NASA Astrophysics Data System (ADS)
Shen, Li; Wu, Linmei; Li, Zhipeng
2016-06-01
Multiscale segmentation is a key prerequisite step for object-based classification methods. However, it is often not possible to determine a sole optimal scale for the image to be classified because in many cases different geo-objects and even an identical geo-object may appear at different scales in one image. In this paper, an object-based classification method based on mutliscale segmentation results in the framework of topic modelling is proposed to classify VHR satellite images in an entirely unsupervised fashion. In the stage of topic modelling, grayscale histogram distributions for each geo-object class and each segment are learned in an unsupervised manner from multiscale segments. In the stage of classification, each segment is allocated a geo-object class label by the similarity comparison between the grayscale histogram distributions of each segment and each geo-object class. Experimental results show that the proposed method can perform better than the traditional methods based on topic modelling.
Lin, Ching-Long; Tawhai, Merryn H; Hoffman, Eric A
2013-01-01
Improved understanding of structure and function relationships in the human lungs in individuals and subpopulations 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.
A multiscale MDCT image-based breathing lung model with time-varying regional ventilation
Yin, Youbing; Choi, Jiwoong; Hoffman, Eric A.; Tawhai, Merryn H.; Lin, Ching-Long
2013-07-01
A novel algorithm is presented that links local structural variables (regional ventilation and deforming central airways) to global function (total lung volume) in the lung over three imaged lung volumes, to derive a breathing lung model for computational fluid dynamics simulation. The algorithm constitutes the core of an integrative, image-based computational framework for subject-specific simulation of the breathing lung. For the first time, the algorithm is applied to three multi-detector row computed tomography (MDCT) volumetric lung images of the same individual. A key technique in linking global and local variables over multiple images is an in-house mass-preserving image registration method. Throughout breathing cycles, cubic interpolation is employed to ensure C{sub 1} continuity in constructing time-varying regional ventilation at the whole lung level, flow rate fractions exiting the terminal airways, and airway deformation. The imaged exit airway flow rate fractions are derived from regional ventilation with the aid of a three-dimensional (3D) and one-dimensional (1D) coupled airway tree that connects the airways to the alveolar tissue. An in-house parallel large-eddy simulation (LES) technique is adopted to capture turbulent-transitional-laminar flows in both normal and deep breathing conditions. The results obtained by the proposed algorithm when using three lung volume images are compared with those using only one or two volume images. The three-volume-based lung model produces physiologically-consistent time-varying pressure and ventilation distribution. The one-volume-based lung model under-predicts pressure drop and yields un-physiological lobar ventilation. The two-volume-based model can account for airway deformation and non-uniform regional ventilation to some extent, but does not capture the non-linear features of the lung.
A multiscale MDCT image-based breathing lung model with time-varying regional ventilation
NASA Astrophysics Data System (ADS)
Yin, Youbing; Choi, Jiwoong; Hoffman, Eric A.; Tawhai, Merryn H.; Lin, Ching-Long
2013-07-01
A novel algorithm is presented that links local structural variables (regional ventilation and deforming central airways) to global function (total lung volume) in the lung over three imaged lung volumes, to derive a breathing lung model for computational fluid dynamics simulation. The algorithm constitutes the core of an integrative, image-based computational framework for subject-specific simulation of the breathing lung. For the first time, the algorithm is applied to three multi-detector row computed tomography (MDCT) volumetric lung images of the same individual. A key technique in linking global and local variables over multiple images is an in-house mass-preserving image registration method. Throughout breathing cycles, cubic interpolation is employed to ensure C1 continuity in constructing time-varying regional ventilation at the whole lung level, flow rate fractions exiting the terminal airways, and airway deformation. The imaged exit airway flow rate fractions are derived from regional ventilation with the aid of a three-dimensional (3D) and one-dimensional (1D) coupled airway tree that connects the airways to the alveolar tissue. An in-house parallel large-eddy simulation (LES) technique is adopted to capture turbulent-transitional-laminar flows in both normal and deep breathing conditions. The results obtained by the proposed algorithm when using three lung volume images are compared with those using only one or two volume images. The three-volume-based lung model produces physiologically-consistent time-varying pressure and ventilation distribution. The one-volume-based lung model under-predicts pressure drop and yields un-physiological lobar ventilation. The two-volume-based model can account for airway deformation and non-uniform regional ventilation to some extent, but does not capture the non-linear features of the lung.
NASA Astrophysics Data System (ADS)
Bultreys, Tom; Van Hoorebeke, Luc; Cnudde, Veerle
2016-09-01
The two-phase flow properties of natural rocks depend strongly on their pore structure and wettability, both of which are often heterogeneous throughout the rock. To better understand and predict these properties, image-based models are being developed. Resulting simulations are however problematic in several important classes of rocks with broad pore-size distributions. We present a new multiscale pore network model to simulate secondary waterflooding in these rocks, which may undergo wettability alteration after primary drainage. This novel approach permits to include the effect of microporosity on the imbibition sequence without the need to describe each individual micropore. Instead, we show that fluid transport through unresolved pores can be taken into account in an upscaled fashion, by the inclusion of symbolic links between macropores, resulting in strongly decreased computational demands. Rules to describe the behavior of these links in the quasistatic invasion sequence are derived from percolation theory. The model is validated by comparison to a fully detailed network representation, which takes each separate micropore into account. Strongly and weakly water-and oil-wet simulations show good results, as do mixed-wettability scenarios with different pore-scale wettability distributions. We also show simulations on a network extracted from a micro-CT scan of Estaillades limestone, which yields good agreement with water-wet and mixed-wet experimental results.
Sander, Edward A.; Stylianopoulos, Triantafyllos; Tranquillo, Robert T.; Barocas, Victor H.
2009-01-01
The mechanical environment plays an important role in cell signaling and tissue homeostasis. Unraveling connections between externally applied loads and the cellular response is often confounded by extracellular matrix (ECM) heterogeneity. Image-based multiscale models provide a foundation for examining the fine details of tissue behavior, but they require validation at multiple scales. In this study, we developed a multiscale model that captured the anisotropy and heterogeneity of a cell-compacted collagen gel subjected to an off-axis hold mechanical test and subsequently to biaxial extension. In both the model and experiments, the ECM reorganized in a nonaffine and heterogeneous manner that depended on multiscale interactions between the fiber networks. Simulations predicted that tensile and compressive fiber forces were produced to accommodate macroscopic displacements. Fiber forces in the simulation ranged from −11.3 to 437.7 nN, with a significant fraction of fibers under compression (12.1% during off-axis stretch). The heterogeneous network restructuring predicted by the model serves as an example of how multiscale modeling techniques provide a theoretical framework for understanding relationships between ECM structure and tissue-level mechanical properties and how microscopic fiber rearrangements could lead to mechanotransductive cell signaling. PMID:19805118
MacLeod, R.S.; Stinstra, J.G.; Lew, S.; Whitaker, R.T.; Swenson, D.J.; Cole, M.J.; Krüger, J.; Brooks, D.H.; Johnson, C.R.
2009-01-01
Many simulation studies in biomedicine are based on a similar sequence of processing steps, starting from images and running through geometric model generation, assignment of tissue properties, numerical simulation and visualization of the results—a process known as image-based geometric modelling and simulation. We present an overview of software systems for implementing such a sequence both within highly integrated problem-solving environments and in the form of loosely integrated pipelines. Loose integration in this case indicates that individual programs function largely independently but communicate through files of a common format and support simple scripting, so as to automate multiple executions wherever possible. We then describe three specific applications of such pipelines to translational biomedical research in electrophysiology. PMID:19414456
MacLeod, R S; Stinstra, J G; Lew, S; Whitaker, R T; Swenson, D J; Cole, M J; Krüger, J; Brooks, D H; Johnson, C R
2009-06-13
Many simulation studies in biomedicine are based on a similar sequence of processing steps, starting from images and running through geometric model generation, assignment of tissue properties, numerical simulation and visualization of the results--a process known as image-based geometric modelling and simulation. We present an overview of software systems for implementing such a sequence both within highly integrated problem-solving environments and in the form of loosely integrated pipelines. Loose integration in this case indicates that individual programs function largely independently but communicate through files of a common format and support simple scripting, so as to automate multiple executions wherever possible. We then describe three specific applications of such pipelines to translational biomedical research in electrophysiology.
Image-based multi-scale modelling and validation of radio-frequency ablation in liver tumours.
Payne, Stephen; Flanagan, Ronan; Pollari, Mika; Alhonnoro, Tuomas; Bost, Claire; O'Neill, David; Peng, Tingying; Stiegler, Philipp
2011-11-13
The treatment of cancerous tumours in the liver remains clinically challenging, despite the wide range of treatment possibilities, including radio-frequency ablation (RFA), high-intensity focused ultrasound and resection, which are currently available. Each has its own advantages and disadvantages. For non- or minimally invasive modalities, such as RFA, considered here, it is difficult to monitor the treatment in vivo. This is particularly problematic in the liver, where large blood vessels act as heat sinks, dissipating delivered heat and shrinking the size of the lesion (the volume damaged by the heat treatment) locally; considerable experience is needed on the part of the clinician to optimize the heat treatment to prevent recurrence. In this paper, we outline our work towards developing a simulation tool kit that could be used both to optimize treatment protocols in advance and to train the less-experienced clinicians for RFA treatment of liver tumours. This tool is based on a comprehensive mathematical model of bio-heat transfer and cell death. We show how simulations of ablations in two pigs, based on individualized imaging data, compare directly with experimentally measured lesion sizes and discuss the likely sources of error and routes towards clinical implementation. This is the first time that such a 'loop' of mathematical modelling and experimental validation in vivo has been performed in this context, and such validation enables us to make quantitative estimates of error.
Change detection in high resolution SAR images based on multiscale texture features
NASA Astrophysics Data System (ADS)
Wen, Caihuan; Gao, Ziqiang
2011-12-01
This paper studied on change detection algorithm of high resolution (HR) Synthetic Aperture Radar (SAR) images based on multi-scale texture features. Firstly, preprocessed multi-temporal Terra-SAR images were decomposed by 2-D dual tree complex wavelet transform (DT-CWT), and multi-scale texture features were extracted from those images. Then, log-ratio operation was utilized to get difference images, and the Bayes minimum error theory was used to extract change information from difference images. Lastly, precision assessment was done. Meanwhile, we compared with the result of method based on texture features extracted from gray-level cooccurrence matrix (GLCM). We had a conclusion that, change detection algorithm based on multi-scale texture features has a great more improvement, which proves an effective method to change detect of high spatial resolution SAR images.
Guo, Xingye; Hu, Bin; Wei, Changdong; Sun, Jiangang; Jung, Yeon-Gil; Li, Li; Knapp, James; Zhang, Jing
2016-09-01
Lanthanum zirconate (La2Zr2O7) is a promising candidate material for thermal barrier coating (TBC) applications due to its low thermal conductivity and high-temperature phase stability. In this work, a novel image-based multi-scale simulation framework combining molecular dynamics (MD) and finite element (FE) calculations is proposed to study the thermal conductivity of La2Zr2O7 coatings. Since there is no experimental data of single crystal La2Zr2O7 thermal conductivity, a reverse non-equilibrium molecular dynamics (reverse NEMD) approach is first employed to compute the temperature-dependent thermal conductivity of single crystal La2Zr2O7. The single crystal data is then passed to a FE model which takes into account of realistic thermal barrier coating microstructures. The predicted thermal conductivities from the FE model are in good agreement with experimental validations using both flash laser technique and pulsed thermal imaging-multilayer analysis. The framework proposed in this work provides a powerful tool for future design of advanced coating systems. (C) 2016 Elsevier Ltd. All rights reserved.
Multiscale Cloud System Modeling
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo; Moncrieff, Mitchell W.
2009-01-01
The central theme of this paper is to describe how cloud system resolving models (CRMs) of grid spacing approximately 1 km have been applied to various important problems in atmospheric science across a wide range of spatial and temporal scales and how these applications relate to other modeling approaches. A long-standing problem concerns the representation of organized precipitating convective cloud systems in weather and climate models. Since CRMs resolve the mesoscale to large scales of motion (i.e., 10 km to global) they explicitly address the cloud system problem. By explicitly representing organized convection, CRMs bypass restrictive assumptions associated with convective parameterization such as the scale gap between cumulus and large-scale motion. Dynamical models provide insight into the physical mechanisms involved with scale interaction and convective organization. Multiscale CRMs simulate convective cloud systems in computational domains up to global and have been applied in place of contemporary convective parameterizations in global models. Multiscale CRMs pose a new challenge for model validation, which is met in an integrated approach involving CRMs, operational prediction systems, observational measurements, and dynamical models in a new international project: the Year of Tropical Convection, which has an emphasis on organized tropical convection and its global effects.
Multiscale Cloud System Modeling
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo; Moncrieff, Mitchell W.
2009-01-01
The central theme of this paper is to describe how cloud system resolving models (CRMs) of grid spacing approximately 1 km have been applied to various important problems in atmospheric science across a wide range of spatial and temporal scales and how these applications relate to other modeling approaches. A long-standing problem concerns the representation of organized precipitating convective cloud systems in weather and climate models. Since CRMs resolve the mesoscale to large scales of motion (i.e., 10 km to global) they explicitly address the cloud system problem. By explicitly representing organized convection, CRMs bypass restrictive assumptions associated with convective parameterization such as the scale gap between cumulus and large-scale motion. Dynamical models provide insight into the physical mechanisms involved with scale interaction and convective organization. Multiscale CRMs simulate convective cloud systems in computational domains up to global and have been applied in place of contemporary convective parameterizations in global models. Multiscale CRMs pose a new challenge for model validation, which is met in an integrated approach involving CRMs, operational prediction systems, observational measurements, and dynamical models in a new international project: the Year of Tropical Convection, which has an emphasis on organized tropical convection and its global effects.
Multiscale modeling of proteins.
Tozzini, Valentina
2010-02-16
The activity within a living cell is based on a complex network of interactions among biomolecules, exchanging information and energy through biochemical processes. These events occur on different scales, from the nano- to the macroscale, spanning about 10 orders of magnitude in the space domain and 15 orders of magnitude in the time domain. Consequently, many different modeling techniques, each proper for a particular time or space scale, are commonly used. In addition, a single process often spans more than a single time or space scale. Thus, the necessity arises for combining the modeling techniques in multiscale approaches. In this Account, I first review the different modeling methods for bio-systems, from quantum mechanics to the coarse-grained and continuum-like descriptions, passing through the atomistic force field simulations. Special attention is devoted to their combination in different possible multiscale approaches and to the questions and problems related to their coherent matching in the space and time domains. These aspects are often considered secondary, but in fact, they have primary relevance when the aim is the coherent and complete description of bioprocesses. Subsequently, applications are illustrated by means of two paradigmatic examples: (i) the green fluorescent protein (GFP) family and (ii) the proteins involved in the human immunodeficiency virus (HIV) replication cycle. The GFPs are currently one of the most frequently used markers for monitoring protein trafficking within living cells; nanobiotechnology and cell biology strongly rely on their use in fluorescence microscopy techniques. A detailed knowledge of the actions of the virus-specific enzymes of HIV (specifically HIV protease and integrase) is necessary to study novel therapeutic strategies against this disease. Thus, the insight accumulated over years of intense study is an excellent framework for this Account. The foremost relevance of these two biomolecular systems was
MULTISCALE THERMOHYDROLOGIC MODEL
T.A. Buscheck
2001-12-21
The purpose of the Multiscale Thermohydrologic Model (MSTHM) is to describe the thermohydrologic evolution of the near-field environment (NFE) and engineered barrier system (EBS) throughout the potential high-level nuclear waste repository at Yucca Mountain for a particular engineering design (CRWMS M&O 2000c). The process-level model will provide thermohydrologic (TH) information and data (such as in-drift temperature, relative humidity, liquid saturation, etc.) for use in other technical products. This data is provided throughout the entire repository area as a function of time. The MSTHM couples the Smeared-heat-source Drift-scale Thermal-conduction (SDT), Line-average-heat-source Drift-scale Thermohydrologic (LDTH), Discrete-heat-source Drift-scale Thermal-conduction (DDT), and Smeared-heat-source Mountain-scale Thermal-conduction (SMT) submodels such that the flow of water and water vapor through partially-saturated fractured rock is considered. The MSTHM accounts for 3-D drift-scale and mountain-scale heat flow, repository-scale variability of stratigraphy and infiltration flux, and waste package (WP)-to-WP variability in heat output from WPs. All submodels use the nonisothermal unsaturated-saturated flow and transport (NUFT) simulation code. The MSTHM is implemented in several data-processing steps. The four major steps are: (1) submodel input-file preparation, (2) execution of the four submodel families with the use of the NUFT code, (3) execution of the multiscale thermohydrologic abstraction code (MSTHAC), and (4) binning and post-processing (i.e., graphics preparation) of the output from MSTHAC. Section 6 describes the MSTHM in detail. The objectives of this Analyses and Model Report (AMR) are to investigate near field (NF) and EBS thermohydrologic environments throughout the repository area at various evolution periods, and to provide TH data that may be used in other process model reports.
Multiscale Thermohydrologic Model
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'' (BSC 2004 [DIRS 170033]); (6) ''Ventilation Model and Analysis Report'' (BSC 2004 [DIRS 169862]); (7) ''Heat Capacity
MULTISCALE THERMOHYDROLOGIC MODEL
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
NASA Astrophysics Data System (ADS)
Arshadi, Amir
Image-based simulation of complex materials is a very important tool for understanding their mechanical behavior and an effective tool for successful design of composite materials. In this thesis an image-based multi-scale finite element approach is developed to predict the mechanical properties of asphalt mixtures. In this approach the "up-scaling" and homogenization of each scale to the next is critically designed to improve accuracy. In addition to this multi-scale efficiency, this study introduces an approach for consideration of particle contacts at each of the scales in which mineral particles exist. One of the most important pavement distresses which seriously affects the pavement performance is fatigue cracking. As this cracking generally takes place in the binder phase of the asphalt mixture, the binder fatigue behavior is assumed to be one of the main factors influencing the overall pavement fatigue performance. It is also known that aggregate gradation, mixture volumetric properties, and filler type and concentration can affect damage initiation and progression in the asphalt mixtures. This study was conducted to develop a tool to characterize the damage properties of the asphalt mixtures at all scales. In the present study the Viscoelastic continuum damage model is implemented into the well-known finite element software ABAQUS via the user material subroutine (UMAT) in order to simulate the state of damage in the binder phase under the repeated uniaxial sinusoidal loading. The inputs are based on the experimentally derived measurements for the binder properties. For the scales of mastic and mortar, the artificially 2-Dimensional images of mastic and mortar scales were generated and used to characterize the properties of those scales. Finally, the 2D scanned images of asphalt mixtures are used to study the asphalt mixture fatigue behavior under loading. In order to validate the proposed model, the experimental test results and the simulation results were
Multiscale modeling methods in biomechanics.
Bhattacharya, Pinaki; Viceconti, Marco
2017-01-19
More and more frequently, computational biomechanics deals with problems where the portion of physical reality to be modeled spans over such a large range of spatial and temporal dimensions, that it is impossible to represent it as a single space-time continuum. We are forced to consider multiple space-time continua, each representing the phenomenon of interest at a characteristic space-time scale. Multiscale models describe a complex process across multiple scales, and account for how quantities transform as we move from one scale to another. This review offers a set of definitions for this emerging field, and provides a brief summary of the most recent developments on multiscale modeling in biomechanics. Of all possible perspectives, we chose that of the modeling intent, which vastly affect the nature and the structure of each research activity. To the purpose we organized all papers reviewed in three categories: 'causal confirmation,' where multiscale models are used as materializations of the causation theories; 'predictive accuracy,' where multiscale modeling is aimed to improve the predictive accuracy; and 'determination of effect,' where multiscale modeling is used to model how a change at one scale manifests in an effect at another radically different space-time scale. Consistent with how the volume of computational biomechanics research is distributed across application targets, we extensively reviewed papers targeting the musculoskeletal and the cardiovascular systems, and covered only a few exemplary papers targeting other organ systems. The review shows a research subdomain still in its infancy, where causal confirmation papers remain the most common. For further resources related to this article, please visit the WIREs website.
Multiscale models for synthetic biology.
Kaznessis, Yiannis N
2009-01-01
Reacting systems away from the thermodynamic limit cannot be accurately modeled with ordinary differential equations. These continuous-deterministic modeling formalisms, traditionally developed and used by chemical engineers can be distinctly false if the number of molecules of reacting chemical species is very small, or if reaction events are very rare. Then stochastic-discrete representations are appropriate. Importantly, in cases where in a network of reactions there are some parts that must be modeled discretely and stochastically, yet others can be modeled continuously and deterministically, the need for development of multiscale models emerges naturally. In computational synthetic biology, such cases arise often. In this work we present the development of multiscale models for synthetic biology applications, demonstrating accuracy, computational efficiency and utility.
Image-based modelling of organogenesis.
Iber, Dagmar; Karimaddini, Zahra; Ünal, Erkan
2016-07-01
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks-and how can they change as a result of mutations? Morphogenesis provides an excellent model system to study how simple molecular networks robustly control complex processes on the macroscopic scale despite molecular noise, and how important functional variants can emerge from small genetic changes. Recent advancements in three-dimensional imaging technologies, computer algorithms and computer power now allow us to develop and analyse increasingly realistic models of biological control. Here, we present our pipeline for image-based modelling that includes the segmentation of images, the determination of displacement fields and the solution of systems of partial differential equations on the growing, embryonic domains. The development of suitable mathematical models, the data-based inference of parameter sets and the evaluation of competing models are still challenging, and current approaches are discussed.
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
2014-12-01
the mineral content at each level will be tracked for comparison at the macro level. Table 9 displays the mineral content of the two fibril models...surface view (SSV). By continuously etching and imaging a section of material, the three dimensional structure is revealed. Reznikov et al. [12] has...orientations of three samples were calculated. The samples were taken from a 20 year- old female, a 59 year- old male, and a 77 year- old male. The results
Multiscale modelling of DNA mechanics
NASA Astrophysics Data System (ADS)
Dršata, Tomáš; Lankaš, Filip
2015-08-01
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.
Automatic Method to Classify Images Based on Multiscale Fractal Descriptors and Paraconsistent Logic
NASA Astrophysics Data System (ADS)
Pavarino, E.; Neves, L. A.; Nascimento, M. Z.; Godoy, M. F.; Arruda, P. F.; Neto, D. S.
2015-01-01
In this study is presented an automatic method to classify images from fractal descriptors as decision rules, such as multiscale fractal dimension and lacunarity. The proposed methodology was divided in three steps: quantification of the regions of interest with fractal dimension and lacunarity, techniques under a multiscale approach; definition of reference patterns, which are the limits of each studied group; and, classification of each group, considering the combination of the reference patterns with signals maximization (an approach commonly considered in paraconsistent logic). The proposed method was used to classify histological prostatic images, aiming the diagnostic of prostate cancer. The accuracy levels were important, overcoming those obtained with Support Vector Machine (SVM) and Best- first Decicion Tree (BFTree) classifiers. The proposed approach allows recognize and classify patterns, offering the advantage of giving comprehensive results to the specialists.
Towards a Multiscale Approach to Cybersecurity Modeling
Hogan, Emilie A.; Hui, Peter SY; Choudhury, Sutanay; Halappanavar, Mahantesh; Oler, Kiri J.; Joslyn, Cliff A.
2013-11-12
We propose a multiscale approach to modeling cyber networks, with the goal of capturing a view of the network and overall situational awareness with respect to a few key properties--- connectivity, distance, and centrality--- for a system under an active attack. We focus on theoretical and algorithmic foundations of multiscale graphs, coming from an algorithmic perspective, with the goal of modeling cyber system defense as a specific use case scenario. We first define a notion of \\emph{multiscale} graphs, in contrast with their well-studied single-scale counterparts. We develop multiscale analogs of paths and distance metrics. As a simple, motivating example of a common metric, we present a multiscale analog of the all-pairs shortest-path problem, along with a multiscale analog of a well-known algorithm which solves it. From a cyber defense perspective, this metric might be used to model the distance from an attacker's position in the network to a sensitive machine. In addition, we investigate probabilistic models of connectivity. These models exploit the hierarchy to quantify the likelihood that sensitive targets might be reachable from compromised nodes. We believe that our novel multiscale approach to modeling cyber-physical systems will advance several aspects of cyber defense, specifically allowing for a more efficient and agile approach to defending these systems.
MULTISCALE MODELING OF POLYMER NANOCOMPOSITES
Maiti, A
2007-07-16
Polymer Nanocomposites are an important class of nanomaterials with potential applications including but not limited to structural and cushion materials, electromagnetic and heat shields, conducting plastics, sensors, and catalysts for various chemical and bio processes. Success in most such applications hinges on molecular-level control of structure and assembly, and a deep understanding of how the overall morphology of various components and the interfaces between them affect the composite properties at the macroscale. The length and time-scales associated with such assemblies are prohibitively large for a full atomistic modeling. Instead we adopt a multiscale methodology in which atomic-level interactions between different components of a composite are incorporated into a coarse-grained simulation of the mesoscale morphology, which is then represented on a numerical grid and the macroscopic properties computed using a finite-elements method.
Multiscale Modeling of Hematologic Disorders
Fedosov, Dmitry A.; Pivkin, Igor; Pan, Wenxiao; Dao, Ming; Caswell, Bruce; Karniadakis, George E.
2012-01-28
Parasitic infectious diseases and other hereditary hematologic disorders are often associated with major changes in the shape and viscoelastic properties of red blood cells (RBCs). Such changes can disrupt blood flow and even brain perfusion, as in the case of cerebral malaria. Modeling of these hematologic disorders requires a seamless multiscale approach, where blood cells and blood flow in the entire arterial tree are represented accurately using physiologically consistent parameters. In this chapter, we present a computational methodology based on dissipative particle dynamics (DPD) which models RBCs as well as whole blood in health and disease. DPD is a Lagrangian method that can be derived from systematic coarse-graining of molecular dynamics but can scale efficiently up to small arteries and can also be used to model RBCs down to spectrin level. To this end, we present two complementary mathematical models for RBCs and describe a systematic procedure on extracting the relevant input parameters from optical tweezers and microfluidic experiments for single RBCs. We then use these validated RBC models to predict the behavior of whole healthy blood and compare with experimental results. The same procedure is applied to modeling malaria, and results for infected single RBCs and whole blood are presented.
Efficient postprocessing scheme for block-coded images based on multiscale edge detection
NASA Astrophysics Data System (ADS)
Wu, Shuanhu; Yan, Hong; Tan, Zheng
2001-09-01
The block discrete cosine transform (BDCT) is the most widely used technique for the compression of both still and moving images, a major problem related with the BDCT techniques is that the decoded images, especially at low bit rate, exhibit visually annoying blocking effects. In this paper, based on Mallets multiscale edge detection, we proposed an efficient deblocking algorithm to further improved the coding performance. The advantage of our algorithm is that it can efficiently preserve texture structure in the original decompressed images. Our method is similar to that of Z. Xiong's, where the Z.Xiong's method is not suitable for images with a large portion of texture; for instance, the Barbara Image. The difference of our method and the Z.Xiong's is that our method adopted a new thresholding scheme for multi-scale edge detection instead of exploiting cross-scale correlation for edge detection. Numerical experiment results show that our scheme not only outperforms Z.Xiong's for various images in the case of the same computational complexity, but also preserve texture structure in the decompressed images at the same time. Compared with the best iterative-based method (POCS) reported in the literature, our algorithm can achieve the same peak signal-to-noise ratio (PSNR) improvement and give visually very pleasing images as well.
A framework for multi-scale modelling
Chopard, B.; Borgdorff, Joris; Hoekstra, A. G.
2014-01-01
We review a methodology to design, implement and execute multi-scale and multi-science numerical simulations. We identify important ingredients of multi-scale modelling and give a precise definition of them. Our framework assumes that a multi-scale model can be formulated in terms of a collection of coupled single-scale submodels. With concepts such as the scale separation map, the generic submodel execution loop (SEL) and the coupling templates, one can define a multi-scale modelling language which is a bridge between the application design and the computer implementation. Our approach has been successfully applied to an increasing number of applications from different fields of science and technology. PMID:24982249
Feature and contrast enhancement of mammographic image based on multiscale analysis and morphology.
Wu, Shibin; Yu, Shaode; Yang, Yuhan; Xie, Yaoqin
2013-01-01
A new algorithm for feature and contrast enhancement of mammographic images is proposed in this paper. The approach bases on multiscale transform and mathematical morphology. First of all, the Laplacian Gaussian pyramid operator is applied to transform the mammography into different scale subband images. In addition, the detail or high frequency subimages are equalized by contrast limited adaptive histogram equalization (CLAHE) and low-pass subimages are processed by mathematical morphology. Finally, the enhanced image of feature and contrast is reconstructed from the Laplacian Gaussian pyramid coefficients modified at one or more levels by contrast limited adaptive histogram equalization and mathematical morphology, respectively. The enhanced image is processed by global nonlinear operator. The experimental results show that the presented algorithm is effective for feature and contrast enhancement of mammogram. The performance evaluation of the proposed algorithm is measured by contrast evaluation criterion for image, signal-noise-ratio (SNR), and contrast improvement index (CII).
Feature and Contrast Enhancement of Mammographic Image Based on Multiscale Analysis and Morphology
Wu, Shibin; Xie, Yaoqin
2013-01-01
A new algorithm for feature and contrast enhancement of mammographic images is proposed in this paper. The approach bases on multiscale transform and mathematical morphology. First of all, the Laplacian Gaussian pyramid operator is applied to transform the mammography into different scale subband images. In addition, the detail or high frequency subimages are equalized by contrast limited adaptive histogram equalization (CLAHE) and low-pass subimages are processed by mathematical morphology. Finally, the enhanced image of feature and contrast is reconstructed from the Laplacian Gaussian pyramid coefficients modified at one or more levels by contrast limited adaptive histogram equalization and mathematical morphology, respectively. The enhanced image is processed by global nonlinear operator. The experimental results show that the presented algorithm is effective for feature and contrast enhancement of mammogram. The performance evaluation of the proposed algorithm is measured by contrast evaluation criterion for image, signal-noise-ratio (SNR), and contrast improvement index (CII). PMID:24416072
Multiscale modelling of evolving foams
NASA Astrophysics Data System (ADS)
Saye, R. I.; Sethian, J. A.
2016-06-01
We present a set of multi-scale interlinked algorithms to model the dynamics of evolving foams. These algorithms couple the key effects of macroscopic bubble rearrangement, thin film drainage, and membrane rupture. For each of the mechanisms, we construct consistent and accurate algorithms, and couple them together to work across the wide range of space and time scales that occur in foam dynamics. These algorithms include second order finite difference projection methods for computing incompressible fluid flow on the macroscale, second order finite element methods to solve thin film drainage equations in the lamellae and Plateau borders, multiphase Voronoi Implicit Interface Methods to track interconnected membrane boundaries and capture topological changes, and Lagrangian particle methods for conservative liquid redistribution during rearrangement and rupture. We derive a full set of numerical approximations that are coupled via interface jump conditions and flux boundary conditions, and show convergence for the individual mechanisms. We demonstrate our approach by computing a variety of foam dynamics, including coupled evolution of three-dimensional bubble clusters attached to an anchored membrane and collapse of a foam cluster.
Multiscale Modeling of Cortical Neural Networks
NASA Astrophysics Data System (ADS)
Torben-Nielsen, Benjamin; Stiefel, Klaus M.
2009-09-01
In this study, we describe efforts at modeling the electrophysiological dynamics of cortical networks in a multi-scale manner. Specifically, we describe the implementation of a network model composed of simple single-compartmental neuron models, in which a single complex multi-compartmental model of a pyramidal neuron is embedded. The network is capable of generating Δ (2 Hz, observed during deep sleep states) and γ (40 Hz, observed during wakefulness) oscillations, which are then imposed onto the multi-compartmental model, thus providing realistic, dynamic boundary conditions. We furthermore discuss the challenges and chances involved in multi-scale modeling of neural function.
Image based modeling of tumor growth.
Meghdadi, N; Soltani, M; Niroomand-Oscuii, H; Ghalichi, F
2016-09-01
Tumors are a main cause of morbidity and mortality worldwide. Despite the efforts of the clinical and research communities, little has been achieved in the past decades in terms of improving the treatment of aggressive tumors. Understanding the underlying mechanism of tumor growth and evaluating the effects of different therapies are valuable steps in predicting the survival time and improving the patients' quality of life. Several studies have been devoted to tumor growth modeling at different levels to improve the clinical outcome by predicting the results of specific treatments. Recent studies have proposed patient-specific models using clinical data usually obtained from clinical images and evaluating the effects of various therapies. The aim of this review is to highlight the imaging role in tumor growth modeling and provide a worthwhile reference for biomedical and mathematical researchers with respect to tumor modeling using the clinical data to develop personalized models of tumor growth and evaluating the effect of different therapies.
Experience With Bayesian Image Based Surface Modeling
NASA Technical Reports Server (NTRS)
Stutz, John C.
2005-01-01
Bayesian surface modeling from images requires modeling both the surface and the image generation process, in order to optimize the models by comparing actual and generated images. Thus it differs greatly, both conceptually and in computational difficulty, from conventional stereo surface recovery techniques. But it offers the possibility of using any number of images, taken under quite different conditions, and by different instruments that provide independent and often complementary information, to generate a single surface model that fuses all available information. I describe an implemented system, with a brief introduction to the underlying mathematical models and the compromises made for computational efficiency. I describe successes and failures achieved on actual imagery, where we went wrong and what we did right, and how our approach could be improved. Lastly I discuss how the same approach can be extended to distinct types of instruments, to achieve true sensor fusion.
Multiscale Computational Models of Complex Biological Systems
Walpole, Joseph; Papin, Jason A.; Peirce, Shayn M.
2014-01-01
Integration of data across spatial, temporal, and functional scales is a primary focus of biomedical engineering efforts. The advent of powerful computing platforms, coupled with quantitative data from high-throughput experimental platforms, has allowed multiscale modeling to expand as a means to more comprehensively investigate biological phenomena in experimentally relevant ways. This review aims to highlight recently published multiscale models of biological systems while using their successes to propose the best practices for future model development. We demonstrate that coupling continuous and discrete systems best captures biological information across spatial scales by selecting modeling techniques that are suited to the task. Further, we suggest how to best leverage these multiscale models to gain insight into biological systems using quantitative, biomedical engineering methods to analyze data in non-intuitive ways. These topics are discussed with a focus on the future of the field, the current challenges encountered, and opportunities yet to be realized. PMID:23642247
Multiscale model approach for magnetization dynamics simulations
NASA Astrophysics Data System (ADS)
De Lucia, Andrea; Krüger, Benjamin; Tretiakov, Oleg A.; Kläui, Mathias
2016-11-01
Simulations of magnetization dynamics in a multiscale environment enable the rapid evaluation of the Landau-Lifshitz-Gilbert equation in a mesoscopic sample with nanoscopic accuracy in areas where such accuracy is required. We have developed a multiscale magnetization dynamics simulation approach that can be applied to large systems with spin structures that vary locally on small length scales. To implement this, the conventional micromagnetic simulation framework has been expanded to include a multiscale solving routine. The software selectively simulates different regions of a ferromagnetic sample according to the spin structures located within in order to employ a suitable discretization and use either a micromagnetic or an atomistic model. To demonstrate the validity of the multiscale approach, we simulate the spin wave transmission across the regions simulated with the two different models and different discretizations. We find that the interface between the regions is fully transparent for spin waves with frequency lower than a certain threshold set by the coarse scale micromagnetic model with no noticeable attenuation due to the interface between the models. As a comparison to exact analytical theory, we show that in a system with a Dzyaloshinskii-Moriya interaction leading to spin spirals, the simulated multiscale result is in good quantitative agreement with the analytical calculation.
Multiscale modeling of polymer nanocomposites
NASA Astrophysics Data System (ADS)
Sheidaei, Azadeh
In recent years, polymer nano-composites (PNCs) have increasingly gained more attention due to their improved mechanical, barrier, thermal, optical, electrical and biodegradable properties in comparison with the conventional micro-composites or pristine polymer. With a modest addition of nanoparticles (usually less than 5wt. %), PNCs offer a wide range of improvements in moduli, strength, heat resistance, biodegradability, as well as decrease in gas permeability and flammability. Although PNCs offer enormous opportunities to design novel material systems, development of an effective numerical modeling approach to predict their properties based on their complex multi-phase and multiscale structure is still at an early stage. Developing a computational framework to predict the mechanical properties of PNC is the focus of this dissertation. A computational framework has been developed to predict mechanical properties of polymer nano-composites. In chapter 1, a microstructure inspired material model has been developed based on statistical technique and this technique has been used to reconstruct the microstructure of Halloysite nanotube (HNT) polypropylene composite. This technique also has been used to reconstruct exfoliated Graphene nanoplatelet (xGnP) polymer composite. The model was able to successfully predict the material behavior obtained from experiment. Chapter 2 is the summary of the experimental work to support the numerical work. First, different processing techniques to make the polymer nanocomposites have been reviewed. Among them, melt extrusion followed by injection molding was used to manufacture high density polyethylene (HDPE)---xGnP nanocomposties. Scanning electron microscopy (SEM) also was performed to determine particle size and distribution and to examine fracture surfaces. Particle size was measured from these images and has been used for calculating the probability density function for GNPs in chapter 1. A series of nanoindentation tests have
A bidirectional coupling procedure applied to multiscale respiratory modeling
NASA Astrophysics Data System (ADS)
Kuprat, A. P.; Kabilan, S.; Carson, J. P.; Corley, R. A.; Einstein, D. R.
2013-07-01
In this study, we present a novel multiscale computational framework for efficiently linking multiple lower-dimensional models describing the distal lung mechanics to imaging-based 3D computational fluid dynamics (CFDs) models of the upper pulmonary airways in order to incorporate physiologically appropriate outlet boundary conditions. The framework is an extension of the modified Newton's method with nonlinear Krylov accelerator developed by Carlson and Miller [1], Miller [2] and Scott and Fenves [3]. Our extensions include the retention of subspace information over multiple timesteps, and a special correction at the end of a timestep that allows for corrections to be accepted with verified low residual with as little as a single residual evaluation per timestep on average. In the case of a single residual evaluation per timestep, the method has zero additional computational cost compared to uncoupled or unidirectionally coupled simulations. We expect these enhancements to be generally applicable to other multiscale coupling applications where timestepping occurs. In addition we have developed a "pressure-drop" residual which allows for stable coupling of flows between a 3D incompressible CFD application and another (lower-dimensional) fluid system. We expect this residual to also be useful for coupling non-respiratory incompressible fluid applications, such as multiscale simulations involving blood flow. The lower-dimensional models that are considered in this study are sets of simple ordinary differential equations (ODEs) representing the compliant mechanics of symmetric human pulmonary airway trees. To validate the method, we compare the predictions of hybrid CFD-ODE models against an ODE-only model of pulmonary airflow in an idealized geometry. Subsequently, we couple multiple sets of ODEs describing the distal lung to an imaging-based human lung geometry. Boundary conditions in these models consist of atmospheric pressure at the mouth and intrapleural
A Bidirectional Coupling Procedure Applied to Multiscale Respiratory Modeling.
Kuprat, A P; Kabilan, S; Carson, J P; Corley, R A; Einstein, D R
2013-07-01
In this study, we present a novel multiscale computational framework for efficiently linking multiple lower-dimensional models describing the distal lung mechanics to imaging-based 3D computational fluid dynamics (CFD) models of the upper pulmonary airways in order to incorporate physiologically appropriate outlet boundary conditions. The framework is an extension of the Modified Newton's Method with nonlinear Krylov accelerator developed by Carlson and Miller [1, 2, 3]. Our extensions include the retention of subspace information over multiple timesteps, and a special correction at the end of a timestep that allows for corrections to be accepted with verified low residual with as little as a single residual evaluation per timestep on average. In the case of a single residual evaluation per timestep, the method has zero additional computational cost compared to uncoupled or unidirectionally coupled simulations. We expect these enhancements to be generally applicable to other multiscale coupling applications where timestepping occurs. In addition we have developed a "pressure-drop" residual which allows for stable coupling of flows between a 3D incompressible CFD application and another (lower-dimensional) fluid system. We expect this residual to also be useful for coupling non-respiratory incompressible fluid applications, such as multiscale simulations involving blood flow. The lower-dimensional models that are considered in this study are sets of simple ordinary differential equations (ODEs) representing the compliant mechanics of symmetric human pulmonary airway trees. To validate the method, we compare the predictions of hybrid CFD-ODE models against an ODE-only model of pulmonary airflow in an idealized geometry. Subsequently, we couple multiple sets of ODEs describing the distal lung to an imaging-based human lung geometry. Boundary conditions in these models consist of atmospheric pressure at the mouth and intrapleural pressure applied to the multiple sets
A Bidirectional Coupling Procedure Applied to Multiscale Respiratory Modeling
Kuprat, Andrew P.; Kabilan, Senthil; Carson, James P.; Corley, Richard A.; Einstein, Daniel R.
2013-07-01
In this study, we present a novel multiscale computational framework for efficiently linking multiple lower-dimensional models describing the distal lung mechanics to imaging-based 3D computational fluid dynamics (CFD) models of the upper pulmonary airways in order to incorporate physiologically appropriate outlet boundary conditions. The framework is an extension of the Modified Newton’s Method with nonlinear Krylov accelerator developed by Carlson and Miller [1, 2, 3]. Our extensions include the retention of subspace information over multiple timesteps, and a special correction at the end of a timestep that allows for corrections to be accepted with verified low residual with as little as a single residual evaluation per timestep on average. In the case of a single residual evaluation per timestep, the method has zero additional computational cost compared to uncoupled or unidirectionally coupled simulations. We expect these enhancements to be generally applicable to other multiscale coupling applications where timestepping occurs. In addition we have developed a “pressure-drop” residual which allows for stable coupling of flows between a 3D incompressible CFD application and another (lower-dimensional) fluid system. We expect this residual to also be useful for coupling non-respiratory incompressible fluid applications, such as multiscale simulations involving blood flow. The lower-dimensional models that are considered in this study are sets of simple ordinary differential equations (ODEs) representing the compliant mechanics of symmetric human pulmonary airway trees. To validate the method, we compare the predictions of hybrid CFD-ODE models against an ODE-only model of pulmonary airflow in an idealized geometry. Subsequently, we couple multiple sets of ODEs describing the distal lung to an imaging-based human lung geometry. Boundary conditions in these models consist of atmospheric pressure at the mouth and intrapleural pressure applied to the multiple
A bidirectional coupling procedure applied to multiscale respiratory modeling
Kuprat, A.P.; Kabilan, S.; Carson, J.P.; Corley, R.A.; Einstein, D.R.
2013-07-01
In this study, we present a novel multiscale computational framework for efficiently linking multiple lower-dimensional models describing the distal lung mechanics to imaging-based 3D computational fluid dynamics (CFDs) models of the upper pulmonary airways in order to incorporate physiologically appropriate outlet boundary conditions. The framework is an extension of the modified Newton’s method with nonlinear Krylov accelerator developed by Carlson and Miller [1], Miller [2] and Scott and Fenves [3]. Our extensions include the retention of subspace information over multiple timesteps, and a special correction at the end of a timestep that allows for corrections to be accepted with verified low residual with as little as a single residual evaluation per timestep on average. In the case of a single residual evaluation per timestep, the method has zero additional computational cost compared to uncoupled or unidirectionally coupled simulations. We expect these enhancements to be generally applicable to other multiscale coupling applications where timestepping occurs. In addition we have developed a “pressure-drop” residual which allows for stable coupling of flows between a 3D incompressible CFD application and another (lower-dimensional) fluid system. We expect this residual to also be useful for coupling non-respiratory incompressible fluid applications, such as multiscale simulations involving blood flow. The lower-dimensional models that are considered in this study are sets of simple ordinary differential equations (ODEs) representing the compliant mechanics of symmetric human pulmonary airway trees. To validate the method, we compare the predictions of hybrid CFD–ODE models against an ODE-only model of pulmonary airflow in an idealized geometry. Subsequently, we couple multiple sets of ODEs describing the distal lung to an imaging-based human lung geometry. Boundary conditions in these models consist of atmospheric pressure at the mouth and intrapleural
Multiscale Modeling and Multifunctional Composites
2013-07-17
8) Here, Frs and Drs represent stress and the strain influence functions. The phase transformation fields, ,λ µ , appearing in Eqs...concentration factors Ar , Br , and influence functions Drs , Frs , , 1,=r s Q . Two applications are presented; one is a benchmark, classical...Journal for Multiscale Computational Engineering 8, 69-80. Berger, H., Kari S., Gabbert U., Rodriguez- Ramos , R., Guinovart, R., Otero, J.A., Bravo
Multiscale Modeling of Ceramic Matrix Composites
NASA Technical Reports Server (NTRS)
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.
Multiscale vascular surface model generation from medical imaging data using hierarchical features.
Bekkers, Eric J; Taylor, Charles A
2008-03-01
Computational fluid dynamics (CFD) modeling of blood flow from image-based patient specific models can provide useful physiologic information for guiding clinical decision making. A novel method for the generation of image-based, 3-D, multiscale vascular surface models for CFD is presented. The method generates multiscale surfaces based on either a linear triangulated or a globally smooth nonuniform rational B-spline (NURB) representation. A robust local curvature analysis is combined with a novel global feature analysis to set mesh element size. The method is particularly useful for CFD modeling of complex vascular geometries that have a wide range of vasculature size scales, in conditions where 1) initial surface mesh density is an important consideration for balancing surface accuracy with manageable size volumetric meshes, 2) adaptive mesh refinement based on flow features makes an underlying explicit smooth surface representation desirable, and 3) semi-automated detection and trimming of a large number of inlet and outlet vessels expedites model construction.
Image based 3D city modeling : Comparative study
NASA Astrophysics Data System (ADS)
Singh, S. P.; Jain, K.; Mandla, V. R.
2014-06-01
3D city model is a digital representation of the Earth's surface and it's related objects such as building, tree, vegetation, and some manmade feature belonging to urban area. The demand of 3D city modeling is increasing rapidly for various engineering and non-engineering applications. Generally four main image based approaches were used for virtual 3D city models generation. In first approach, researchers were used Sketch based modeling, second method is Procedural grammar based modeling, third approach is Close range photogrammetry based modeling and fourth approach is mainly based on Computer Vision techniques. SketchUp, CityEngine, Photomodeler and Agisoft Photoscan are the main softwares to represent these approaches respectively. These softwares have different approaches & methods suitable for image based 3D city modeling. Literature study shows that till date, there is no complete such type of comparative study available to create complete 3D city model by using images. This paper gives a comparative assessment of these four image based 3D modeling approaches. This comparative study is mainly based on data acquisition methods, data processing techniques and output 3D model products. For this research work, study area is the campus of civil engineering department, Indian Institute of Technology, Roorkee (India). This 3D campus acts as a prototype for city. This study also explains various governing parameters, factors and work experiences. This research work also gives a brief introduction, strengths and weakness of these four image based techniques. Some personal comment is also given as what can do or what can't do from these softwares. At the last, this study shows; it concluded that, each and every software has some advantages and limitations. Choice of software depends on user requirements of 3D project. For normal visualization project, SketchUp software is a good option. For 3D documentation record, Photomodeler gives good result. For Large city
Towards multiscale modeling of influenza infection
Murillo, Lisa N.; Murillo, Michael S.; Perelson, Alan S.
2013-01-01
Aided by recent advances in computational power, algorithms, and higher fidelity data, increasingly detailed theoretical models of infection with influenza A virus are being developed. We review single scale models as they describe influenza infection from intracellular to global scales, and, in particular, we consider those models that capture details specific to influenza and can be used to link different scales. We discuss the few multiscale models of influenza infection that have been developed in this emerging field. In addition to discussing modeling approaches, we also survey biological data on influenza infection and transmission that is relevant for constructing influenza infection models. We envision that, in the future, multiscale models that capitalize on technical advances in experimental biology and high performance computing could be used to describe the large spatial scale epidemiology of influenza infection, evolution of the virus, and transmission between hosts more accurately. PMID:23608630
Multiscale information modelling for heart morphogenesis
NASA Astrophysics Data System (ADS)
Abdulla, T.; Imms, R.; Schleich, J. M.; Summers, R.
2010-07-01
Science is made feasible by the adoption of common systems of units. As research has become more data intensive, especially in the biomedical domain, it requires the adoption of a common system of information models, to make explicit the relationship between one set of data and another, regardless of format. This is being realised through the OBO Foundry to develop a suite of reference ontologies, and NCBO Bioportal to provide services to integrate biomedical resources and functionality to visualise and create mappings between ontology terms. Biomedical experts tend to be focused at one level of spatial scale, be it biochemistry, cell biology, or anatomy. Likewise, the ontologies they use tend to be focused at a particular level of scale. There is increasing interest in a multiscale systems approach, which attempts to integrate between different levels of scale to gain understanding of emergent effects. This is a return to physiological medicine with a computational emphasis, exemplified by the worldwide Physiome initiative, and the European Union funded Network of Excellence in the Virtual Physiological Human. However, little work has been done on how information modelling itself may be tailored to a multiscale systems approach. We demonstrate how this can be done for the complex process of heart morphogenesis, which requires multiscale understanding in both time and spatial domains. Such an effort enables the integration of multiscale metrology.
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
Multi-scale modeling in cell biology
Meier-Schellersheim, Martin; Fraser, Iain D. C.; Klauschen, Frederick
2009-01-01
Biomedical research frequently involves performing experiments and developing hypotheses that link different scales of biological systems such as, for instance, the scales of intracellular molecular interactions to the scale of cellular behavior and beyond to the behavior of cell populations. Computational modeling efforts that aim at exploring such multi-scale systems quantitatively with the help of simulations have to incorporate several different simulation techniques due to the different time and space scales involved. Here, we provide a non-technical overview of how different scales of experimental research can be combined with the appropriate computational modeling techniques. We also show that current modeling software permits building and simulating multi-scale models without having to become involved with the underlying technical details of computational modeling. PMID:20448808
Multiscale Models of Breast Cancer Progression
Chakrabarti, Anirikh; Verbridge, Scott; Stroock, Abraham D.; Fischbach, Claudia; Varner, Jeffrey D.
2013-01-01
Breast cancer initiation, invasion and metastasis span multiple length and time scales. Molecular events at short length scales lead to an initial tumorigenic population, which left unchecked by immune action, acts at increasingly longer length scales until eventually the cancer cells escape from the primary tumor site. This series of events is highly complex, involving multiple cell types interacting with (and shaping) the microenvironment. Multiscale mathematical models have emerged as a powerful tool to quantitatively integrate the convective-diffusion-reaction processes occurring on the systemic scale, with the molecular signaling processes occurring on the cellular and subcellular scales. In this study, we reviewed the current state of the art in cancer modeling across multiple length scales, with an emphasis on the integration of intracellular signal transduction models with pro-tumorigenic chemical and mechanical microenvironmental cues. First, we reviewed the underlying biomolecular origin of breast cancer, with a special emphasis on angiogenesis. Then, we summarized the development of tissue engineering platforms which could provide highfidelity ex vivo experimental models to identify and validate multiscale simulations. Lastly, we reviewed top-down and bottom-up multiscale strategies that integrate subcellular networks with the microenvironment. We present models of a variety of cancers, in addition to breast cancer specific models. Taken together, we expect as the sophistication of the simulations increase, that multiscale modeling and bottom-up agent-based models in particular will become an increasingly important platform technology for basic scientific discovery, as well as the identification and validation of potentially novel therapeutic targets. PMID:23008097
Multiscale Modeling of Multiphase Fluid Flow
2016-08-01
models. 5.1 Introduction Heat and mass transfer in thin evaporating liquid films is of interest in a variety of technological and industrial...modeling of evaporative heat and mass transfer in thin films presents a multiscale problem where the intermolecular interactions between the substrate...Iskrenova, S.S. Patnaik, J. Heat Transfer , 137 (2015) 080912. [12] E.K. Iskrenova, S.S. Patnaik, International Journal of Heat and Mass Transfer , 100
Multiscale modelling of hydraulic conductivity in vuggy porous media.
Daly, K R; Roose, T
2014-02-08
Flow in both saturated and non-saturated vuggy porous media, i.e. soil, is inherently multiscale. The complex microporous structure of the soil aggregates and the wider vugs provides a multitude of flow pathways and has received significant attention from the X-ray computed tomography (CT) community with a constant drive to image at higher resolution. Using multiscale homogenization, we derive averaged equations to study the effects of the microscale structure on the macroscopic flow. The averaged model captures the underlying geometry through a series of cell problems and is verified through direct comparison to numerical simulations of the full structure. These methods offer significant reductions in computation time and allow us to perform three-dimensional calculations with complex geometries on a desktop PC. The results show that the surface roughness of the aggregate has a significantly greater effect on the flow than the microstructure within the aggregate. Hence, this is the region in which the resolution of X-ray CT for image-based modelling has the greatest impact.
Multiscale modeling of failure in composites under model parameter uncertainty
NASA Astrophysics Data System (ADS)
Bogdanor, Michael J.; Oskay, Caglar; Clay, Stephen B.
2015-09-01
This manuscript presents a multiscale stochastic failure modeling approach for fiber reinforced composites. A homogenization based reduced-order multiscale computational model is employed to predict the progressive damage accumulation and failure in the composite. Uncertainty in the composite response is modeled at the scale of the microstructure by considering the constituent material (i.e., matrix and fiber) parameters governing the evolution of damage as random variables. Through the use of the multiscale model, randomness at the constituent scale is propagated to the scale of the composite laminate. The probability distributions of the underlying material parameters are calibrated from unidirectional composite experiments using a Bayesian statistical approach. The calibrated multiscale model is exercised to predict the ultimate tensile strength of quasi-isotropic open-hole composite specimens at various loading rates. The effect of random spatial distribution of constituent material properties on the composite response is investigated.
Concurrent Multiscale Modeling of Embedded Nanomechanics
Rudd, R E
2001-04-13
We discuss concurrent multiscale simulations of dynamic and temperature-dependent processes found in nanomechanical systems coupled to larger scale surroundings. We focus on the behavior of sub-micron Micro-Electro-Mechanical Systems (MEMS), especially micro-resonators. The coupling of length scales methodology we have developed for MEMS employs an atomistic description of small but key regions of the system, consisting of millions of atoms, coupled concurrently to a finite element model of the periphery. The result is a model that accurately describes the behavior of the mechanical components of MEMS down to the atomic scale. This paper reviews some of the general issues involved in concurrent multiscale simulation, extends the methodology to metallic systems and describes how it has been used to identify atomistic effects in sub-micron resonators.
Stochastic multiscale model for carbonate rocks.
Biswal, B; Oren, P-E; Held, R J; Bakke, S; Hilfer, R
2007-06-01
A multiscale model for the diagenesis of carbonate rocks is proposed. It captures important pore scale characteristics of carbonate rocks: wide range of length scales in the pore diameters; large variability in the permeability; and strong dependence of the geometrical and transport parameters on the resolution. A pore scale microstructure of an oolithic dolostone with generic diagenetic features is successfully generated. The continuum representation of a reconstructed cubic sample of side length 2mm contains roughly 42 x 10{6} crystallites and pore diameters varying over many decades. Petrophysical parameters are computed on discretized samples of sizes up to 1000{3}. The model can be easily adapted to represent the multiscale microstructure of a wide variety of carbonate rocks.
Image based Monte Carlo Modeling for Computational Phantom
NASA Astrophysics Data System (ADS)
Cheng, Mengyun; Wang, Wen; Zhao, Kai; Fan, Yanchang; Long, Pengcheng; Wu, Yican
2014-06-01
The evaluation on the effects of ionizing radiation and the risk of radiation exposure on human body has been becoming one of the most important issues for radiation protection and radiotherapy fields, which is helpful to avoid unnecessary radiation and decrease harm to human body. In order to accurately evaluate the dose on human body, it is necessary to construct more realistic computational phantom. However, manual description and verfication of the models for Monte carlo(MC)simulation are very tedious, error-prone and time-consuming. In addiation, it is difficult to locate and fix the geometry error, and difficult to describe material information and assign it to cells. MCAM (CAD/Image-based Automatic Modeling Program for Neutronics and Radiation Transport Simulation) was developed as an interface program to achieve both CAD- and image-based automatic modeling by FDS Team (Advanced Nuclear Energy Research Team, http://www.fds.org.cn). The advanced version (Version 6) of MCAM can achieve automatic conversion from CT/segmented sectioned images to computational phantoms such as MCNP models. Imaged-based automatic modeling program(MCAM6.0) has been tested by several medical images and sectioned images. And it has been applied in the construction of Rad-HUMAN. Following manual segmentation and 3D reconstruction, a whole-body computational phantom of Chinese adult female called Rad-HUMAN was created by using MCAM6.0 from sectioned images of a Chinese visible human dataset. Rad-HUMAN contains 46 organs/tissues, which faithfully represented the average anatomical characteristics of the Chinese female. The dose conversion coefficients(Dt/Ka) from kerma free-in-air to absorbed dose of Rad-HUMAN were calculated. Rad-HUMAN can be applied to predict and evaluate dose distributions in the Treatment Plan System (TPS), as well as radiation exposure for human body in radiation protection.
PDF-based heterogeneous multiscale filtration model.
Gong, Jian; Rutland, Christopher J
2015-04-21
Motivated by modeling of gasoline particulate filters (GPFs), a probability density function (PDF) based heterogeneous multiscale filtration (HMF) model is developed to calculate filtration efficiency of clean particulate filters. A new methodology based on statistical theory and classic filtration theory is developed in the HMF model. Based on the analysis of experimental porosimetry data, a pore size probability density function is introduced to represent heterogeneity and multiscale characteristics of the porous wall. The filtration efficiency of a filter can be calculated as the sum of the contributions of individual collectors. The resulting HMF model overcomes the limitations of classic mean filtration models which rely on tuning of the mean collector size. Sensitivity analysis shows that the HMF model recovers the classical mean model when the pore size variance is very small. The HMF model is validated by fundamental filtration experimental data from different scales of filter samples. The model shows a good agreement with experimental data at various operating conditions. The effects of the microstructure of filters on filtration efficiency as well as the most penetrating particle size are correctly predicted by the model.
Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM).
Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei
2015-11-28
Gaussian network model (GNM) and anisotropic network model (ANM) are some of the most popular methods for the study of protein flexibility and related functions. In this work, we propose generalized GNM (gGNM) and ANM methods and show that the GNM Kirchhoff matrix can be built from the ideal low-pass filter, which is a special case of a wide class of correlation functions underpinning the linear scaling flexibility-rigidity index (FRI) method. Based on the mathematical structure of correlation functions, we propose a unified framework to construct generalized Kirchhoff matrices whose matrix inverse leads to gGNMs, whereas, the direct inverse of its diagonal elements gives rise to FRI method. With this connection, we further introduce two multiscale elastic network models, namely, multiscale GNM (mGNM) and multiscale ANM (mANM), which are able to incorporate different scales into the generalized Kirchhoff matrices or generalized Hessian matrices. We validate our new multiscale methods with extensive numerical experiments. We illustrate that gGNMs outperform the original GNM method in the B-factor prediction of a set of 364 proteins. We demonstrate that for a given correlation function, FRI and gGNM methods provide essentially identical B-factor predictions when the scale value in the correlation function is sufficiently large. More importantly, we reveal intrinsic multiscale behavior in protein structures. The proposed mGNM and mANM are able to capture this multiscale behavior and thus give rise to a significant improvement of more than 11% in B-factor predictions over the original GNM and ANM methods. We further demonstrate the benefits of our mGNM through the B-factor predictions of many proteins that fail the original GNM method. We show that the proposed mGNM can also be used to analyze protein domain separations. Finally, we showcase the ability of our mANM for the analysis of protein collective motions.
Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM)
NASA Astrophysics Data System (ADS)
Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei
2015-11-01
Gaussian network model (GNM) and anisotropic network model (ANM) are some of the most popular methods for the study of protein flexibility and related functions. In this work, we propose generalized GNM (gGNM) and ANM methods and show that the GNM Kirchhoff matrix can be built from the ideal low-pass filter, which is a special case of a wide class of correlation functions underpinning the linear scaling flexibility-rigidity index (FRI) method. Based on the mathematical structure of correlation functions, we propose a unified framework to construct generalized Kirchhoff matrices whose matrix inverse leads to gGNMs, whereas, the direct inverse of its diagonal elements gives rise to FRI method. With this connection, we further introduce two multiscale elastic network models, namely, multiscale GNM (mGNM) and multiscale ANM (mANM), which are able to incorporate different scales into the generalized Kirchhoff matrices or generalized Hessian matrices. We validate our new multiscale methods with extensive numerical experiments. We illustrate that gGNMs outperform the original GNM method in the B-factor prediction of a set of 364 proteins. We demonstrate that for a given correlation function, FRI and gGNM methods provide essentially identical B-factor predictions when the scale value in the correlation function is sufficiently large. More importantly, we reveal intrinsic multiscale behavior in protein structures. The proposed mGNM and mANM are able to capture this multiscale behavior and thus give rise to a significant improvement of more than 11% in B-factor predictions over the original GNM and ANM methods. We further demonstrate the benefits of our mGNM through the B-factor predictions of many proteins that fail the original GNM method. We show that the proposed mGNM can also be used to analyze protein domain separations. Finally, we showcase the ability of our mANM for the analysis of protein collective motions.
Multiscale Models of Antibiotic Probiotics
Kaznessis, Yiannis N.
2014-01-01
The discovery of antibiotics is one of the most important advances in the history of humankind. For eighty years human life expectancy and standards of living improved greatly thanks to antibiotics. But bacteria have been fighting back, developing resistance to our most potent molecules. New, alternative strategies must be explored as antibiotic therapies become obsolete because of bacterial resistance. Mathematical models and simulations guide the development of complex technologies, such as aircrafts, bridges, communication systems and transportation systems. Herein, models are discussed that guide the development of new antibiotic technologies. These models span multiple molecular and cellular scales, and facilitate the development of a technology that addresses a significant societal challenge. We argue that simulations can be a creative source of knowledge. PMID:25313349
Multiscale Stochastic Simulation and Modeling
James Glimm; Xiaolin Li
2006-01-10
Acceleration driven instabilities of fluid mixing layers include the classical cases of Rayleigh-Taylor instability, driven by a steady acceleration and Richtmyer-Meshkov instability, driven by an impulsive acceleration. Our program starts with high resolution methods of numerical simulation of two (or more) distinct fluids, continues with analytic analysis of these solutions, and the derivation of averaged equations. A striking achievement has been the systematic agreement we obtained between simulation and experiment by using a high resolution numerical method and improved physical modeling, with surface tension. Our study is accompanies by analysis using stochastic modeling and averaged equations for the multiphase problem. We have quantified the error and uncertainty using statistical modeling methods.
Multiscale Modeling with Carbon Nanotubes
Maiti, A
2006-02-21
Technologically important nanomaterials come in all shapes and sizes. They can range from small molecules to complex composites and mixtures. Depending upon the spatial dimensions of the system and properties under investigation computer modeling of such materials can range from equilibrium and nonequilibrium Quantum Mechanics, to force-field-based Molecular Mechanics and kinetic Monte Carlo, to Mesoscale simulation of evolving morphology, to Finite-Element computation of physical properties. This brief review illustrates some of the above modeling techniques through a number of recent applications with carbon nanotubes: nano electromechanical sensors (NEMS), chemical sensors, metal-nanotube contacts, and polymer-nanotube composites.
Multiscale modeling of polyelectrolyte gels
NASA Astrophysics Data System (ADS)
Wallmersperger, Thomas; Wittel, Falk K.; Kröplin, Bernd H.
2006-03-01
Electrolyte polymer gels are a very attractive class of actuation materials with remarkable electronic and mechanical properties having a great similarity to biological contractile tissues. They consist of a polymer network with ionizable groups and a liquid phase with mobile ions. Absorption and delivery of solvent lead to a considerably large change of volume. Due to this capability, they can be used as actuators for technical applications, where large swelling and shrinkage is desired. In the present work chemically and electrically stimulated polymer gels in a solution bath are investigated. To describe the different complicated phenomena occurring in these gels adequately, the modeling can be conducted on different scales. Therefore, models based on the statistical theory and porous media theory, as well as a multi-field model and a discrete element formulation are derived. A refinement of the different theories from global macroscopic to microscopic are presented in this paper: The statistical theory is a macroscopic theory capable to describe the global swelling or bending e.g. of a gel film, while the general theory of porous media (TPM) is a macroscopic continuum theory which is based on the theory of mixtures extended by the concept of volume fractions. The TPM is a homogenized model, i.e. all geometrical and physical quantities can be seen as statistical averages of the real quantities. The presented chemo-electro-mechanical multi-field formulation is a mesoscopic theory. It is capable of giving the concentrations and the electric potential in the whole domain. Finally the (micromechanical) discrete element (DE) theory is employed. In this case, the continuum is represented by distributed particles with local interaction relations combined with balance equations for the chemical field. This method is predestined for problems involving large displacements, strains and discontinuities. The presented formulations are compared and conclusions on their
Multiscale modeling of lipids and lipid bilayers.
Lyubartsev, Alexander P
2005-12-01
A multiscale modeling approach is applied for simulations of lipids and lipid assemblies on mesoscale. First, molecular dynamics simulation of initially disordered system of lipid molecules in water within all-atomic model was carried out. On the next stage, structural data obtained from the molecular dynamics (MD) simulation were used to build a coarse-grained (ten sites) lipid model, with effective interaction potentials computed by the inverse Monte Carlo method. Finally, several simulations of the coarse-grained model on longer length- and time-scale were performed, both within Monte Carlo and molecular dynamics simulations: a periodical sample of lipid molecules ordered in bilayer, a free sheet of such bilayer without periodic boundary conditions, formation of vesicle from a plain membrane, process of self-assembly of lipids randomly dispersed in volume. It was shown that the coarse-grained model, developed exclusively from all-atomic simulation data, reproduces well all the basic features of lipids in water solution.
Scheibe, Timothy D.; Murphy, Ellyn M.; Chen, Xingyuan; Rice, Amy K.; Carroll, Kenneth C.; Palmer, Bruce J.; Tartakovsky, Alexandre M.; Battiato, Ilenia; Wood, Brian D.
2015-01-01
One of the most significant challenges facing hydrogeologic modelers is the disparity between those spatial and temporal scales at which fundamental flow, transport and reaction processes can best be understood and quantified (e.g., microscopic to pore scales, seconds to days) and those at which practical model predictions are needed (e.g., plume to aquifer scales, years to centuries). While the multiscale nature of hydrogeologic problems is widely recognized, technological limitations in computational and characterization restrict most practical modeling efforts to fairly coarse representations of heterogeneous properties and processes. For some modern problems, the necessary level of simplification is such that model parameters may lose physical meaning and model predictive ability is questionable for any conditions other than those to which the model was calibrated. Recently, there has been broad interest across a wide range of scientific and engineering disciplines in simulation approaches that more rigorously account for the multiscale nature of systems of interest. In this paper, we review a number of such approaches and propose a classification scheme for defining different types of multiscale simulation methods and those classes of problems to which they are most applicable. Our classification scheme is presented in terms of a flow chart (Multiscale Analysis Platform or MAP), and defines several different motifs of multiscale simulation. Within each motif, the member methods are reviewed and example applications are discussed. We focus attention on hybrid multiscale methods, in which two or more models with different physics described at fundamentally different scales are directly coupled within a single simulation. Very recently these methods have begun to be applied to groundwater flow and transport simulations, and we discuss these applications in the context of our classification scheme. As computational and characterization capabilities continue to
Institute for Multiscale Modeling of Biological Interactions
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.
Multiscale Modeling of Microbial Communities
NASA Astrophysics Data System (ADS)
Blanchard, Andrew
Although bacteria are single-celled organisms, they exist in nature primarily in the form of complex communities, participating in a vast array of social interactions through regulatory gene networks. The social interactions between individual cells drive the emergence of community structures, resulting in an intricate relationship across multiple spatiotemporal scales. Here, I present my work towards developing and applying the tools necessary to model the complex dynamics of bacterial communities. In Chapter 2, I utilize a reaction-diffusion model to determine the population dynamics for a population with two species. One species (CDI+) utilizes contact dependent inhibition to kill the other sensitive species (CDI-). The competition can produce diverse patterns, including extinction, coexistence, and localized aggregation. The emergence, relative abundance, and characteristic features of these patterns are collectively determined by the competitive benefit of CDI and its growth disadvantage for a given rate of population diffusion. The results provide a systematic and statistical view of CDI-based bacterial population competition, expanding the spectrum of our knowledge about CDI systems and possibly facilitating new experimental tests for a deeper understanding of bacterial interactions. In the following chapter, I present a systematic computational survey on the relationship between social interaction types and population structures for two-species communities by developing and utilizing a hybrid computational framework that combines discrete element techniques with reaction-diffusion equations. The impact of deleterious and beneficial interactions on the community are quantified. Deleterious interactions generate an increased variance in relative abundance, a drastic decrease in surviving lineages, and a rough expanding front. In contrast, beneficial interactions contribute to a reduced variance in relative abundance, an enhancement in lineage number, and a
A multiscale strength model in HYDRA
NASA Astrophysics Data System (ADS)
Marinak, M. M.; Barton, N. R.
2016-10-01
We describe a multiscale strength model recently implemented in HYDRA. The model incorporates results from a hierarchy of methods which span from the atomistic to the continuum level. Those are obtained from focused physics codes that treat density functional theory, molecular statics, molecular dynamics, dislocation dynamics and continuum mechanics. The model is designed to handle extreme pressures and temperatures, and is especially appropriate for strain rates in excess of 104 s-1. As such it can be used to provide insight into HEDP experimental observations. The model has demonstrated success in capturing planar Rayleigh-Taylor growth for 1 Mbar shocks in Ta and V. This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344.
Multiscale Models in the Biomechanics of Plant Growth
Fozard, John A.
2015-01-01
Plant growth occurs through the coordinated expansion of tightly adherent cells, driven by regulated softening of cell walls. It is an intrinsically multiscale process, with the integrated properties of multiple cell walls shaping the whole tissue. Multiscale models encode physical relationships to bring new understanding to plant physiology and development. PMID:25729061
Variational multiscale models for charge transport.
Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin
2012-01-01
This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle
Variational multiscale models for charge transport
Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin
2012-01-01
This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle
A Multiscale Model for Virus Capsid Dynamics
Chen, Changjun; Saxena, Rishu; Wei, Guo-Wei
2010-01-01
Viruses are infectious agents that can cause epidemics and pandemics. The understanding of virus formation, evolution, stability, and interaction with host cells is of great importance to the scientific community and public health. Typically, a virus complex in association with its aquatic environment poses a fabulous challenge to theoretical description and prediction. In this work, we propose a differential geometry-based multiscale paradigm to model complex biomolecule systems. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum domain of the fluid mechanical description of the aquatic environment from the microscopic discrete domain of the atomistic description of the biomolecule. A multiscale action functional is constructed as a unified framework to derive the governing equations for the dynamics of different scales. We show that the classical Navier-Stokes equation for the fluid dynamics and Newton's equation for the molecular dynamics can be derived from the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. PMID:20224756
Multiscale measurement error models for aggregated small area health data.
Aregay, Mehreteab; Lawson, Andrew B; Faes, Christel; Kirby, Russell S; Carroll, Rachel; Watjou, Kevin
2016-08-01
Spatial data are often aggregated from a finer (smaller) to a coarser (larger) geographical level. The process of data aggregation induces a scaling effect which smoothes the variation in the data. To address the scaling problem, multiscale models that link the convolution models at different scale levels via the shared random effect have been proposed. One of the main goals in aggregated health data is to investigate the relationship between predictors and an outcome at different geographical levels. In this paper, we extend multiscale models to examine whether a predictor effect at a finer level hold true at a coarser level. To adjust for predictor uncertainty due to aggregation, we applied measurement error models in the framework of multiscale approach. To assess the benefit of using multiscale measurement error models, we compare the performance of multiscale models with and without measurement error in both real and simulated data. We found that ignoring the measurement error in multiscale models underestimates the regression coefficient, while it overestimates the variance of the spatially structured random effect. On the other hand, accounting for the measurement error in multiscale models provides a better model fit and unbiased parameter estimates.
Multiscale modeling of shock-loaded materials
NASA Astrophysics Data System (ADS)
Ortiz, Michael
2001-06-01
I will describe efforts within Caltech's ASCI/ASAP Center to develop a Virtual Testing Facility (VTF) for investigating the dynamic properties of materials subjected to extreme conditions of pressure, temperature and strain rate. The facility combines an Eulerian description of HE materials, with a Lagrangian description of solids. We subscribe to the multiscale modeling paradigm as the means of developing material models with a minimum of empiricism by a systematic bridging of lengthscales, from atomistic to macroscopic. For instance, we have developed a multiscale model of bcc Ta in which we specifically consider the following unit processes: double-kink formation and thermally activated motion of kinks; the close-range interactions between primary and forest dislocation, leading to the formation of jogs; the percolation motion of dislocations through a random array of forest dislocations introducing short-range obstacles of different strengths; dislocation multiplication due to breeding by double cross-slip; and dislocation pair-annihilation. These models contained parameters representing well-characterized physical properties of the material. All essential parameters of the model have been determined by recourse to atomistic calculations based on empirical potentials fitted to first-principles quantum mechanical calculations. In addition, the volumetric equation of state and the pressure and temperature dependence of the material have been determined directly from first-principles quantum mechanical calculations. The model is found to capture salient experimentally observed features of the behavior of Ta crystals. The VTF also includes cohesive descriptions of fracture enabling the simulation of fragmentation. The performance and scalability of the VTF on ASCI platforms has been extensively assessed. As an overarching application which tests the integration of all its components, the VTF is being applied to the simulation of detonation-induced shock loading of
Image-based modeling of flow and reactive transport in porous media
NASA Astrophysics Data System (ADS)
Qin, Chao-Zhong; Hoang, Tuong; Verhoosel, Clemens V.; Harald van Brummelen, E.; Wijshoff, Herman M. A.
2017-04-01
Brummelen, and A. Reali (2016), Mixed Isogeometric Finite Cell Methods for the Stokes problem, Computer Methods in Applied Mechanics and Engineering, doi:10.1016/j.cma.2016.07.027. Scheibe, T. D., W. A. Perkins, M. C. Richmond, M. I. McKinley, P. D. J. Romero-Gomez, M. Oostrom, T. W. Wietsma, J. A. Serkowski, and J. M. Zachara (2015), Pore-scale and multiscale numerical simulation of flow and transport in a laboratory-scale column, Water Resources Research, 51(2), 1023-1035, doi:10.1002/2014WR015959. Verhoosel, C. V., G. J. van Zwieten, B. van Rietbergen, and R. de Borst (2015), Image-based goal-oriented adaptive isogeometric analysis with application to the micro-mechanical modeling of trabecular bone, Computer Methods in Applied Mechanics and Engineering, 284(February), 138-164, doi:10.1016/j.cma.2014.07.009.
Multiscale modelling of nucleosome core particle aggregation
NASA Astrophysics Data System (ADS)
Lyubartsev, Alexander P.; Korolev, Nikolay; Fan, Yanping; Nordenskiöld, Lars
2015-02-01
The nucleosome core particle (NCP) is the basic building block of chromatin. Under the influence of multivalent cations, isolated mononucleosomes exhibit a rich phase behaviour forming various columnar phases with characteristic NCP-NCP stacking. NCP stacking is also a regular element of chromatin structure in vivo. Understanding the mechanism of nucleosome stacking and the conditions leading to self-assembly of NCPs is still incomplete. Due to the complexity of the system and the need to describe electrostatics properly by including the explicit mobile ions, novel modelling approaches based on coarse-grained (CG) methods at the multiscale level becomes a necessity. In this work we present a multiscale CG computer simulation approach to modelling interactions and self-assembly of solutions of NCPs induced by the presence of multivalent cations. Starting from continuum simulations including explicit three-valent cobalt(III)hexammine (CoHex3+) counterions and 20 NCPs, based on a previously developed advanced CG NCP model with one bead per amino acid and five beads per two DNA base pair unit (Fan et al 2013 PLoS One 8 e54228), we use the inverse Monte Carlo method to calculate effective interaction potentials for a ‘super-CG’ NCP model consisting of seven beads for each NCP. These interaction potentials are used in large-scale simulations of up to 5000 NCPs, modelling self-assembly induced by CoHex3+. The systems of ‘super-CG’ NCPs form a single large cluster of stacked NCPs without long-range order in agreement with experimental data for NCPs precipitated by the three-valent polyamine, spermidine3+.
Multiscale agent-based consumer market modeling.
North, M. J.; Macal, C. M.; St. Aubin, J.; Thimmapuram, P.; Bragen, M.; Hahn, J.; Karr, J.; Brigham, N.; Lacy, M. E.; Hampton, D.; Decision and Information Sciences; Procter & Gamble Co.
2010-05-01
Consumer markets have been studied in great depth, and many techniques have been used to represent them. These have included regression-based models, logit models, and theoretical market-level models, such as the NBD-Dirichlet approach. Although many important contributions and insights have resulted from studies that relied on these models, there is still a need for a model that could more holistically represent the interdependencies of the decisions made by consumers, retailers, and manufacturers. When the need is for a model that could be used repeatedly over time to support decisions in an industrial setting, it is particularly critical. Although some existing methods can, in principle, represent such complex interdependencies, their capabilities might be outstripped if they had to be used for industrial applications, because of the details this type of modeling requires. However, a complementary method - agent-based modeling - shows promise for addressing these issues. Agent-based models use business-driven rules for individuals (e.g., individual consumer rules for buying items, individual retailer rules for stocking items, or individual firm rules for advertizing items) to determine holistic, system-level outcomes (e.g., to determine if brand X's market share is increasing). We applied agent-based modeling to develop a multi-scale consumer market model. We then conducted calibration, verification, and validation tests of this model. The model was successfully applied by Procter & Gamble to several challenging business problems. In these situations, it directly influenced managerial decision making and produced substantial cost savings.
Image-based modelling of skeletal muscle oxygenation
Clough, G. F.
2017-01-01
The supply of oxygen in sufficient quantity is vital for the correct functioning of all organs in the human body, in particular for skeletal muscle during exercise. Disease is often associated with both an inhibition of the microvascular supply capability and is thought to relate to changes in the structure of blood vessel networks. Different methods exist to investigate the influence of the microvascular structure on tissue oxygenation, varying over a range of application areas, i.e. biological in vivo and in vitro experiments, imaging and mathematical modelling. Ideally, all of these methods should be combined within the same framework in order to fully understand the processes involved. This review discusses the mathematical models of skeletal muscle oxygenation currently available that are based upon images taken of the muscle microvasculature in vivo and ex vivo. Imaging systems suitable for capturing the blood vessel networks are discussed and respective contrasting methods presented. The review further informs the association between anatomical characteristics in health and disease. With this review we give the reader a tool to understand and establish the workflow of developing an image-based model of skeletal muscle oxygenation. Finally, we give an outlook for improvements needed for measurements and imaging techniques to adequately investigate the microvascular capability for oxygen exchange. PMID:28202595
Image-based modelling of skeletal muscle oxygenation.
Zeller-Plumhoff, B; Roose, T; Clough, G F; Schneider, P
2017-02-01
The supply of oxygen in sufficient quantity is vital for the correct functioning of all organs in the human body, in particular for skeletal muscle during exercise. Disease is often associated with both an inhibition of the microvascular supply capability and is thought to relate to changes in the structure of blood vessel networks. Different methods exist to investigate the influence of the microvascular structure on tissue oxygenation, varying over a range of application areas, i.e. biological in vivo and in vitro experiments, imaging and mathematical modelling. Ideally, all of these methods should be combined within the same framework in order to fully understand the processes involved. This review discusses the mathematical models of skeletal muscle oxygenation currently available that are based upon images taken of the muscle microvasculature in vivo and ex vivo Imaging systems suitable for capturing the blood vessel networks are discussed and respective contrasting methods presented. The review further informs the association between anatomical characteristics in health and disease. With this review we give the reader a tool to understand and establish the workflow of developing an image-based model of skeletal muscle oxygenation. Finally, we give an outlook for improvements needed for measurements and imaging techniques to adequately investigate the microvascular capability for oxygen exchange.
Multiscale modeling of three-dimensional genome
NASA Astrophysics Data System (ADS)
Zhang, Bin; Wolynes, Peter
The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.
An approach to multiscale modelling with graph grammars
Ong, Yongzhi; Streit, Katarína; Henke, Michael; Kurth, Winfried
2014-01-01
Background and Aims 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. Methods 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. Key Results 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. Conclusions 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. PMID:25134929
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 models for vertebrate limb development.
Newman, Stuart A; Christley, Scott; Glimm, Tilmann; Hentschel, H G E; Kazmierczak, Bogdan; Zhang, Yong-Tao; Zhu, Jianfeng; Alber, Mark
2008-01-01
Dynamical systems in which geometrically extended model cells produce and interact with diffusible (morphogen) and nondiffusible (extracellular matrix) chemical fields have proved very useful as models for developmental processes. The embryonic vertebrate limb is an apt system for such mathematical and computational modeling since it has been the subject of hundreds of experimental studies, and its normal and variant morphologies and spatiotemporal organization of expressed genes are well known. Because of its stereotypical proximodistally generated increase in the number of parallel skeletal elements, the limb lends itself to being modeled by Turing-type systems which are capable of producing periodic, or quasiperiodic, arrangements of spot- and stripe-like elements. This chapter describes several such models, including, (i) a system of partial differential equations in which changing cell density enters into the dynamics explicitly, (ii) a model for morphogen dynamics alone, derived from the latter system in the "morphostatic limit" where cell movement relaxes on a much slower time-scale than cell differentiation, (iii) a discrete stochastic model for the simplified pattern formation that occurs when limb cells are placed in planar culture, and (iv) several hybrid models in which continuum morphogen systems interact with cells represented as energy-minimizing mesoscopic entities. Progress in devising computational methods for handling 3D, multiscale, multimodel simulations of organogenesis is discussed, as well as for simulating reaction-diffusion dynamics in domains of irregular shape.
Multiscale Modeling of Mesoscale and Interfacial Phenomena
NASA Astrophysics Data System (ADS)
Petsev, Nikolai Dimitrov
we provide a novel and general framework for multiscale modeling of systems featuring one or more dissolved species. This makes it possible to retain molecular detail for parts of the problem that require it while using a simple, continuum description for parts where high detail is unnecessary, reducing the number of degrees of freedom (i.e. number of particles) dramatically. This opens the possibility for modeling ion transport in biological processes and biomolecule assembly in ionic solution, as well as electrokinetic phenomena at interfaces such as corrosion. The number of particles in the system is further reduced through an integrated boundary approach, which we apply to colloidal suspensions. In this thesis, we describe this general framework for multiscale modeling single- and multicomponent systems, provide several simple equilibrium and non-equilibrium case studies, and discuss future applications.
NASA Astrophysics Data System (ADS)
Li, Dengwang; Li, Hongsheng; Wan, Honglin; Chen, Jinhu; Gong, Guanzhong; Wang, Hongjun; Wang, Liming; Yin, Yong
2012-08-01
Mutual information (MI) is a well-accepted similarity measure for image registration in medical systems. However, MI-based registration faces the challenges of high computational complexity and a high likelihood of being trapped into local optima due to an absence of spatial information. In order to solve these problems, multi-scale frameworks can be used to accelerate registration and improve robustness. Traditional Gaussian pyramid representation is one such technique but it suffers from contour diffusion at coarse levels which may lead to unsatisfactory registration results. In this work, a new multi-scale registration framework called edge preserving multiscale registration (EPMR) was proposed based upon an edge preserving total variation L1 norm (TV-L1) scale space representation. TV-L1 scale space is constructed by selecting edges and contours of images according to their size rather than the intensity values of the image features. This ensures more meaningful spatial information with an EPMR framework for MI-based registration. Furthermore, we design an optimal estimation of the TV-L1 parameter in the EPMR framework by training and minimizing the transformation offset between the registered pairs for automated registration in medical systems. We validated our EPMR method on both simulated mono- and multi-modal medical datasets with ground truth and clinical studies from a combined positron emission tomography/computed tomography (PET/CT) scanner. We compared our registration framework with other traditional registration approaches. Our experimental results demonstrated that our method outperformed other methods in terms of the accuracy and robustness for medical images. EPMR can always achieve a small offset value, which is closer to the ground truth both for mono-modality and multi-modality, and the speed can be increased 5-8% for mono-modality and 10-14% for multi-modality registration under the same condition. Furthermore, clinical application by adaptive
Multiscale retinocortical model of contrast processing
NASA Astrophysics Data System (ADS)
Moorhead, Ian R.; Haig, Nigel D.
1996-04-01
Visual performance models have in the past, typically been empirical, relying on the user to supply numerical values such as target contrast and background luminance to describe the performance of the visual system, when undertaking a specified task. However, it is becoming increasingly easy to obtain computer images using for example digital cameras, scanners, imaging photometers and radiometers. We have therefore been examining the possibility of producing a quantitative model of human vision that is capable of directly processing images in order to provide predictions of performance. We are particularly interested in being able to process images of 'real' scenes. The model is inspired by human vision and the components have analogies with parts of the human visual system but their properties are governed primarily by existing psychophysical data. The first stage of the model generates a multiscale, difference of Gaussian (DoG) representation of the image (Burton, Haig and Moorhead), with a central foveal region of high resolution, and with a resolution that declines with eccentricity as the scale of the filter increases. Incorporated into this stage is a gain control process which ensures that the contrast sensitivity is consistent with the psychophysical data of van Nes and Bouman. The second stage incorporates a model of perceived contrast proposed by Cannon and Fullenkamp. Their model assumes the image is analyzed by oriented (Gabor) filters and produces a representation of the image in terms of perceived contrast.
Multi-scale modeling of chemotactic interactions
NASA Astrophysics Data System (ADS)
Grima, Ramon
Biological complexity emerges from the synthesis of biochemical, chemical and physical phenomena. In recent years there has been an intense effort in modeling various cellular systems of interest to understand how the observed complexity emerges from the underlying mechanisms. Most modeling approaches are based on a population description of the cells: these methods, though usually amenable to calculation, are only valid in the limit of large numbers of interacting cells. Many systems of interest involve the interaction of a relatively small number of cells; even biological systems composed of thousands of cells have spatially extended regions over which the number density of cells is small. For the latter cases, population descriptions are not valid and individual based models become a necessity. Such models, usually cellular automaton models, have been numerically studied in recent years; however, these models are not usually amenable to analytic calculation. The work presented in this thesis seeks to fulfill a gap in modeling approaches to the understanding of biocomplexity by constructing an individual based model on which analysis is possible, through the methods of statistical physics and the theory of stochastic processes. This model will be used to study the differences between individual based and population based models and the range of applicability of the latter. For the sake of comparison of the two, new efficient computational algorithms are devised for the simulation of both types of models. We finally complete our multiscale study of modeling by investigating the robustness of individual based models; this meaning a comparison of the results of different microscopic descriptions modeling the same underlying phenomena.
NASA Astrophysics Data System (ADS)
Yoon, Jayoung; Kim, Gerard J.
2003-04-01
Traditionally, three dimension models have been used for building virtual worlds, and a data structure called the "scene graph" is often employed to organize these 3D objects in the virtual space. On the other hand, image-based rendering has recently been suggested as a probable alternative VR platform for its photo-realism, however, due to limited interactivity, it has only been used for simple navigation systems. To combine the merits of these two approaches to object/scene representations, this paper proposes for a scene graph structure in which both 3D models and various image-based scenes/objects can be defined, traversed, and rendered together. In fact, as suggested by Shade et al., these different representations can be used as different LOD's for a given object. For instance, an object might be rendered using a 3D model at close range, a billboard at an intermediate range, and as part of an environment map at far range. The ultimate objective of this mixed platform is to breath more interactivity into the image based rendered VE's by employing 3D models as well. There are several technical challenges in devising such a platform: designing scene graph nodes for various types of image based techniques, establishing criteria for LOD/representation selection, handling their transitions, implementing appropriate interaction schemes, and correctly rendering the overall scene. Currently, we have extended the scene graph structure of the Sense8's WorldToolKit, to accommodate new node types for environment maps billboards, moving textures and sprites, "Tour-into-the-Picture" structure, and view interpolated objects. As for choosing the right LOD level, the usual viewing distance and image space criteria are used, however, the switching between the image and 3D model occurs at a distance from the user where the user starts to perceive the object's internal depth. Also, during interaction, regardless of the viewing distance, a 3D representation would be used, it if
Integrating Multiscale Modeling with Drug Effects for Cancer Treatment.
Li, Xiangfang L; Oduola, Wasiu O; Qian, Lijun; Dougherty, Edward R
2015-01-01
In this paper, we review multiscale modeling for cancer treatment with the incorporation of drug effects from an applied system's pharmacology perspective. Both the classical pharmacology and systems biology are inherently quantitative; however, systems biology focuses more on networks and multi factorial controls over biological processes rather than on drugs and targets in isolation, whereas systems pharmacology has a strong focus on studying drugs with regard to the pharmacokinetic (PK) and pharmacodynamic (PD) relations accompanying drug interactions with multiscale physiology as well as the prediction of dosage-exposure responses and economic potentials of drugs. Thus, it requires multiscale methods to address the need for integrating models from the molecular levels to the cellular, tissue, and organism levels. It is a common belief that tumorigenesis and tumor growth can be best understood and tackled by employing and integrating a multifaceted approach that includes in vivo and in vitro experiments, in silico models, multiscale tumor modeling, continuous/discrete modeling, agent-based modeling, and multiscale modeling with PK/PD drug effect inputs. We provide an example application of multiscale modeling employing stochastic hybrid system for a colon cancer cell line HCT-116 with the application of Lapatinib drug. It is observed that the simulation results are similar to those observed from the setup of the wet-lab experiments at the Translational Genomics Research Institute.
Multiscale modeling of integrated CCS systems
NASA Astrophysics Data System (ADS)
Alhajaj, Ahmed; Shah, Nilay
2015-01-01
The world will continue consuming fossil fuel within the coming decades to meet its growing energy demand; however, this source must be cleaner through implementation of carbon capture, transport and storage (CCTS). This process is complex and involves multiple phases, owned by different operational companies and stakeholders with different business models and regulatory framework. The objective of this work is to develop a multiscale modeling approach to link process models, post-combustion capture plant model and network design models under an optimization framework in order to design and analyse the cost optimal CO2 infrastructure that match CO2 sources and sinks in capacity and time. The network comprises a number of CO2 sources at fixed locations and a number of potential CO2 storage sites. The decisions to be determined include from which sources it is appropriate to capture CO2 and the cost-optimal degree-of-capture (DOC) for a given source and the infrastructural layout of the CO2 transmission network.
Multiscale Modeling of Cavitating Bubbly Flows
NASA Astrophysics Data System (ADS)
Ma, J.; Hsiao, C.-T.; Chahine, G. L.
2013-03-01
Modeling of cavitating bubbly flows is challenging due to the wide range of characteristic lengths of the physics at play: from micrometers (e.g., bubble nuclei radius) to meters (e.g., propeller diameter or sheet cavity length). To address this, we present here a multiscale approach which integrates a Discrete Bubble Model for dispersed microbubbles and a level set N-S solver for macro cavities, along with a mesoscale transition model to bridge the two. This approach was implemented in 3DYNAFScopyright and used to simulate sheet-to-cloud cavitation over a hydrofoil. The hybrid model captures well the full cavitation process starting from free field nuclei and nucleation from solid surfaces. In low pressure region of the foil small nuclei are seen to grow large and eventually merge to form a large scale sheet cavity. A reentrant jet forms under the cavity, travels upstream, and breaks it, resulting in a bubble cloud of a large amount of microbubbles as the broken pockets shrink and travel downstream. This is in good agreement with experimental observations based of sheet lengths and frequency of lift force oscillation. DOE-SBIR, ONR (monitored by Dr. Ki-Han Kim)
Structurally Governed Cell Mechanotransduction through Multiscale Modeling
Kang, John; Puskar, Kathleen M.; Ehrlicher, Allen J.; LeDuc, Philip R.; Schwartz, Russell S.
2015-01-01
Mechanotransduction has been divided into mechanotransmission, mechanosensing, and mechanoresponse, although how a cell performs all three functions using the same set of structural components is still highly debated. Here, we bridge the gap between emerging molecular and systems-level understandings of mechanotransduction through a multiscale model linking these three phases. Our model incorporates a discrete network of actin filaments and associated proteins that responds to stretching through geometric relaxation. We assess three potential activating mechanisms at mechanosensitive crosslinks as inputs to a mixture model of molecular release and benchmark each using experimental data of mechanically-induced Rho GTPase FilGAP release from actin-filamin crosslinks. Our results suggest that filamin-FilGAP mechanotransduction response is best explained by a bandpass mechanism favoring release when crosslinking angles fall outside of a specific range. Our model further investigates the difference between ordered versus disordered networks and finds that a more disordered actin network may allow a cell to more finely tune control of molecular release enabling a more robust response. PMID:25722249
Multiscale approach to equilibrating model polymer melts
NASA Astrophysics Data System (ADS)
Svaneborg, Carsten; Karimi-Varzaneh, Hossein Ali; Hojdis, Nils; Fleck, Frank; Everaers, Ralf
2016-09-01
We present an effective and simple multiscale method for equilibrating Kremer Grest model polymer melts of varying stiffness. In our approach, we progressively equilibrate the melt structure above the tube scale, inside the tube and finally at the monomeric scale. We make use of models designed to be computationally effective at each scale. Density fluctuations in the melt structure above the tube scale are minimized through a Monte Carlo simulated annealing of a lattice polymer model. Subsequently the melt structure below the tube scale is equilibrated via the Rouse dynamics of a force-capped Kremer-Grest model that allows chains to partially interpenetrate. Finally the Kremer-Grest force field is introduced to freeze the topological state and enforce correct monomer packing. We generate 15 melts of 500 chains of 10.000 beads for varying chain stiffness as well as a number of melts with 1.000 chains of 15.000 monomers. To validate the equilibration process we study the time evolution of bulk, collective, and single-chain observables at the monomeric, mesoscopic, and macroscopic length scales. Extension of the present method to longer, branched, or polydisperse chains, and/or larger system sizes is straightforward.
Modelling approaches for evaluating multiscale tendon mechanics
Fang, Fei; Lake, Spencer P.
2016-01-01
Tendon exhibits anisotropic, inhomogeneous and viscoelastic mechanical properties that are determined by its complicated hierarchical structure and varying amounts/organization of different tissue constituents. Although extensive research has been conducted to use modelling approaches to interpret tendon structure–function relationships in combination with experimental data, many issues remain unclear (i.e. the role of minor components such as decorin, aggrecan and elastin), and the integration of mechanical analysis across different length scales has not been well applied to explore stress or strain transfer from macro- to microscale. This review outlines mathematical and computational models that have been used to understand tendon mechanics at different scales of the hierarchical organization. Model representations at the molecular, fibril and tissue levels are discussed, including formulations that follow phenomenological and microstructural approaches (which include evaluations of crimp, helical structure and the interaction between collagen fibrils and proteoglycans). Multiscale modelling approaches incorporating tendon features are suggested to be an advantageous methodology to understand further the physiological mechanical response of tendon and corresponding adaptation of properties owing to unique in vivo loading environments. PMID:26855747
Multiscale physics-based modeling of friction
NASA Astrophysics Data System (ADS)
Eriten, Melih
Frictional contacts between solids exist in nature and in a wide range of engineering applications. Friction causes energy loss, and it is the main source of wear and surface degradation which limits the lifetime of mechanical systems. Yet, friction is needed to walk, run, accelerate, slow down or stop moving systems. Whether desirable or not, friction is a very complex physical phenomenon. The behavior of systems with friction is nonlinear, and the physical mechanisms governing friction behavior span a wide range of spatial and temporal scales. A thorough study of friction should employ experimentalists and theoreticians in chemistry, materials science, tribology, mechanics, dynamics, and structural engineering. High spatial and temporal resolutions are required to capture and model essential physics of a frictional contact. However, such a detailed model is impractical in large-scale structural dynamics simulations; especially since frictional contacts can be numerous in a given application. Reduced-order models (ROMs) achieve broader applicability by compromising several aspects and accounting for the important physics. Hence, rather simple Coulomb friction is still the most ubiquitous model in the modeling and simulation literature. As an alternative, a reduced-order friction model built-up from micromechanics of surfaces is proposed in this work. Continuum-scale formulation of pre-sliding friction behavior is combined with material-strength-based friction coefficients to develop a physics-based friction model at asperity-scale. Then, the statistical summation technique is utilized to build a multiscale modeling framework. A novel joint fretting setup is designed for friction experiments in a practical setting, and the developed models are tested. Both asperity and rough surface friction models show good agreement with experimental data. The influences of materials, surface roughness and contact contamination on the friction are also studied. Finally, the
Multiscale imaging and computational modeling of blood flow in the tumor vasculature.
Kim, Eugene; Stamatelos, Spyros; Cebulla, Jana; Bhujwalla, Zaver M; Popel, Aleksander S; Pathak, Arvind P
2012-11-01
The evolution in our understanding of tumor angiogenesis has been the result of pioneering imaging and computational modeling studies spanning the endothelial cell, microvasculature and tissue levels. Many of these primary data on the tumor vasculature are in the form of images from pre-clinical tumor models that provide a wealth of qualitative and quantitative information in many dimensions and across different spatial scales. However, until recently, the visualization of changes in the tumor vasculature across spatial scales remained a challenge due to a lack of techniques for integrating micro- and macroscopic imaging data. Furthermore, the paucity of three-dimensional (3-D) tumor vascular data in conjunction with the challenges in obtaining such data from patients presents a serious hurdle for the development and validation of predictive, multiscale computational models of tumor angiogenesis. In this review, we discuss the development of multiscale models of tumor angiogenesis, new imaging techniques capable of reproducing the 3-D tumor vascular architecture with high fidelity, and the emergence of "image-based models" of tumor blood flow and molecular transport. Collectively, these developments are helping us gain a fundamental understanding of the cellular and molecular regulation of tumor angiogenesis that will benefit the development of new cancer therapies. Eventually, we expect this exciting integration of multiscale imaging and mathematical modeling to have widespread application beyond the tumor vasculature to other diseases involving a pathological vasculature, such as stroke and spinal cord injury.
Multiscale modeling of polyisoprene on graphite
Pandey, Yogendra Narayan; Brayton, Alexander; Doxastakis, Manolis; Burkhart, Craig; Papakonstantopoulos, George J.
2014-02-07
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.
Multiscale Concrete Modeling of Aging Degradation
Hammi, Yousseff; Gullett, Philipp; Horstemeyer, Mark F.
2015-07-31
In this work a numerical finite element framework is implemented to enable the integration of coupled multiscale and multiphysics transport processes. A User Element subroutine (UEL) in Abaqus is used to simultaneously solve stress equilibrium, heat conduction, and multiple diffusion equations for 2D and 3D linear and quadratic elements. Transport processes in concrete structures and their degradation mechanisms are presented along with the discretization of the governing equations. The multiphysics modeling framework is theoretically extended to the linear elastic fracture mechanics (LEFM) by introducing the eXtended Finite Element Method (XFEM) and based on the XFEM user element implementation of Giner et al. [2009]. A damage model that takes into account the damage contribution from the different degradation mechanisms is theoretically developed. The total contribution of damage is forwarded to a Multi-Stage Fatigue (MSF) model to enable the assessment of the fatigue life and the deterioration of reinforced concrete structures in a nuclear power plant. Finally, two examples are presented to illustrate the developed multiphysics user element implementation and the XFEM implementation of Giner et al. [2009].
Multiscale Atmospheric Physics Modeled by Cumulant Expansions
NASA Astrophysics Data System (ADS)
Marston, Brad; Chini, Greg
2014-03-01
We investigate a systematic and physically based approach to modeling subgrid physics statistically with the use of an expansion in equal-time cumulants. To accomplish this we replace the zonal average employed in previous work with a low-pass filter that separates small and large scales in the zonal direction. The statistics are non-local, inhomogeneous, and anisotropic; the sole approximation is the neglect of 3-point and higher correlation functions. The closure respects the conservation of energy, enstrophy, and angular momentum. An advantage of the formulation is that correlations between large and small scale processes are treated explicitly without the introduction of phenomenological parameterizations. The approach is tested against full numerical simulation of idealized 1- and 2-layer models of the atmospheric general circulation and shown to yield accurate low-order statistics. (The computer model used to perform these tests runs on OS X and is publicly available.) We identify important multiscale interactions and discuss the computational cost of the new scheme. Supported in part by NSF DMR-1306806 and CCF-1048701.
Microphysics in Multi-scale Modeling System with Unified Physics
NASA Technical Reports Server (NTRS)
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.
Multiscale Imaging and Computational Modeling of Blood Flow in the Tumor Vasculature
Kim, Eugene; Stamatelos, Spyros; Cebulla, Jana; Bhujwalla, Zaver M.; Popel, Aleksander S.; Pathak, Arvind P.
2013-01-01
The evolution in our understanding of tumor angiogenesis has been the result of pioneering imaging and computational modeling studies spanning the endothelial cell, microvasculature and tissue levels. Many of these primary data on the tumor vasculature are in the form of images from pre-clinical tumor models that provide a wealth of qualitative and quantitative information in many dimensions and across different spatial scales. However, until recently, the visualization of changes in the tumor vasculature across spatial scales remained a challenge due to a lack of techniques for integrating micro- and macroscopic imaging data. Furthermore, the paucity of three-dimensional (3-D) tumor vascular data in conjunction with the challenges in obtaining such data from patients presents a serious hurdle for the development and validation of predictive, multiscale computational models of tumor angiogenesis. In this review, we discuss the development of multiscale models of tumor angiogenesis, new imaging techniques capable of reproducing the 3-D tumor vascular architecture with high fidelity, and the emergence of “image-based models”of tumor blood flow and molecular transport. Collectively, these developments are helping us gain a fundamental understanding of the cellular and molecular regulation of tumor angiogenesis that will benefit the development of new cancer therapies. Eventually, we expect this exciting integration of multiscale imaging and mathematical modeling to have widespread application beyond the tumor vasculature to other diseases involving a pathological vasculature, such as stroke and spinal cord injury. PMID:22565817
Multiscale Modeling of UHTC: Thermal Conductivity
NASA Technical Reports Server (NTRS)
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.
Multiscale model of platelet translocation and collision
NASA Astrophysics Data System (ADS)
Wang, Weiwei; Mody, Nipa A.; King, Michael R.
2013-07-01
The tethering of platelets on the injured vessel surface mediated by glycoprotein Ibα (GPIbα) - Von Willebrand factor (vWF) bonds, as well as the interaction between flowing platelets and adherent platelets, are two key events that take place immediately following blood vessel injury. This early-stage platelet deposition and accumulation triggers the initiation of hemostasis, a self-defensive mechanism to prevent the body from excessive blood loss. To understand and predict this complex process, one must integrate experimentally determined information on the mechanics and biochemical kinetics of participating receptors over very small time frames (1-1000 μs) and length scales (10-100 nm), to collective phenomena occurring over seconds and tens of microns. In the present study, a unique three dimensional multiscale computational model, Platelet Adhesive Dynamics (PAD), was applied to elucidate the unique physics of (i) a non-spherical, disk-shaped platelet interacting and tethering onto the damaged vessel wall followed by (ii) collisional interactions between a flowing platelet with a downstream adherent platelet. By analyzing numerous simulations under different physiological conditions, we conclude that the platelet's unique spheroid-shape provides heterogeneous, orientation-dependent translocation (rolling) behavior which enhances cell-wall interactions. We also conclude that platelet-platelet near field interactions are critical for cell-cell communication during the initiation of microthrombi. The PAD model described here helps to identify the physical factors that control the initial stages of platelet capture during this process.
Discovering Molecular Targets in Cancer with Multiscale Modeling
Wang, Zhihui; Bordas, Veronika; Deisboeck, Thomas S.
2011-01-01
Multiscale modeling is increasingly being recognized as a promising research area in computational cancer systems biology. Here, exemplified by two pioneering studies, we attempt to explain why and how such a multiscale approach paired with an innovative cross-scale analytical technique can be useful in identifying high-value molecular therapeutic targets. This novel, integrated approach has the potential to offer a more effective in silico framework for target discovery and represents an important technical step towards systems medicine. PMID:21572568
A review of predictive nonlinear theories for multiscale modeling of heterogeneous materials
NASA Astrophysics Data System (ADS)
Matouš, Karel; Geers, Marc G. D.; Kouznetsova, Varvara G.; Gillman, Andrew
2017-02-01
Since the beginning of the industrial age, material performance and design have been in the midst of innovation of many disruptive technologies. Today's electronics, space, medical, transportation, and other industries are enriched by development, design and deployment of composite, heterogeneous and multifunctional materials. As a result, materials innovation is now considerably outpaced by other aspects from component design to product cycle. In this article, we review predictive nonlinear theories for multiscale modeling of heterogeneous materials. Deeper attention is given to multiscale modeling in space and to computational homogenization in addressing challenging materials science questions. Moreover, we discuss a state-of-the-art platform in predictive image-based, multiscale modeling with co-designed simulations and experiments that executes on the world's largest supercomputers. Such a modeling framework consists of experimental tools, computational methods, and digital data strategies. Once fully completed, this collaborative and interdisciplinary framework can be the basis of Virtual Materials Testing standards and aids in the development of new material formulations. Moreover, it will decrease the time to market of innovative products.
Multiscale mechanical modeling of soft biological tissues
NASA Astrophysics Data System (ADS)
Stylianopoulos, Triantafyllos
2008-10-01
Soft biological tissues include both native and artificial tissues. In the human body, tissues like the articular cartilage, arterial wall, and heart valve leaflets are examples of structures composed of an underlying network of collagen fibers, cells, proteins and molecules. Artificial tissues are less complex than native tissues and mainly consist of a fiber polymer network with the intent of replacing lost or damaged tissue. Understanding of the mechanical function of these materials is essential for many clinical treatments (e.g. arterial clamping, angioplasty), diseases (e.g. arteriosclerosis) and tissue engineering applications (e.g. engineered blood vessels or heart valves). This thesis presents the derivation and application of a multiscale methodology to describe the macroscopic mechanical function of soft biological tissues incorporating directly their structural architecture. The model, which is based on volume averaging theory, accounts for structural parameters such as the network volume fraction and orientation, the realignment of the fibers in response to strain, the interactions among the fibers and the interactions between the fibers and the interstitial fluid in order to predict the overall tissue behavior. Therefore, instead of using a constitutive equation to relate strain to stress, the tissue microstructure is modeled within a representative volume element (RVE) and the macroscopic response at any point in the tissue is determined by solving a micromechanics problem in the RVE. The model was applied successfully to acellular collagen gels, native blood vessels, and electrospun polyurethane scaffolds and provided accurate predictions for permeability calculations in isotropic and oriented fiber networks. The agreement of model predictions with experimentally determined mechanical properties provided insights into the mechanics of tissues and tissue constructs, while discrepancies revealed limitations of the model framework.
Multi-scale models for cell adhesion
NASA Astrophysics Data System (ADS)
Wu, Yinghao; Chen, Jiawen; Xie, Zhong-Ru
2014-03-01
The interactions of membrane receptors during cell adhesion play pivotal roles in tissue morphogenesis during development. Our lab focuses on developing multi-scale models to decompose the mechanical and chemical complexity in cell adhesion. Recent experimental evidences show that clustering is a generic process for cell adhesive receptors. However, the physical basis of such receptor clustering is not understood. We introduced the effect of molecular flexibility to evaluate the dynamics of receptors. By delivering new theory to quantify the changes of binding free energy in different cellular environments, we revealed that restriction of molecular flexibility upon binding of membrane receptors from apposing cell surfaces (trans) causes large entropy loss, which dramatically increases their lateral interactions (cis). This provides a new molecular mechanism to initialize receptor clustering on the cell-cell interface. By using the subcellular simulations, we further found that clustering is a cooperative process requiring both trans and cis interactions. The detailed binding constants during these processes are calculated and compared with experimental data from our collaborator's lab.
Multiscale Modeling in the Clinic: Drug Design and Development.
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
2016-09-01
A wide range of length and time scales are relevant to pharmacology, especially in drug development, drug design and drug delivery. Therefore, multiscale computational modeling and simulation methods and paradigms that advance the linkage of phenomena occurring at these multiple scales have become increasingly important. Multiscale 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 multiscale modeling in drug design and development. We demonstrate the impact of multiple scales of modeling in this field. We indicate the common mathematical and computational techniques employed for multiscale modeling approaches used in pharmacometric and systems pharmacology models in drug development and present several examples illustrating the current state-of-the-art models for (1) excitable systems and applications in cardiac disease; (2) stem cell driven complex biosystems; (3) nanoparticle delivery, with applications to angiogenesis and cancer therapy; (4) host-pathogen interactions and their use in metabolic disorders, inflammation and sepsis; and (5) computer-aided design of nanomedical systems. We conclude with a focus on barriers to successful clinical translation of drug development, drug design and drug delivery multiscale models.
Multiscale Modeling in the Clinic: Drug Design and Development
An, Gary; Cannon, William R; Liu, Yaling; May, Elebeoba E.; Ortoleva, Peter; Popel, Aleksander S.; Sluka, James P.; Su, Jing; Vicini, Paolo; Zhou, Xiaobo
2016-01-01
A wide range of length and time scales are relevant to pharmacology, especially in drug development, drug design and drug delivery. Therefore, multiscale computational modeling and simulation methods and paradigms that advance the linkage of phenomena occurring at these multiple scales have become increasingly important. Multiscale 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 multiscale modeling in drug design and development. We demonstrate the impact of multiple scales of modeling in this field. We indicate the common mathematical and computational techniques employed for multiscale modeling approaches used in pharmacometric and systems pharmacology models in drug development and present several examples illustrating the current state-of-the-art models for (i) excitable systems and applications in cardiac disease; (ii) stem cell driven complex biosystems; (iii) nanoparticle delivery, with applications to angiogenesis and cancer therapy; (iv) host-pathogen interactions and their use in metabolic disorders, inflammation and sepsis; and (v) computer-aided design of nanomedical systems. We conclude with a focus on barriers to successful clinical translation of drug development, drug design and drug delivery multiscale models. PMID:26885640
Computational technology of multiscale modeling the gas flows in microchannels
NASA Astrophysics Data System (ADS)
Podryga, V. O.
2016-11-01
The work is devoted to modeling the gas mixture flows in engineering microchannels under conditions of many scales of computational domain. The computational technology of using the multiscale approach combining macro - and microscopic models is presented. At macrolevel the nature of the flow and the external influence on it are considered. As a model the system of quasigasdynamic equations is selected. At microlevel the correction of gasdynamic parameters and the determination of boundary conditions are made. As a numerical model the Newton's equations and the molecular dynamics method are selected. Different algorithm types used for implementation of multiscale modeling are considered. The results of the model problems for separate stages are given.
Multiscale Modeling in the Clinic: Drug Design and Development
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.
Multiscale modeling of growth plate cartilage mechanobiology.
Gao, Jie; Williams, John L; Roan, Esra
2017-04-01
Growth plate chondrocytes are responsible for bone growth through proliferation and differentiation. However, the way they experience physiological loads and regulate bone formation, especially during the later developmental phase in the mature growth plate, is still under active investigation. In this study, a previously developed multiscale finite element model of the growth plate is utilized to study the stress and strain distributions within the cartilage at the cellular level when rapidly compressed to 20 %. Detailed structures of the chondron are included in the model to examine the hypothesis that the same combination of mechanoregulatory signals shown to maintain cartilage or stimulate osteogenesis or fibrogenesis in the cartilage anlage or fracture callus also performs the same function at the cell level within the chondrons of growth plate cartilage. Our cell-level results are qualitatively and quantitatively in agreement with tissue-level theories when both hydrostatic cellular stress and strain are considered simultaneously in a mechanoregulatory phase diagram similar to that proposed at the tissue level by Claes and Heigele for fracture healing. Chondrocytes near the reserve/proliferative zone border are subjected to combinations of high compressive hydrostatic stresses ([Formula: see text] MPa), and cell height and width strains of [Formula: see text] to [Formula: see text] respectively, that maintain cartilage and keep chondrocytes from differentiating and provide conditions favorable for cell division, whereas chondrocytes closer to the hypertrophic/calcified zone undergo combinations of lower compressive hydrostatic stress ([Formula: see text] MPa) and cell height and width strains as low as [Formula: see text] to +4 %, respectively, that promote cell differentiation toward osteogenesis; cells near the outer periphery of the growth plate structure experience a combination of low compressive hydrostatic stress (0 to [Formula: see text] MPa) and
Stochastic multiscale modeling of polycrystalline materials
NASA Astrophysics Data System (ADS)
Wen, Bin
provides a new outlook to multi-scale materials modeling accounting for microstructure and process uncertainties. Predictive materials modeling will accelerate the development of new materials and processes for critical applications in industry.
AUGUSTO'S Sundial: Image-Based Modeling for Reverse Engeneering Purposes
NASA Astrophysics Data System (ADS)
Baiocchi, V.; Barbarella, M.; Del Pizzo, S.; Giannone, F.; Troisi, S.; Piccaro, C.; Marcantonio, D.
2017-02-01
A photogrammetric survey of a unique archaeological site is reported in this paper. The survey was performed using both a panoramic image-based solution and by classical procedure. The panoramic image-based solution was carried out employing a commercial solution: the Trimble V10 Imaging Rover (IR). Such instrument is an integrated cameras system that captures 360 degrees digital panoramas, composed of 12 images, with a single push. The direct comparison of the point clouds obtained with traditional photogrammetric procedure and V10 stations, using the same GCP coordinates has been carried out in Cloud Compare, open source software that can provide the comparison between two point clouds supplied by all the main statistical data. The site is a portion of the dial plate of the "Horologium Augusti" inaugurated in 9 B.C.E. in the area of Campo Marzio and still present intact in the same position, in a cellar of a building in Rome, around 7 meter below the present ground level.
Nanomechanics and Multiscale Modeling of Sustainable Concretes
NASA Astrophysics Data System (ADS)
Zanjani Zadeh, Vahid
The work presented in this dissertation is aimed to implement and further develop the recent advances in material characterization for porous and heterogeneous materials and apply these advances to sustainable concretes. The studied sustainable concretes were concrete containing fly ash and slag, Kenaf fiber reinforced concrete, and lightweight aggregate concrete. All these cement-based materials can be categorized as sustainable concrete, by achieving concrete with high strength while reducing cement consumption. The nanoindentation technique was used to infer the nanomechanical properties of the active hydration phases in bulk cement paste. Moreover, the interfacial transition zone (ITZ) of lightweight aggregate, normal aggregate, and Kenaf fibers were investigated using nanoindentation and imagine techniques, despite difficulties regarding characterizing this region. Samples were also tested after exposure to high temperature to evaluate the damage mechanics of sustainable concretes. It has been shown that there is a direct correlation between the nature of the nanoscale structure of a cement-based material with its macroscopic properties. This was addressed in two steps in this dissertation: (i) Nanoscale characterization of sustainable cementitious materials to understand the different role of fly ash, slag, lightweight aggregate, and Kenaf fibers on nanoscale (ii) Link the nanoscale mechanical properties to macroscale ones with multiscale modeling. The grid indentation technique originally developed for normal concrete was extended to sustainable concretes with more complex microstructure. The relation between morphology of cement paste materials and submicron mechanical properties, indentation modulus, hardness, and dissipated energy is explained in detail. Extensive experimental and analytical approaches were focused on description of the materials' heterogeneous microstructure as function of their composition and physical phenomenon. Quantitative
Foundations for a multiscale collaborative Earth model
NASA Astrophysics Data System (ADS)
Afanasiev, Michael; Peter, Daniel; Sager, Korbinian; Simutė, Saulė; Ermert, Laura; Krischer, Lion; Fichtner, Andreas
2016-01-01
of the CSEM development, the broad global updates mostly act to remove artefacts from the assembly of the initial CSEM. During the future evolution of the CSEM, the reference data set will be used to account for the influence of small-scale refinements on large-scale global structure. 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 of concept, future refinements and additions will require community involvement, which is welcome at this stage already.
A Multiscale Meshfree Approach for Modeling Fragment Penetration into Ultra High-Strength Concrete
2011-09-01
material deformation and damage mechanisms, multiscale homogenization based on the energy bridging theory pertinent to fragment penetration modeling...problems associated with contact-impact simulations as well as multiscale modeling of material damage have been performed to examine the effectiveness...15 3 Multiscale Microcrack Informed Damage Model..................................................................... 18 Model
Multiscale Constitutive Modeling of Asphalt Concrete
NASA Astrophysics Data System (ADS)
Underwood, Benjamin Shane
Multiscale modeling of asphalt concrete has become a popular technique for gaining improved insight into the physical mechanisms that affect the material's behavior and ultimately its performance. This type of modeling considers asphalt concrete, not as a homogeneous mass, but rather as an assemblage of materials at different characteristic length scales. For proper modeling these characteristic scales should be functionally definable and should have known properties. Thus far, research in this area has not focused significant attention on functionally defining what the characteristic scales within asphalt concrete should be. Instead, many have made assumptions on the characteristic scales and even the characteristic behaviors of these scales with little to no support. This research addresses these shortcomings by directly evaluating the microstructure of the material and uses these results to create materials of different characteristic length scales as they exist within the asphalt concrete mixture. The objectives of this work are to; 1) develop mechanistic models for the linear viscoelastic (LVE) and damage behaviors in asphalt concrete at different length scales and 2) develop a mechanistic, mechanistic/empirical, or phenomenological formulation to link the different length scales into a model capable of predicting the effects of microstructural changes on the linear viscoelastic behaviors of asphalt concrete mixture, e.g., a microstructure association model for asphalt concrete mixture. Through the microstructural study it is found that asphalt concrete mixture can be considered as a build-up of three different phases; asphalt mastic, fine aggregate matrix (FAM), and finally the coarse aggregate particles. The asphalt mastic is found to exist as a homogenous material throughout the mixture and FAM, and the filler content within this material is consistent with the volumetric averaged concentration, which can be calculated from the job mix formula. It is also
A perspective on modeling the multiscale response of energetic materials
NASA Astrophysics Data System (ADS)
Rice, Betsy M.
2017-01-01
The response of an energetic material to insult is perhaps one of the most difficult processes to model due to concurrent chemical and physical phenomena occurring over scales ranging from atomistic to continuum. Unraveling the interdependencies of these complex processes across the scales through modeling can only be done within a multiscale framework. In this paper, I will describe progress in the development of a predictive, experimentally validated multiscale reactive modeling capability for energetic materials at the Army Research Laboratory. I will also describe new challenges and research opportunities that have arisen in the course of our development which should be pursued in the future.
A Liver-centric Multiscale Modeling Framework for Xenobiotics ...
We describe a multi-scale framework for modeling acetaminophen-induced liver toxicity. Acetaminophen is a widely used analgesic. Overdose of acetaminophen can result in liver injury via its biotransformation into toxic product, which further induce massive necrosis. Our study focuses on developing a multi-scale computational model to characterize both phase I and phase II metabolism of acetaminophen, by bridging Physiologically Based Pharmacokinetic (PBPK) modeling at the whole body level, cell movement and blood flow at the tissue level and cell signaling and drug metabolism at the sub-cellular level. To validate the model, we estimated our model parameters by fi?tting serum concentrations of acetaminophen and its glucuronide and sulfate metabolites to experiments, and carried out sensitivity analysis on 35 parameters selected from three modules. Our study focuses on developing a multi-scale computational model to characterize both phase I and phase II metabolism of acetaminophen, by bridging Physiologically Based Pharmacokinetic (PBPK) modeling at the whole body level, cell movement and blood flow at the tissue level and cell signaling and drug metabolism at the sub-cellular level. This multiscale model bridges the CompuCell3D tool used by the Virtual Tissue project with the httk tool developed by the Rapid Exposure and Dosimetry project.
A Liver-centric Multiscale Modeling Framework for Xenobiotics ...
We describe a multi-scale framework for modeling acetaminophen-induced liver toxicity. Acetaminophen is a widely used analgesic. Overdose of acetaminophen can result in liver injury via its biotransformation into toxic product, which further induce massive necrosis. Our study focuses on developing a multi-scale computational model to characterize both phase I and phase II metabolism of acetaminophen, by bridging Physiologically Based Pharmacokinetic (PBPK) modeling at the whole body level, cell movement and blood flow at the tissue level and cell signaling and drug metabolism at the sub-cellular level. To validate the model, we estimated our model parameters by fi?tting serum concentrations of acetaminophen and its glucuronide and sulfate metabolites to experiments, and carried out sensitivity analysis on 35 parameters selected from three modules. Our study focuses on developing a multi-scale computational model to characterize both phase I and phase II metabolism of acetaminophen, by bridging Physiologically Based Pharmacokinetic (PBPK) modeling at the whole body level, cell movement and blood flow at the tissue level and cell signaling and drug metabolism at the sub-cellular level. This multiscale model bridges the CompuCell3D tool used by the Virtual Tissue project with the httk tool developed by the Rapid Exposure and Dosimetry project.
Multiscale modeling of thermal conductivity of polycrystalline graphene sheets.
Mortazavi, Bohayra; Pötschke, Markus; Cuniberti, Gianaurelio
2014-03-21
We developed a multiscale approach to explore the effective thermal conductivity of polycrystalline graphene sheets. By performing equilibrium molecular dynamics (EMD) simulations, the grain size effect on the thermal conductivity of ultra-fine grained polycrystalline graphene sheets is investigated. Our results reveal that the ultra-fine grained graphene structures have thermal conductivity one order of magnitude smaller than that of pristine graphene. Based on the information provided by the EMD simulations, we constructed finite element models of polycrystalline graphene sheets to probe the thermal conductivity of samples with larger grain sizes. Using the developed multiscale approach, we also investigated the effects of grain size distribution and thermal conductivity of grains on the effective thermal conductivity of polycrystalline graphene. The proposed multiscale approach on the basis of molecular dynamics and finite element methods could be used to evaluate the effective thermal conductivity of polycrystalline graphene and other 2D structures.
NASA Astrophysics Data System (ADS)
Macioł, Piotr; Regulski, Krzysztof
2016-08-01
We present a process of semantic meta-model development for data management in an adaptable multiscale modeling framework. The main problems in ontology design are discussed, and a solution achieved as a result of the research is presented. The main concepts concerning the application and data management background for multiscale modeling were derived from the AM3 approach—object-oriented Agile multiscale modeling methodology. The ontological description of multiscale models enables validation of semantic correctness of data interchange between submodels. We also present a possibility of using the ontological model as a supervisor in conjunction with a multiscale model controller and a knowledge base system. Multiscale modeling formal ontology (MMFO), designed for describing multiscale models' data and structures, is presented. A need for applying meta-ontology in the MMFO development process is discussed. Examples of MMFO application in describing thermo-mechanical treatment of metal alloys are discussed. Present and future applications of MMFO are described.
A Liver-centric Multiscale Modeling Framework for Xenobiotics
We describe a multi-scale framework for modeling acetaminophen-induced liver toxicity. Acetaminophen is a widely used analgesic. Overdose of acetaminophen can result in liver injury via its biotransformation into toxic product, which further induce massive necrosis. Our study foc...
Multiscale modeling and simulation of brain blood flow.
Perdikaris, Paris; Grinberg, Leopold; Karniadakis, George Em
2016-02-01
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.
A Liver-centric Multiscale Modeling Framework for Xenobiotics
We describe a multi-scale framework for modeling acetaminophen-induced liver toxicity. Acetaminophen is a widely used analgesic. Overdose of acetaminophen can result in liver injury via its biotransformation into toxic product, which further induce massive necrosis. Our study foc...
Multiscale modeling and simulation of brain blood flow
NASA Astrophysics Data System (ADS)
Perdikaris, Paris; Grinberg, Leopold; Karniadakis, George Em
2016-02-01
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.
Multiscale modeling and simulation of brain blood flow
Perdikaris, Paris; Grinberg, Leopold; Karniadakis, George Em
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.
Multiscale modeling and simulation of brain blood flow
Perdikaris, Paris; Grinberg, Leopold; Karniadakis, George Em
2016-01-01
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. PMID:26909005
Mathematical and Numerical Analyses of Peridynamics for Multiscale Materials Modeling
Du, Qiang
2014-11-12
The rational design of materials, the development of accurate and efficient material simulation algorithms, and the determination of the response of materials to environments and loads occurring in practice all require an understanding of mechanics at disparate spatial and temporal scales. The project addresses mathematical and numerical analyses for material problems for which relevant scales range from those usually treated by molecular dynamics all the way up to those most often treated by classical elasticity. The prevalent approach towards developing a multiscale material model couples two or more well known models, e.g., molecular dynamics and classical elasticity, each of which is useful at a different scale, creating a multiscale multi-model. However, the challenges behind such a coupling are formidable and largely arise because the atomistic and continuum models employ nonlocal and local models of force, respectively. The project focuses on a multiscale analysis of the peridynamics materials model. Peridynamics can be used as a transition between molecular dynamics and classical elasticity so that the difficulties encountered when directly coupling those two models are mitigated. In addition, in some situations, peridynamics can be used all by itself as a material model that accurately and efficiently captures the behavior of materials over a wide range of spatial and temporal scales. Peridynamics is well suited to these purposes because it employs a nonlocal model of force, analogous to that of molecular dynamics; furthermore, at sufficiently large length scales and assuming smooth deformation, peridynamics can be approximated by classical elasticity. The project will extend the emerging mathematical and numerical analysis of peridynamics. One goal is to develop a peridynamics-enabled multiscale multi-model that potentially provides a new and more extensive mathematical basis for coupling classical elasticity and molecular dynamics, thus enabling next
Image-Based Empirical Modeling of the Plasmasphere
NASA Technical Reports Server (NTRS)
Adrian, Mark L.; Gallagher, D. L.
2008-01-01
A new suite of empirical models of plasmaspheric plasma based on remote, global images from the IMAGE EUV instrument is proposed for development. The purpose of these empirical models is to establish the statistical properties of the plasmasphere as a function of conditions. This suite of models will mark the first time the plasmaspheric plume is included in an empirical model. Development of these empirical plasmaspheric models will support synoptic studies (such as for wave propagation and growth, energetic particle loss through collisions and dust transport as influenced by charging) and serves as a benchmark against which physical models can be tested. The ability to know that a specific global density distribution occurs in response to specific magnetospheric and solar wind factors is a huge advantage over all previous in-situ based empirical models. The consequence of creating these new plasmaspheric models will be to provide much higher fidelity and much richer quantitative descriptions of the statistical properties of plasmaspheric plasma in the inner magnetosphere, whether that plasma is in the main body of the plasmasphere, nearby during recovery or in the plasmaspheric plume. Model products to be presented include statistical probabilities for being in the plasmasphere, near thermal He+ density boundaries and the complexity of its spatial structure.
Image-Based Empirical Modeling of the Plasmasphere
NASA Technical Reports Server (NTRS)
Adrian, Mark L.; Gallagher, D. L.
2008-01-01
A new suite of empirical models of plasmaspheric plasma based on remote, global images from the IMAGE EUV instrument is proposed for development. The purpose of these empirical models is to establish the statistical properties of the plasmasphere as a function of conditions. This suite of models will mark the first time the plasmaspheric plume is included in an empirical model. Development of these empirical plasmaspheric models will support synoptic studies (such as for wave propagation and growth, energetic particle loss through collisions and dust transport as influenced by charging) and serves as a benchmark against which physical models can be tested. The ability to know that a specific global density distribution occurs in response to specific magnetospheric and solar wind factors is a huge advantage over all previous in-situ based empirical models. The consequence of creating these new plasmaspheric models will be to provide much higher fidelity and much richer quantitative descriptions of the statistical properties of plasmaspheric plasma in the inner magnetosphere, whether that plasma is in the main body of the plasmasphere, nearby during recovery or in the plasmaspheric plume. Model products to be presented include statistical probabilities for being in the plasmasphere, near thermal He+ density boundaries and the complexity of its spatial structure.
Modeling crack propagation in polycrystalline microstructure using variational multiscale method
Sun, Shang; Sundararaghavan, Veera
2016-01-01
Crack propagation in a polycrystalline microstructure is analyzed using a novel multiscale model. The model includes an explicit microstructural representation at critical regions (stress concentrators such as notches and cracks) and a reduced order model that statistically captures the microstructure at regions far away from stress concentrations. Crack propagation is modeled in these critical regions using the variational multiscale method. In this approach, a discontinuous displacement field is added to elements that exceed the critical values of normal or tangential tractions during loading. Compared to traditional cohesive zone modeling approaches, the method does not require the use of any specialmore » interface elements in the microstructure and thus can model arbitrary crack paths. As a result, the capability of the method in predicting both intergranular and transgranular failure modes in an elastoplastic polycrystal is demonstrated under tensile and three-point bending loads.« less
Multiscale Modeling of Virus Entry via Receptor-Mediated Endocytosis
NASA Astrophysics Data System (ADS)
Liu, Jin
2012-11-01
Virus infections are ubiquitous and remain major threats to human health worldwide. Viruses are intracellular parasites and must enter host cells to initiate infection. Receptor-mediated endocytosis is the most common entry pathway taken by viruses, the whole process is highly complex and dictated by various events, such as virus motions, membrane deformations, receptor diffusion and ligand-receptor reactions, occurring at multiple length and time scales. We develop a multiscale model for virus entry through receptor-mediated endocytosis. The binding of virus to cell surface is based on a mesoscale three dimensional stochastic adhesion model, the internalization (endocytosis) of virus and cellular membrane deformation is based on the discretization of Helfrich Hamiltonian in a curvilinear space using Monte Carlo method. The multiscale model is based on the combination of these two models. We will implement this model to study the herpes simplex virus entry into B78 cells and compare the model predictions with experimental measurements.
Final Report for Integrated Multiscale Modeling of Molecular Computing Devices
Glotzer, Sharon C.
2013-08-28
In collaboration with researchers at Vanderbilt University, North Carolina State University, Princeton and Oakridge National Laboratory we developed multiscale modeling and simulation methods capable of modeling the synthesis, assembly, and operation of molecular electronics devices. Our role in this project included the development of coarse-grained molecular and mesoscale models and simulation methods capable of simulating the assembly of millions of organic conducting molecules and other molecular components into nanowires, crossbars, and other organized patterns.
Multiscale numerical modeling of the spherically symmetric cryosurgery problem
NASA Astrophysics Data System (ADS)
Kudryashov, N. A.; Shilnikov, K. E.
2017-01-01
The work is concerned with the numerical studying of the cryogenic biotissue destruction by a spherically symmetric tip. The multiscale bioheat transfer model is used for the describing of the biological solutions crystallization features. An explicit finite volume based approximation is applied for the numerical modeling of the processes taking place during the cryosurgery. The phase averaging method is applied as an computationally economic approach for the numerical modeling of the problem under study.
Image-based modeling of objects and human faces
NASA Astrophysics Data System (ADS)
Zhang, Zhengyou
2000-12-01
In this paper, provided is an overview of our project on 3D object and face modeling from images taken by a free-moving camera. We strive to advance the state of the art in 3D computer vision, and develop flexible and robust techniques for ordinary users to gain 3D experience from a ste of casually collected 2D images. Applications include product advertisement on the Web, virtual conference, and interactive games. We briefly cover the following topics: camera calibration, stereo rectification, image matching, 3D photo editing, object modeling, and face modeling. Demos on the last three topics will be shown during the conference.
Multiscale Combination of Physically-Based Registration and Deformation Modeling
Tsap, L.; Goldgof, D.B.; Sarkar, S.
1999-11-08
In this paper the authors present a novel multiscale approach to recovery of nonrigid motion from sequences of registered intensity and range images. The main idea of the approach is that a finite element (FEM) model can naturally handle both registration and deformation modeling using a single model-driving strategy. The method includes a multiscale iterative algorithm based on analysis of the undirected Hausdorff distance to recover correspondences. The method is evaluated with respect to speed, accuracy, and noise sensitivity. Advantages of the proposed approach are demonstrated using man-made elastic materials and human skin motion. Experiments with regular grid features are used for performance comparison with a conventional approach (separate snakes and FEM models). It is shown that the new method does not require a grid and can adapt the model to available object features.
NASA Astrophysics Data System (ADS)
Lan, Hongzhi; Merkow, Jameson; Updegrove, Adam; Schiavazzi, Daniele; Wilson, Nathan; Shadden, Shawn; Marsden, Alison
2015-11-01
SimVascular (www.simvascular.org) is currently the only fully open source software package that provides a complete pipeline from medical image based modeling to patient specific blood flow simulation and analysis. It was initially released in 2007 and has contributed to numerous advances in fundamental hemodynamics research, surgical planning, and medical device design. However, early versions had several major barriers preventing wider adoption by new users, large-scale application in clinical and research studies, and educational access. In the past years, SimVascular 2.0 has made significant progress by integrating open source alternatives for the expensive commercial libraries previously required for anatomic modeling, mesh generation and the linear solver. In addition, it simplified the across-platform compilation process, improved the graphical user interface and launched a comprehensive documentation website. Many enhancements and new features have been incorporated for the whole pipeline, such as 3-D segmentation, Boolean operation for discrete triangulated surfaces, and multi-scale coupling for closed loop boundary conditions. In this presentation we will briefly overview the modeling/simulation pipeline and advances of the new SimVascular 2.0.
Image-Based Structural Modeling of the Cardiac Purkinje Network
Liu, Benjamin R.; Cherry, Elizabeth M.
2015-01-01
The Purkinje network is a specialized conduction system within the heart that ensures the proper activation of the ventricles to produce effective contraction. Its role during ventricular arrhythmias is less clear, but some experimental studies have suggested that the Purkinje network may significantly affect the genesis and maintenance of ventricular arrhythmias. Despite its importance, few structural models of the Purkinje network have been developed, primarily because current physical limitations prevent examination of the intact Purkinje network. In previous modeling efforts Purkinje-like structures have been developed through either automated or hand-drawn procedures, but these networks have been created according to general principles rather than based on real networks. To allow for greater realism in Purkinje structural models, we present a method for creating three-dimensional Purkinje networks based directly on imaging data. Our approach uses Purkinje network structures extracted from photographs of dissected ventricles and projects these flat networks onto realistic endocardial surfaces. Using this method, we create models for the combined ventricle-Purkinje system that can fully activate the ventricles through a stimulus delivered to the Purkinje network and can produce simulated activation sequences that match experimental observations. The combined models have the potential to help elucidate Purkinje network contributions during ventricular arrhythmias. PMID:26583120
Hybrid multiscale modeling and prediction of cancer cell behavior.
Zangooei, Mohammad Hossein; Habibi, Jafar
2017-01-01
Understanding cancer development crossing several spatial-temporal scales is of great practical significance to better understand and treat cancers. It is difficult to tackle this challenge with pure biological means. Moreover, hybrid modeling techniques have been proposed that combine the advantages of the continuum and the discrete methods to model multiscale problems. In light of these problems, we have proposed a new hybrid vascular model to facilitate the multiscale modeling and simulation of cancer development with respect to the agent-based, cellular automata and machine learning methods. The purpose of this simulation is to create a dataset that can be used for prediction of cell phenotypes. By using a proposed Q-learning based on SVR-NSGA-II method, the cells have the capability to predict their phenotypes autonomously that is, to act on its own without external direction in response to situations it encounters. Computational simulations of the model were performed in order to analyze its performance. The most striking feature of our results is that each cell can select its phenotype at each time step according to its condition. We provide evidence that the prediction of cell phenotypes is reliable. Our proposed model, which we term a hybrid multiscale modeling of cancer cell behavior, has the potential to combine the best features of both continuum and discrete models. The in silico results indicate that the 3D model can represent key features of cancer growth, angiogenesis, and its related micro-environment and show that the findings are in good agreement with biological tumor behavior. To the best of our knowledge, this paper is the first hybrid vascular multiscale modeling of cancer cell behavior that has the capability to predict cell phenotypes individually by a self-generated dataset.
Blood Flow: Multi-scale Modeling and Visualization (July 2011)
2011-01-01
Multi-scale modeling of arterial blood flow can shed light on the interaction between events happening at micro- and meso-scales (i.e., adhesion of red blood cells to the arterial wall, clot formation) and at macro-scales (i.e., change in flow patterns due to the clot). Coupled numerical simulations of such multi-scale flow require state-of-the-art computers and algorithms, along with techniques for multi-scale visualizations. This animation presents early results of two studies used in the development of a multi-scale visualization methodology. The fisrt illustrates a flow of healthy (red) and diseased (blue) blood cells with a Dissipative Particle Dynamics (DPD) method. Each blood cell is represented by a mesh, small spheres show a sub-set of particles representing the blood plasma, while instantaneous streamlines and slices represent the ensemble average velocity. In the second we investigate the process of thrombus (blood clot) formation, which may be responsible for the rupture of aneurysms, by concentrating on the platelet blood cells, observing as they aggregate on the wall of an aneruysm. Simulation was performed on Kraken at the National Institute for Computational Sciences. Visualization was produced using resources of the Argonne Leadership Computing Facility at Argonne National Laboratory.
Multiscale geometric modeling of macromolecules II: Lagrangian representation
Feng, Xin; Xia, Kelin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei
2013-01-01
Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X-ray, NMR and cryo-EM, and theoretical/mathematical models, such as molecular dynamics, the Poisson-Boltzmann equation and the Nernst-Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger’s functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent-solute interaction, and ion channel dynamics, while our coarse resolution representations highlight the compatibility of protein-ligand bindings and possibility of protein-protein interactions. PMID:23813599
Tawhai, Merryn; Bischoff, Jeff; Einstein, Daniel R.; Erdemir, Ahmet; Guess, Trent; Reinbolt, Jeff
2009-05-01
Abstract In this article, we describe some current multiscale modeling issues in computational biomechanics from the perspective of the musculoskeletal and respiratory systems and mechanotransduction. First, we outline the necessity of multiscale simulations in these biological systems. Then we summarize challenges inherent to multiscale biomechanics modeling, regardless of the subdiscipline, followed by computational challenges that are system-specific. We discuss some of the current tools that have been utilized to aid research in multiscale mechanics simulations, and the priorities to further the field of multiscale biomechanics computation.
Multiscale modelling and nonlinear simulation of vascular tumour growth
Macklin, Paul; Anderson, Alexander R. A.; Chaplain, Mark A. J.; Cristini, Vittorio
2011-01-01
In this article, we present a new multiscale mathematical model for solid tumour growth which couples an improved model of tumour invasion with a model of tumour-induced angiogenesis. We perform nonlinear simulations of the multi-scale model that demonstrate the importance of the coupling between the development and remodeling of the vascular network, the blood flow through the network and the tumour progression. Consistent with clinical observations, the hydrostatic stress generated by tumour cell proliferation shuts down large portions of the vascular network dramatically affecting the flow, the subsequent network remodeling, the delivery of nutrients to the tumour and the subsequent tumour progression. In addition, extracellular matrix degradation by tumour cells is seen to have a dramatic affect on both the development of the vascular network and the growth response of the tumour. In particular, the newly developing vessels tend to encapsulate, rather than penetrate, the tumour and are thus less effective in delivering nutrients. PMID:18781303
Moist multi-scale models for the hurricane embryo
Majda, Andrew J.; Xing, Yulong; Mohammadian, Majid
2010-01-01
Determining the finite-amplitude preconditioned states in the hurricane embryo, which lead to tropical cyclogenesis, is a central issue in contemporary meteorology. In the embryo there is competition between different preconditioning mechanisms involving hydrodynamics and moist thermodynamics, which can lead to cyclogenesis. Here systematic asymptotic methods from applied mathematics are utilized to develop new simplified moist multi-scale models starting from the moist anelastic equations. Three interesting multi-scale models emerge in the analysis. The balanced mesoscale vortex (BMV) dynamics and the microscale balanced hot tower (BHT) dynamics involve simplified balanced equations without gravity waves for vertical vorticity amplification due to moist heat sources and incorporate nonlinear advective fluxes across scales. The BMV model is the central one for tropical cyclogenesis in the embryo. The moist mesoscale wave (MMW) dynamics involves simplified equations for mesoscale moisture fluctuations, as well as linear hydrostatic waves driven by heat sources from moisture and eddy flux divergences. A simplified cloud physics model for deep convection is introduced here and used to study moist axisymmetric plumes in the BHT model. A simple application in periodic geometry involving the effects of mesoscale vertical shear and moist microscale hot towers on vortex amplification is developed here to illustrate features of the coupled multi-scale models. These results illustrate the use of these models in isolating key mechanisms in the embryo in a simplified content.
Blood Flow: Multi-scale Modeling and Visualization
2010-01-01
Multi-scale modeling of arterial blood flow can shed light on the interaction between events happening at micro- and meso-scales (i.e., adhesion of red blood cells to the arterial wall, clot formation) and at macro-scales (i.e., change in flow patterns due to the clot). Coupled numerical simulations of such multi-scale flow require state-of-the-art computers and algorithms. Along with developing methods for multi-scale computations, techniques for multi-scale visualizations must be designed. This animation presents early results of joint efforts of teams from Brown University and Argonne National Laboratory to develop a multi-scale visualization methodology. It illustrates a flow of healthy (red) and diseased (blue) blood cells with a Dissipative Particle Dynamics (DPD) method. Each blood cell is represented by a mesh made of 500 DPD-particles, and small spheres show a sub-set of the DPD particles representing the blood plasma, while instantaneous streamlines and slices represent the ensemble average velocity. Credits: Science: Leopold Grinberg and George Karniadakis, Brown University Visualization: Joseph A. Insley and Michael E. Papka, Argonne National Laboratory This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357. This research was supported in part by the National Science Foundation through the PetaApps program and used TeraGrid resources provided by National Institute for Computational Sciences.
Image-based numerical modeling of HIFU-induced lesions
NASA Astrophysics Data System (ADS)
Almekkaway, Mohamed K.; Shehata, Islam A.; Haritonova, Alyona; Ballard, John; Casper, Andrew; Ebbini, Emad
2017-03-01
Atherosclerosis is a chronic vascular disease affecting large and medium sized arteries. Several treatment options are already available for treatment of this disease. Targeting atherosclerotic plaques by high intensity focused ultrasound (HIFU) using dual mode ultrasound arrays (DMUA) was recently introduced in literature. We present a finite difference time domain (FDTD) simulation modeling of the wave propagation in heterogeneous medium from the surface of a 3.5 MHz array prototype with 32-elements. After segmentation of the ultrasound image obtained for the treatment region in-vivo, we integrated this anatomical information into our simulation to account for different parameters that may be caused by these multi-region anatomical complexities. The simulation program showed that HIFU was able to induce damage in the prefocal region instead of the target area. The HIFU lesions, as predicted by our simulation, were well correlated with the actual damage detected in histology.
Multiscale Models for Reactive Transport in Porous Media
NASA Astrophysics Data System (ADS)
Tartakovsky, A. M.
2012-12-01
Under certain conditions, Darcy-scale reactive transport equations cannot provide sufficiently accurate predictions of multiphase flow and reactive transport. Pore-scale models are based on fundamental conservation laws and, in general, are more accurate than the Darcy-scale models. But, for domains of practical importance, number of unknowns in the pore-sale models may be on the order of billions or trillions and a direct solution of the pore-scale equations is often unfeasible even on modern super-computes. Several novel multiscale methods including a Langevin approach and a dimension reduction method based on a computational closure will be presented. The purpose of these methods is to provide an accurate description of the system averages while retaining critical pore-scale information. The advantages, range of applicability and limitations of the mentioned above multiscale methods will be discussed.
Image-based modeling of radiation-induced foci
NASA Astrophysics Data System (ADS)
Costes, Sylvain; Cucinotta, Francis A.; Ponomarev, Artem; Barcellos-Hoff, Mary Helen; Chen, James; Chou, William; Gascard, Philippe
Several proteins involved in the response to DNA double strand breaks (DSB) form microscopically visible nuclear domains, or foci, after exposure to ionizing radiation. Radiation-induced foci (RIF) are believed to be located where DNA damage occurs. To test this assumption, we used Monte Carlo simulations to predict the spatial distribution of DSB in human nuclei exposed to high or low-LET radiation. We then compared these predictions to the distribution patterns of three DNA damage sensing proteins, i.e. 53BP1, phosphorylated ATM and γH2AX in human mammary epithelial. The probability to induce DSB can be derived from DNA fragment data measured experimentally by pulsed-field gel electrophoresis. We first used this probability in Monte Carlo simulations to predict DSB locations in synthetic nuclei geometrically described by a complete set of human chromosomes, taking into account microscope optics from real experiments. Simulations showed a very good agreement for high-LET, predicting 0.7 foci/µm along the path of a 1 GeV/amu Fe particle against measurement of 0.69 to 0.82 foci/µm for various RIF 5 min following exposure (LET 150 keV/µm). On the other hand, discrepancies were shown in foci frequency for low-LET, with measurements 20One drawback using a theoretical model for the nucleus is that it assumes a simplistic and static pattern for DNA densities. However DNA damage pattern is highly correlated to DNA density pattern (i.e. the more DNA, the more likely to have a break). Therefore, we generalized our Monte Carlo approach to real microscope images, assuming pixel intensity of DAPI in the nucleus was directly proportional to the amount of DNA in that pixel. With such approach we could predict DNA damage pattern in real images on a per nucleus basis. Since energy is randomly deposited along high-LET particle paths, RIF along these paths should also be randomly distributed. As expected, simulations produced DNA-weighted random (Poisson) distributions. In
Multiscale Modeling of Irradiation effects in Fusion Materials
Hussein Zbib
2004-12-23
The aim of this collaborative research work was to apply predictive, physically based multiscale modeling to improve understanding of the underlying mechanisms of material changes in the fusion environment, with the ultimate objective to aid development of advanced materials. The multiscale modeling methodology involved a hierarchical approach, integrating ab initio electronic structure calculations, molecular dynamics (MD) simulations, kinetic Monte Carlo (KMC), and three dimensional dislocation dynamics (DD) simulations, over the relevant length and time scales to model the fates of defects and solutes (including hydrogen and helium) and thus, predict microstructural evolution in ferritic/martensitic and vanadium based alloys. The main task at WSU was to investigate changes in mechanical properties as a result of the production of a varied population of nanostructural features and to be obtained from three dimensional dislocation dynamics simulation (DD). The initial dislocation structure and microstructure could be obtained from electron microscopy characterization and the appropriate nanostructural features produced during irradiation are introduced from predictions of the multiscale modeling. The dislocation structure was then allowed to evolve under an applied load, taking into account all possible forces and reactions between the dislocations with the radiation induced nanostructure as well as network dislocations. In this manner, quantitative predictions of irradiation hardening would result without the use of empirical constants within the framework of dispersed barrier hardening models.
Automatic brain segmentation and validation: image-based versus atlas-based deformable models
NASA Astrophysics Data System (ADS)
Aboutanos, Georges B.; Dawant, Benoit M.
1997-04-01
Due to the complexity of the brain surface, there is at present no segmentation method that proves to work automatically and consistently on any 3-D magnetic resonance (MR) images of the head. There is a definite lack of validation studies related to automatic brain extraction. In this work we present an image-base automatic method for brain segmentation and use its results as an input to a deformable model method which we call image-based deformable model. Combining image-based methods with a deformable model can lead to a robust segmentation method without requiring registration of the image volumes into a standardized space, the automation of which remains challenging for pathological cases. We validate our segmentation results on 3-D MP-RAGE (magnetization-prepared rapid gradient-echo) volumes for the image model prior- and post-deformation and compare it to an atlas model prior- and post-deformation. Our validation is based on volume measurement comparison to manually segmented data. Our analysis shows that the improvement afforded by the deformable model methods are statistically significant, however there are no significant differences between the image-based and atlas-based deformable model methods.
Multiscale Modeling of Particles Embedded in High Speed Flows
NASA Astrophysics Data System (ADS)
Davis, Sean; Sen, Oishik; Jacobs, Gustaaf; Udaykumar, H. S.
2015-06-01
Problems involving propagation of shock waves through a cloud of particles are inherently multiscale. The system scale is governed by macro-scale conservation equations, which average over solid and fluid phases. The averaging process results in source terms that represent the unresolved momentum exchange between the solid phase and the fluid phase. Typically, such source terms are modeled using empirical correlations derived from physical experiments conducted in a limited parameter space. The focus of the current research is to advance the multiscale modeling of shocked particle-laden gas flows; particle- (i.e. meso-)scale computations are performed to resolve the dynamics of ensembles of particles and closure laws are obtained from the meso-scale for use in the macro-scale equations. Closure models are constructed from meso-scale simulations using the Dynamic Kriging method. The presentation will demonstrate the multiscale approach by connecting meso-scale simulations to an Eulerian-Lagrangian macro-scale model of particle laden flows. The technique is applied to study shock interactions with particle curtains in shock tubes and the results are compared with experimental data in such systems. We gratefully acknowledge the financial support by the Air Force Office of Scientific Research under Grant Number FA9550-12-1-0115 and the National Science Foundation under grant number DMS-115631.
Cohesive Zone Approach to Multiscale Modeling of Nanotube Reinforced Composites
2007-11-18
2007 FINAL Aug 1, 2004 to July 31 , 2005 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Cohesive Zone Approach to Multiscale Modeling of Nanotube Reinforced... 8050 11. SPONSOR/MONITOR’S REPORT ~ NUMBER(S) 12. DISTRIBUTION I AVAILABILITY STATEMENT Unlimited AFRL-SR-AR-TR-07_0 43 6 13. SUPPLEMENTARY NOTES 14...been applied to study CNTs and CNT based composites, which are essentially nanoscale systems. For example, Yakobson [ 5 ] has shown that predictions of
Multiscale Aspects of Modeling Gas-Phase Nanoparticle Synthesis
Buesser, B.; Gröhn, A.J.
2013-01-01
Aerosol reactors are utilized to manufacture nanoparticles in industrially relevant quantities. The development, understanding and scale-up of aerosol reactors can be facilitated with models and computer simulations. This review aims to provide an overview of recent developments of models and simulations and discuss their interconnection in a multiscale approach. A short introduction of the various aerosol reactor types and gas-phase particle dynamics is presented as a background for the later discussion of the models and simulations. Models are presented with decreasing time and length scales in sections on continuum, mesoscale, molecular dynamics and quantum mechanics models. PMID:23729992
A Goddard Multi-Scale Modeling System with Unified Physics
NASA Technical Reports Server (NTRS)
Tao, W.K.; Anderson, D.; Atlas, R.; Chern, J.; Houser, P.; Hou, A.; Lang, S.; Lau, W.; Peters-Lidard, C.; Kakar, R.; Kumar, S.; Lapenta, W.; Li, X.; Matsui, T.; Rienecker, M.; Shen, B.W.; Shi, J.J.; Simpson, J.; Zeng, X.
2008-01-01
Numerical cloud resolving models (CRMs), which are based the non-hydrostatic equations of motion, have been extensively applied to cloud-scale and mesoscale processes during the past four decades. Recent GEWEX Cloud System Study (GCSS) model comparison projects have indicated that CRMs agree with observations in simulating various types of clouds and cloud systems from different geographic locations. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that Numerical Weather Prediction (NWP) and regional scale model can be run in grid size similar to cloud resolving model through nesting technique. Current and future NASA satellite programs can provide cloud, precipitation, aerosol and other data at very fine spatial and temporal scales. It requires a coupled global circulation model (GCM) and cloud-scale model (termed a szrper-parameterization or multi-scale modeling -framework, MMF) to use these satellite data to improve the understanding of the physical processes that are responsible for the variation in global and regional climate and hydrological systems. The use of a GCM will enable global coverage, and the use of a CRM will allow for better and more sophisticated physical parameterization. NASA satellite and field campaign can provide initial conditions as well as validation through utilizing the Earth Satellite simulators. At Goddard, we have developed a multi-scale modeling system with unified physics. The modeling system consists a coupled GCM-CRM (or MMF); a state-of-the-art weather research forecast model (WRF) and a cloud-resolving model (Goddard Cumulus Ensemble model). In these models, the same microphysical schemes (2ICE, several 3ICE), radiation (including explicitly calculated cloud optical properties), and surface models are applied. In addition, a comprehensive unified Earth Satellite
Multiscale modeling for materials design: Molecular square catalysts
NASA Astrophysics Data System (ADS)
Majumder, Debarshi
In a wide variety of materials, including a number of heterogeneous catalysts, the properties manifested at the process scale are a consequence of phenomena that occur at different time and length scales. Recent experimental developments allow materials to be designed precisely at the nanometer scale. However, the optimum design of such materials requires capabilities to predict the properties at the process scale based on the phenomena occurring at the relevant scales. The thesis research reported here addresses this need to develop multiscale modeling strategies for the design of new materials. As a model system, a new system of materials called molecular squares was studied in this research. Both serial and parallel multiscale strategies and their components were developed as parts of this work. As a serial component, a parameter estimation tool was developed that uses a hierarchical protocol and consists of two different search elements: a global search method implemented using a genetic algorithm that is capable of exploring large parametric space, and a local search method using gradient search techniques that accurately finds the optimum in a localized space. As an essential component of parallel multiscale modeling, different standard as well as specialized computational fluid dynamics (CFD) techniques were explored and developed in order to identify a technique that is best suited to solve a membrane reactor model employing layered films of molecular squares as the heterogeneous catalyst. The coupled set of non-linear partial differential equations (PDEs) representing the continuum model was solved numerically using three different classes of methods: a split-step method using finite difference (FD); domain decomposition in two different forms, one involving three overlapping subdomains and the other involving a gap-tooth scheme; and the multiple-timestep method that was developed in this research. The parallel multiscale approach coupled continuum
Numerical Simulations of a Multiscale Model of Stratified Langmuir Circulation
NASA Astrophysics Data System (ADS)
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 model updating of a curved highway bridge
NASA Astrophysics Data System (ADS)
Mensah-Bonsu, Priscilla; Jang, Shinae
2012-04-01
Finite element model updating based on a multi-scale data is demonstrated on a skewed in-service highway bridge. The multi-scale data approach provides an evidence-based method to create a bound of model class to ensure that the optimum model retains physical connectivity to the real structure. The need for this hybrid approach to model selection comes from the challenges of applying model updating to online structural health monitoring (SHM) strategy based on output-only measurements of in-service highway bridges, which should consider various uncertainties. In vibration-based FE model updating methods, the optimum model is selected by minimizing the error between modal parameters of the model and the real structure. A major drawback of model selection is the probability that the optimum model has no physical connectivity with the real structure. This is because a large set of updating parameters is required to increase accuracy. In this paper, an evidence-based approach to model selection using temperature-induced tilts is implemented in which the cyclical static behavior of a bridge is used to create a bound of possible models. This approach has a strong potential to be applicable to large civil structures with sparse array of sensors.
LLNL's program on multiscale modeling of polycrystal plasticity
Diaz De La Rubia, T.; Holmes, N. H.; King, W. E.; Lassila, D. H.; Moriarty, J. A.; Nikkel, D. J.
1998-04-27
At LLNL a multiscale modeling program based on information-passing has been established for modeling the strength properties of a body-centered-cubic metal (tantalum) ,. under conditions of extreme plastic deformation. The plastic deformation experienced by an explosively-formed shaped-charge jet is an example of "extreme deformation". The shaped charge liner material undergoes high strain rate deformation at high hydrostatic pressure. The constitutive model for flow stress, which describes the deformation, is highly dependent on pressure, temperature, and strain-rate. Current material models can not be extrapolated to these extreme conditions because the underlying mechanisms of plastic deformation are poorly reflected in the models and laboratory experiments are limited to pressures orders of magnitude less than actual pressures. This disparity between actual deformation conditions and those that can be attained in laboratory experiments is the principle motivation behind the multiscale modeling program. The fundamental elements of LLNL's multiscale modeling program are distinct models at the atomistic, microscale and mesoscale/continuum length scales. The information that needs to be passed from the lower to higher length scales has been carefully defined to bound the levels of effort required to ''bridge'' length scales. Information that needs to be generated by the different simulations has been specified by a multidisciplinary steering group comprised of physicists, materials scientists and engineers. The ultimate goal of the program is to provide critical information on strength properties to be used in continuum computer code simulations. The technical work-plan involves three principle areas which are highly coupled: 1) simulation development, 2) deformation experiments and 3) characterizations of deformed crystals. The three work areas are presented which provide examples of the progress of LLNL's program.
Multi-scale modeling for sustainable chemical production.
Zhuang, Kai; Bakshi, Bhavik R; Herrgård, Markus J
2013-09-01
With recent advances in metabolic engineering, it is now technically possible to produce a wide portfolio of existing petrochemical products from biomass feedstock. In recent years, a number of modeling approaches have been developed to support the engineering and decision-making processes associated with the development and implementation of a sustainable biochemical industry. The temporal and spatial scales of modeling approaches for sustainable chemical production vary greatly, ranging from metabolic models that aid the design of fermentative microbial strains to material and monetary flow models that explore the ecological impacts of all economic activities. Research efforts that attempt to connect the models at different scales have been limited. Here, we review a number of existing modeling approaches and their applications at the scales of metabolism, bioreactor, overall process, chemical industry, economy, and ecosystem. In addition, we propose a multi-scale approach for integrating the existing models into a cohesive framework. The major benefit of this proposed framework is that the design and decision-making at each scale can be informed, guided, and constrained by simulations and predictions at every other scale. In addition, the development of this multi-scale framework would promote cohesive collaborations across multiple traditionally disconnected modeling disciplines to achieve sustainable chemical production.
Bayesian multi-scale modeling for aggregated disease mapping data.
Aregay, Mehreteab; Lawson, Andrew B; Faes, Christel; Kirby, Russell S
2015-09-29
In disease mapping, a scale effect due to an aggregation of data from a finer resolution level to a coarser level is a common phenomenon. This article addresses this issue using a hierarchical Bayesian modeling framework. We propose four different multiscale models. The first two models use a shared random effect that the finer level inherits from the coarser level. The third model assumes two independent convolution models at the finer and coarser levels. The fourth model applies a convolution model at the finer level, but the relative risk at the coarser level is obtained by aggregating the estimates at the finer level. We compare the models using the deviance information criterion (DIC) and Watanabe-Akaike information criterion (WAIC) that are applied to real and simulated data. The results indicate that the models with shared random effects outperform the other models on a range of criteria.
Multiscale Modeling of Red Blood Cells Squeezing through Submicron Slits
NASA Astrophysics Data System (ADS)
Peng, Zhangli; Lu, Huijie
2016-11-01
A multiscale model is applied to study the dynamics of healthy red blood cells (RBCs), RBCs in hereditary spherocytosis, and sickle cell disease squeezing through submicron slits. This study is motivated by the mechanical filtration of RBCs by inter-endothelial slits in the spleen. First, the model is validated by comparing the simulation results with experiments. Secondly, the deformation of the cytoskeleton in healthy RBCs is investigated. Thirdly, the mechanisms of damage in hereditary spherocytosis are investigated. Finally, the effects of cytoplasm and membrane viscosities, especially in sickle cell disease, are examined. The simulations results provided guidance for future experiments to explore the dynamics of RBCs under extreme deformation.
Community Multiscale Air Quality (CMAQ) Modeling for ...
The CMAQ model is a Eulerian model that produces gridded values of atmospheric concentration and deposition. Recent updates to the model are highlighted that impact estimates of dry and wet deposition of nitrogen, sulfur and base cations. Output from the CMAQ model is used in the measurement-model fusion method used to create the National Atmospheric Program's (NADP) Total Deposition (TDEP) map product. The National Exposure Research Laboratory (NERL) Computational Exposure Division (CED) develops and evaluates data, decision-support tools, and models to be applied to media-specific or receptor-specific problem areas. CED uses modeling-based approaches to characterize exposures, evaluate fate and transport, and support environmental diagnostics/forensics with input from multiple data sources. It also develops media- and receptor-specific models, process models, and decision support tools for use both within and outside of EPA.
Community Multiscale Air Quality (CMAQ) Modeling for ...
The CMAQ model is a Eulerian model that produces gridded values of atmospheric concentration and deposition. Recent updates to the model are highlighted that impact estimates of dry and wet deposition of nitrogen, sulfur and base cations. Output from the CMAQ model is used in the measurement-model fusion method used to create the National Atmospheric Program's (NADP) Total Deposition (TDEP) map product. The National Exposure Research Laboratory (NERL) Computational Exposure Division (CED) develops and evaluates data, decision-support tools, and models to be applied to media-specific or receptor-specific problem areas. CED uses modeling-based approaches to characterize exposures, evaluate fate and transport, and support environmental diagnostics/forensics with input from multiple data sources. It also develops media- and receptor-specific models, process models, and decision support tools for use both within and outside of EPA.
Multiscale modeling of bone tissue with surface and permeability control.
Gonçalves Coelho, Pedro; Rui Fernandes, Paulo; Carriço Rodrigues, Helder
2011-01-11
Natural biological materials usually present a hierarchical arrangement with various structural levels. The biomechanical behavior of the complex hierarchical structure of bone is investigated with models that address the various levels corresponding to different scales. Models that simulate the bone remodeling process concurrently at different scales are in development. We present a multiscale model for bone tissue adaptation that considers the two top levels, whole bone and trabecular architecture. The bone density distribution is calculated at the macroscale (whole bone) level, and the trabecular structure at the microscale level takes into account its mechanical properties as well as surface density and permeability. The bone remodeling process is thus formulated as a material distribution problem at both scales. At the local level, the biologically driven information of surface density and permeability characterizes the trabecular structure. The model is tested by a three-dimensional simulation of bone tissue adaptation for the human femur. The density distribution of the model shows good agreement with the actual bone density distribution. Permeability at the microstructural level assures interconnectivity of pores, which mimics the interconnectivity of trabecular bone essential for vascularization and transport of nutrients. The importance of this multiscale model relays on the flexibility to control the morphometric parameters that characterize the trabecular structure. Therefore, the presented model can be a valuable tool to define bone quality, to assist with diagnosis of osteoporosis, and to support the development of bone substitutes.
Multiscale modeling of chemotaxis in homogeneous porous media
NASA Astrophysics Data System (ADS)
Porter, Mark L.; ValdéS-Parada, Francisco J.; Wood, Brian D.
2011-06-01
We present a predictive, multiscale modeling framework for chemotaxis in porous media. This model results from volume averaging the governing equations for bacterial transport at the microscale and is expressed in terms of effective medium coefficients that are predicted from the solution of the associated closure problems. As a result, the averaged chemotactic velocity is an explicit function of the attractant concentration field and diffusivity, rather than an empirical effective chemotactic sensitivity coefficient. The model was validated by comparing the transverse bacterial concentration profiles with experimental measurements for Escherichia coli HCB1 in a T-sensor. The averaged chemotactic velocity predicted by the model was found to be within the range of values reported in the literature. Reasonable agreement (approximately 10% mean absolute error) between theory and experiments was found for several flow rates. In order to assess the potential for decreasing the computational demands of the model, the macroscale domain was divided into subdomains for the coupling of bacterial transport to that of the attractant. Sensitivity analysis was performed regarding the number of subdomains chosen, and the results indicate that bacterial transport (as measured by concentration profiles) was not highly affected by this choice. Overall, these results suggest that the predictive, multiscale modeling framework is reliable for modeling chemotaxis in porous media when chemotactic transport is significant compared to convective transport.
Multiscale Modeling of Carbon Nanotube-Epoxy Nanocomposites
NASA Astrophysics Data System (ADS)
Fasanella, Nicholas A.
Epoxy-composites are widely used in the aerospace industry. In order to improve upon stiffness and thermal conductivity; carbon nanotube additives to epoxies are being explored. This dissertation presents multiscale modeling techniques to study the engineering properties of single walled carbon nanotube (SWNT)-epoxy nanocomposites, consisting of pristine and covalently functionalized systems. Using Molecular Dynamics (MD), thermomechanical properties were calculated for a representative polymer unit cell. Finite Element (FE) and orientation distribution function (ODF) based methods were used in a multiscale framework to obtain macroscale properties. An epoxy network was built using the dendrimer growth approach. The epoxy model was verified by matching the experimental glass transition temperature, density, and dilatation. MD, via the constant valence force field (CVFF), was used to explore the mechanical and dilatometric effects of adding pristine and functionalized SWNTs to epoxy. Full stiffness matrices and linear coefficient of thermal expansion vectors were obtained. The Green-Kubo method was used to investigate the thermal conductivity as a function of temperature for the various nanocomposites. Inefficient phonon transport at the ends of nanotubes is an important factor in the thermal conductivity of the nanocomposites, and for this reason discontinuous nanotubes were modeled in addition to long nanotubes. To obtain continuum-scale elastic properties from the MD data, multiscale modeling was considered to give better control over the volume fraction of nanotubes, and investigate the effects of nanotube alignment. Two methods were considered; an FE based method, and an ODF based method. The FE method probabilistically assigned elastic properties of elements from the MD lattice results based on the desired volume fraction and alignment of the nanotubes. For the ODF method, a distribution function was generated based on the desired amount of nanotube alignment
Multiscale modelling approaches for assessing cosmetic ingredients safety.
Bois, Frédéric Y; Ochoa, Juan G Diaz; Gajewska, Monika; Kovarich, Simona; Mauch, Klaus; Paini, Alicia; Péry, Alexandre; Benito, Jose Vicente Sala; Teng, Sophie; Worth, Andrew
2016-06-04
The European Union's ban on animal testing for cosmetic ingredients and products has generated a strong momentum for the development of in silico and in vitro alternative methods. One of the focus of the COSMOS project was ab initio prediction of kinetics and toxic effects through multiscale pharmacokinetic modeling and in vitro data integration. In our experience, mathematical or computer modeling and in vitro experiments are complementary. We present here a summary of the main models and results obtained within the framework of the project on these topics. A first section presents our work at the organelle and cellular level. We then go toward modeling cell levels effects (monitored continuously), multiscale physiologically based pharmacokinetic and effect models, and route to route extrapolation. We follow with a short presentation of the automated KNIME workflows developed for dissemination and easy use of the models. We end with a discussion of two challenges to the field: our limited ability to deal with massive data and complex computations. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.
Multiscale Eulerian Model Within NCEP's National Environmental Modeling System
NASA Astrophysics Data System (ADS)
Janjic, Z.; Black, T.; Vasic, R.; Rogers, E.; Dimego, G.
2010-12-01
The unified Non-hydrostatic Multi-scale Model on the B grid (NMMB) is being developed at NCEP as a part of the National Environmental Modeling System (NEMS). The finite-volume horizontal differencing employed in the model preserves important properties of differential operators and conserves a variety of basic and derived dynamical and quadratic quantities. Among these, conservation of energy and enstrophy improves the accuracy of nonlinear dynamics. The nonhydrostatic dynamics were formulated in such a way as to avoid overspecification. In the global limit, “across the pole” polar boundary conditions are used, and the polar filter selectively slows down the wave components that would otherwise propagate faster in the zonal direction than the fastest wave propagating in the meridional direction. The physical package of the model has been developed from the standard NCEP’s WRF NMM physics. A global forecasting system based on the NMMB was run for more than a year in order to test and tune the model, and in particular, to examine its potential for medium range weather forecasting. The system was initialized and verified using the analyses of NCEP’s Global Forecasting System (GFS). The skill of the large scale medium range forecasts produced by the system has been comparable to that of other major medium range forecasting systems. The computational efficiency of the model on parallel computers has been competitive with that of other major global systems. Interestingly, even though the NMMB and GFS were starting from the same analyses, the skill of the two individual medium range forecasts was often disparate. When one model produced a bad forecast, the forecast from the other model could be quite good. Such behavior appears potentially advantageous for application of the two models for ensemble forecasting. On the mesoscales, the NMMB is planned to replace the WRF NMM in operations as the North American Model (NAM), and in a number of nested high resolution
Multiscale geometric modeling of macromolecules I: Cartesian representation
Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo Wei
2013-01-01
This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computational instabilities in molecular simulations, and violate the physical principle of surface free energy minimization. Variational multiscale surface definitions are proposed based on geometric flows and solvation analysis of biomolecular systems. Our approach leads to geometric and potential driven Laplace-Beltrami flows for biomolecular surface evolution and formation. The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system. High order partial differential equation (PDE)-based nonlinear filters are employed for EMDB data processing. We show the efficacy of this approach in feature-preserving noise reduction. After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions. Apart from the classical Gaussian curvature and mean curvature, maximum curvature, minimum curvature, shape index, and curvedness are also applied to macromolecular surface analysis for the first time. Our curvature analysis is uniquely coupled to the analysis of electrostatic surface potential, which is a by-product of our variational multiscale solvation models. As an expository investigation, we particularly emphasize the numerical algorithms and computational protocols for practical applications of the above multiscale geometric models. Such information may otherwise be scattered over the vast literature on this topic. Based on the curvature and electrostatic analysis from our multiresolution surfaces, we introduce a new concept, the
Multiscale geometric modeling of macromolecules I: Cartesian representation.
Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo Wei
2014-01-01
This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computational instabilities in molecular simulations, and violate the physical principle of surface free energy minimization. Variational multiscale surface definitions are proposed based on geometric flows and solvation analysis of biomolecular systems. Our approach leads to geometric and potential driven Laplace-Beltrami flows for biomolecular surface evolution and formation. The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system. High order partial differential equation (PDE)-based nonlinear filters are employed for EMDB data processing. We show the efficacy of this approach in feature-preserving noise reduction. After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions. Apart from the classical Gaussian curvature and mean curvature, maximum curvature, minimum curvature, shape index, and curvedness are also applied to macromolecular surface analysis for the first time. Our curvature analysis is uniquely coupled to the analysis of electrostatic surface potential, which is a by-product of our variational multiscale solvation models. As an expository investigation, we particularly emphasize the numerical algorithms and computational protocols for practical applications of the above multiscale geometric models. Such information may otherwise be scattered over the vast literature on this topic. Based on the curvature and electrostatic analysis from our multiresolution surfaces, we introduce a new concept, the
Multiscale geometric modeling of macromolecules I: Cartesian representation
NASA Astrophysics Data System (ADS)
Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei
2014-01-01
This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computational instabilities in molecular simulations, and violate the physical principle of surface free energy minimization. Variational multiscale surface definitions are proposed based on geometric flows and solvation analysis of biomolecular systems. Our approach leads to geometric and potential driven Laplace-Beltrami flows for biomolecular surface evolution and formation. The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system. High order partial differential equation (PDE)-based nonlinear filters are employed for EMDB data processing. We show the efficacy of this approach in feature-preserving noise reduction. After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions. Apart from the classical Gaussian curvature and mean curvature, maximum curvature, minimum curvature, shape index, and curvedness are also applied to macromolecular surface analysis for the first time. Our curvature analysis is uniquely coupled to the analysis of electrostatic surface potential, which is a by-product of our variational multiscale solvation models. As an expository investigation, we particularly emphasize the numerical algorithms and computational protocols for practical applications of the above multiscale geometric models. Such information may otherwise be scattered over the vast literature on this topic. Based on the curvature and electrostatic analysis from our multiresolution surfaces, we introduce a new concept, the
Multiscale geometric modeling of macromolecules I: Cartesian representation
Xia, Kelin; Feng, Xin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei
2014-01-15
This paper focuses on the geometric modeling and computational algorithm development of biomolecular structures from two data sources: Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) in the Eulerian (or Cartesian) representation. Molecular surface (MS) contains non-smooth geometric singularities, such as cusps, tips and self-intersecting facets, which often lead to computational instabilities in molecular simulations, and violate the physical principle of surface free energy minimization. Variational multiscale surface definitions are proposed based on geometric flows and solvation analysis of biomolecular systems. Our approach leads to geometric and potential driven Laplace–Beltrami flows for biomolecular surface evolution and formation. The resulting surfaces are free of geometric singularities and minimize the total free energy of the biomolecular system. High order partial differential equation (PDE)-based nonlinear filters are employed for EMDB data processing. We show the efficacy of this approach in feature-preserving noise reduction. After the construction of protein multiresolution surfaces, we explore the analysis and characterization of surface morphology by using a variety of curvature definitions. Apart from the classical Gaussian curvature and mean curvature, maximum curvature, minimum curvature, shape index, and curvedness are also applied to macromolecular surface analysis for the first time. Our curvature analysis is uniquely coupled to the analysis of electrostatic surface potential, which is a by-product of our variational multiscale solvation models. As an expository investigation, we particularly emphasize the numerical algorithms and computational protocols for practical applications of the above multiscale geometric models. Such information may otherwise be scattered over the vast literature on this topic. Based on the curvature and electrostatic analysis from our multiresolution surfaces, we introduce a new concept, the
Multi-scale modelling of elastic moduli of trabecular bone
Hamed, Elham; Jasiuk, Iwona; Yoo, Andrew; Lee, YikHan; Liszka, Tadeusz
2012-01-01
We model trabecular bone as a nanocomposite material with hierarchical structure and predict its elastic properties at different structural scales. The analysis involves a bottom-up multi-scale approach, starting with nanoscale (mineralized collagen fibril) and moving up the scales to sub-microscale (single lamella), microscale (single trabecula) and mesoscale (trabecular bone) levels. Continuum micromechanics methods, composite materials laminate theory and finite-element methods are used in the analysis. Good agreement is found between theoretical and experimental results. PMID:22279160
The Total Variation Regularized L1 Model for Multiscale Decomposition
2006-01-01
measure theory approach, and Vixie and Esedoglu’s [43] work on characterizing the solutions of (1.2) below. In this paper we extend the existing...no person shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control ...2r . THE TV-L1 MODEL FOR MULTISCALE DECOMPOSITION 5 In general the minimizer of the TV-L1 is nonunique . In the above disk example, if λ = 2/r
Multiscale Materials Modeling in an Industrial Environment.
Weiß, Horst; Deglmann, Peter; In 't Veld, Pieter J; Cetinkaya, Murat; Schreiner, Eduard
2016-06-07
In this review, we sketch the materials modeling process in industry. We show that predictive and fast modeling is a prerequisite for successful participation in research and development processes in the chemical industry. Stable and highly automated workflows suitable for handling complex systems are a must. In particular, we review approaches to build and parameterize soft matter systems. By satisfying these prerequisites, efficiency for the development of new materials can be significantly improved, as exemplified here for formulation polymer development. This is in fact in line with recent Materials Genome Initiative efforts sponsored by the US government. Valuable contributions to product development are possible today by combining existing modeling techniques in an intelligent fashion, provided modeling and experiment work hand in hand.
Community Multiscale Air Quality Modeling System (CMAQ)
CMAQ is a computational tool used for air quality management. It models air pollutants including ozone, particulate matter and other air toxics to help determine optimum air quality management scenarios.
Standard Model in multiscale theories and observational constraints
NASA Astrophysics Data System (ADS)
Calcagni, Gianluca; Nardelli, Giuseppe; Rodríguez-Fernández, David
2016-08-01
We construct and analyze the Standard Model of electroweak and strong interactions in multiscale spacetimes with (i) weighted derivatives and (ii) q -derivatives. Both theories can be formulated in two different frames, called fractional and integer picture. By definition, the fractional picture is where physical predictions should be made. (i) In the theory with weighted derivatives, it is shown that gauge invariance and the requirement of having constant masses in all reference frames make the Standard Model in the integer picture indistinguishable from the ordinary one. Experiments involving only weak and strong forces are insensitive to a change of spacetime dimensionality also in the fractional picture, and only the electromagnetic and gravitational sectors can break the degeneracy. For the simplest multiscale measures with only one characteristic time, length and energy scale t*, ℓ* and E*, we compute the Lamb shift in the hydrogen atom and constrain the multiscale correction to the ordinary result, getting the absolute upper bound t*<10-23 s . For the natural choice α0=1 /2 of the fractional exponent in the measure, this bound is strengthened to t*<10-29 s , corresponding to ℓ*<10-20 m and E*>28 TeV . Stronger bounds are obtained from the measurement of the fine-structure constant. (ii) In the theory with q -derivatives, considering the muon decay rate and the Lamb shift in light atoms, we obtain the independent absolute upper bounds t*<10-13 s and E*>35 MeV . For α0=1 /2 , the Lamb shift alone yields t*<10-27 s , ℓ*<10-19 m and E*>450 GeV .
A Goddard Multi-Scale Modeling System with Unified Physics
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo
2008-01-01
A multi-scale modeling system with unified physics has been developed at NASA Goddard Space Flight Center (GSFC). The system consists of an MMF, the coupled NASA Goddard finite-volume GCM (fvGCM) and Goddard Cumulus Ensemble model (GCE, a CRM); the state-of-the-art Weather Research and Forecasting model (WRF) and the stand alone GCE. These models can share the same microphysical schemes, radiation (including explicitly calculated cloud optical properties), and surface models that have been developed, improved and tested for different environments. The following is presented in this report: (1) a brief review of the GCE model and its applications on the impact of aerosols on deep precipitation processes, (2) the Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) a discussion on the Goddard WRF version (its developments and applications).
Multiscale modeling of virus replication and spread.
Kumberger, Peter; Frey, Felix; Schwarz, Ulrich S; Graw, Frederik
2016-07-01
Replication and spread of human viruses is based on the simultaneous exploitation of many different host functions, bridging multiple scales in space and time. Mathematical modeling is essential to obtain a systems-level understanding of how human viruses manage to proceed through their life cycles. Here, we review corresponding advances for viral systems of large medical relevance, such as human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV). We will outline how the combination of mathematical models and experimental data has advanced our quantitative knowledge about various processes of these pathogens, and how novel quantitative approaches promise to fill remaining gaps. © 2016 Federation of European Biochemical Societies.
Pope, Bernard J; Fitch, Blake G; Pitman, Michael C; Rice, John J; Reumann, Matthias
2011-01-01
Future multiscale and multiphysics models must use the power of high performance computing (HPC) systems to enable research into human disease, translational medical science, and treatment. Previously we showed that computationally efficient multiscale models will require the use of sophisticated hybrid programming models, mixing distributed message passing processes (e.g. the message passing interface (MPI)) with multithreading (e.g. OpenMP, POSIX pthreads). The objective of this work is to compare the performance of such hybrid programming models when applied to the simulation of a lightweight multiscale cardiac model. Our results show that the hybrid models do not perform favourably when compared to an implementation using only MPI which is in contrast to our results using complex physiological models. Thus, with regards to lightweight multiscale cardiac models, the user may not need to increase programming complexity by using a hybrid programming approach. However, considering that model complexity will increase as well as the HPC system size in both node count and number of cores per node, it is still foreseeable that we will achieve faster than real time multiscale cardiac simulations on these systems using hybrid programming models.
MODELS-3 COMMUNITY MULTISCALE AIR QUALITY (CMAQ) MODEL AEROSOL COMPONENT 1: MODEL DESCRIPTION
The aerosol component of the Community Multiscale Air Quality (CMAQ) model is designed to be an efficient and economical depiction of aerosol dynamics in the atmosphere. The approach taken represents the particle size distribution as the superposition of three lognormal subdis...
MODELS-3 COMMUNITY MULTISCALE AIR QUALITY (CMAQ) MODEL AEROSOL COMPONENT 1: MODEL DESCRIPTION
The aerosol component of the Community Multiscale Air Quality (CMAQ) model is designed to be an efficient and economical depiction of aerosol dynamics in the atmosphere. The approach taken represents the particle size distribution as the superposition of three lognormal subdis...
Multiscale modeling of brain blow flow
NASA Astrophysics Data System (ADS)
Karniadakis, George
2014-11-01
Cardiovascular pathologies, such as brain aneurysms, 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, 3D or 1D) 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 will present a physical model of the brain vasculature consisting at the macro level of all major arteries (about 200 down to 0.5 mm), at the mesoscale the fractal arteriolar tree (more than 10 millions down to 20 nm) and at the microscale the capillary bed. Correspondingly, we employ three different methods to model the total brain vasculature by developing proper interface conditions at each level. We will present examples from aneurysms and other hematological diseases, where red blood cell rheology is modeled explicitly.
Multi-scale modelling and dynamics
NASA Astrophysics Data System (ADS)
Müller-Plathe, Florian
Moving from a fine-grained particle model to one of lower resolution leads, with few exceptions, to an acceleration of molecular mobility, higher diffusion coefficient, lower viscosities and more. On top of that, the level of acceleration is often different for different dynamical processes as well as for different state points. While the reasons are often understood, the fact that coarse-graining almost necessarily introduces unpredictable acceleration of the molecular dynamics severely limits its usefulness as a predictive tool. There are several attempts under way to remedy these shortcoming of coarse-grained models. On the one hand, we follow bottom-up approaches. They attempt already when the coarse-graining scheme is conceived to estimate their impact on the dynamics. This is done by excess-entropy scaling. On the other hand, we also pursue a top-down development. Here we start with a very coarse-grained model (dissipative particle dynamics) which in its native form produces qualitatively wrong polymer dynamics, as its molecules cannot entangle. This model is modified by additional temporary bonds, so-called slip springs, to repair this defect. As a result, polymer melts and solutions described by the slip-spring DPD model show correct dynamical behaviour. Read more: ``Excess entropy scaling for the segmental and global dynamics of polyethylene melts'', E. Voyiatzis, F. Müller-Plathe, and M.C. Böhm, Phys. Chem. Chem. Phys. 16, 24301-24311 (2014). [DOI: 10.1039/C4CP03559C] ``Recovering the Reptation Dynamics of Polymer Melts in Dissipative Particle Dynamics Simulations via Slip-Springs'', M. Langeloth, Y. Masubuchi, M. C. Böhm, and F. Müller-Plathe, J. Chem. Phys. 138, 104907 (2013). [DOI: 10.1063/1.4794156].
Angelis, G I; Reader, A J; Markiewicz, P J; Kotasidis, F A; Lionheart, W R; Matthews, J C
2013-08-07
Recent studies have demonstrated the benefits of a resolution model within iterative reconstruction algorithms in an attempt to account for effects that degrade the spatial resolution of the reconstructed images. However, these algorithms suffer from slower convergence rates, compared to algorithms where no resolution model is used, due to the additional need to solve an image deconvolution problem. In this paper, a recently proposed algorithm, which decouples the tomographic and image deconvolution problems within an image-based expectation maximization (EM) framework, was evaluated. This separation is convenient, because more computational effort can be placed on the image deconvolution problem and therefore accelerate convergence. Since the computational cost of solving the image deconvolution problem is relatively small, multiple image-based EM iterations do not significantly increase the overall reconstruction time. The proposed algorithm was evaluated using 2D simulations, as well as measured 3D data acquired on the high-resolution research tomograph. Results showed that bias reduction can be accelerated by interleaving multiple iterations of the image-based EM algorithm solving the resolution model problem, with a single EM iteration solving the tomographic problem. Significant improvements were observed particularly for voxels that were located on the boundaries between regions of high contrast within the object being imaged and for small regions of interest, where resolution recovery is usually more challenging. Minor differences were observed using the proposed nested algorithm, compared to the single iteration normally performed, when an optimal number of iterations are performed for each algorithm. However, using the proposed nested approach convergence is significantly accelerated enabling reconstruction using far fewer tomographic iterations (up to 70% fewer iterations for small regions). Nevertheless, the optimal number of nested image-based EM
Multiscale Models of Melting Arctic Sea Ice
2013-09-30
understanding the evolution of melt ponds and sea ice albedo remains a significant challenge to improving climate models. Our research is focused on...Mathematics, U. of Utah) Don Perovich ( Research Geophysicist, ERDC-CRREL) Tolga Tasdizen (Associate Professor, Department of Electrical and Computer...Chris Polashenski ( Research Geophysicist, ERDC-CRREL) Ivan Sudakov (Lorenz Postdoc in Mathematics of Climate, U. of Utah) Report Documentation
Multi-Scale Modeling of Magnetospheric Dynamics
NASA Technical Reports Server (NTRS)
Kuznetsova, M. M.; Hesse, M.; Toth, G.
2012-01-01
Magnetic reconnection is a key element in many phenomena in space plasma, e.g. Coronal mass Ejections, Magnetosphere substorms. One of the major challenges in modeling the dynamics of large-scale systems involving magnetic reconnection is to quantifY the interaction between global evolution of the magnetosphere and microphysical kinetic processes in diffusion regions near reconnection sites. Recent advances in small-scale kinetic modeling of magnetic reconnection significantly improved our understanding of physical mechanisms controlling the dissipation in the vicinity of the reconnection site in collisionless plasma. However the progress in studies of small-scale geometries was not very helpful for large scale simulations. Global magnetosphere simulations usually include non-ideal processes in terms of numerical dissipation and/or ad hoc anomalous resistivity. Comparative studies of magnetic reconnection in small scale geometries demonstrated that MHD simulations that included non-ideal processes in terms of a resistive term 11 J did not produce fast reconnection rates observed in kinetic simulations. In collisionless magnetospheric plasma, the primary mechanism controlling the dissipation in the vicinity of the reconnection site is nongyrotropic pressure effects with spatial scales comparable with the particle Larmor radius. We utilize the global MHD code BATSRUS and replace ad hoc parameters such as "critical current density" and "anomalous resistivity" with a physically motivated model of dissipation. The primary mechanism controlling the dissipation in the vicinity of the reconnection site in incorporated into MHD description in terms of non-gyrotropic corrections to the induction equation. We will demonstrate that kinetic nongyrotropic effects can significantly alter the global magnetosphere evolution. Our approach allowed for the first time to model loading/unloading cycle in response to steady southward IMF driving. The role of solar wind parameters and
Stochastic Multiscale Modeling of Polycrystalline Materials
2013-01-01
2.16 Explicit structure of a (γ+γ′) grain and its equivalent homoge- nized model. The gray background on the left grain represents γ matrix, while...effective strength . . . . . . . . . . . . . . . . . . . . . . . 129 3.14 Convergence test of the mean field of the properties of the forged product...microstructure input. The variabil- ity of strain, stress and strength fields over the workpiece after forging is inves- tigated. The microstructures in the
Multiscale Modeling of Solar Coronal Magnetic Reconnection
NASA Astrophysics Data System (ADS)
Antiochos, S. K.; Karpen, J. T.; DeVore, C. R.
2010-12-01
Magnetic reconnection is widely believed to be the primary process by which the magnetic field releases energy to plasma in the Sun's corona. For example, in the breakout model for the initiation of coronal mass ejections/eruptive flares, reconnection is responsible for the catastrophic destabilizing of magnetic force balance in the corona, leading to explosive energy release. A critical requirement for the reconnection is that it have a "switch-on' nature in that the reconnection stays off until a large store of magnetic free energy has built up, and then it turn on abruptly and stay on until most of this free energy has been released. We discuss the implications of this requirement for reconnection in the context of the breakout model for CMEs/flares. We argue that it imposes stringent constraints on the properties of the flux breaking mechanism, which is expected to operate in the corona on kinetic scales. We present numerical simulations demonstrating how the reconnection and the eruption depend on the effective resistivity, i.e., the effective Lundquist number, and propose a model for incorporating kinetic flux-breaking mechanisms into MHD calculation of CMEs/flares. This work has been supported by the NASA HTP, SR&T, and LWS programs. High-resolution simulation of a breakout CME showing details of the reconnection region (Karpen et al 2010).
Multiscale Systems Modeling of Male Reproductive Tract ...
The reproductive tract is a complex, integrated organ system with diverse embryology and unique sensitivity to prenatal environmental exposures that disrupt morphoregulatory processes and endocrine signaling. U.S. EPA’s in vitro high-throughput screening (HTS) database (ToxCastDB) was used to profile the bioactivity of 54 chemicals with male developmental consequences across ~800 molecular and cellular features [Leung et al., accepted manuscript]. The in vitro bioactivity on molecular targets could be condensed into 156 gene annotations in a bipartite network. These results highlighted the role of estrogen and androgen signaling pathways in male reproductive tract development, and importantly, broadened the list of molecular targets to include GPCRs, cytochrome-P450s, vascular remodeling proteins, and retinoic acid signaling. A multicellular agent-based model was used to simulate the complex interactions between morphoregulatory, endocrine, and environmental influences during genital tubercle (GT) development. Spatially dynamic signals (e.g., SHH, FGF10, and androgen) were implemented in the model to address differential adhesion, cell motility, proliferation, and apoptosis. Urethral tube closure was an emergent feature of the model that was linked to gender-specific rates of ventral mesenchymal proliferation and urethral plate endodermal apoptosis, both under control of androgen signaling [Leung et al., manuscript in preparation]. A systemic parameter sweep w
A tantalum strength model using a multiscale approach: version 2
Becker, R; Arsenlis, A; Hommes, G; Marian, J; Rhee, M; Yang, L H
2009-09-21
A continuum strength model for tantalum was developed in 2007 using a multiscale approach. This was our first attempt at connecting simulation results from atomistic to continuum length scales, and much was learned that we were not able to incorporate into the model at that time. The tantalum model described in this report represents a second cut at pulling together multiscale simulation results into a continuum model. Insight gained in creating previous multiscale models for tantalum and vanadium was used to guide the model construction and functional relations for the present model. While the basic approach follows that of the vanadium model, there are significant departures. Some of the recommendations from the vanadium report were followed, but not all. Results from several new analysis techniques have not yet been incorporated due to technical difficulties. Molecular dynamics simulations of single dislocation motion at several temperatures suggested that the thermal activation barrier was temperature dependent. This dependency required additional temperature functions be included within the assumed Arrhenius relation. The combination of temperature dependent functions created a complex model with a non unique parameterization and extra model constants. The added complexity had no tangible benefits. The recommendation was to abandon the strict Arrhenius form and create a simpler curve fit to the molecular dynamics data for shear stress versus dislocation velocity. Functions relating dislocation velocity and applied shear stress were constructed vor vanadium for both edge and screw dislocations. However, an attempt to formulate a robust continuum constitutive model for vanadium using both dislocation populations was unsuccessful; the level of coupling achieved was inadequate to constrain the dislocation evolution properly. Since the behavior of BCC materials is typically assumed to be dominated by screw dislocations, the constitutive relations were ultimately
Adaptive Multiscale Modeling of Geochemical Impacts on Fracture Evolution
NASA Astrophysics Data System (ADS)
Molins, S.; Trebotich, D.; Steefel, C. I.; Deng, H.
2016-12-01
Understanding fracture evolution is essential for many subsurface energy applications, including subsurface storage, shale gas production, fracking, CO2 sequestration, and geothermal energy extraction. Geochemical processes in particular play a significant role in the evolution of fractures through dissolution-driven widening, fines migration, and/or fracture sealing due to precipitation. One obstacle to understanding and exploiting geochemical fracture evolution is that it is a multiscale process. However, current geochemical modeling of fractures cannot capture this multi-scale nature of geochemical and mechanical impacts on fracture evolution, and is limited to either a continuum or pore-scale representation. Conventional continuum-scale models treat fractures as preferential flow paths, with their permeability evolving as a function (often, a cubic law) of the fracture aperture. This approach has the limitation that it oversimplifies flow within the fracture in its omission of pore scale effects while also assuming well-mixed conditions. More recently, pore-scale models along with advanced characterization techniques have allowed for accurate simulations of flow and reactive transport within the pore space (Molins et al., 2014, 2015). However, these models, even with high performance computing, are currently limited in their ability to treat tractable domain sizes (Steefel et al., 2013). Thus, there is a critical need to develop an adaptive modeling capability that can account for separate properties and processes, emergent and otherwise, in the fracture and the rock matrix at different spatial scales. Here we present an adaptive modeling capability that treats geochemical impacts on fracture evolution within a single multiscale framework. Model development makes use of the high performance simulation capability, Chombo-Crunch, leveraged by high resolution characterization and experiments. The modeling framework is based on the adaptive capability in Chombo
Multiscale Model for the Dielectric Permittivity
NASA Astrophysics Data System (ADS)
Pérez-Madrid, Agustín; Lapas, Luciano C.; Rubí, J. Miguel
2017-02-01
We present a generalisation of the Debye relaxation model for the dielectric permittivity in the case in which the global relaxation process is the result of many elementary excitations. The relaxation dynamics is in this case non-Markovian. In the case of many events, for which the central limit theorem holds and Gaussianity as well as the assumption of independency are both plausible, the global relaxation time is given by a log-normal function. The hierarchy of relaxation times leads to a generalised expression of the dielectric permittivity.
Multiscale computational modelling of the heart
NASA Astrophysics Data System (ADS)
Smith, N. P.; Nickerson, D. P.; Crampin, E. J.; Hunter, P. J.
A computational framework is presented for integrating the electrical, mechanical and biochemical functions of the heart. Finite element techniques are used to solve the large-deformation soft tissue mechanics using orthotropic constitutive laws based in the measured fibre-sheet structure of myocardial (heart muscle) tissue. The reaction-diffusion equations governing electrical current flow in the heart are solved on a grid of deforming material points which access systems of ODEs representing the cellular processes underlying the cardiac action potential. Navier-Stokes equations are solved for coronary blood flow in a system of branching blood vessels embedded in the deforming myocardium and the delivery of oxygen and metabolites is coupled to the energy-dependent cellular processes. The framework presented here for modelling coupled physical conservation laws at the tissue and organ levels is also appropriate for other organ systems in the body and we briefly discuss applications to the lungs and the musculo-skeletal system. The computational framework is also designed to reach down to subcellular processes, including signal transduction cascades and metabolic pathways as well as ion channel electrophysiology, and we discuss the development of ontologies and markup language standards that will help link the tissue and organ level models to the vast array of gene and protein data that are now available in web-accessible databases.
Multiscale modeling for fluid transport in nanosystems.
Lee, Jonathan W.; Jones, Reese E.; Mandadapu, Kranthi Kiran; Templeton, Jeremy Alan; Zimmerman, Jonathan A.
2013-09-01
Atomistic-scale behavior drives performance in many micro- and nano-fluidic systems, such as mircrofludic mixers and electrical energy storage devices. Bringing this information into the traditionally continuum models used for engineering analysis has proved challenging. This work describes one such approach to address this issue by developing atomistic-to-continuum multi scale and multi physics methods to enable molecular dynamics (MD) representations of atoms to incorporated into continuum simulations. Coupling is achieved by imposing constraints based on fluxes of conserved quantities between the two regions described by one of these models. The impact of electric fields and surface charges are also critical, hence, methodologies to extend finite-element (FE) MD electric field solvers have been derived to account for these effects. Finally, the continuum description can have inconsistencies with the coarse-grained MD dynamics, so FE equations based on MD statistics were derived to facilitate the multi scale coupling. Examples are shown relevant to nanofluidic systems, such as pore flow, Couette flow, and electric double layer.
Quantitative modeling of multiscale neural activity
NASA Astrophysics Data System (ADS)
Robinson, Peter A.; Rennie, Christopher J.
2007-01-01
The electrical activity of the brain has been observed for over a century and is widely used to probe brain function and disorders, chiefly through the electroencephalogram (EEG) recorded by electrodes on the scalp. However, the connections between physiology and EEGs have been chiefly qualitative until recently, and most uses of the EEG have been based on phenomenological correlations. A quantitative mean-field model of brain electrical activity is described that spans the range of physiological and anatomical scales from microscopic synapses to the whole brain. Its parameters measure quantities such as synaptic strengths, signal delays, cellular time constants, and neural ranges, and are all constrained by independent physiological measurements. Application of standard techniques from wave physics allows successful predictions to be made of a wide range of EEG phenomena, including time series and spectra, evoked responses to stimuli, dependence on arousal state, seizure dynamics, and relationships to functional magnetic resonance imaging (fMRI). Fitting to experimental data also enables physiological parameters to be infered, giving a new noninvasive window into brain function, especially when referenced to a standardized database of subjects. Modifications of the core model to treat mm-scale patchy interconnections in the visual cortex are also described, and it is shown that resulting waves obey the Schroedinger equation. This opens the possibility of classical cortical analogs of quantum phenomena.
Multi-Scale Modeling of Magnetospheric Reconnection
NASA Technical Reports Server (NTRS)
Kuznetsova, M. M.; Hesse, M.; Rastatter, L.; Toth, G.; Dezeeuw, D.; Gomobosi, T.
2007-01-01
One of the major challenges in modeling the magnetospheric magnetic reconnection is to quantify the interaction between large-scale global magnetospheric dynamics and microphysical processes in diffusion regions near reconnection sites. There is still considerable debate as to what degree microphysical processes on kinetic scales affect the global evolution and how important it is to substitute numerical dissipation and/or ad hoc anomalous resistivity by a physically motivated model of dissipation. Comparative studies of magnetic reconnection in small scale geometries demonstrated that MHD simulations that included non-ideal processes in terms of a resistive term $\\eta J$ did not produce the fast reconnection rates observed in kinetic simulations. For a broad range of physical parameters in collisionless magnetospheric plasma, the primary mechanism controlling the dissipation in the vicinity of the reconnection site is non-gyrotropic effects with spatial scales comparable with the particle Larmor radius. We utilize the global MHD code BATSRUS and incorporate nongyrotropic effects in diffusion regions in terms of corrections to the induction equation. We developed an algorithm to search for magnetotail reconnection sites, specifically where the magnetic field components perpendicular to the local current direction approaches zero and form an X-type configuration. Spatial scales of the diffusion region and magnitude of the reconnection electric field are calculated selfconsistently using MHD plasma and field parameters in the vicinity of the reconnection site. The location of the reconnection sites is updated during the simulations. To clarify the role of nongyrotropic effects in diffusion region on the global magnetospheric dynamic we perform simulations with steady southward IMF driving of the magnetosphere. Ideal MHD simulations with magnetic reconnection supported by numerical resistivity produce steady configuration with almost stationary near-earth neutral
Multi-Scale Modeling of Magnetospheric Reconnection
NASA Technical Reports Server (NTRS)
Kuznetsova, M. M.; Hesse, M.; Rastatter, L.; Toth, G.; Dezeeuw, D.; Gomobosi, T.
2007-01-01
One of the major challenges in modeling the magnetospheric magnetic reconnection is to quantify the interaction between large-scale global magnetospheric dynamics and microphysical processes in diffusion regions near reconnection sites. There is still considerable debate as to what degree microphysical processes on kinetic scales affect the global evolution and how important it is to substitute numerical dissipation and/or ad hoc anomalous resistivity by a physically motivated model of dissipation. Comparative studies of magnetic reconnection in small scale geometries demonstrated that MHD simulations that included non-ideal processes in terms of a resistive term $\\eta J$ did not produce the fast reconnection rates observed in kinetic simulations. For a broad range of physical parameters in collisionless magnetospheric plasma, the primary mechanism controlling the dissipation in the vicinity of the reconnection site is non-gyrotropic effects with spatial scales comparable with the particle Larmor radius. We utilize the global MHD code BATSRUS and incorporate nongyrotropic effects in diffusion regions in terms of corrections to the induction equation. We developed an algorithm to search for magnetotail reconnection sites, specifically where the magnetic field components perpendicular to the local current direction approaches zero and form an X-type configuration. Spatial scales of the diffusion region and magnitude of the reconnection electric field are calculated selfconsistently using MHD plasma and field parameters in the vicinity of the reconnection site. The location of the reconnection sites is updated during the simulations. To clarify the role of nongyrotropic effects in diffusion region on the global magnetospheric dynamic we perform simulations with steady southward IMF driving of the magnetosphere. Ideal MHD simulations with magnetic reconnection supported by numerical resistivity produce steady configuration with almost stationary near-earth neutral
Multiscale modeling and computation of optically manipulated nano devices
Bao, Gang; Liu, Di; Luo, Songting
2016-07-01
We present a multiscale modeling and computational scheme for optical-mechanical responses of nanostructures. The multi-physical nature of the problem is a result of the interaction between the electromagnetic (EM) field, the molecular motion, and the electronic excitation. To balance accuracy and complexity, we adopt the semi-classical approach that the EM field is described classically by the Maxwell equations, and the charged particles follow the Schrödinger equations quantum mechanically. To overcome the numerical challenge of solving the high dimensional multi-component many-body Schrödinger equations, we further simplify the model with the Ehrenfest molecular dynamics to determine the motion of the nuclei, and use the Time-Dependent Current Density Functional Theory (TD-CDFT) to calculate the excitation of the electrons. This leads to a system of coupled equations that computes the electromagnetic field, the nuclear positions, and the electronic current and charge densities simultaneously. In the regime of linear responses, the resonant frequencies initiating the out-of-equilibrium optical-mechanical responses can be formulated as an eigenvalue problem. A self-consistent multiscale method is designed to deal with the well separated space scales. The isomerization of azobenzene is presented as a numerical example.
Multiscale modeling of blood flow in cerebral malaria
NASA Astrophysics Data System (ADS)
Fedosov, Dmitry; Caswell, Bruce; Karniadakis, George
2009-11-01
The main characteristics of the malaria disease are progressing changes in red blood cell (RBC) mechanical properties and geometry, and its cytoadhesion to the vascular endothelium. Malaria-infected RBCs become considerably stiff compared to healthy ones, and may bind to the vascular endothelium of arterioles and venules. This leads to a significant reduction of blood flow, and eventual vessel obstruction. Due to a non-trivial malaria-infected RBC adhesive dynamics and obstruction formations the blood flow in cerebral malaria is extremely complex. Here, we employ multiscale modeling to couple nanometer scales at the binding level, micrometer scales at the cell level and millimeter scales at the arteriole level. Blood flow in cerebral malaria is modeled using a coarse-grained RBC model developed in our group. The RBC adhesion is simulated based on the stochastic bond formation/breakage model, which is validated against recent experiments.
Multiscale thermohydrologic model sensitivity analysis/011/011/011
Buscheck, T.A., LLNL
1998-07-31
A multiscale, thermohydrologic (TH) modeling approach (or methodology) has been developed that integrates the results from one- dimensional (1-D), two-dimensional (2-D), and three-dimensional (3-D) drift-scale models and a 3-D mountain-scale model to calculate the near-field TH variables affecting the performance of the engineered barrier system (EBS) of the potential repository at Yucca Mountain. This information is required by Total System Performance Assessment- Viability Assessment (TSPA-VA) to assess waste-package (WP) corrosion, waste-form dissolution, and radionuclide transport in the EBS. This methodology is a computationally efficient, flexible means of determining EBS TH conditions; such determination would otherwise require millions of grid blocks if a brute-force numerical model were used. The methodology determines EBS TH conditions as a function of location within the repository and WP type.
Multi-Scale Modeling of Plasma Thrusters
NASA Astrophysics Data System (ADS)
Batishchev, Oleg
2004-11-01
Plasma thrusters are characterized with multiple spatial and temporal scales, which are due to the intrinsic physical processes such as gas ionization, wall effects and plasma acceleration. Characteristic times for hot plasma and cold gas are differing by 6-7 orders of magnitude. The typical collisional mean-free-paths vary by 3-5 orders along the devices. These make questionable a true self-consistent modeling of the thrusters. The latter is vital to the understanding of complex physics, non-linear dynamics and optimization of the performance. To overcome this problem we propose the following approach. All processes are divided into two groups: fast and slow. The slow ones include gas evolution with known sources and ionization sink. The ionization rate, transport coefficients, energy sources are defined during "fast step". Both processes are linked through external iterations. Multiple spatial scales are handled using moving adaptive mesh. Development and application of this method to the VASIMR helicon plasma source and other thrusters will be discussed. Supported by NASA.
Integrated Multiscale Modeling of Molecular Computing Devices
Jerzy Bernholc
2011-02-03
will some day reach a miniaturization limit, forcing designers of Si-based electronics to pursue increased performance by other means. Any other alternative approach would have the unenviable task of matching the ability of Si technology to pack more than a billion interconnected and addressable devices on a chip the size of a thumbnail. Nevertheless, the prospects of developing alternative approaches to fabricate electronic devices have spurred an ever-increasing pace of fundamental research. One of the promising possibilities is molecular electronics (ME), self-assembled molecular-based electronic systems composed of single-molecule devices in ultra dense, ultra fast molecular-sized components. This project focused on developing accurate, reliable theoretical modeling capabilities for describing molecular electronics devices. The participants in the project are given in Table 1. The primary outcomes of this fundamental computational science grant are publications in the open scientific literature. As listed below, 62 papers have been published from this project. In addition, the research has also been the subject of more than 100 invited talks at conferences, including several plenary or keynote lectures. Many of the goals of the original proposal were completed. Specifically, the multi-disciplinary group developed a unique set of capabilities and tools for investigating electron transport in fabricated and self-assembled nanostructures at multiple length and time scales.
Parallelization of fine-scale computation in Agile Multiscale Modelling Methodology
NASA Astrophysics Data System (ADS)
Macioł, Piotr; Michalik, Kazimierz
2016-10-01
Nowadays, multiscale modelling of material behavior is an extensively developed area. An important obstacle against its wide application is high computational demands. Among others, the parallelization of multiscale computations is a promising solution. Heterogeneous multiscale models are good candidates for parallelization, since communication between sub-models is limited. In this paper, the possibility of parallelization of multiscale models based on Agile Multiscale Methodology framework is discussed. A sequential, FEM based macroscopic model has been combined with concurrently computed fine-scale models, employing a MatCalc thermodynamic simulator. The main issues, being investigated in this work are: (i) the speed-up of multiscale models with special focus on fine-scale computations and (ii) on decreasing the quality of computations enforced by parallel execution. Speed-up has been evaluated on the basis of Amdahl's law equations. The problem of `delay error', rising from the parallel execution of fine scale sub-models, controlled by the sequential macroscopic sub-model is discussed. Some technical aspects of combining third-party commercial modelling software with an in-house multiscale framework and a MPI library are also discussed.
A new approach towards image based virtual 3D city modeling by using close range photogrammetry
NASA Astrophysics Data System (ADS)
Singh, S. P.; Jain, K.; Mandla, V. R.
2014-05-01
3D city model is a digital representation of the Earth's surface and it's related objects such as building, tree, vegetation, and some manmade feature belonging to urban area. The demand of 3D city modeling is increasing day to day for various engineering and non-engineering applications. Generally three main image based approaches are using for virtual 3D city models generation. In first approach, researchers used Sketch based modeling, second method is Procedural grammar based modeling and third approach is Close range photogrammetry based modeling. Literature study shows that till date, there is no complete solution available to create complete 3D city model by using images. These image based methods also have limitations This paper gives a new approach towards image based virtual 3D city modeling by using close range photogrammetry. This approach is divided into three sections. First, data acquisition process, second is 3D data processing, and third is data combination process. In data acquisition process, a multi-camera setup developed and used for video recording of an area. Image frames created from video data. Minimum required and suitable video image frame selected for 3D processing. In second section, based on close range photogrammetric principles and computer vision techniques, 3D model of area created. In third section, this 3D model exported to adding and merging of other pieces of large area. Scaling and alignment of 3D model was done. After applying the texturing and rendering on this model, a final photo-realistic textured 3D model created. This 3D model transferred into walk-through model or in movie form. Most of the processing steps are automatic. So this method is cost effective and less laborious. Accuracy of this model is good. For this research work, study area is the campus of department of civil engineering, Indian Institute of Technology, Roorkee. This campus acts as a prototype for city. Aerial photography is restricted in many country
Toward a multiscale modeling framework for understanding serotonergic function
Wong-Lin, KongFatt; Wang, Da-Hui; Moustafa, Ahmed A; Cohen, Jeremiah Y; Nakamura, Kae
2017-01-01
Despite its importance in regulating emotion and mental wellbeing, the complex structure and function of the serotonergic system present formidable challenges toward understanding its mechanisms. In this paper, we review studies investigating the interactions between serotonergic and related brain systems and their behavior at multiple scales, with a focus on biologically-based computational modeling. We first discuss serotonergic intracellular signaling and neuronal excitability, followed by neuronal circuit and systems levels. At each level of organization, we will discuss the experimental work accompanied by related computational modeling work. We then suggest that a multiscale modeling approach that integrates the various levels of neurobiological organization could potentially transform the way we understand the complex functions associated with serotonin. PMID:28417684
A High-Order Multiscale Global Atmospheric Model
NASA Astrophysics Data System (ADS)
Nair, R. D.
2015-12-01
The High-Order Method Modeling Environment (HOMME), developed at NCAR, is a petascale hydrostatic framework, which employs the cubed-sphere grid system and high-order continuous or discontinuous Galerkin (DG) methods. Recently, the HOMME framework is being extended to a non-hydrostatic dynamical core, named as the "High-Order Multiscale Atmospheric Model (HOMAM)." The spatial discretization for HOMAM is based on DG or high-order finite-volume methods. Orography is handled by the terrain-following height-based coordinate system. To alleviate the stringent CFL stability requirement resulting from the vertical aspects of the dynamics, an operator-splitting time integration scheme based on the horizontally explicit and vertically implicit (HEVI) philosophy is adopted for HOMAM. Preliminary results with the benchmark test cases proposed in the Dynamical Core Model Intercomparison project (DCMIP) test-suite will be presented in the seminar.
A High-Order Multiscale Global Atmospheric Model
NASA Astrophysics Data System (ADS)
Nair, Ram
2016-04-01
The High-Order Method Modeling Environment (HOMME), developed at NCAR, is a petascale hydrostatic framework, which employs the cubed-sphere grid system and high-order continuous or discontinuous Galerkin (DG) methods. Recently, the HOMME framework is being extended to a non-hydrostatic dynamical core, named as the "High-Order Multiscale Atmospheric Model (HOMAM)." The spatial discretization is based on DG or high-order finite-volume methods. Orography is handled by the terrain-following height-based coordinate system. To alleviate the stringent CFL stability requirement resulting from the vertical aspects of the dynamics, an operator-splitting time integration scheme based on the horizontally explicit and vertically implicit (HEVI) philosophy is adopted for HOMAM. Preliminary results with the benchmark test cases proposed in the Dynamical Core Model Intercomparison project (DCMIP) test-suite will be presented in the seminar.
NASA Astrophysics Data System (ADS)
Trinks, I.; Wallner, M.; Kucera, M.; Verhoeven, G.; Torrejón Valdelomar, J.; Löcker, K.; Nau, E.; Sevara, C.; Aldrian, L.; Neubauer, E.; Klein, M.
2017-02-01
The excavated architecture of the exceptional prehistoric site of Akrotiri on the Greek island of Thera/Santorini is endangered by gradual decay, damage due to accidents, and seismic shocks, being located on an active volcano in an earthquake-prone area. Therefore, in 2013 and 2014 a digital documentation project has been conducted with support of the National Geographic Society in order to generate a detailed digital model of Akrotiri's architecture using terrestrial laser scanning and image-based modeling. Additionally, non-invasive geophysical prospection has been tested in order to investigate its potential to explore and map yet buried archaeological remains. This article describes the project and the generated results.
Identity in agent-based models : modeling dynamic multiscale social processes.
Ozik, J.; Sallach, D. L.; Macal, C. M.; Decision and Information Sciences; Univ. of Chicago
2008-07-01
Identity-related issues play central roles in many current events, including those involving factional politics, sectarianism, and tribal conflicts. Two popular models from the computational-social-science (CSS) literature - the Threat Anticipation Program and SharedID models - incorporate notions of identity (individual and collective) and processes of identity formation. A multiscale conceptual framework that extends some ideas presented in these models and draws other capabilities from the broader CSS literature is useful in modeling the formation of political identities. The dynamic, multiscale processes that constitute and transform social identities can be mapped to expressive structures of the framework
A Novel Spectral Approach to Multi-Scale Modeling
NASA Astrophysics Data System (ADS)
Landi, Giacomo
2011-12-01
In this work, we present a novel approach for predicting the elastic, thermo-elastic and plastic fields in three-dimensional (3-D) voxel-based microstructure datasets subjected to uniform periodic boundary conditions. Such localization relationships (linkages) lie at the core of all multi-scale modeling frameworks and can be efficiently formulated in a Discrete Fourier Transforms (DFT) -based knowledge system. This new formalism has its theoretical roots in the statistical continuum theories developed originally by Kroner [1]. However, in the approach described by Kroner, the terms in the series were established by selecting a reference medium and numerically evaluating a complex series of nested convolution integrals. This approach is largely hampered by the principal value problem, and exhibits high sensitivity to the properties of the selected reference medium. In the present work, the same series expressions have been recast into much more computationally efficient representations using DFTs. The spectral analysis transforms the complex integral relations into relatively simple algebraic expressions involving polynomials of structure parameters and morphology-independent influence coefficients. These coefficients need to be established only once for a given material system. The main advantage of the new DFT-based framework is that it allows easy calibration of Kroner's expansions to results from finite element methods, thereby overcoming all of the main obstacles associated with the principal value problem and the need to select a reference medium. This approach can be seen as an efficient procedure for data-mining the results from computationally expensive numerical models and establishing the underlying knowledge systems at a selected length scale in multi-scale modeling problems. The set of influence coefficients described above constitutes the underlying knowledge for a given deformation and can be easily stored and recalled as and when needed in a multi-scale
Three-Dimensional Multiscale MHD Model of Cometary Plasma Environments
NASA Technical Reports Server (NTRS)
Gombosi, Tamas I.; DeZeeuw, Darren L.; Haberli, Roman M.; Powell, Kenneth G.
1996-01-01
First results of a three-dimensional multiscale MHD model of the interaction of an expanding cometary atmosphere with the magnetized solar wind are presented. The model starts with a supersonic and super-Alfvenic solar wind far upstream of the comet (25 Gm upstream of the nucleus) with arbitrary interplanetary magnetic field orientation. The solar wind is continuously mass loaded with cometary ions originating from a 10-km size nucleus. The effects of photoionization, electron impact ionization, recombination, and ion-neutral frictional drag are taken into account in the model. The governing equations are solved on an adaptively refined unstructured Cartesian grid using our new multiscale upwind scalar conservation laws-type numerical technique (MUSCL). We have named this the multiscale adaptive upwind scheme for MHD (MAUS-MHD). The combination of the adaptive refinement with the MUSCL-scheme allows the entire cometary atmosphere to be modeled, while still resolving both the shock and the diamagnetic cavity of the comet. The main findings are the following: (1) Mass loading decelerates the solar wind flow upstream of the weak cometary shock wave (M approximately equals 2, M(sub A) approximately equals 2), which forms at a subsolar standoff distance of about 0.35 Gm. (2) A cometary plasma cavity is formed at around 3 x 10(exp 3) km from the nucleus. Inside this cavity the plasma expands outward due to the frictional interaction between ions and neutrals. On the nightside this plasma cavity considerably narrows and a relatively fast and dense cometary plasma beam is ejected into the tail. (3) Inside the plasma cavity a teardrop-shaped inner shock is formed, which is terminated by a Mach disk on the nightside. Only the region inside the inner shock is the 'true' diamagnetic cavity. (4) The model predicts four distinct current systems in the inner coma: the density peak current, the cavity boundary current, the inner shock current, and finally the cross-tail current
A Liver-Centric Multiscale Modeling Framework for Xenobiotics.
Sluka, James P; Fu, Xiao; Swat, Maciej; Belmonte, Julio M; Cosmanescu, Alin; Clendenon, Sherry G; Wambaugh, John F; Glazier, James A
2016-01-01
We describe a multi-scale, liver-centric in silico modeling framework for acetaminophen pharmacology and metabolism. We focus on a computational model to characterize whole body uptake and clearance, liver transport and phase I and phase II metabolism. We do this by incorporating sub-models that span three scales; Physiologically Based Pharmacokinetic (PBPK) modeling of acetaminophen uptake and distribution at the whole body level, cell and blood flow modeling at the tissue/organ level and metabolism at the sub-cellular level. We have used standard modeling modalities at each of the three scales. In particular, we have used the Systems Biology Markup Language (SBML) to create both the whole-body and sub-cellular scales. Our modeling approach allows us to run the individual sub-models separately and allows us to easily exchange models at a particular scale without the need to extensively rework the sub-models at other scales. In addition, the use of SBML greatly facilitates the inclusion of biological annotations directly in the model code. The model was calibrated using human in vivo data for acetaminophen and its sulfate and glucuronate metabolites. We then carried out extensive parameter sensitivity studies including the pairwise interaction of parameters. We also simulated population variation of exposure and sensitivity to acetaminophen. Our modeling framework can be extended to the prediction of liver toxicity following acetaminophen overdose, or used as a general purpose pharmacokinetic model for xenobiotics.
Global Environmental Multiscale model - a platform for integrated environmental predictions
NASA Astrophysics Data System (ADS)
Kaminski, Jacek W.; Struzewska, Joanna; Neary, Lori; Dearden, Frank
2017-04-01
The Global Environmental Multiscale model was developed by the Government of Canada as an operational weather prediction model in the mid-1990s. Subsequently, it was used as the host meteorological model for an on-line implementation of air quality chemistry and aerosols from global to the meso-gamma scale. Further model developments led to the vertical extension of the modelling domain to include stratospheric chemistry, aerosols, and formation of polar stratospheric clouds. In parallel, the modelling platform was used for planetary applications where dynamical, radiative transfer and chemical processes in the atmosphere of Mars were successfully simulated. Undoubtedly, the developed modelling platform can be classified as an example capable of the seamless and coupled modelling of the dynamics and chemistry of planetary atmospheres. We will present modelling results for global, regional, and local air quality episodes and the long-term air quality trends. Upper troposphere and lower stratosphere modelling results will be presented in terms of climate change and subsonic aviation emissions modelling. Model results for the atmosphere of Mars will be presented in the context of the 2016 ExoMars mission and the anticipated observations from the NOMAD instrument. Also, we will present plans and the design to extend the GEM model to the F region with further coupling with a magnetospheric model that extends to 15 Re.
A Liver-Centric Multiscale Modeling Framework for Xenobiotics
Swat, Maciej; Cosmanescu, Alin; Clendenon, Sherry G.; Wambaugh, John F.; Glazier, James A.
2016-01-01
We describe a multi-scale, liver-centric in silico modeling framework for acetaminophen pharmacology and metabolism. We focus on a computational model to characterize whole body uptake and clearance, liver transport and phase I and phase II metabolism. We do this by incorporating sub-models that span three scales; Physiologically Based Pharmacokinetic (PBPK) modeling of acetaminophen uptake and distribution at the whole body level, cell and blood flow modeling at the tissue/organ level and metabolism at the sub-cellular level. We have used standard modeling modalities at each of the three scales. In particular, we have used the Systems Biology Markup Language (SBML) to create both the whole-body and sub-cellular scales. Our modeling approach allows us to run the individual sub-models separately and allows us to easily exchange models at a particular scale without the need to extensively rework the sub-models at other scales. In addition, the use of SBML greatly facilitates the inclusion of biological annotations directly in the model code. The model was calibrated using human in vivo data for acetaminophen and its sulfate and glucuronate metabolites. We then carried out extensive parameter sensitivity studies including the pairwise interaction of parameters. We also simulated population variation of exposure and sensitivity to acetaminophen. Our modeling framework can be extended to the prediction of liver toxicity following acetaminophen overdose, or used as a general purpose pharmacokinetic model for xenobiotics. PMID:27636091
Multiscale modeling of PVDF matrix carbon fiber composites
NASA Astrophysics Data System (ADS)
Greminger, Michael; Haghiashtiani, Ghazaleh
2017-06-01
Self-sensing carbon fiber reinforced composites have the potential to enable structural health monitoring that is inherent to the composite material rather than requiring external or embedded sensors. It has been demonstrated that a self-sensing carbon fiber reinforced polymer composite can be created by using the piezoelectric polymer polyvinylidene difluoride (PVDF) as the matrix material and using a Kevlar layer to separate two carbon fiber layers. In this configuration, the electrically conductive carbon fiber layers act as electrodes and the Kevlar layer acts as a dielectric to prevent the electrical shorting of the carbon fiber layers. This composite material has been characterized experimentally for its effective d 33 and d 31 piezoelectric coefficients. However, for design purposes, it is desirable to obtain a predictive model of the effective piezoelectric coefficients for the final smart composite material. Also, the inverse problem can be solved to determine the degree of polarization obtained in the PVDF material during polarization by comparing the effective d 33 and d 31 values obtained in experiment to those predicted by the finite element model. In this study, a multiscale micromechanics and coupled piezoelectric-mechanical finite element modeling approach is introduced to predict the mechanical and piezoelectric performance of a plain weave carbon fiber reinforced PVDF composite. The modeling results show good agreement with the experimental results for the mechanical and electrical properties of the composite. In addition, the degree of polarization of the PVDF component of the composite is predicted using this multiscale modeling approach and shows that there is opportunity to drastically improve the smart composite’s performance by improving the polarization procedure.
Predictive Multiscale Modeling of Nanocellulose Based Materials and Systems
NASA Astrophysics Data System (ADS)
Kovalenko, Andriy
2014-08-01
Cellulose Nanocrysals (CNC) is a renewable biodegradable biopolymer with outstanding mechanical properties made from highly abundant natural source, and therefore is very attractive as reinforcing additive to replace petroleum-based plastics in biocomposite materials, foams, and gels. Large-scale applications of CNC are currently limited due to its low solubility in non-polar organic solvents used in existing polymerization technologies. The solvation properties of CNC can be improved by chemical modification of its surface. Development of effective surface modifications has been rather slow because extensive chemical modifications destabilize the hydrogen bonding network of cellulose and deteriorate the mechanical properties of CNC. We employ predictive multiscale theory, modeling, and simulation to gain a fundamental insight into the effect of CNC surface modifications on hydrogen bonding, CNC crystallinity, solvation thermodynamics, and CNC compatibilization with the existing polymerization technologies, so as to rationally design green nanomaterials with improved solubility in non-polar solvents, controlled liquid crystal ordering and optimized extrusion properties. An essential part of this multiscale modeling approach is the statistical- mechanical 3D-RISM-KH molecular theory of solvation, coupled with quantum mechanics, molecular mechanics, and multistep molecular dynamics simulation. The 3D-RISM-KH theory provides predictive modeling of both polar and non-polar solvents, solvent mixtures, and electrolyte solutions in a wide range of concentrations and thermodynamic states. It properly accounts for effective interactions in solution such as steric effects, hydrophobicity and hydrophilicity, hydrogen bonding, salt bridges, buffer, co-solvent, and successfully predicts solvation effects and processes in bulk liquids, solvation layers at solid surface, and in pockets and other inner spaces of macromolecules and supramolecular assemblies. This methodology
Multi-Scale Modeling of Hypersonic Gas Flow
NASA Astrophysics Data System (ADS)
Boyd, Iain D.
On March 27, 2004, NASA successfully flew the X-43A hypersonic test flight vehicle at a velocity of 5000 mph to break the aeronautics speed record that had stood for over 35 years. The final flight of the X-43A on November 16, 2004 further increased the speed record to 6,600 mph which is almost ten times the speed of sound. The very high speed attainable by hypersonic airplanes could revolutionize air travel by dramatically reducing inter-continental flight times. For example, a hypersonic flight from New York to Sydney, Australia, a distance of 10,000 miles, would take less than 2 h. Reusable hypersonic vehicles are also being researched to significantly reduce the cost of access to space. Computer modeling of the gas flows around hypersonic vehicles will play a critical part in their development. This article discusses the conditions that can prevail in certain hypersonic gas flows that require a multi-scale modeling approach.
Breakdown parameter for kinetic modeling of multiscale gas flows.
Meng, Jianping; Dongari, Nishanth; Reese, Jason M; Zhang, Yonghao
2014-06-01
Multiscale methods built purely on the kinetic theory of gases provide information about the molecular velocity distribution function. It is therefore both important and feasible to establish new breakdown parameters for assessing the appropriateness of a fluid description at the continuum level by utilizing kinetic information rather than macroscopic flow quantities alone. We propose a new kinetic criterion to indirectly assess the errors introduced by a continuum-level description of the gas flow. The analysis, which includes numerical demonstrations, focuses on the validity of the Navier-Stokes-Fourier equations and corresponding kinetic models and reveals that the new criterion can consistently indicate the validity of continuum-level modeling in both low-speed and high-speed flows at different Knudsen numbers.
Multiscale adaptive basis function modeling of spatiotemporal vectorcardiogram signals.
Gang Liu; Hui Yang
2013-03-01
Mathematical modeling of cardiac electrical signals facilitates the simulation of realistic cardiac electrical behaviors, the evaluation of algorithms, and the characterization of underlying space-time patterns. However, there are practical issues pertinent to model efficacy, robustness, and generality. This paper presents a multiscale adaptive basis function modeling approach to characterize not only temporal but also spatial behaviors of vectorcardiogram (VCG) signals. Model parameters are adaptively estimated by the "best matching" projections of VCG characteristic waves onto a dictionary of nonlinear basis functions. The model performance is experimentally evaluated with respect to the number of basis functions, different types of basis function (i.e., Gaussian, Mexican hat, customized wavelet, and Hermitian wavelets), and various cardiac conditions, including 80 healthy controls and different myocardial infarctions (i.e., 89 inferior, 77 anterior-septal, 56 inferior-lateral, 47 anterior, and 43 anterior-lateral). Multiway analysis of variance shows that the basis function and the model complexity have significant effects on model performances while cardiac conditions are not significant. The customized wavelet is found to be an optimal basis function for the modeling of spacetime VCG signals. The comparison of QT intervals shows small relative errors (<;5%) between model representations and realworld VCG signals when the model complexity is greater than 10. The proposed model shows great potentials to model space-time cardiac pathological behaviors and can lead to potential benefits in feature extraction, data compression, algorithm evaluation, and disease prognostics.
Nonhydrostatic adaptive mesh dynamics for multiscale climate models (Invited)
NASA Astrophysics Data System (ADS)
Collins, W.; Johansen, H.; McCorquodale, P.; Colella, P.; Ullrich, P. A.
2013-12-01
Many of the atmospheric phenomena with the greatest potential impact in future warmer climates are inherently multiscale. Such meteorological systems include hurricanes and tropical cyclones, atmospheric rivers, and other types of hydrometeorological extremes. These phenomena are challenging to simulate in conventional climate models due to the relatively coarse uniform model resolutions relative to the native nonhydrostatic scales of the phenomonological dynamics. To enable studies of these systems with sufficient local resolution for the multiscale dynamics yet with sufficient speed for climate-change studies, we have adapted existing adaptive mesh dynamics for the DOE-NSF Community Atmosphere Model (CAM). In this talk, we present an adaptive, conservative finite volume approach for moist non-hydrostatic atmospheric dynamics. The approach is based on the compressible Euler equations on 3D thin spherical shells, where the radial direction is treated implicitly (using a fourth-order Runga-Kutta IMEX scheme) to eliminate time step constraints from vertical acoustic waves. Refinement is performed only in the horizontal directions. The spatial discretization is the equiangular cubed-sphere mapping, with a fourth-order accurate discretization to compute flux averages on faces. By using both space-and time-adaptive mesh refinement, the solver allocates computational effort only where greater accuracy is needed. The resulting method is demonstrated to be fourth-order accurate for model problems, and robust at solution discontinuities and stable for large aspect ratios. We present comparisons using a simplified physics package for dycore comparisons of moist physics. Hadley cell lifting an advected tracer into upper atmosphere, with horizontal adaptivity
Multiscale modeling for clinical translation in neuropsychiatric disease
Lytton, William W.; Neymotin, Samuel A.; Kerr, Cliff C.
2015-01-01
Multiscale modeling of neuropsychiatric illness bridges scales of clinical importance: from the highest scales (presentation of behavioral signs and symptoms), through intermediate scales (clinical testing and surgical intervention), down to the molecular scale of pharmacotherapy. Modeling of brain disease is difficult compared to modeling of other organs, because dysfunction manifests at scales where measurements are rudimentary due both to inadequate access (memory and cognition) and to complexity (behavior). Nonetheless, we can begin to explore these aspects through the use of information-theoretic measures as stand-ins for meaning at the top scales. We here describe efforts across five disorders: Parkinson’s, Alzheimer’s, stroke, schizophrenia, and epilepsy. We look at the use of therapeutic brain stimulation to replace lost neural signals, a loss that produces diaschisis, defined as activity changes in other brain areas due to missing inputs. These changes may in some cases be compensatory, hence beneficial, but in many cases a primary pathology, whether itself static or dynamic, sets in motion a series of dynamic consequences that produce further pathology. The simulations presented here suggest how diaschisis can be reversed by using a neuroprosthetic signal. Despite having none of the information content of the lost physiological signal, the simplified neuroprosthetic signal can restore a diaschitic area to near-normal patterns of activity. Computer simulation thus begins to explain the remarkable success of stimulation technologies - deep brain stimulation, transcranial magnetic stimulation, ultrasound stimulation, transcranial direct current stimulation - across an extremely broad range of pathologies. Multiscale modeling can help us to optimize and integrate these neuroprosthetic therapies by taking into consideration effects of different stimulation protocols, combinations of stimulation with neuropharmacological therapy, and interplay of these
This paper proposes a general procedure to link meteorological data with air quality models, such as U.S. EPA's Models-3 Community Multi-scale Air Quality (CMAQ) modeling system. CMAQ is intended to be used for studying multi-scale (urban and regional) and multi-pollutant (ozon...
This paper proposes a general procedure to link meteorological data with air quality models, such as U.S. EPA's Models-3 Community Multi-scale Air Quality (CMAQ) modeling system. CMAQ is intended to be used for studying multi-scale (urban and regional) and multi-pollutant (ozon...
On the relative importance of rheology for image-based CFD models of the carotid bifurcation.
Lee, Sang-Wook; Steinman, David A
2007-04-01
Patient-specific computational fluid dynamics (CFD) models derived from medical images often require simplifying assumptions to render the simulations conceptually or computationally tractable. In this study, we investigated the sensitivity of image-based CFD models of the carotid bifurcation to assumptions regarding the blood rheology. CFD simulations of three different patient-specific models were carried out assuming: a reference high-shear Newtonian viscosity, two different non-Newtonian (shear-thinning) rheology models, and Newtonian viscosities based on characteristic shear rates or, equivalently, assumed hematocrits. Sensitivity of wall shear stress (WSS) and oscillatory shear index (OSI) were contextualized with respect to the reproducibility of the reconstructed geometry, and to assumptions regarding the inlet boundary conditions. Sensitivity of WSS to the various rheological assumptions was roughly 1.0 dyn/cm(2) or 8%, nearly seven times less than that due to geometric uncertainty (6.7 dyn/cm(2) or 47%), and on the order of that due to inlet boundary condition assumptions. Similar trends were observed regarding OSI sensitivity. Rescaling the Newtonian viscosity based on time-averaged inlet shear rate served to approximate reasonably, if overestimate slightly, non-Newtonian behavior. For image-based CFD simulations of the normal carotid bifurcation, the assumption of constant viscosity at a nominal hematocrit is reasonable in light of currently available levels of geometric precision, thus serving to obviate the need to acquire patient-specific rheological data.
Reconstructing 3D CAD models for simulation using imaging-based reverse engineering
NASA Astrophysics Data System (ADS)
Voisin, Sophie; Page, David; Koschan, Andreas; Abidi, Mongi
2006-05-01
The purpose of this research is to investigate imaging-based methods to reconstruct 3D CAD models of real-world objects. The methodology uses structured lighting technologies such as coded-pattern projection and laser-based triangulation to sample 3D points on the surfaces of objects and then to reconstruct these surfaces from the dense point samples. This reverse engineering (RE) research presents reconstruction results for a military tire that is important to tire-soil simulations. The limitations of this approach are the current level of accuracy that imaging-based systems offer relative to more traditional CMM modeling systems. The benefit however is the potential for denser point samples and increased scanning speeds of objects, and with time, the imaging technologies should continue to improve to compete with CMM accuracy. This approach to RE should lead to high fidelity models of manufactured and prototyped components for comparison to the original CAD models and for simulation analysis. We focus this paper on the data collection and view registration problems within the RE pipeline.
Multiscale modelling of the feto–placental vasculature
Clark, A. R.; Lin, M.; Tawhai, M.; Saghian, R.; James, J. L.
2015-01-01
The placenta provides all the nutrients required for the fetus through pregnancy. It develops dynamically, and, to avoid rejection of the fetus, there is no mixing of fetal and maternal blood; rather, the branched placental villi ‘bathe’ in blood supplied from the uterine arteries. Within the villi, the feto–placental vasculature also develops a complex branching structure in order to maximize exchange between the placental and maternal circulations. To understand the development of the placenta, we must translate functional information across spatial scales including the interaction between macro- and micro-scale haemodynamics and account for the effects of a dynamically and rapidly changing structure through the time course of pregnancy. Here, we present steps towards an anatomically based and multiscale approach to modelling the feto–placental circulation. We assess the effect of the location of cord insertion on feto–placental blood flow resistance and flow heterogeneity and show that, although cord insertion does not appear to directly influence feto–placental resistance, the heterogeneity of flow in the placenta is predicted to increase from a 19.4% coefficient of variation with central cord insertion to 23.3% when the cord is inserted 2 cm from the edge of the placenta. Model geometries with spheroidal and ellipsoidal shapes, but the same volume, showed no significant differences in flow resistance or heterogeneity, implying that normal asymmetry in shape does not affect placental efficiency. However, the size and number of small capillary vessels is predicted to have a large effect on feto–placental resistance and flow heterogeneity. Using this new model as an example, we highlight the importance of taking an integrated multi-disciplinary and multiscale approach to understand development of the placenta. PMID:25844150
Multiscale modelling of the feto-placental vasculature.
Clark, A R; Lin, M; Tawhai, M; Saghian, R; James, J L
2015-04-06
The placenta provides all the nutrients required for the fetus through pregnancy. It develops dynamically, and, to avoid rejection of the fetus, there is no mixing of fetal and maternal blood; rather, the branched placental villi 'bathe' in blood supplied from the uterine arteries. Within the villi, the feto-placental vasculature also develops a complex branching structure in order to maximize exchange between the placental and maternal circulations. To understand the development of the placenta, we must translate functional information across spatial scales including the interaction between macro- and micro-scale haemodynamics and account for the effects of a dynamically and rapidly changing structure through the time course of pregnancy. Here, we present steps towards an anatomically based and multiscale approach to modelling the feto-placental circulation. We assess the effect of the location of cord insertion on feto-placental blood flow resistance and flow heterogeneity and show that, although cord insertion does not appear to directly influence feto-placental resistance, the heterogeneity of flow in the placenta is predicted to increase from a 19.4% coefficient of variation with central cord insertion to 23.3% when the cord is inserted 2 cm from the edge of the placenta. Model geometries with spheroidal and ellipsoidal shapes, but the same volume, showed no significant differences in flow resistance or heterogeneity, implying that normal asymmetry in shape does not affect placental efficiency. However, the size and number of small capillary vessels is predicted to have a large effect on feto-placental resistance and flow heterogeneity. Using this new model as an example, we highlight the importance of taking an integrated multi-disciplinary and multiscale approach to understand development of the placenta.
Oshima, Marie; Torii, Ryo; Tokuda, Shigefumi; Yamada, Shigeki; Koizumi, Akio
2012-09-01
To develop a targeted drug delivery system for cerebrovascular disorders such as stroke, it is important to obtain detailed information on flow rates and hemodynamics of the human cerebrovascular system for individual patients. A patient-specific integrated numerical simulation system has been developed by the authors such that vascular geometry is constructed from medical images such as magnetic resonance imaging (MRI) or computed tomography (CT) data, and computational conditions are modeled mathematically to represent the realistic in vivo environments. In general, the three-dimensional numerical simulation using a patient-specific model is conducted only for a localized diseased region with atherosclerosis or an aneurysm. Although the analysis region is only a part of the circulatory system, the simulation should include the effects from the entire circulatory system. Since the peripheral network determines the flow distributions in the cerebrovascular system, the paper reviews the recent simulation methods to take into account the network by coupling the image-based three-dimensional simulation with a one- and zero-dimensional simulations as an outflow boundary condition The paper shows the mathematical modeling of the multi-scale outflow boundary condition and its applications to patient- specific models of the arterial circle of Willis. The results are compared to those using the conventional, free-stream boundary condition. As a result, the multi-scale outflow boundary condition shows a significant difference in flow rate of each artery and in flow distribution in the arterial circle of Willis.
Transferring Multi-Scale Approaches from 3d City Modeling to Ifc-Based Tunnel Modeling
NASA Astrophysics Data System (ADS)
Borrmann, A.; Kolbe, T. H.; Donaubauer, A.; Steuer, H.; Jubierre, J. R.
2013-09-01
A multi-scale representation of the built environment is required to provide information with the adequate level of detail (LoD) for different use cases and objectives. This applies not only to the visualization of city and building models, but in particular to their use in the context of planning and analysis tasks. While in the field of Geographic Information Systems, the handling of multi-scale representations is well established and understood, no formal approaches for incorporating multi-scale methods exist in the field of Building Information Modeling (BIM) so far. However, these concepts are much needed to better support highly dynamic planning processes that make use of very rough information about the facility under design in the early stages and provide increasingly detailed and fine-grained information in later stages. To meet these demands, this paper presents a comprehensive concept for incorporating multi-scale representations with infrastructural building information models, with a particular focus on the representation of shield tunnels. Based on a detailed analysis of the data modeling methods used in CityGML for capturing multiscale representations and the requirements present in the context of infrastructure planning projects, we discuss potential extensions to the BIM data model Industry Foundation Classes (IFC). Particular emphasis is put on providing means for preserving the consistency of the representation across the different Levels-of-Detail (LoD). To this end we make use of a procedural geometry description which makes it possible to define explicit dependencies between geometric entities on different LoDs. The modification of an object on a coarse level consequently results in an automated update of all dependent objects on the finer levels. Finally we discuss the transformation of the IFC-based multi-scale tunnel model into a CityGML compliant tunnel representation.
Comparing multilevel and multiscale convolution models for small area aggregated health data.
Aregay, Mehreteab; Lawson, Andrew B; Faes, Christel; Kirby, Russell S; Carroll, Rachel; Watjou, Kevin
2017-08-01
In spatial epidemiology, data are often arrayed hierarchically. The classification of individuals into smaller units, which in turn are grouped into larger units, can induce contextual effects. On the other hand, a scaling effect can occur due to the aggregation of data from smaller units into larger units. In this paper, we propose a shared multilevel model to address the contextual effects. In addition, we consider a shared multiscale model to adjust for both scale and contextual effects simultaneously. We also study convolution and independent multiscale models, which are special cases of shared multilevel and shared multiscale models, respectively. We compare the performance of the models by applying them to real and simulated data sets. We found that the shared multiscale model was the best model across a range of simulated and real scenarios as measured by the deviance information criterion (DIC) and the Watanabe Akaike information criterion (WAIC). Copyright © 2017 Elsevier Ltd. All rights reserved.
Residual stress distribution analysis of heat treated APS TBC using image based modelling.
Li, Chun; Zhang, Xun; Chen, Ying; Carr, James; Jacques, Simon; Behnsen, Julia; di Michiel, Marco; Xiao, Ping; Cernik, Robert
2017-08-01
We carried out a residual stress distribution analysis in a APS TBC throughout the depth of the coatings. The samples were heat treated at 1150 °C for 190 h and the data analysis used image based modelling based on the real 3D images measured by Computed Tomography (CT). The stress distribution in several 2D slices from the 3D model is included in this paper as well as the stress distribution along several paths shown on the slices. Our analysis can explain the occurrence of the "jump" features near the interface between the top coat and the bond coat. These features in the residual stress distribution trend were measured (as a function of depth) by high-energy synchrotron XRD (as shown in our related research article entitled 'Understanding the Residual Stress Distribution through the Thickness of Atmosphere Plasma Sprayed (APS) Thermal Barrier Coatings (TBCs) by high energy Synchrotron XRD; Digital Image Correlation (DIC) and Image Based Modelling') (Li et al., 2017) [1].
A virtual coiling technique for image-based aneurysm models by dynamic path planning.
Morales, Hernán G; Larrabide, Ignacio; Geers, Arjan J; San Román, Luis; Blasco, Jordi; Macho, Juan M; Frangi, Alejandro F
2013-01-01
Computational algorithms modeling the insertion of endovascular devices, such as coil or stents, have gained an increasing interest in recent years. This scientific enthusiasm is due to the potential impact that these techniques have to support clinicians by understanding the intravascular hemodynamics and predicting treatment outcomes. In this work, a virtual coiling technique for treating image-based aneurysm models is proposed. A dynamic path planning was used to mimic the structure and distribution of coils inside aneurysm cavities, and to reach high packing densities, which is desirable by clinicians when treating with coils. Several tests were done to evaluate the performance on idealized and image-based aneurysm models. The proposed technique was validated using clinical information of real coiled aneurysms. The virtual coiling technique reproduces the macroscopic behavior of inserted coils and properly captures the densities, shapes and coil distributions inside aneurysm cavities. A practical application was performed by assessing the local hemodynamic after coiling using computational fluid dynamics (CFD). Wall shear stress and intra-aneurysmal velocities were reduced after coiling. Additionally, CFD simulations show that coils decrease the amount of contrast entering the aneurysm and increase its residence time.
Multiscale Modeling of Metallic Materials Containing Embedded Particles
NASA Technical Reports Server (NTRS)
Phillips, Dawn R.; Iesulauro, Erin; Glaessgen, Edward H.
2004-01-01
Multiscale modeling at small length scales (10(exp -9) to 10(exp -3) m) is discussed for aluminum matrices with embedded particles. A configuration containing one particle surrounded by about 50 grains and subjected to uniform tension and lateral constraint is considered. The analyses are performed to better understand the effects of material configuration on the initiation and progression of debonding of the particles from the surrounding aluminum matrix. Configurational parameters considered include particle aspect ratio and orientation within the surrounding matrix. Both configurational parameters are shown to have a significant effect on the behavior of the materials as a whole. For elliptical particles with the major axis perpendicular to the direction of loading, a particle with a 1:1 aspect ratio completely debonds from the surrounding matrix at higher loads than particles with higher aspect ratios. As the particle major axis is aligned with the direction of the applied load, increasing amounts of load are required to completely debond the particles.
Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids.
Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav; Goloviznin, Vasily
2014-08-06
Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space-time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space-time, a novel hybrid atomistic-fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided.
Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids
Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav; Goloviznin, Vasily
2014-01-01
Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space–time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space–time, a novel hybrid atomistic–fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided. PMID:24982246
Multi-Scale Coupling in Ocean and Climate Modeling
Zhengyu Liu, Leslie Smith
2009-08-14
We have made significant progress on several projects aimed at understanding multi-scale dynamics in geophysical flows. Large-scale flows in the atmosphere and ocean are influenced by stable density stratification and rotation. The presence of stratification and rotation has important consequences through (i) the conservation of potential vorticity q = {omega} {center_dot} {del} {rho}, where {omega} is the total vorticity and {rho} is the density, and (ii) the existence of waves that affect the redistribution of energy from a given disturbance to the flow. Our research is centered on quantifying the effects of potential vorticity conservation and of wave interactions for the coupling of disparate time and space scales in the oceans and the atmosphere. Ultimately we expect the work to help improve predictive capabilities of atmosphere, ocean and climate modelers. The main findings of our research projects are described.
Atomistic simulations for multiscale modeling in bcc metal
Belak, J.; Moriarty, J.A.; Soderlind, P.; Xu, W.; Yang, L.H.; Zhu
1998-09-25
Quantum-based atomistic simulations are being used to study fundamental deformation and defect properties relevant to the multiscale modeling of plasticity in bcc metals at both ambient and extreme conditions. Ab initio electronic-structure calculations on the elastic and ideal-strength properties of Ta and Mo help constrain and validate many-body interatomic potentials used to study grain boundaries and dislocations. The predicted C(capital Sigma)5 (310)[100] grain boundary structure for Mo has recently been confirmed in HREM measurements. The core structure, (small gamma) surfaces, Peierls stress, and kink-pair formation energies associated with the motion of a/2(111) screw dislocations in Ta and Mo have also been calculated. Dislocation mobility and dislocation junction formation and breaking are currently under investigation.
Multiscale and Multiphysics Modeling of Additive Manufacturing of Advanced Materials
NASA Technical Reports Server (NTRS)
Liou, Frank; Newkirk, Joseph; Fan, Zhiqiang; Sparks, Todd; Chen, Xueyang; Fletcher, Kenneth; Zhang, Jingwei; Zhang, Yunlu; Kumar, Kannan Suresh; Karnati, Sreekar
2015-01-01
The objective of this proposed project is to research and develop a prediction tool for advanced additive manufacturing (AAM) processes for advanced materials and develop experimental methods to provide fundamental properties and establish validation data. Aircraft structures and engines demand materials that are stronger, useable at much higher temperatures, provide less acoustic transmission, and enable more aeroelastic tailoring than those currently used. Significant improvements in properties can only be achieved by processing the materials under nonequilibrium conditions, such as AAM processes. AAM processes encompass a class of processes that use a focused heat source to create a melt pool on a substrate. Examples include Electron Beam Freeform Fabrication and Direct Metal Deposition. These types of additive processes enable fabrication of parts directly from CAD drawings. To achieve the desired material properties and geometries of the final structure, assessing the impact of process parameters and predicting optimized conditions with numerical modeling as an effective prediction tool is necessary. The targets for the processing are multiple and at different spatial scales, and the physical phenomena associated occur in multiphysics and multiscale. In this project, the research work has been developed to model AAM processes in a multiscale and multiphysics approach. A macroscale model was developed to investigate the residual stresses and distortion in AAM processes. A sequentially coupled, thermomechanical, finite element model was developed and validated experimentally. The results showed the temperature distribution, residual stress, and deformation within the formed deposits and substrates. A mesoscale model was developed to include heat transfer, phase change with mushy zone, incompressible free surface flow, solute redistribution, and surface tension. Because of excessive computing time needed, a parallel computing approach was also tested. In addition
Multiscale Modeling of Gastrointestinal Electrophysiology and Experimental Validation
Du, Peng; O'Grady, Greg; Davidson, John B.; Cheng, Leo K.; Pullan, Andrew J.
2011-01-01
Normal gastrointestinal (GI) motility results from the coordinated interplay of multiple cooperating mechanisms, both intrinsic and extrinsic to the GI tract. A fundamental component of this activity is an omnipresent electrical activity termed slow waves, which is generated and propagated by the interstitial cells of Cajal (ICCs). The role of ICC loss and network degradation in GI motility disorders is a significant area of ongoing research. This review examines recent progress in the multiscale modeling framework for effectively integrating a vast range of experimental data in GI electrophysiology, and outlines the prospect of how modeling can provide new insights into GI function in health and disease. The review begins with an overview of the GI tract and its electrophysiology, and then focuses on recent work on modeling GI electrical activity, spanning from cell to body biophysical scales. Mathematical cell models of the ICCs and smooth muscle cell are presented. The continuum framework of monodomain and bidomain models for tissue and organ models are then considered, and the forward techniques used to model the resultant body surface potential and magnetic field are discussed. The review then outlines recent progress in experimental support and validation of modeling, and concludes with a discussion on potential future research directions in this field. PMID:21133835
A multiscale strength model for extreme loading conditions
NASA Astrophysics Data System (ADS)
Barton, N. R.; Bernier, J. V.; Becker, R.; Arsenlis, A.; Cavallo, R.; Marian, J.; Rhee, M.; Park, H.-S.; Remington, B. A.; Olson, R. T.
2011-04-01
We present a multiscale strength model in which strength depends on pressure, strain rate, temperature, and evolving dislocation density. Model construction employs an information passing paradigm to span from the atomistic level to the continuum level. Simulation methods in the overall hierarchy include density functional theory, molecular statics, molecular dynamics, dislocation dynamics, and continuum based approaches. Given the nature of the subcontinuum simulations upon which the strength model is based, the model is particularly appropriate to strain rates in excess of 104 s-1. Strength model parameters are obtained entirely from the hierarchy of simulation methods to obtain a full strength model in a range of loading conditions that so far has been inaccessible to direct measurement of material strength. Model predictions compare favorably with relevant high energy density physics (HEDP) experiments that have bearing on material strength. The model is used to provide insight into HEDP experimental observations and to make predictions of what might be observable using dynamic x-ray diffraction based experimental methods.
Simulating cancer growth with multiscale agent-based modeling.
Wang, Zhihui; Butner, Joseph D; Kerketta, Romica; Cristini, Vittorio; Deisboeck, Thomas S
2015-02-01
There have been many techniques developed in recent years to in silico model a variety of cancer behaviors. Agent-based modeling is a specific discrete-based hybrid modeling approach that allows simulating the role of diversity in cell populations as well as within each individual cell; it has therefore become a powerful modeling method widely used by computational cancer researchers. Many aspects of tumor morphology including phenotype-changing mutations, the adaptation to microenvironment, the process of angiogenesis, the influence of extracellular matrix, reactions to chemotherapy or surgical intervention, the effects of oxygen and nutrient availability, and metastasis and invasion of healthy tissues have been incorporated and investigated in agent-based models. In this review, we introduce some of the most recent agent-based models that have provided insight into the understanding of cancer growth and invasion, spanning multiple biological scales in time and space, and we further describe several experimentally testable hypotheses generated by those models. We also discuss some of the current challenges of multiscale agent-based cancer models.
A MULTISCALE, CELL-BASED FRAMEWORK FOR MODELING CANCER DEVELOPMENT
JIANG, YI
2007-01-16
Cancer remains to be one of the leading causes of death due to diseases. We use a systems approach that combines mathematical modeling, numerical simulation, in vivo and in vitro experiments, to develop a predictive model that medical researchers can use to study and treat cancerous tumors. The multiscale, cell-based model includes intracellular regulations, cellular level dynamics and intercellular interactions, and extracellular level chemical dynamics. The intracellular level protein regulations and signaling pathways are described by Boolean networks. The cellular level growth and division dynamics, cellular adhesion and interaction with the extracellular matrix is described by a lattice Monte Carlo model (the Cellular Potts Model). The extracellular dynamics of the signaling molecules and metabolites are described by a system of reaction-diffusion equations. All three levels of the model are integrated through a hybrid parallel scheme into a high-performance simulation tool. The simulation results reproduce experimental data in both avasular tumors and tumor angiogenesis. By combining the model with experimental data to construct biologically accurate simulations of tumors and their vascular systems, this model will enable medical researchers to gain a deeper understanding of the cellular and molecular interactions associated with cancer progression and treatment.
Kirschner, Denise E; Hunt, C Anthony; Marino, Simeone; Fallahi-Sichani, Mohammad; Linderman, Jennifer J
2014-01-01
The use of multi-scale mathematical and computational models to study complex biological processes is becoming increasingly productive. Multi-scale models span a range of spatial and/or temporal scales and can encompass multi-compartment (e.g., multi-organ) models. Modeling advances are enabling virtual experiments to explore and answer questions that are problematic to address in the wet-lab. Wet-lab experimental technologies now allow scientists to observe, measure, record, and analyze experiments focusing on different system aspects at a variety of biological scales. We need the technical ability to mirror that same flexibility in virtual experiments using multi-scale models. Here we present a new approach, tuneable resolution, which can begin providing that flexibility. Tuneable resolution involves fine- or coarse-graining existing multi-scale models at the user's discretion, allowing adjustment of the level of resolution specific to a question, an experiment, or a scale of interest. Tuneable resolution expands options for revising and validating mechanistic multi-scale models, can extend the longevity of multi-scale models, and may increase computational efficiency. The tuneable resolution approach can be applied to many model types, including differential equation, agent-based, and hybrid models. We demonstrate our tuneable resolution ideas with examples relevant to infectious disease modeling, illustrating key principles at work.
Linear theory for filtering nonlinear multiscale systems with model error
Berry, Tyrus; Harlim, John
2014-01-01
In this paper, we study filtering of multiscale dynamical systems with model error arising from limitations in resolving the smaller scale processes. In particular, the analysis assumes the availability of continuous-time noisy observations of all components of the slow variables. Mathematically, this paper presents new results on higher order asymptotic expansion of the first two moments of a conditional measure. In particular, we are interested in the application of filtering multiscale problems in which the conditional distribution is defined over the slow variables, given noisy observation of the slow variables alone. From the mathematical analysis, we learn that for a continuous time linear model with Gaussian noise, there exists a unique choice of parameters in a linear reduced model for the slow variables which gives the optimal filtering when only the slow variables are observed. Moreover, these parameters simultaneously give the optimal equilibrium statistical estimates of the underlying system, and as a consequence they can be estimated offline from the equilibrium statistics of the true signal. By examining a nonlinear test model, we show that the linear theory extends in this non-Gaussian, nonlinear configuration as long as we know the optimal stochastic parametrization and the correct observation model. However, when the stochastic parametrization model is inappropriate, parameters chosen for good filter performance may give poor equilibrium statistical estimates and vice versa; this finding is based on analytical and numerical results on our nonlinear test model and the two-layer Lorenz-96 model. Finally, even when the correct stochastic ansatz is given, it is imperative to estimate the parameters simultaneously and to account for the nonlinear feedback of the stochastic parameters into the reduced filter estimates. In numerical experiments on the two-layer Lorenz-96 model, we find that the parameters estimated online, as part of a filtering procedure
Quasi-3D Multi-scale Modeling Framework Development
NASA Astrophysics Data System (ADS)
Arakawa, A.; Jung, J.
2008-12-01
When models are truncated in or near an energetically active range of the spectrum, model physics must be changed as the resolution changes. The model physics of GCMs and that of CRMs are, however, quite different from each other and at present there is no unified formulation of model physics that automatically provides transition between these model physics. The Quasi-3D (Q3D) Multi-scale Modeling Framework (MMF) is an attempt to bridge this gap. Like the recently proposed Heterogeneous Multiscale Method (HMM) (E and Engquist 2003), MMF combines a macroscopic model, GCM, and a microscopic model, CRM. Unlike the traditional multiscale methods such as the multi-grid and adapted mesh refinement techniques, HMM and MMF are for solving multi-physics problems. They share the common objective "to design combined macroscopic-microscopic computational methods that are much more efficient than solving the full microscopic model and at the same time give the information we need" (E et al. 2008). The question is then how to meet this objective in practice, which can be highly problem dependent. In HHM, the efficiency is gained typically by localization of the microscale problem. Following the pioneering work by Grabowski and Smolarkiewicz (1999) and Grabowski (2001), MMF takes advantage of the fact that 2D CRMs are reasonably successful in simulating deep clouds. In this approach, the efficiency is gained by sacrificing the three-dimensionality of cloud-scale motion. It also "localizes" the algorithm through embedding a CRM in each GCM grid box using cyclic boundary condition. The Q3D MMF is an attempt to reduce the expense due to these constraints by partially including the cloud-scale 3D effects and extending the CRM beyond individual GCM grid boxes. As currently formulated, the Q3D MMF is a 4D estimation/prediction framework that combines a GCM with a 3D anelastic cloud-resolving vector vorticity equation model (VVM) applied to a network of horizontal grids. The network
A Goddard Multi-Scale Modeling System with Unified Physics
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo
2010-01-01
A multi-scale modeling system with unified physics has been developed at NASA Goddard Space Flight Center (GSFC). The system consists of an MMF, the coupled NASA Goddard finite-volume GCM (fvGCM) and Goddard Cumulus Ensemble model (GCE, a CRM); the state-of-the-art Weather Research and Forecasting model (WRF) and the stand alone GCE. These models can share the same microphysical schemes, radiation (including explicitly calculated cloud optical properties), and surface models that have been developed, improved and tested for different environments. In this talk, I will present: (1) A brief review on GCE model and its applications on the impact of the aerosol on deep precipitation processes, (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) A discussion on the Goddard WRF version (its developments and applications). We are also performing the inline tracer calculation to comprehend the physical processes (i.e., boundary layer and each quadrant in the boundary layer) related to the development and structure of hurricanes and mesoscale convective systems. In addition, high - resolution (spatial. 2km, and temporal, I minute) visualization showing the model results will be presented.
Cancer systems biology and modeling: microscopic scale and multiscale approaches.
Masoudi-Nejad, Ali; Bidkhori, Gholamreza; Hosseini Ashtiani, Saman; Najafi, Ali; Bozorgmehr, Joseph H; Wang, Edwin
2015-02-01
Cancer has become known as a complex and systematic disease on macroscopic, mesoscopic and microscopic scales. Systems biology employs state-of-the-art computational theories and high-throughput experimental data to model and simulate complex biological procedures such as cancer, which involves genetic and epigenetic, in addition to intracellular and extracellular complex interaction networks. In this paper, different systems biology modeling techniques such as systems of differential equations, stochastic methods, Boolean networks, Petri nets, cellular automata methods and agent-based systems are concisely discussed. We have compared the mentioned formalisms and tried to address the span of applicability they can bear on emerging cancer modeling and simulation approaches. Different scales of cancer modeling, namely, microscopic, mesoscopic and macroscopic scales are explained followed by an illustration of angiogenesis in microscopic scale of the cancer modeling. Then, the modeling of cancer cell proliferation and survival are examined on a microscopic scale and the modeling of multiscale tumor growth is explained along with its advantages. Copyright © 2014 Elsevier Ltd. All rights reserved.
Systematic multiscale models for deep convection on mesoscales
NASA Astrophysics Data System (ADS)
Klein, Rupert; Majda, Andrew J.
2006-11-01
This paper builds on recent developments of a unified asymptotic approach to meteorological modeling [ZAMM, 80: 765 777, 2000, SIAM Proc. App. Math. 116, 227 289, 2004], which was used successfully in the development of Systematic multiscale models for the tropics in Majda and Klein [J. Atmosph. Sci. 60: 393 408, 2003] and Majda and Biello [PNAS, 101: 4736 4741, 2004]. Biello and Majda [J. Atmosph. Sci. 62: 1694 1720, 2005]. Here we account for typical bulk microphysics parameterizations of moist processes within this framework. The key steps are careful nondimensionalization of the bulk microphysics equations and the choice of appropriate distinguished limits for the various nondimensional small parameters that appear. We are then in a position to study scale interactions in the atmosphere involving moist physics. We demonstrate this by developing two systematic multiscale models that are motivated by our interest in mesoscale organized convection. The emphasis here is on multiple length scales but common time scales. The first of these models describes the short-time evolution of slender, deep convective hot towers with horizontal scale ~ 1 km interacting with the linearized momentum balance on length and time scales of (10 km/3 min). We expect this model to describe how convective inhibition may be overcome near the surface, how the onset of deep convection triggers convective-scale gravity waves, and that it will also yield new insight into how such local convective events may conspire to create larger-scale strong storms. The second model addresses the next larger range of length and time scales (10 km, 100 km, and 20 min) and exhibits mathematical features that are strongly reminiscent of mesoscale organized convection. In both cases, the asymptotic analysis reveals how the stiffness of condensation/evaporation processes induces highly nonlinear dynamics. Besides providing new theoretical insights, the derived models may also serve as a theoretical devices
Multi-scale modeling of the CD8 immune response
Barbarroux, Loic; Michel, Philippe; Adimy, Mostafa; Crauste, Fabien
2016-06-08
During the primary CD8 T-Cell immune response to an intracellular pathogen, CD8 T-Cells undergo exponential proliferation and continuous differentiation, acquiring cytotoxic capabilities to address the infection and memorize the corresponding antigen. After cleaning the organism, the only CD8 T-Cells left are antigen-specific memory cells whose role is to respond stronger and faster in case they are presented this very same antigen again. That is how vaccines work: a small quantity of a weakened pathogen is introduced in the organism to trigger the primary response, generating corresponding memory cells in the process, giving the organism a way to defend himself in case it encounters the same pathogen again. To investigate this process, we propose a non linear, multi-scale mathematical model of the CD8 T-Cells immune response due to vaccination using a maturity structured partial differential equation. At the intracellular scale, the level of expression of key proteins is modeled by a delay differential equation system, which gives the speeds of maturation for each cell. The population of cells is modeled by a maturity structured equation whose speeds are given by the intracellular model. We focus here on building the model, as well as its asymptotic study. Finally, we display numerical simulations showing the model can reproduce the biological dynamics of the cell population for both the primary response and the secondary responses.
Bayesian Multiscale Modeling of Closed Curves in Point Clouds.
Gu, Kelvin; Pati, Debdeep; Dunson, David B
2014-10-01
Modeling object boundaries based on image or point cloud data is frequently necessary in medical and scientific applications ranging from detecting tumor contours for targeted radiation therapy, to the classification of organisms based on their structural information. In low-contrast images or sparse and noisy point clouds, there is often insufficient data to recover local segments of the boundary in isolation. Thus, it becomes critical to model the entire boundary in the form of a closed curve. To achieve this, we develop a Bayesian hierarchical model that expresses highly diverse 2D objects in the form of closed curves. The model is based on a novel multiscale deformation process. By relating multiple objects through a hierarchical formulation, we can successfully recover missing boundaries by borrowing structural information from similar objects at the appropriate scale. Furthermore, the model's latent parameters help interpret the population, indicating dimensions of significant structural variability and also specifying a 'central curve' that summarizes the collection. Theoretical properties of our prior are studied in specific cases and efficient Markov chain Monte Carlo methods are developed, evaluated through simulation examples and applied to panorex teeth images for modeling teeth contours and also to a brain tumor contour detection problem.
A Goddard Multi-Scale Modeling System with Unified Physics
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo
2010-01-01
A multi-scale modeling system with unified physics has been developed at NASA Goddard Space Flight Center (GSFC). The system consists of an MMF, the coupled NASA Goddard finite-volume GCM (fvGCM) and Goddard Cumulus Ensemble model (GCE, a CRM); the state-of-the-art Weather Research and Forecasting model (WRF) and the stand alone GCE. These models can share the same microphysical schemes, radiation (including explicitly calculated cloud optical properties), and surface models that have been developed, improved and tested for different environments. In this talk, I will present: (1) A brief review on GCE model and its applications on the impact of the aerosol on deep precipitation processes, (2) The Goddard MMF and the major difference between two existing MMFs (CSU MMF and Goddard MMF), and preliminary results (the comparison with traditional GCMs), and (3) A discussion on the Goddard WRF version (its developments and applications). We are also performing the inline tracer calculation to comprehend the ph ysical processes (i.e., boundary layer and each quadrant in the boundary layer) related to the development and structure of hurricanes and mesoscale convective systems.
Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework
Osborne, James M
2015-01-01
Colorectal cancer (CRC) is one of the major causes of death in the developed world and forms a canonical example of tumorigenesis. CRC arises from a string of mutations of individual cells in the colorectal crypt, making it particularly suited for multiscale multicellular modeling, where mutations of individual cells can be clearly represented and their effects readily tracked. In this paper, we present a multicellular model of the onset of colorectal cancer, utilizing the cellular Potts model (CPM). We use the model to investigate how, through the modification of their mechanical properties, mutant cells colonize the crypt. Moreover, we study the influence of mutations on the shape of cells in the crypt, suggesting possible cell- and tissue-level indicators for identifying early-stage cancerous crypts. Crucially, we discuss the effect that the motility parameters of the model (key factors in the behavior of the CPM) have on the distribution of cells within a homeostatic crypt, resulting in an optimal parameter regime that accurately reflects biological assumptions. In summary, the key results of this paper are 1) how to couple the CPM with processes occurring on other spatial scales, using the example of the crypt to motivate suitable motility parameters; 2) modeling mutant cells with the CPM; 3) and investigating how mutations influence the shape of cells in the crypt. PMID:26461973
Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework.
Osborne, James M
2015-01-01
Colorectal cancer (CRC) is one of the major causes of death in the developed world and forms a canonical example of tumorigenesis. CRC arises from a string of mutations of individual cells in the colorectal crypt, making it particularly suited for multiscale multicellular modeling, where mutations of individual cells can be clearly represented and their effects readily tracked. In this paper, we present a multicellular model of the onset of colorectal cancer, utilizing the cellular Potts model (CPM). We use the model to investigate how, through the modification of their mechanical properties, mutant cells colonize the crypt. Moreover, we study the influence of mutations on the shape of cells in the crypt, suggesting possible cell- and tissue-level indicators for identifying early-stage cancerous crypts. Crucially, we discuss the effect that the motility parameters of the model (key factors in the behavior of the CPM) have on the distribution of cells within a homeostatic crypt, resulting in an optimal parameter regime that accurately reflects biological assumptions. In summary, the key results of this paper are 1) how to couple the CPM with processes occurring on other spatial scales, using the example of the crypt to motivate suitable motility parameters; 2) modeling mutant cells with the CPM; 3) and investigating how mutations influence the shape of cells in the crypt.
Multi-scale modeling of the CD8 immune response
NASA Astrophysics Data System (ADS)
Barbarroux, Loic; Michel, Philippe; Adimy, Mostafa; Crauste, Fabien
2016-06-01
During the primary CD8 T-Cell immune response to an intracellular pathogen, CD8 T-Cells undergo exponential proliferation and continuous differentiation, acquiring cytotoxic capabilities to address the infection and memorize the corresponding antigen. After cleaning the organism, the only CD8 T-Cells left are antigen-specific memory cells whose role is to respond stronger and faster in case they are presented this very same antigen again. That is how vaccines work: a small quantity of a weakened pathogen is introduced in the organism to trigger the primary response, generating corresponding memory cells in the process, giving the organism a way to defend himself in case it encounters the same pathogen again. To investigate this process, we propose a non linear, multi-scale mathematical model of the CD8 T-Cells immune response due to vaccination using a maturity structured partial differential equation. At the intracellular scale, the level of expression of key proteins is modeled by a delay differential equation system, which gives the speeds of maturation for each cell. The population of cells is modeled by a maturity structured equation whose speeds are given by the intracellular model. We focus here on building the model, as well as its asymptotic study. Finally, we display numerical simulations showing the model can reproduce the biological dynamics of the cell population for both the primary response and the secondary responses.
A multiscale model for red blood cell mechanics.
Hartmann, Dirk
2010-02-01
The objective of this article is the derivation of a continuum model for mechanics of red blood cells via multiscale analysis. On the microscopic level, we consider realistic discrete models in terms of energy functionals defined on networks/lattices. Using concepts of Gamma-convergence, convergence results as well as explicit homogenisation formulae are derived. Based on a characterisation via energy functionals, appropriate macroscopic stress-strain relationships (constitutive equations) can be determined. Further, mechanical moduli of the derived macroscopic continuum model are directly related to microscopic moduli. As a test case we consider optical tweezers experiments, one of the most common experiments to study mechanical properties of cells. Our simulations of the derived continuum model are based on finite element methods and account explicitly for membrane mechanics and its coupling with bulk mechanics. Since the discretisation of the continuum model can be chosen freely, rather than it is given by the topology of the microscopic cytoskeletal network, the approach allows a significant reduction of computational efforts. Our approach is highly flexible and can be generalised to many other cell models, also including biochemical control.
Image-Based Airborne LiDAR Point Cloud Encoding for 3d Building Model Retrieval
NASA Astrophysics Data System (ADS)
Chen, Yi-Chen; Lin, Chao-Hung
2016-06-01
With the development of Web 2.0 and cyber city modeling, an increasing number of 3D models have been available on web-based model-sharing platforms with many applications such as navigation, urban planning, and virtual reality. Based on the concept of data reuse, a 3D model retrieval system is proposed to retrieve building models similar to a user-specified query. The basic idea behind this system is to reuse these existing 3D building models instead of reconstruction from point clouds. To efficiently retrieve models, the models in databases are compactly encoded by using a shape descriptor generally. However, most of the geometric descriptors in related works are applied to polygonal models. In this study, the input query of the model retrieval system is a point cloud acquired by Light Detection and Ranging (LiDAR) systems because of the efficient scene scanning and spatial information collection. Using Point clouds with sparse, noisy, and incomplete sampling as input queries is more difficult than that by using 3D models. Because that the building roof is more informative than other parts in the airborne LiDAR point cloud, an image-based approach is proposed to encode both point clouds from input queries and 3D models in databases. The main goal of data encoding is that the models in the database and input point clouds can be consistently encoded. Firstly, top-view depth images of buildings are generated to represent the geometry surface of a building roof. Secondly, geometric features are extracted from depth images based on height, edge and plane of building. Finally, descriptors can be extracted by spatial histograms and used in 3D model retrieval system. For data retrieval, the models are retrieved by matching the encoding coefficients of point clouds and building models. In experiments, a database including about 900,000 3D models collected from the Internet is used for evaluation of data retrieval. The results of the proposed method show a clear superiority
Multiscale forward electromagnetic model of uterine contractions during pregnancy
2012-01-01
Background Analyzing and monitoring uterine contractions during pregnancy is relevant to the field of reproductive health assessment. Its clinical importance is grounded in the need to reliably predict the onset of labor at term and pre-term. Preterm births can cause health problems or even be fatal for the fetus. Currently, there are no objective methods for consistently predicting the onset of labor based on sensing of the mechanical or electrophysiological aspects of uterine contractions. Therefore, modeling uterine contractions could help to better interpret such measurements and to develop more accurate methods for predicting labor. In this work, we develop a multiscale forward electromagnetic model of myometrial contractions during pregnancy. In particular, we introduce a model of myometrial current source densities and compute its magnetic field and action potential at the abdominal surface, using Maxwell’s equations and a four-compartment volume conductor geometry. To model the current source density at the myometrium we use a bidomain approach. We consider a modified version of the Fitzhugh-Nagumo (FHN) equation for modeling ionic currents in each myocyte, assuming a plateau-type transmembrane potential, and we incorporate the anisotropic nature of the uterus by designing conductivity-tensor fields. Results We illustrate our modeling approach considering a spherical uterus and one pacemaker located in the fundus. We obtained a travelling transmembrane potential depolarizing from −56 mV to −16 mV and an average potential in the plateau area of −25 mV with a duration, before hyperpolarization, of 35 s, which is a good approximation with respect to the average recorded transmembrane potentials at term reported in the technical literature. Similarly, the percentage of myometrial cells contracting as a function of time had the same symmetric properties and duration as the intrauterine pressure waveforms of a pregnant human myometrium at term
Cummings, P. T.
2010-02-08
This document reports the outcomes of the Computational Nanoscience Project, "Integrated Multiscale Modeling of Molecular Computing Devices". It includes a list of participants and publications arising from the research supported.
Multiscale Modeling of Wave-induced Flow in Vegetation Canopy
NASA Astrophysics Data System (ADS)
Zhu, L.; Chen, Q. J.; Chakrabarti, A.; Ma, G.
2016-12-01
Coastal vegetation dissipates the wave energy and alters local hydrodynamics by enhancing within-canopy turbulence, and introducing significant spatial variability to the flow. The modeling of flows and waves through vegetation has attracted the attention of coastal and hydraulics engineers for decades. The ability to predict instantaneous flow characteristics and turbulent flow structures accurately is of great significance for modeling wave attenuation and sediment transport in vegetated area. Two widely used types of modeling approaches are the Reynolds-averaged Navier-Stokes (RANS) and the Large Eddy Simulations (LES). The high level of detail delivered by the LES model comes with significantly large computational costs. The objective of this study is to investigate the flow structure and turbulence properties predicted by both methods and explore the applicability of multi-scale modeling of wave-induced flow in vegetation canopy. In this study, two models, NHWAVE and OpenFOAM, are utilized to simulate wave-induced flows in emergent and submerged vegetation. A standard k-ɛ turbulence model and a LES model are used in NHWAVE and OpenFOAM, respectively. NHWAVE employs a Morrison-type quadratic equation to approximate the wave-induced drag on vegetation stems, whereas OpenFOAM adopts a direct approach and resolves flow structure within the canopy using the high-resolution LES-based turbulence model. Both models are firstly validated against laboratory data for free surface and vertical variation of mean velocity. Reynolds stresses calculated directly from the LES model is compared with modeled Reynolds stresses from the RANS model and the influence of vertical variation of the turbulence structures on the mean canopy flow elucidated. Implications on wave energy dissipation and sediment transport are discussed.
Extreme Precipitation in a Multi-Scale Modeling Framework
NASA Astrophysics Data System (ADS)
Phillips, M.; Denning, S.; Arabi, M.
2015-12-01
Extreme precipitation events are characterized by infrequent but large magnitude accummulatations that generally occur on scales belowthat resolved by the typical Global Climate Model. The Multi-scale Modeling Framework allows for information about the precipitation on these scales to be simulated for long periods of time without the large computational resources required for the use of a full cloud permitting model. The Community Earth System Model was run for 30 years in both its MMF and GCM modes, and the annual maximum series of 24 hour precipitation accumulations were used to estimate the parameters of statistical distributions. The distributions generated from model ouput were then fit to a General Extreme Value distribution and evaluated against observations. These results indicate that the MMF produces extreme precipitation with a statistical distribution that closely resembles that of observations and motivates the continued use of the MMF for analysis of extreme precipitation, and shows an improvement over the traditional GCM. The improvement in statistical distributions of annual maxima is greatest in regions that are dominated by convective precipitation where the small-scale information provided by the MMF heavily influences precipitation processes.
Bayesian Multiscale Modeling of Closed Curves in Point Clouds
Gu, Kelvin; Pati, Debdeep; Dunson, David B.
2014-01-01
Modeling object boundaries based on image or point cloud data is frequently necessary in medical and scientific applications ranging from detecting tumor contours for targeted radiation therapy, to the classification of organisms based on their structural information. In low-contrast images or sparse and noisy point clouds, there is often insufficient data to recover local segments of the boundary in isolation. Thus, it becomes critical to model the entire boundary in the form of a closed curve. To achieve this, we develop a Bayesian hierarchical model that expresses highly diverse 2D objects in the form of closed curves. The model is based on a novel multiscale deformation process. By relating multiple objects through a hierarchical formulation, we can successfully recover missing boundaries by borrowing structural information from similar objects at the appropriate scale. Furthermore, the model’s latent parameters help interpret the population, indicating dimensions of significant structural variability and also specifying a ‘central curve’ that summarizes the collection. Theoretical properties of our prior are studied in specific cases and efficient Markov chain Monte Carlo methods are developed, evaluated through simulation examples and applied to panorex teeth images for modeling teeth contours and also to a brain tumor contour detection problem. PMID:25544786
Multiscale modeling of droplet interface bilayer membrane networks
Freeman, Eric C.; Farimani, Amir B.; Aluru, Narayana R.; Philen, Michael K.
2015-01-01
Droplet interface bilayer (DIB) networks are considered for the development of stimuli-responsive membrane-based materials inspired by cellular mechanics. These DIB networks are often modeled as combinations of electrical circuit analogues, creating complex networks of capacitors and resistors that mimic the biomolecular structures. These empirical models are capable of replicating data from electrophysiology experiments, but these models do not accurately capture the underlying physical phenomena and consequently do not allow for simulations of material functionalities beyond the voltage-clamp or current-clamp conditions. The work presented here provides a more robust description of DIB network behavior through the development of a hierarchical multiscale model, recognizing that the macroscopic network properties are functions of their underlying molecular structure. The result of this research is a modeling methodology based on controlled exchanges across the interfaces of neighboring droplets. This methodology is validated against experimental data, and an extension case is provided to demonstrate possible future applications of droplet interface bilayer networks. PMID:26594262
The multi-scale modelling of coronary blood flow.
Lee, Jack; Smith, Nicolas P
2012-11-01
Coronary flow is governed by a number of determinants including network anatomy, systemic afterload and the mechanical interaction with the myocardium throughout the cardiac cycle. The range of spatial scales and multi-physics nature of coronary perfusion highlights a need for a multiscale framework that captures the relevant details at each level of the network. The goal of this review is to provide a compact and accessible introduction to the methodology and current state of the art application of the modelling frameworks that have been used to study the coronary circulation. We begin with a brief description of the seminal experimental observations that have motivated the development of mechanistic frameworks for understanding how myocardial mechanics influences coronary flow. These concepts are then linked to an overview of the lumped parameter models employed to test these hypotheses. We then outline the full and reduced-order (3D and 1D) continuum mechanics models based on the Navier-Stokes equations and highlight, with examples, their application regimes. At the smaller spatial scales the case for the importance of addressing the microcirculation is presented, with an emphasis on the poroelastic approach that is well-suited to bridge an existing gap in the development of an integrated whole heart model. Finally, the recent accomplishments of the wave intensity analysis and related approaches are presented and the clinical outlook for coronary flow modelling discussed.
Relational grounding facilitates development of scientifically useful multiscale models
2011-01-01
We review grounding issues that influence the scientific usefulness of any biomedical multiscale model (MSM). Groundings are the collection of units, dimensions, and/or objects to which a variable or model constituent refers. To date, models that primarily use continuous mathematics rely heavily on absolute grounding, whereas those that primarily use discrete software paradigms (e.g., object-oriented, agent-based, actor) typically employ relational grounding. We review grounding issues and identify strategies to address them. We maintain that grounding issues should be addressed at the start of any MSM project and should be reevaluated throughout the model development process. We make the following points. Grounding decisions influence model flexibility, adaptability, and thus reusability. Grounding choices should be influenced by measures, uncertainty, system information, and the nature of available validation data. Absolute grounding complicates the process of combining models to form larger models unless all are grounded absolutely. Relational grounding facilitates referent knowledge embodiment within computational mechanisms but requires separate model-to-referent mappings. Absolute grounding can simplify integration by forcing common units and, hence, a common integration target, but context change may require model reengineering. Relational grounding enables synthesis of large, composite (multi-module) models that can be robust to context changes. Because biological components have varying degrees of autonomy, corresponding components in MSMs need to do the same. Relational grounding facilitates achieving such autonomy. Biomimetic analogues designed to facilitate translational research and development must have long lifecycles. Exploring mechanisms of normal-to-disease transition requires model components that are grounded relationally. Multi-paradigm modeling requires both hyperspatial and relational grounding. PMID:21951817
NASA Astrophysics Data System (ADS)
Mizokami, Naoya; Nakahata, Kazuyuki; Ogi, Keiji; Yamawaki, Hisashi; Shiwa, Mitsuharu
2017-02-01
The use of fiber reinforced plastics (FRPs) as structural components has significantly increased in recent years. FRPs are made of stacks of plies, each of which is reinforced by fibers. When modeling ultrasonic wave propagation in FRPs, it is important to introduce three-dimensional mesoscopic and microscopic structures to account for the anisotropy and heterogeneity caused by fiber orientation and the lay-up of laminates. In this study, a finite element method using an image-based modeling is applied to simulation of ultrasonic wave propagation in a carbon FRP (CFRP). Here, the elastic stiffness of a single ply is determined using a homogenization method, where a CFRP microstructure is incorporated on the basis of a two-scale asymptotic expansion. The wave propagation in a CFRP specimen composed of unidirectionally aligned fibers is calculated, and the simulation results are compared to visualization results obtained for ultrasonic wave propagation using a laser scanning device.
Use of Image Based Modelling for Documentation of Intricately Shaped Objects
NASA Astrophysics Data System (ADS)
Marčiš, M.; Barták, P.; Valaška, D.; Fraštia, M.; Trhan, O.
2016-06-01
In the documentation of cultural heritage, we can encounter three dimensional shapes and structures which are complicated to measure. Such objects are for example spiral staircases, timber roof trusses, historical furniture or folk costume where it is nearly impossible to effectively use the traditional surveying or the terrestrial laser scanning due to the shape of the object, its dimensions and the crowded environment. The actual methods of digital photogrammetry can be very helpful in such cases with the emphasis on the automated processing of the extensive image data. The created high resolution 3D models and 2D orthophotos are very important for the documentation of architectural elements and they can serve as an ideal base for the vectorization and 2D drawing documentation. This contribution wants to describe the various usage of image based modelling in specific interior spaces and specific objects. The advantages and disadvantages of the photogrammetric measurement of such objects in comparison to other surveying methods are reviewed.
Multiscale modeling of nerve agent hydrolysis mechanisms: a tale of two Nobel Prizes
NASA Astrophysics Data System (ADS)
Field, Martin J.; Wymore, Troy W.
2014-10-01
The 2013 Nobel Prize in Chemistry was awarded for the development of multiscale models for complex chemical systems, whereas the 2013 Peace Prize was given to the Organisation for the Prohibition of Chemical Weapons for their efforts to eliminate chemical warfare agents. This review relates the two by introducing the field of multiscale modeling and highlighting its application to the study of the biological mechanisms by which selected chemical weapon agents exert their effects at an atomic level.
A Multi-Scale Modeling and Experimental Program for the Dynamic Mechanical Response of Tissue
2014-12-09
Einstein relation and microrheology analysis , Journal of Non-Newtonian Fluid Mechanics , (10 2013): 3. doi: 10.1016/j.jnnfm.2012.08.002 Cédric Zeltz...A Multi-Scale Modeling and Experimental Program for the Dynamic Mechanical Response of Tissue We study the mechanical properties of collagen, which...is the most prevalent protein in humans, and largely responsible for the mechanical properties of tissue. We use both a multiscale modeling approach
NASA Astrophysics Data System (ADS)
Macioł, Piotr; Gotfryd, Leszek; Macioł, Andrzej
2012-09-01
The hereby paper concerns the issue of solution of runtime controlling of multiscale model of ion-exchange solvent extraction. It is based on cooperation of a framework applying Agile Multiscale Modeling Methodology (AM3), and the REBIT Knowledge Based System. Ion-exchange solvent extraction has been shortly introduced. Design assumptions of AM3 and theoretical basis of REBIT have been described. Designed workflows and rules for simple laminar/ turbulent flow and extraction processes have been shown.
Multiscale model for pedestrian and infection dynamics during air travel
NASA Astrophysics Data System (ADS)
Namilae, Sirish; Derjany, Pierrot; Mubayi, Anuj; Scotch, Mathew; Srinivasan, Ashok
2017-05-01
In this paper we develop a multiscale model combining social-force-based pedestrian movement with a population level stochastic infection transmission dynamics framework. The model is then applied to study the infection transmission within airplanes and the transmission of the Ebola virus through casual contacts. Drastic limitations on air-travel during epidemics, such as during the 2014 Ebola outbreak in West Africa, carry considerable economic and human costs. We use the computational model to evaluate the effects of passenger movement within airplanes and air-travel policies on the geospatial spread of infectious diseases. We find that boarding policy by an airline is more critical for infection propagation compared to deplaning policy. Enplaning in two sections resulted in fewer infections than the currently followed strategy with multiple zones. In addition, we found that small commercial airplanes are better than larger ones at reducing the number of new infections in a flight. Aggregated results indicate that passenger movement strategies and airplane size predicted through these network models can have significant impact on an event like the 2014 Ebola epidemic. The methodology developed here is generic and can be readily modified to incorporate the impact from the outbreak of other directly transmitted infectious diseases.
A multiscale model of Earth's inner-core anisotropy
NASA Astrophysics Data System (ADS)
Merkel, Sébastien; Lincot, Ainhoa; Deguen, Renaud; Cardin, Philippe
2016-04-01
The Earth's solid inner-core exhibits a global seismic anisotropy of several percents. It results from a coherent alignment of anisotropic Fe-alloy crystals through the inner-core history that can be sampled by present-day seismic observations. By combining self-consistent polycrystal plasticity, inner-core formation models, Monte-Carlo search for elastic moduli, and simulations of seismic measurements, we introduce a multiscale model that can reproduce a global seismic anisotropy of several percents aligned with the Earth's rotation axis. Cubic-structured Fe-alloy fail at producing significant global scale anisotropy. Conditions for a successful model are an hexagonal-close-packed structure for the inner-core Fe-alloy, plastic deformation by pyramidal ⟨c + a⟩ slip, and large-scale flow induced by a low-degree inner-core formation model. For global anisotropies ranging between 1 and 3%, the elastic anisotropy in the single crystal ranges from 5 to 20% with larger velocities along the c-axis.
Improving NASA's Multiscale Modeling Framework for Tropical Cyclone Climate Study
NASA Technical Reports Server (NTRS)
Shen, Bo-Wen; Nelson, Bron; Cheung, Samson; Tao, Wei-Kuo
2013-01-01
One of the current challenges in tropical cyclone (TC) research is how to improve our understanding of TC interannual variability and the impact of climate change on TCs. Recent advances in global modeling, visualization, and supercomputing technologies at NASA show potential for such studies. In this article, the authors discuss recent scalability improvement to the multiscale modeling framework (MMF) that makes it feasible to perform long-term TC-resolving simulations. The MMF consists of the finite-volume general circulation model (fvGCM), supplemented by a copy of the Goddard cumulus ensemble model (GCE) at each of the fvGCM grid points, giving 13,104 GCE copies. The original fvGCM implementation has a 1D data decomposition; the revised MMF implementation retains the 1D decomposition for most of the code, but uses a 2D decomposition for the massive copies of GCEs. Because the vast majority of computation time in the MMF is spent computing the GCEs, this approach can achieve excellent speedup without incurring the cost of modifying the entire code. Intelligent process mapping allows differing numbers of processes to be assigned to each domain for load balancing. The revised parallel implementation shows highly promising scalability, obtaining a nearly 80-fold speedup by increasing the number of cores from 30 to 3,335.
Multi-Scale Modeling of Global of Magnetospheric Dynamics
NASA Technical Reports Server (NTRS)
Kuznetsova, M. M.; Hesse, M.; Rastatter, L.; Toth, G.; DeZeeuw, D.; Gombosi, T.
2010-01-01
To understand the role of magnetic reconnection in global evolution of magnetosphere and to place spacecraft observations into global context it is essential to perform global simulations with physically motivated model of dissipation that is capable to reproduce reconnection rates predicted by kinetic models. In our efforts to bridge the gap between small scale kinetic modeling and global simulations we introduced an approach that allows to quantify the interaction between large-scale global magnetospheric dynamics and microphysical processes in diffusion regions near reconnection sites. We utilized the high resolution global MHD code BATSRUS and incorporate primary mechanism controlling the dissipation in the vicinity of reconnection sites in terms of kinetic corrections to induction and energy equations. One of the key elements of the multiscale modeling of magnetic reconnection is identification of reconnection sites and boundaries of surrounding diffusion regions where non-MHD corrections are required. Reconnection site search in the equatorial plane implemented in our previous studies is extended to cusp and magnetopause reconnection, as well as for magnetotail reconnection in realistic asymmetric configurations. The role of feedback between the non-ideal effects in diffusion regions and global magnetosphere structure and dynamics will be discussed.
Upscalling processes in an ocean-atmosphere multiscale coupled model
NASA Astrophysics Data System (ADS)
Masson, S. G.; Berthet, S.; Samson, G.; Crétat, J.; Colas, F.; Echevin, V.; Jullien, S.; Hourdin, C.
2015-12-01
This work explores new pathways toward a better representation of the multi-scale physics that drive climate variability. We are analysing the key upscaling processes by which small-scale localized errors have a knock-on effect onto global climate. We focus on the Peru-Chilli coastal upwelling, an area known to hold among the strongest models biases in the Tropics. Our approach is based on the development of a multiscale coupling interface allowing us to couple WRF with the NEMO oceanic model in a configuration including 2-way nested zooms in the oceanic and/or the atmospheric component of the coupled model. Upscalling processes are evidenced and quantified by comparing three 20-year long simulations of a tropical channel (45°S-45°N), which differ by their horizontal resolution: 0.75° everywhere, 0.75°+0.25° zoom in the southeastern Pacific or 0.25° everywhere. This set of three 20-year long simulations was repeated with 3 different sets of parameterizations to assess the robustness of our results. Our results show that adding an embedded zoom over the southeastern Pacific only in the atmosphere cools down the SST along the Peru-Chili coast, which is a clear improvement. This change is associated with a displacement of the low-level cloud cover, which moves closer to the coast cooling further the coastal area SST. Offshore, we observe the opposite effect with a reduction of the cloud cover with higher resolution, which increases solar radiation and warms the SST. Increasing the resolution in the oceanic component show contrasting results according to the different set parameterization used in the experiments. Some experiment shows a coastal cooling as expected, whereas, in other cases, we observe a counterintuitive response with a warming of the coastal SST. Using at the same time an oceanic and an atmospheric zoom mostly combines the results obtained when using the 2-way nesting in only one component of the coupled model. In the best case, we archive by this
Statistical Inverse Ray Tracing for Image-Based 3D Modeling.
Liu, Shubao; Cooper, David B
2014-10-01
This paper proposes a new formulation and solution to image-based 3D modeling (aka "multi-view stereo") based on generative statistical modeling and inference. The proposed new approach, named statistical inverse ray tracing, models and estimates the occlusion relationship accurately through optimizing a physically sound image generation model based on volumetric ray tracing. Together with geometric priors, they are put together into a Bayesian formulation known as Markov random field (MRF) model. This MRF model is different from typical MRFs used in image analysis in the sense that the ray clique, which models the ray-tracing process, consists of thousands of random variables instead of two to dozens. To handle the computational challenges associated with large clique size, an algorithm with linear computational complexity is developed by exploiting, using dynamic programming, the recursive chain structure of the ray clique. We further demonstrate the benefit of exact modeling and accurate estimation of the occlusion relationship by evaluating the proposed algorithm on several challenging data sets.
Multi-Scale Modeling of Cross-Linked Nanotube Materials
NASA Technical Reports Server (NTRS)
Frankland, S. J. V.; Odegard, G. M.; Herzog, M. N.; Gates, T. S.; Fay, C. C.
2005-01-01
The effect of cross-linking single-walled carbon nanotubes on the Young's modulus of a nanotube-reinforced composite is modeled with a multi-scale method. The Young's modulus is predicted as a function of nanotube volume fraction and cross-link density. In this method, the constitutive properties of molecular representative volume elements are determined using molecular dynamics simulation and equivalent-continuum modeling. The Young's modulus is subsequently calculated for cross-linked nanotubes in a matrix which consists of the unreacted cross-linking agent. Two different cross-linking agents are used in this study, one that is short and rigid (Molecule A), and one that is long and flexible (Molecule B). Direct comparisons between the predicted elastic constants are made for the models in which the nanotubes are either covalently bonded or not chemically bonded to the cross-linking agent. At a nanotube volume fraction of 10%, the Young's modulus of Material A is not affected by nanotube crosslinking, while the Young's modulus of Material B is reduced by 64% when the nanotubes are cross-linked relative to the non-cross-linked material with the same matrix.
Multi-Scale Modeling of Cross-Linked Nanotube Materials
NASA Technical Reports Server (NTRS)
Frankland, S. J. V.; Odegard, G. M.; Herzog, M. N.; Gates, T. S.; Fay, C. C.
2005-01-01
The effect of cross-linking single-walled carbon nanotubes on the Young's modulus of a nanotube-reinforced composite is modeled with a multi-scale method. The Young's modulus is predicted as a function of nanotube volume fraction and cross-link density. In this method, the constitutive properties of molecular representative volume elements are determined using molecular dynamics simulation and equivalent-continuum modeling. The Young's modulus is subsequently calculated for cross-linked nanotubes in a matrix which consists of the unreacted cross-linking agent. Two different cross-linking agents are used in this study, one that is short and rigid (Molecule A), and one that is long and flexible (Molecule B). Direct comparisons between the predicted elastic constants are made for the models in which the nanotubes are either covalently bonded or not chemically bonded to the cross-linking agent. At a nanotube volume fraction of 10%, the Young's modulus of Material A is not affected by nanotube crosslinking, while the Young's modulus of Material B is reduced by 64% when the nanotubes are cross-linked relative to the non-cross-linked material with the same matrix.
Multiscale modelling of hydrothermal biomass pretreatment for chip size optimization.
Hosseini, Seyed Ali; Shah, Nilay
2009-05-01
The objective of this work is to develop a relationship between biomass chip size and the energy requirement of hydrothermal pretreatment processes using a multiscale modelling approach. The severity factor or modified severity factor is currently used to characterize some hydrothermal pretreatment methods. Although these factors enable an easy comparison of experimental results to facilitate process design and operation, they are not representative of all the factors affecting the efficiency of pretreatment, because processes with the same temperature, residence time, and pH will not have same effect on biomass chips of different size. In our study, a model based on the diffusion of liquid or steam in the biomass that takes into account the interrelationship between chip size and time is developed. With the aid of our developed model, a method to find the optimum chip size that minimizes the energy requirement of grinding and pretreatment processes is proposed. We show that with the proposed optimization method, an average saving equivalent to a 5% improvement in the yield of biomass to ethanol conversion process can be achieved.
Multiscale Modeling of Heat Conduction in Carbon Nanotube Aerogels
NASA Astrophysics Data System (ADS)
Gong, Feng; Papavassiliou, Dimitrios; Duong, Hai
Carbon nanotube (CNT) aerogels have attracted a lot of interest due to their ultrahigh strength/weight and surface area/weight ratios. They are promising advanced materials used in energy storage systems, hydrogen storage media and weight-conscious devices such as satellites, because of their ultralight and highly porous quality. CNT aerogels can have excellent electrical conductivity and mechanical strength. However, the thermal conductivity of CNT aerogels are as low as 0.01-0.1 W/mK, which is five orders of magnitude lower than that of CNT (2000-5000 W/mK). To investigate the mechanisms for the low thermal conductivity of CNT aerogels, multiscale models are built in this study. Molecular dynamic (MD) simulations are first carried out to investigate the heat transfer between CNT and different gases (e.g. nitrogen and hydrogen), and the thermal conductance at CNT-CNT interface. The interfacial thermal resistances of CNT-gas and CNT-CNT are estimated from the MD simulations. Mesoscopic modeling of CNT aerogels are then built using an off-lattice Monte Carlo (MC) simulations to replicate the realistic CNT aerogels. The interfacial thermal resistances estimated from MD simulations are used as inputs in the MC models to predict the thermal conductivity of CNT aerogels. The volume fractions and the complex morphologies of CNTs are also quantified to study their effects on the thermal conductivity of CNT aerogels. The quantitative findings may help researchers to obtain the CNT aerogels with expected thermal conductivity.
Modeling multiscale evolution of numerous voids in shocked brittle material.
Yu, Yin; Wang, Wenqiang; He, Hongliang; Lu, Tiecheng
2014-04-01
The influence of the evolution of numerous voids on macroscopic properties of materials is a multiscale problem that challenges computational research. A shock-wave compression model for brittle material, which can obtain both microscopic evolution and macroscopic shock properties, was developed using discrete element methods (lattice model). Using a model interaction-parameter-mapping procedure, qualitative features, as well as trends in the calculated shock-wave profiles, are shown to agree with experimental results. The shock wave splits into an elastic wave and a deformation wave in porous brittle materials, indicating significant shock plasticity. Void collapses in the deformation wave were the natural reason for volume shrinkage and deformation. However, media slippage and rotation deformations indicated by complex vortex patterns composed of relative velocity vectors were also confirmed as an important source of shock plasticity. With increasing pressure, the contribution from slippage deformation to the final plastic strain increased. Porosity was found to determine the amplitude of the elastic wave; porosity and shock stress together determine propagation speed of the deformation wave, as well as stress and strain on the final equilibrium state. Thus, shock behaviors of porous brittle material can be systematically designed for specific applications.
Multi-Scale Modeling of Wave Attenuation by Vegetation
NASA Astrophysics Data System (ADS)
Chen, Q. J.; Zhu, L.; Chakrabarti, A.
2016-02-01
In the past decade, interest in wave attenuation by vegetation has increased considerably as coastal scientists and engineers search for sustainable solutions to mitigate the impacts of climate change and natural hazards. It is well known that vegetation in wetlands can effectively reduce the flow speed, modify turbulence structure, attenuate wave energy, and affect sediment dynamics. Restoring coastal wetlands and reducing flood risks require improved understanding and better predictive capability of wave and surge attenuation over inundated coastal landscapes with vegetation. The interactions of surface weaves and natural vegetation span over a large range of scales, from turbulence and eddies at the vegetation stem scale to wave generation in vast inundated wetlands of hundreds of square miles under hurricane conditions. The study is focused on a phase-averaged energy-based model and phase-resolving Euler and Navier-Stokes (N-S) solvers with different representations of submerged vegetation. We will present recent advances in multi-scale modeling of wave attenuation by wetland vegetation. Numerical modeling results ranging from vegetation-resolved large eddy simulation under idealized conditions to incorporating vegetation-induced drag forces into conservation laws of momentum and energy for engineering applications will be shown. Effects of vegetation flexibility, turbulence closure, and various wave theories on the prediction of wave attenuation and the choice of vegetation drag coefficients will be discussed.
NASA Astrophysics Data System (ADS)
Jiang, Hai; Zhang, Bingchen; Lin, Yueguan; Hong, Wen; Wu, Yirong
2011-11-01
Recent theory of compressed sensing (CS) has been widely used in many application areas. In this paper, we mainly concentrate on the CS in radar and analyze the distinguishing ability of CS radar image based on information theory model. The information content contained in the CS radar echoes is analyzed by simplifying the information transmission channel as a parallel Gaussian channel, and the relationship among the signal-to-noise ratio (SNR) of the echo signal, the number of required samples, the length of the sparse targets and the distinguishing level of the radar image is gotten. Based on this result, we introduced the distinguishing ability of the CS radar image and some of its properties are also gotten. Real IECAS advanced scanning two-dimensional railway observation (ASTRO) data experiment demonstrates our conclusions.
Toward unification of the multiscale modeling of the atmosphere
NASA Astrophysics Data System (ADS)
Arakawa, A.; Jung, J.-H.; Wu, C.-M.
2011-01-01
This paper suggests two possible routes to achieve the unification of model physics in coarse- and fine-resolution atmospheric models. As far as representation of deep moist convection is concerned, only two kinds of model physics are used at present: highly parameterized as in the conventional general circulation models (GCMs) and explicitly simulated as in the cloud-resolving models (CRMs). Ideally, these two kinds of model physics should be unified so that a continuous transition of model physics from one kind to the other takes place as the resolution changes. With such unification, the GCM can converge to a global CRM (GCRM) as the grid size is refined. ROUTE I for unification continues to follow the parameterization approach, but uses a unified parameterization that is applicable to any horizontal resolutions between those typically used by GCMs and CRMs. It is shown that a key to construct such a unified parameterization is to eliminate the assumption of small fractional area covered by convective clouds, which is commonly used in the conventional cumulus parameterizations either explicitly or implicitly. A preliminary design of the unified parameterization is presented, which demonstrates that such an assumption can be eliminated through a relatively minor modification of the existing mass-flux based parameterizations. Partial evaluations of the unified parameterization are also presented. ROUTE II for unification follows the "multi-scale modeling framework (MMF)" approach, which takes advantage of explicit representation of deep moist convection and associated cloud-scale processes by CRMs. The Quasi-3-D (Q3-D) MMF is an attempt to broaden the applicability of MMF without necessarily using a fully three-dimensional CRM. This is accomplished using a network of cloud-resolving grids with gaps. An outline of the Q3-D algorithm and highlights of preliminary results are reviewed.
Multi-scale Modeling of Plasticity in Tantalum.
Lim, Hojun; Battaile, Corbett Chandler.; Carroll, Jay; Buchheit, Thomas E.; Boyce, Brad; Weinberger, Christopher
2015-12-01
In this report, we present a multi-scale computational model to simulate plastic deformation of tantalum and validating experiments. In atomistic/ dislocation level, dislocation kink- pair theory is used to formulate temperature and strain rate dependent constitutive equations. The kink-pair theory is calibrated to available data from single crystal experiments to produce accurate and convenient constitutive laws. The model is then implemented into a BCC crystal plasticity finite element method (CP-FEM) model to predict temperature and strain rate dependent yield stresses of single and polycrystalline tantalum and compared with existing experimental data from the literature. Furthermore, classical continuum constitutive models describing temperature and strain rate dependent flow behaviors are fit to the yield stresses obtained from the CP-FEM polycrystal predictions. The model is then used to conduct hydro- dynamic simulations of Taylor cylinder impact test and compared with experiments. In order to validate the proposed tantalum CP-FEM model with experiments, we introduce a method for quantitative comparison of CP-FEM models with various experimental techniques. To mitigate the effects of unknown subsurface microstructure, tantalum tensile specimens with a pseudo-two-dimensional grain structure and grain sizes on the order of millimeters are used. A technique combining an electron back scatter diffraction (EBSD) and high resolution digital image correlation (HR-DIC) is used to measure the texture and sub-grain strain fields upon uniaxial tensile loading at various applied strains. Deformed specimens are also analyzed with optical profilometry measurements to obtain out-of- plane strain fields. These high resolution measurements are directly compared with large-scale CP-FEM predictions. This computational method directly links fundamental dislocation physics to plastic deformations in the grain-scale and to the engineering-scale applications. Furthermore, direct
Multiscale mathematical modeling of the hypothalamo-pituitary-gonadal axis.
Clément, Frédérique
2016-07-01
Although the fields of systems and integrative biology are in full expansion, few teams are involved worldwide into the study of reproductive function from the mathematical modeling viewpoint. This may be due to the fact that the reproductive function is not compulsory for individual organism survival, even if it is for species survival. Alternatively, the complexity of reproductive physiology may be discouraging. Indeed, the hypothalamo-pituitary-gonadal (HPG) axis involves not only several organs and tissues but also intricate time (from the neuronal millisecond timescale to circannual rhythmicity) and space (from molecules to organs) scales. Yet, mathematical modeling, and especially multiscale modeling, can renew our approaches of the molecular, cellular, and physiological processes underlying the control of reproductive functions. In turn, the remarkable dynamic features exhibited by the HPG axis raise intriguing and challenging questions to modelers and applied mathematicians. In this article, we draw a panoramic review of some mathematical models designed in the framework of the female HPG, with a special focus on the gonadal and central control of follicular development. On the gonadal side, the modeling of follicular development calls to the generic formalism of structured cell populations, that allows one to make mechanistic links between the control of cell fate (proliferation, differentiation, or apoptosis) and that of the follicle fate (ovulation or degeneration) or to investigate how the functional interactions between the oocyte and its surrounding cells shape the follicle morphogenesis. On the central, mainly hypothalamic side, models based on dynamical systems with multiple timescales allow one to represent within a single framework both the pulsatile and surge patterns of the neurohormone GnRH. Beyond their interest in basic research investigations, mathematical models can also be at the source of useful tools to study the encoding and decoding of
Multiscale Modeling of the Orthotropic Behaviour of PA6-6 overmoulded Composites using MMI Approach
Bikard, Jerome; Robert, Gilles; Moulinjeune, Olivier
2011-05-04
In this study the MMI ConfidentDesign multiscale approach (consisting in a non-linear multiscale simulation based on DIGIMAT registered including the injection modeling of the filled polymer and a multiscale mechanical model using the fiber orientation tensor resulting from the injection) has been combined with an orthotropic damageable elastic simulation. The anisotropic properties (including rupture criterion) are estimated and a multiscale simulation including the heterogeneous material properties issued from injection process is done. The impact of fiber ratios is then investigated. The structural simulation predicts stresses localized close to the punch, as well in injected PA66 than in composite part. Greater the fiber volume ratio, greater the modulus and more brittle the composite.
Multiscale Parameter Regionalization for consistent global water resources modelling
NASA Astrophysics Data System (ADS)
Wanders, Niko; Wood, Eric; Pan, Ming; Samaniego, Luis; Thober, Stephan; Kumar, Rohini; Sutanudjaja, Edwin; van Beek, Rens; Bierkens, Marc F. P.
2017-04-01
Due to an increasing demand for high- and hyper-resolution water resources information, it has become increasingly important to ensure consistency in model simulations across scales. This consistency can be ensured by scale independent parameterization of the land surface processes, even after calibration of the water resource model. Here, we use the Multiscale Parameter Regionalization technique (MPR, Samaniego et al. 2010, WRR) to allow for a novel, spatially consistent, scale independent parameterization of the global water resource model PCR-GLOBWB. The implementation of MPR in PCR-GLOBWB allows for calibration at coarse resolutions and subsequent parameter transfer to the hyper-resolution. In this study, the model was calibrated at 50 km resolution over Europe and validation carried out at resolutions of 50 km, 10 km and 1 km. MPR allows for a direct transfer of the calibrated transfer function parameters across scales and we find that we can maintain consistent land-atmosphere fluxes across scales. Here we focus on the 2003 European drought and show that the new parameterization allows for high-resolution calibrated simulations of water resources during the drought. For example, we find a reduction from 29% to 9.4% in the percentile difference in the annual evaporative flux across scales when compared against default simulations. Soil moisture errors are reduced from 25% to 6.9%, clearly indicating the benefits of the MPR implementation. This new parameterization allows us to show more spatial detail in water resources simulations that are consistent across scales and also allow validation of discharge for smaller catchments, even with calibrations at a coarse 50 km resolution. The implementation of MPR allows for novel high-resolution calibrated simulations of a global water resources model, providing calibrated high-resolution model simulations with transferred parameter sets from coarse resolutions. The applied methodology can be transferred to other
Multiscale modeling and simulation of microtubule-motor-protein assemblies
NASA Astrophysics Data System (ADS)
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 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
A multiscale crack-bridging model of cellulose nanopaper
NASA Astrophysics Data System (ADS)
Meng, Qinghua; Li, Bo; Li, Teng; Feng, Xi-Qiao
2017-06-01
The conflict between strength and toughness is a long-standing challenge in advanced materials design. Recently, a fundamental bottom-up material design strategy has been demonstrated using cellulose nanopaper to achieve significant simultaneous increase in both strength and toughness. Fertile opportunities of such a design strategy aside, mechanistic understanding is much needed to thoroughly explore its full potential. To this end, here we establish a multiscale crack-bridging model to reveal the toughening mechanisms in cellulose nanopaper. A cohesive law is developed to characterize the interfacial properties between cellulose nanofibrils by considering their hydrogen bonding nature. In the crack-bridging zone, the hydrogen bonds between neighboring cellulose nanofibrils may break and reform at the molecular scale, rendering a superior toughness at the macroscopic scale. It is found that cellulose nanofibrils exhibit a distinct size-dependence in enhancing the fracture toughness of cellulose nanopaper. An optimal range of the length-to-radius ratio of nanofibrils is required to achieve higher fracture toughness of cellulose nanopaper. A unified law is proposed to correlate the fracture toughness of cellulose nanopaper with its microstructure and material parameters. The results obtained from this model agree well with relevant experiments. This work not only helps decipher the fundamental mechanisms underlying the remarkable mechanical properties of cellulose nanopaper but also provides a guide to design a wide range of advanced functional materials.
Theory and Modeling for the Magnetospheric Multiscale Mission
NASA Astrophysics Data System (ADS)
Hesse, M.; Aunai, N.; Birn, J.; Cassak, P.; Denton, R. E.; Drake, J. F.; Gombosi, T.; Hoshino, M.; Matthaeus, W.; Sibeck, D.; Zenitani, S.
2016-03-01
The Magnetospheric Multiscale (MMS) mission will provide measurement capabilities, which will exceed those of earlier and even contemporary missions by orders of magnitude. MMS will, for the first time, be able to measure directly and with sufficient resolution key features of the magnetic reconnection process, down to the critical electron scales, which need to be resolved to understand how reconnection works. Owing to the complexity and extremely high spatial resolution required, no prior measurements exist, which could be employed to guide the definition of measurement requirements, and consequently set essential parameters for mission planning and execution. Insight into expected details of the reconnection process could hence only been obtained from theory and modern kinetic modeling. This situation was recognized early on by MMS leadership, which supported the formation of a fully integrated Theory and Modeling Team (TMT). The TMT participated in all aspects of mission planning, from the proposal stage to individual aspects of instrument performance characteristics. It provided and continues to provide to the mission the latest insights regarding the kinetic physics of magnetic reconnection, as well as associated particle acceleration and turbulence, assuring that, to the best of modern knowledge, the mission is prepared to resolve the inner workings of the magnetic reconnection process. The present paper provides a summary of key recent results or reconnection research by TMT members.
Multiscale Modeling of Discontinuous Precipitation in U-Nb
NASA Astrophysics Data System (ADS)
Duong, Thien C.; Arroyave, Raymundo
Discontinuous precipitation (DP) was experimentally observed in the uranium-niobium nuclear fuel. The reaction is undesirable as it degrades the fuel's corrosion resistance and ductility. To minimize the impacts, it is important to understand the fundamental thermodynamics and kinetics of DP. In this work, we proposed to study the microstructure evolution of DP using a multiscale approach. In particular, three combinatorial methodologies including (1) first-principles calculations, (2) CALPHAD and (3) phase-field modeling were practiced. Initially, first-principle calculations were carried out to calculate for the ground-state formation energy of U-Nb's bcc phase. The ab initio energetic data were then used in CALPHAD assessment to achieve for a self-consistent thermodynamic description of U-Nb system. Next, atomic mobilities and diffusivities of the bcc phase was estimated also in the framework of CALPHAD. Finally, phase-field simulation was carried out to model the microstructure evolution of DP's lamellae, using the achieved thermodynamic and kinetic information. Results show good agreements with experiments.
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 Modeling of Shock-Induced Phase Transitions in Iron
NASA Astrophysics Data System (ADS)
Carter, Emily; Caspersen, Kyle; Lew, Adrian; Ortiz, Michael
2004-03-01
Multiscale Modeling of Shock-Induced Phase Transitions in Iron Emily Carter, Kyle Caspersen, Adrian Lew and Michael Ortiz We investigate the bcc to hcp phase transition in iron under both pressure and shear. We use DFT to map out the energy landscape of uniformly deformed iron, including its equation of state and its elastic moduli as a function of volume. >From these data we construct a nonlinear-elastic energy density which gives the energy density for arbitrary - not necessarily small - deformations. The energy density contains two wells corresponding to the bcc and hcp phases. We take this multi-well energy density as a basis for the investigation of the effect of shear on the phase diagram of iron. We allow for mixed states consisting alternating lamellae of bcc and hcp phases, and, for each macroscopic deformation, we determine the optimal microstructure of the mixed state by energy minimization using a sequential-lamination algorithm. We find that the superposition of shearing deformation on a volume change has the effect of inducing mixed states of varying spatial complexity, and of markedly lowering the critical transformation pressure. Indeed, we find that shear must be taken into consideration in order to obtain agreement with measured transformation pressures. Finally, we demonstrate how the microstructure model can be integrated into large-scale finite element calculations of shocked iron.
Multiscale computational modeling of a radiantly driven solar thermal collector
NASA Astrophysics Data System (ADS)
Ponnuru, Koushik
The objectives of the master's thesis are to present, discuss and apply sequential multiscale modeling that combines analytical, numerical (finite element-based) and computational fluid dynamic (CFD) analysis to assist in the development of a radiantly driven macroscale solar thermal collector for energy harvesting. The solar thermal collector is a novel green energy system that converts solar energy to heat and utilizes dry air as a working heat transfer fluid (HTF). This energy system has important advantages over competitive technologies: it is self-contained (no energy sources are needed), there are no moving parts, no oil or supplementary fluids are needed and it is environmentally friendly since it is powered by solar radiation. This work focuses on the development of multi-physics and multiscale models for predicting the performance of the solar thermal collector. Model construction and validation is organized around three distinct and complementary levels. The first level involves an analytical analysis of the thermal transpiration phenomenon and models for predicting the associated mass flow pumping that occurs in an aerogel membrane in the presence of a large thermal gradient. Within the aerogel, a combination of convection, conduction and radiation occurs simultaneously in a domain where the pore size is comparable to the mean free path of the gas molecules. CFD modeling of thermal transpiration is not possible because all the available commercial CFD codes solve the Navier Stokes equations only for continuum flow, which is based on the assumption that the net molecular mass diffusion is zero. However, thermal transpiration occurs in a flow regime where a non-zero net molecular mass diffusion exists. Thus these effects are modeled by using Sharipov's [2] analytical expression for gas flow characterized by high Knudsen number. The second level uses a detailed CFD model solving Navier Stokes equations for momentum, heat and mass transfer in the various
Toward unification of the multiscale modeling of the atmosphere
NASA Astrophysics Data System (ADS)
Arakawa, A.; Jung, J.-H.; Wu, C.-M.
2011-04-01
As far as the representation of deep moist convection is concerned, only two kinds of model physics are used at present: highly parameterized as in the conventional general circulation models (GCMs) and explicitly simulated as in the cloud-resolving models (CRMs). Ideally, these two kinds of model physics should be unified so that a continuous transition of model physics from one kind to the other takes place as the resolution changes. With such unification, the GCM can converge to a global CRM (GCRM) as the grid size is refined. This paper suggests two possible routes to achieve the unification. ROUTE I continues to follow the parameterization approach, but uses a unified parameterization that is applicable to any horizontal resolutions between those typically used by GCMs and CRMs. It is shown that a key to construct such a unified parameterization is to eliminate the assumption of small fractional area covered by convective clouds, which is commonly used in the conventional cumulus parameterizations either explicitly or implicitly. A preliminary design of the unified parameterization is presented, which demonstrates that such an assumption can be eliminated through a relatively minor modification of the existing mass-flux based parameterizations. Partial evaluations of the unified parameterization are also presented. ROUTE II follows the "multi-scale modeling framework (MMF)" approach, which takes advantage of explicit representation of deep moist convection and associated cloud-scale processes by CRMs. The Quasi-3-D (Q3-D) MMF is an attempt to broaden the applicability of MMF without necessarily using a fully three-dimensional CRM. This is accomplished using a network of cloud-resolving grids with large gaps. An outline of the Q3-D algorithm and highlights of preliminary results are reviewed.
Multiscale models for synoptic-mesoscale interactions in the ocean
NASA Astrophysics Data System (ADS)
Grooms, Ian; Shafer Smith, K.; Majda, Andrew J.
2012-11-01
Multiscale analysis is used to derive two sets of coupled models, each based on the same distinguished limit, to represent the interaction of the midlatitude oceanic synoptic scale-where coherent features such as jets and rings form-and the mesoscale, defined by the internal deformation scale. The synoptic scale and mesoscale overlap at low and mid latitudes, and are hence synonymous in much of the oceanographic literature; at higher latitudes the synoptic scale can be an order of magnitude larger than the deformation scale, which motivates our asymptotic approach and our nonstandard terminology. In the first model the synoptic dynamics are described by ‘Large Amplitude Geostrophic’ (LAG) equations while the eddy dynamics are quasigeostrophic. This model has order one isopycnal variation on the synoptic scale; the synoptic dynamics respond to an eddy momentum flux while the eddy dynamics respond to the baroclinically unstable synoptic density gradient. The second model assumes small isopycnal variation on the synoptic scale, but allows for a planetary scale background density gradient that may be fixed or evolved on a slower time scale. Here the large-scale equations are just the barotropic quasigeostrophic equations, and the mesoscale is modeled by the baroclinic quasigeostrophic equations. The synoptic dynamics now respond to both eddy momentum and buoyancy fluxes, but the small-scale eddy dynamics are simply advected by the synoptic-scale flow-there is no baroclinic production term in the eddy equations. The energy budget is closed by deriving an equation for the slow evolution of the eddy energy, which ensures that energy gained or lost by the synoptic-scale flow is reflected in a corresponding loss or gain by the eddies. This latter model, aided by the eddy energy equation-a key result of this paper-provides a conceptual basis through which to understand the classic baroclinic turbulence cycle.
Image-based models of cardiac structure in health and disease
Vadakkumpadan, Fijoy; Arevalo, Hermenegild; Prassl, Anton J.; Chen, Junjie; Kickinger, Ferdinand; Kohl, Peter; Plank, Gernot; Trayanova, Natalia
2010-01-01
Computational approaches to investigating the electromechanics of healthy and diseased hearts are becoming essential for the comprehensive understanding of cardiac function. In this article, we first present a brief review of existing image-based computational models of cardiac structure. We then provide a detailed explanation of a processing pipeline which we have recently developed for constructing realistic computational models of the heart from high resolution structural and diffusion tensor (DT) magnetic resonance (MR) images acquired ex vivo. The presentation of the pipeline incorporates a review of the methodologies that can be used to reconstruct models of cardiac structure. In this pipeline, the structural image is segmented to reconstruct the ventricles, normal myocardium, and infarct. A finite element mesh is generated from the segmented structural image, and fiber orientations are assigned to the elements based on DTMR data. The methods were applied to construct seven different models of healthy and diseased hearts. These models contain millions of elements, with spatial resolutions in the order of hundreds of microns, providing unprecedented detail in the representation of cardiac structure for simulation studies. PMID:20582162
Image-Based Personalization of Cardiac Anatomy for Coupled Electromechanical Modeling.
Crozier, A; Augustin, C M; Neic, A; Prassl, A J; Holler, M; Fastl, T E; Hennemuth, A; Bredies, K; Kuehne, T; Bishop, M J; Niederer, S A; Plank, G
2016-01-01
Computational models of cardiac electromechanics (EM) are increasingly being applied to clinical problems, with patient-specific models being generated from high fidelity imaging and used to simulate patient physiology, pathophysiology and response to treatment. Current structured meshes are limited in their ability to fully represent the detailed anatomical data available from clinical images and capture complex and varied anatomy with limited geometric accuracy. In this paper, we review the state of the art in image-based personalization of cardiac anatomy for biophysically detailed, strongly coupled EM modeling, and present our own tools for the automatic building of anatomically and structurally accurate patient-specific models. Our method relies on using high resolution unstructured meshes for discretizing both physics, electrophysiology and mechanics, in combination with efficient, strongly scalable solvers necessary to deal with the computational load imposed by the large number of degrees of freedom of these meshes. These tools permit automated anatomical model generation and strongly coupled EM simulations at an unprecedented level of anatomical and biophysical detail.
Image-based Modeling of PSF Deformation with Application to Limited Angle PET Data.
Matej, Samuel; Li, Yusheng; Panetta, Joseph; Karp, Joel S; Surti, Suleman
2016-10-01
The point-spread-functions (PSFs) of reconstructed images can be deformed due to detector effects such as resolution blurring and parallax error, data acquisition geometry such as insufficient sampling or limited angular coverage in dual-panel PET systems, or reconstruction imperfections/simplifications. PSF deformation decreases quantitative accuracy and its spatial variation lowers consistency of lesion uptake measurement across the imaging field-of-view (FOV). This can be a significant problem with dual panel PET systems even when using TOF data and image reconstruction models of the detector and data acquisition process. To correct for the spatially variant reconstructed PSF distortions we propose to use an image-based resolution model (IRM) that includes such image PSF deformation effects. Originally the IRM was mostly used for approximating data resolution effects of standard PET systems with full angular coverage in a computationally efficient way, but recently it was also used to mitigate effects of simplified geometric projectors. Our work goes beyond this by including into the IRM reconstruction imperfections caused by combination of the limited angle, parallax errors, and any other (residual) deformation effects and testing it for challenging dual panel data with strongly asymmetric and variable PSF deformations. We applied and tested these concepts using simulated data based on our design for a dedicated breast imaging geometry (B-PET) consisting of dual-panel, time-of-flight (TOF) detectors. We compared two image-based resolution models; i) a simple spatially invariant approximation to PSF deformation, which captures only the general PSF shape through an elongated 3D Gaussian function, and ii) a spatially variant model using a Gaussian mixture model (GMM) to more accurately capture the asymmetric PSF shape in images reconstructed from data acquired with the B-PET scanner geometry. Results demonstrate that while both IRMs decrease the overall uptake
Facing the challenges of multiscale modelling of bacterial and fungal pathogen–host interactions
Schleicher, Jana; Conrad, Theresia; Gustafsson, Mika; Cedersund, Gunnar; Guthke, Reinhard
2017-01-01
Abstract Recent and rapidly evolving progress on high-throughput measurement techniques and computational performance has led to the emergence of new disciplines, such as systems medicine and translational systems biology. At the core of these disciplines lies the desire to produce multiscale models: mathematical models that integrate multiple scales of biological organization, ranging from molecular, cellular and tissue models to organ, whole-organism and population scale models. Using such models, hypotheses can systematically be tested. In this review, we present state-of-the-art multiscale modelling of bacterial and fungal infections, considering both the pathogen and host as well as their interaction. Multiscale modelling of the interactions of bacteria, especially Mycobacterium tuberculosis, with the human host is quite advanced. In contrast, models for fungal infections are still in their infancy, in particular regarding infections with the most important human pathogenic fungi, Candida albicans and Aspergillus fumigatus. We reflect on the current availability of computational approaches for multiscale modelling of host–pathogen interactions and point out current challenges. Finally, we provide an outlook for future requirements of multiscale modelling. PMID:26857943
Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions.
Schleicher, Jana; Conrad, Theresia; Gustafsson, Mika; Cedersund, Gunnar; Guthke, Reinhard; Linde, Jörg
2017-03-01
Recent and rapidly evolving progress on high-throughput measurement techniques and computational performance has led to the emergence of new disciplines, such as systems medicine and translational systems biology. At the core of these disciplines lies the desire to produce multiscale models: mathematical models that integrate multiple scales of biological organization, ranging from molecular, cellular and tissue models to organ, whole-organism and population scale models. Using such models, hypotheses can systematically be tested. In this review, we present state-of-the-art multiscale modelling of bacterial and fungal infections, considering both the pathogen and host as well as their interaction. Multiscale modelling of the interactions of bacteria, especially Mycobacterium tuberculosis, with the human host is quite advanced. In contrast, models for fungal infections are still in their infancy, in particular regarding infections with the most important human pathogenic fungi, Candida albicans and Aspergillus fumigatus. We reflect on the current availability of computational approaches for multiscale modelling of host-pathogen interactions and point out current challenges. Finally, we provide an outlook for future requirements of multiscale modelling. © The Author 2016. Published by Oxford University Press.
Modeling of Multi-Scale Channeling Phenomena in Porous Flow
NASA Astrophysics Data System (ADS)
Räss, Ludovic; Omlin, Samuel; Yarushina, Viktoriya; Simon, Nina; Podladchikov, Yuri
2015-04-01
Predictive modeling of fluid percolation through tight porous rocks is critical to evaluate environmental risks associated with waste storage and reservoir operations. To understand the evolution of two-phase mixtures of fluid and solid it is insufficient to only combine single-phase fluid flow methods and solid mechanics. A proper coupling of these two different multi-scales physical processes is required to describe the complex evolution of permeability and porosity in space and in time. We conduct numerical modeling experiments in geometrically simple but physically complex systems of stressed rocks containing self-focusing porous flow. Our model is physically and thermodynamically consistent and describes the formation and evolution of fluid pathways. The model consists of a system of coupled equations describing poro-elasto-viscous deformation and flow. Nonlinearity of the solid rheology is also taken into account. We have developed a numerical application based on an iterative finite difference scheme that runs on mutli-GPUs cluster in parallel. In order to validate these models, we consider the largest CO2 sequestration project in operation at the Sleipner field in the Norwegian North Sea. Attempts to match the observations at Sleipner using conventional reservoir simulations fail to capture first order observations, such as the seemingly effortless vertical flow of CO2 through low permeability shale layers and the formation of focused flow channels or chimneys. Conducted high-resolution three-dimensional numerical simulations predict the formation of dynamically evolving high porosity and permeability pathways as a natural outcome of porous flow nonlinearly coupled with rock deformation, which may trigger leakage through low permeability barriers.
Multiscale Modeling of Hybrid Structural Composites with Integrated Damping Features
NASA Astrophysics Data System (ADS)
Martone, Alfonso; Giordano, Michele
2008-08-01
The aim of this work is to propose a design approach for a multifunctional hybrid composite material that integrates high damping performances while withstanding the required structural features. Hybrid composite consists in a three phases composite where a viscoelastic material is added to the conventional structural long fibers/polymeric matrix laminate. Design addresses the problem of integrating the viscoelastic material within the laminate architecture to exploit its maximum damping efficiency. Key aspect is the definition of a viscoelastic multiscale model starting from the constituents to the lamina, and further to the hybrid laminate properties. An analytical procedure has been developed that uses the strain energy method to evaluate the specific damping capacity for all dimensional scales and classical lamination theory was extended to include the transverse shear effects. The method potentiality has been tested against experimental data from Literature. Possible configurations of hybrid laminates have been simulated where viscoelastic material is added as laminae or distributed as long fibers within the structural laminate.
Mechanism of the Exchange Reaction in HRAS from Multiscale Modeling
Kapoor, Abhijeet; Travesset, Alex
2014-01-01
HRAS regulates cell growth promoting signaling processes by cycling between active (GTP-bound) and inactive (GDP-bound) states. Understanding the transition mechanism is central for the design of small molecules to inhibit the formation of RAS-driven tumors. Using a multiscale approach involving coarse-grained (CG) simulations, all-atom classical molecular dynamics (CMD; total of 3.02 µs), and steered molecular dynamics (SMD) in combination with Principal Component Analysis (PCA), we identified the structural features that determine the nucleotide (GDP) exchange reaction. We show that weakening the coupling between the SwitchI (residues 25–40) and SwitchII (residues 59–75) accelerates the opening of SwitchI; however, an open conformation of SwitchI is unstable in the absence of guanine nucleotide exchange factors (GEFs) and rises up towards the bound nucleotide to close the nucleotide pocket. Both I21 and Y32, play a crucial role in SwitchI transition. We show that an open SwitchI conformation is not necessary for GDP destabilization but is required for GDP/Mg escape from the HRAS. Further, we present the first simulation study showing displacement of GDP/Mg away from the nucleotide pocket. Both SwitchI and SwitchII, delays the escape of displaced GDP/Mg in the absence of GEF. Based on these results, a model for the mechanism of GEF in accelerating the exchange process is hypothesized. PMID:25272152
NASA Astrophysics Data System (ADS)
Zhang, Qingfu; Huang, Zhaoqin; Yao, Jun; Wang, Yueying; Li, Yang
2017-09-01
A multiscale mimetic method is developed for the simulation of multiphase flow in fractured porous media in the context of an embedded discrete fracture model (EDFM). The EDFM constructs independent grids for matrix and fracture system. Therefore, it is an efficient and practical flow model as it avoids the complicated unstructured grid subdivision and computing process. In order to extend the EDFM to field-scale applications, we integrate EDFM into a multiscale mimetic method. In this work, we use the multiscale basis functions to capture the detailed interactions between the fractures and the background. The multiscale basis functions are calculated numerically by solving EDFM on the local fine-grid with mimetic finite difference (MFD) method. The MFD method is conservative and robust, which makes it possible to deal with highly complex grid systems. Through combination of multiscale mimetic method and EDFM, this formulation can generate accurate velocity field and pressure field on the fine-scale grid more efficiently than the traditional methods. Numerical results are presented for verification of this multiscale mimetic approach for embedded discrete fracture media, and demonstrate its computational efficiency. The results show that this method is an accurate and efficient method for flow simulation in real-field fractured heterogeneous reservoirs.
Zhang, Xueqing; Bieberle-Hütter, Anja
2016-06-08
This review summarizes recent developments, challenges, and strategies in the field of modeling and simulations of photoelectrochemical (PEC) water oxidation. We focus on water splitting by metal-oxide semiconductors and discuss topics such as theoretical calculations of light absorption, band gap/band edge, charge transport, and electrochemical reactions at the electrode-electrolyte interface. In particular, we review the mechanisms of the oxygen evolution reaction, strategies to lower overpotential, and computational methods applied to PEC systems with particular focus on multiscale modeling. The current challenges in modeling PEC interfaces and their processes are summarized. At the end, we propose a new multiscale modeling approach to simulate the PEC interface under conditions most similar to those of experiments. This approach will contribute to identifying the limitations at PEC interfaces. Its generic nature allows its application to a number of electrochemical systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Report of the proceedings of the Colloquium and Workshop on Multiscale Coupled Modeling
NASA Technical Reports Server (NTRS)
Koch, Steven E. (Editor)
1993-01-01
The Colloquium and Workshop on Multiscale Coupled Modeling was held for the purpose of addressing modeling issues of importance to planning for the Cooperative Multiscale Experiment (CME). The colloquium presentations attempted to assess the current ability of numerical models to accurately simulate the development and evolution of mesoscale cloud and precipitation systems and their cycling of water substance, energy, and trace species. The primary purpose of the workshop was to make specific recommendations for the improvement of mesoscale models prior to the CME, their coupling with cloud, cumulus ensemble, hydrology, air chemistry models, and the observational requirements to initialize and verify these models.
MIDA: A Multimodal Imaging-Based Detailed Anatomical Model of the Human Head and Neck
Iacono, Maria Ida; Neufeld, Esra; Akinnagbe, Esther; Bower, Kelsey; Wolf, Johanna; Vogiatzis Oikonomidis, Ioannis; Sharma, Deepika; Lloyd, Bryn; Wilm, Bertram J.; Wyss, Michael; Pruessmann, Klaas P.; Jakab, Andras; Makris, Nikos; Cohen, Ethan D.; Kuster, Niels; Kainz, Wolfgang; Angelone, Leonardo M.
2015-01-01
Computational modeling and simulations are increasingly being used to complement experimental testing for analysis of safety and efficacy of medical devices. Multiple voxel- and surface-based whole- and partial-body models have been proposed in the literature, typically with spatial resolution in the range of 1–2 mm and with 10–50 different tissue types resolved. We have developed a multimodal imaging-based detailed anatomical model of the human head and neck, named “MIDA”. The model was obtained by integrating three different magnetic resonance imaging (MRI) modalities, the parameters of which were tailored to enhance the signals of specific tissues: i) structural T1- and T2-weighted MRIs; a specific heavily T2-weighted MRI slab with high nerve contrast optimized to enhance the structures of the ear and eye; ii) magnetic resonance angiography (MRA) data to image the vasculature, and iii) diffusion tensor imaging (DTI) to obtain information on anisotropy and fiber orientation. The unique multimodal high-resolution approach allowed resolving 153 structures, including several distinct muscles, bones and skull layers, arteries and veins, nerves, as well as salivary glands. The model offers also a detailed characterization of eyes, ears, and deep brain structures. A special automatic atlas-based segmentation procedure was adopted to include a detailed map of the nuclei of the thalamus and midbrain into the head model. The suitability of the model to simulations involving different numerical methods, discretization approaches, as well as DTI-based tensorial electrical conductivity, was examined in a case-study, in which the electric field was generated by transcranial alternating current stimulation. The voxel- and the surface-based versions of the models are freely available to the scientific community. PMID:25901747
MIDA: A Multimodal Imaging-Based Detailed Anatomical Model of the Human Head and Neck.
Iacono, Maria Ida; Neufeld, Esra; Akinnagbe, Esther; Bower, Kelsey; Wolf, Johanna; Vogiatzis Oikonomidis, Ioannis; Sharma, Deepika; Lloyd, Bryn; Wilm, Bertram J; Wyss, Michael; Pruessmann, Klaas P; Jakab, Andras; Makris, Nikos; Cohen, Ethan D; Kuster, Niels; Kainz, Wolfgang; Angelone, Leonardo M
2015-01-01
Computational modeling and simulations are increasingly being used to complement experimental testing for analysis of safety and efficacy of medical devices. Multiple voxel- and surface-based whole- and partial-body models have been proposed in the literature, typically with spatial resolution in the range of 1-2 mm and with 10-50 different tissue types resolved. We have developed a multimodal imaging-based detailed anatomical model of the human head and neck, named "MIDA". The model was obtained by integrating three different magnetic resonance imaging (MRI) modalities, the parameters of which were tailored to enhance the signals of specific tissues: i) structural T1- and T2-weighted MRIs; a specific heavily T2-weighted MRI slab with high nerve contrast optimized to enhance the structures of the ear and eye; ii) magnetic resonance angiography (MRA) data to image the vasculature, and iii) diffusion tensor imaging (DTI) to obtain information on anisotropy and fiber orientation. The unique multimodal high-resolution approach allowed resolving 153 structures, including several distinct muscles, bones and skull layers, arteries and veins, nerves, as well as salivary glands. The model offers also a detailed characterization of eyes, ears, and deep brain structures. A special automatic atlas-based segmentation procedure was adopted to include a detailed map of the nuclei of the thalamus and midbrain into the head model. The suitability of the model to simulations involving different numerical methods, discretization approaches, as well as DTI-based tensorial electrical conductivity, was examined in a case-study, in which the electric field was generated by transcranial alternating current stimulation. The voxel- and the surface-based versions of the models are freely available to the scientific community.
Multi-scale model of food drying: Current status and challenges.
Rahman, M M; Joardder, Mohammad U H; Khan, M I H; Pham, Nghia Duc; Karim, M A
2016-09-19
For a long time, food engineers have been trying to describe the physical phenomena that occur during food processing especially drying. Physics-based theoretical modeling is an important tool for the food engineers to reduce the hurdles of experimentation. Drying of food is a multi-physics phenomenon such as coupled heat and mass transfer. Moreover, food structure is multi-scale in nature, and the microstructural features play a great role in the food processing specially in drying. Previously simple macroscopic model was used to describe the drying phenomena which can give a little description about the smaller scale. The multiscale modeling technique can handle all the phenomena that occur during drying. In this special kind of modeling approach, the single scale models from bigger to smaller scales are interconnected. With the help of multiscale modeling framework, the transport process associated with drying can be studied on a smaller scale and the resulting information can be transferred to the bigger scale. This article is devoted to discussing the state of the art multi-scale modeling, its prospect and challenges in the field of drying technology. This article has also given some directions to how to overcome the challenges for successful implementation of multi-scale modeling.
De Jesus, Aribet M; Aghvami, Maziar; Sander, Edward A
2016-01-01
Many cell types remodel the extracellular matrix of the tissues they inhabit in response to a wide range of environmental stimuli, including mechanical cues. Such is the case in dermal wound healing, where fibroblast migrate into and remodel the provisional fibrin matrix in a complex manner that depends in part on the local mechanical environment and the evolving multi-scale mechanical interactions of the system. In this study, we report on the development of an image-based multi-scale mechanical model that predicts the short-term (24 hours), structural reorganization of a fibrin gel by fibroblasts. These predictive models are based on an in vitro experimental system where clusters of fibroblasts (i.e., explants) were spatially arranged into a triangular geometry onto the surface of fibrin gels that were subjected to either Fixed or Free in-plane mechanical constraints. Experimentally, regional differences in short-term structural remodeling and cell migration were observed for the two gel boundary conditions. A pilot experiment indicated that these small differences in the short-term remodeling of the fibrin gel translate into substantial differences in long-term (4 weeks) remodeling, particularly in terms of collagen production. The multi-scale models were able to predict some regional differences in remodeling and qualitatively similar reorganization patterns for the two boundary conditions. However, other aspects of the model, such as the magnitudes and rates of deformation of gel, did not match the experiments. These discrepancies between model and experiment provide fertile ground for challenging model assumptions and devising new experiments to enhance our understanding of how this multi-scale system functions. These efforts will ultimately improve the predictions of the remodeling process, particularly as it relates to dermal wound healing and the reduction of patient scarring. Such models could be used to recommend patient-specific mechanical
2016-01-01
Many cell types remodel the extracellular matrix of the tissues they inhabit in response to a wide range of environmental stimuli, including mechanical cues. Such is the case in dermal wound healing, where fibroblast migrate into and remodel the provisional fibrin matrix in a complex manner that depends in part on the local mechanical environment and the evolving multi-scale mechanical interactions of the system. In this study, we report on the development of an image-based multi-scale mechanical model that predicts the short-term (24 hours), structural reorganization of a fibrin gel by fibroblasts. These predictive models are based on an in vitro experimental system where clusters of fibroblasts (i.e., explants) were spatially arranged into a triangular geometry onto the surface of fibrin gels that were subjected to either Fixed or Free in-plane mechanical constraints. Experimentally, regional differences in short-term structural remodeling and cell migration were observed for the two gel boundary conditions. A pilot experiment indicated that these small differences in the short-term remodeling of the fibrin gel translate into substantial differences in long-term (4 weeks) remodeling, particularly in terms of collagen production. The multi-scale models were able to predict some regional differences in remodeling and qualitatively similar reorganization patterns for the two boundary conditions. However, other aspects of the model, such as the magnitudes and rates of deformation of gel, did not match the experiments. These discrepancies between model and experiment provide fertile ground for challenging model assumptions and devising new experiments to enhance our understanding of how this multi-scale system functions. These efforts will ultimately improve the predictions of the remodeling process, particularly as it relates to dermal wound healing and the reduction of patient scarring. Such models could be used to recommend patient-specific mechanical
Multiscale Model for the Assembly Kinetics of Protein Complexes.
Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao
2016-02-04
The assembly of proteins into high-order complexes is a general mechanism for these biomolecules to implement their versatile functions in cells. Natural evolution has developed various assembling pathways for specific protein complexes to maintain their stability and proper activities. Previous studies have provided numerous examples of the misassembly of protein complexes leading to severe biological consequences. Although the research focusing on protein complexes has started to move beyond the static representation of quaternary structures to the dynamic aspect of their assembly, the current understanding of the assembly mechanism of protein complexes is still largely limited. To tackle this problem, we developed a new multiscale modeling framework. This framework combines a lower-resolution rigid-body-based simulation with a higher-resolution Cα-based simulation method so that protein complexes can be assembled with both structural details and computational efficiency. We applied this model to a homotrimer and a heterotetramer as simple test systems. Consistent with experimental observations, our simulations indicated very different kinetics between protein oligomerization and dimerization. The formation of protein oligomers is a multistep process that is much slower than dimerization but thermodynamically more stable. Moreover, we showed that even the same protein quaternary structure can have very diverse assembly pathways under different binding constants between subunits, which is important for regulating the functions of protein complexes. Finally, we revealed that the binding between subunits in a complex can be synergistically strengthened during assembly without considering allosteric regulation or conformational changes. Therefore, our model provides a useful tool to understand the general principles of protein complex assembly.
A multiscale model of the bone marrow and hematopoiesis
Silva, Ariosto S; Anderson, Alexander R.A.
2013-01-01
The bone marrow is necessary for renewal of all hematopoietic cells and critical for maintenance of a wide range of physiologic functions. Multiple human diseases result from bone marrow dysfunction. It is also the site in which “liquid” tumors, including leukemia and multiple myeloma, develop as well as a frequent site of metastases. Understanding the complex cellular and microenvironmental interactions that govern normal bone marrow function as well as diseases and cancers of the bone marrow would be a valuable medical advance. Our goal is the development of a spatially-explicit in silico model of the bone marrow to understand both its normal function and the evolutionary dynamics that govern the emergence of bone marrow malignancy. Here we introduce a multiscale computational model of the bone marrow that incorporates three distinct spatial scales, cell, hematopoietic subunit, whole marrow. Implemented as a fixed lattice 3D cellular automaton, it reproduces the spatial characteristics of the normal bone marrow and is validated against data from the daily production of mature blood cells and response of hematopoiesis after irradiation. The major mechanisms modeled in this work are: (1) replication, specialization and migration of hematopoietic cells, (2) optimized spatial configuration of sinuses and hematopoietic compartments and, (3) intravasation of mature hematopoietic cells into sinuses. Our results, using parameter estimates from literature, recapitulates normal bone marrow function and suggest an explanation for the fractal-like structure of trabeculae and sinuses in the marrow, which would be an optimization of the hematopoietic function in order to maximize the number of mature blood cells produced daily within the volumetric restrictions of the marrow. PMID:21631151
Jagiella, Nick; Rickert, Dennis; Theis, Fabian J; Hasenauer, Jan
2017-02-22
Mechanistic understanding of multi-scale biological processes, such as cell proliferation in a changing biological tissue, is readily facilitated by computational models. While tools exist to construct and simulate multi-scale models, the statistical inference of the unknown model parameters remains an open problem. Here, we present and benchmark a parallel approximate Bayesian computation sequential Monte Carlo (pABC SMC) algorithm, tailored for high-performance computing clusters. pABC SMC is fully automated and returns reliable parameter estimates and confidence intervals. By running the pABC SMC algorithm for ∼10(6) hr, we parameterize multi-scale models that accurately describe quantitative growth curves and histological data obtained in vivo from individual tumor spheroid growth in media droplets. The models capture the hybrid deterministic-stochastic behaviors of 10(5)-10(6) of cells growing in a 3D dynamically changing nutrient environment. The pABC SMC algorithm reliably converges to a consistent set of parameters. Our study demonstrates a proof of principle for robust, data-driven modeling of multi-scale biological systems and the feasibility of multi-scale model parameterization through statistical inference.
Zhao, Fu; Landis, Heather R; Skerlos, Steven J
2005-01-01
A methodology for producing a pore-scale, 3D computational model of porous filter permeability is developed that is based on the analysis of 2D images of the filter matrix and first principles. The computationally reconstructed porous filter model retains statistical details of porosity and the spatial correlations of porosity within the filter and can be used to calculate permeability for either isotropic or 1D anisotropic porous filters. In the isotropic case, validation of the methodology was conducted using 0.2 and 0.8 microm ceramic membrane filters,forwhich it is shown that the image-based computational models provide a viable statistical reproduction of actual porosity characteristics. It is also shown that these models can predict water flux directly from first principles with deviations from experimental measurements in the range of experimental error. In the anisotropic case, validation of the methodology was conducted using a natural river sand filter. For this case, it is shown that the methodology yields predictions of filtration velocity that are similar or better than predictions offered by existing filtration models. It was found for the sand filter that the deviation between observation and prediction was mostly due to swelling during the preparation of the sand filter for imaging and can be reduced significantly using alternative methods reported in the literature. On the basis of these results, it is concluded that the computational reconstruction methodology is valid for porous filter modeling, and given that it captures pore-scale details, it has potential application to the investigation of permeability decline underthe influence of pore-scale fouling mechanisms.
Sport helmet design and virtual impact test by image-based finite element modeling.
Luo, Yunhua; Liang, Zhaoyang
2013-01-01
Head injury has been a major concern in various sports, especially in contact sports such as football and ice hockey. Helmet has been adopted as a protective device in such sports, aiming at preventing or at least alleviating head injuries. However, there exist two challenges in current helmet design and test. One is that the helmet does not fit the subject's head well; the other is that current helmet testing methods are not able to provide accurate information about intracranial pressure and stress/strain level in brain tissues during impact. To meet the challenges, an image-based finite element modeling procedure was proposed to design subject-specific helmet and to conduct virtual impact test. In the procedure, a set of medical images such as computed tomography (CT) and magnetic resonance image (MRI) of the subject's head was used to construct geometric shape of the helmet and to develop a helmet-head finite element model that can be used in the virtual impact test.
Multiscale modeling and surgical planning for single ventricle heart patients
NASA Astrophysics Data System (ADS)
Marsden, Alison
2011-11-01
Single ventricle heart patients are among the most challenging for pediatric cardiologists to treat, and typically undergo a palliative course of three open-heart surgeries starting immediately after birth. We will present recent tools for modeling blood flow in single ventricle heart patients using a multiscale approach that couples a 3D Navier-Stokes domain to a 0D closed loop lumped parameter network comprised of circuit elements. This coupling allows us to capture the effect of changes in local geometry, such as shunt sizes, on global circulatory dynamics, such as cardiac output. A semi-implicit numerical method is formulated to solve the coupled system in which flow and pressure information is passed between the two domains at the inlets and outlets of the model. A finite element method with outflow stabilization is applied in the 3D Navier-Stokes domain, and the LPN system of ordinary differential equations is solved numerically using a Runge-Kutta method. These tools are coupled via automated scripts to a derivative-free optimization method. Optimization is used to systematically explore surgical designs using clinically relevant cost functions for two stages of single ventricle repair. First, we will present results from optimization of the first stage Blalock Taussig Shunt. Second, we will present results from optimization of a new Y-graft design for the third stage of single ventricle repair called the Fontan surgery. The Y-graft is shown, in simulations, to successfully improve hepatic flow distribution, a known clinical problem. Preliminary clinical experience with the Y-graft will be discussed.
Computational Modeling of Multi-Scale Material Features in Cement Paste - An Overview
2015-05-25
material chemistry level config- uration of hydrated cement paste CSH Jennite structure. 3 MICRO SCALE MODELING The advent of scalable computing ...ABSTRACT 16. SECURITY CLASSIFICATION OF: Computational modeling of complex, heterogeneous, multi-scale features of cement paste requires starting from...that in-fluence the properties and behavior of materials through associated computational , material and mechanistic models. Such modeling starting
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology.
Starruß, Jörn; de Back, Walter; Brusch, Lutz; Deutsch, Andreas
2014-05-01
Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale models in biological terms and mathematical expressions rather than programming code. Its graphical user interface supports the entire workflow from model construction and simulation to visualization, archiving and batch processing.
Research on texture feature of RS image based on cloud model
NASA Astrophysics Data System (ADS)
Wang, Zuocheng; Xue, Lixia
2008-10-01
This paper presents a new method applied to texture feature representation in RS image based on cloud model. Aiming at the fuzziness and randomness of RS image, we introduce the cloud theory into RS image processing in a creative way. The digital characteristics of clouds well integrate the fuzziness and randomness of linguistic terms in a unified way and map the quantitative and qualitative concepts. We adopt texture multi-dimensions cloud to accomplish vagueness and randomness handling of texture feature in RS image. The method has two steps: 1) Correlativity analyzing of texture statistical parameters in Grey Level Co-occurrence Matrix (GLCM) and parameters fuzzification. GLCM can be used to representing the texture feature in many aspects perfectly. According to the expressive force of texture statistical parameters and by Correlativity analyzing of texture statistical parameters, we can abstract a few texture statistical parameters that can best represent the texture feature. By the fuzziness algorithm, the texture statistical parameters can be mapped to fuzzy cloud space. 2) Texture multi-dimensions cloud model constructing. Based on the abstracted texture statistical parameters and fuzziness cloud space, texture multi-dimensions cloud model can be constructed in micro-windows of image. According to the membership of texture statistical parameters, we can achieve the samples of cloud-drop. By backward cloud generator, the digital characteristics of texture multi-dimensions cloud model can be achieved and the Mathematical Expected Hyper Surface(MEHS) of multi-dimensions cloud of micro-windows can be constructed. At last, the weighted sum of the 3 digital characteristics of micro-window cloud model was proposed and used in texture representing in RS image. The method we develop is demonstrated by applying it to texture representing in many RS images, various performance studies testify that the method is both efficient and effective. It enriches the cloud
Full field spatially-variant image-based resolution modelling reconstruction for the HRRT.
Angelis, Georgios I; Kotasidis, Fotis A; Matthews, Julian C; Markiewicz, Pawel J; Lionheart, William R; Reader, Andrew J
2015-03-01
Accurate characterisation of the scanner's point spread function across the entire field of view (FOV) is crucial in order to account for spatially dependent factors that degrade the resolution of the reconstructed images. The HRRT users' community resolution modelling reconstruction software includes a shift-invariant resolution kernel, which leads to transaxially non-uniform resolution in the reconstructed images. Unlike previous work to date in this field, this work is the first to model the spatially variant resolution across the entire FOV of the HRRT, which is the highest resolution human brain PET scanner in the world. In this paper we developed a spatially variant image-based resolution modelling reconstruction dedicated to the HRRT, using an experimentally measured shift-variant resolution kernel. Previously, the system response was measured and characterised in detail across the entire FOV of the HRRT, using a printed point source array. The newly developed resolution modelling reconstruction was applied on measured phantom, as well as clinical data and was compared against the HRRT users' community resolution modelling reconstruction, which is currently in use. Results demonstrated improvements both in contrast and resolution recovery, particularly for regions close to the edges of the FOV, with almost uniform resolution recovery across the entire transverse FOV. In addition, because the newly measured resolution kernel is slightly broader with wider tails, compared to the deliberately conservative kernel employed in the HRRT users' community software, the reconstructed images appear to have not only improved contrast recovery (up to 20% for small regions), but also better noise characteristics.
NASA Astrophysics Data System (ADS)
Bhattacharjee, Satyaki; Matouš, Karel
2016-05-01
A new manifold-based reduced order model for nonlinear problems in multiscale modeling of heterogeneous hyperelastic materials is presented. The model relies on a global geometric framework for nonlinear dimensionality reduction (Isomap), and the macroscopic loading parameters are linked to the reduced space using a Neural Network. The proposed model provides both homogenization and localization of the multiscale solution in the context of computational homogenization. To construct the manifold, we perform a number of large three-dimensional simulations of a statistically representative unit cell using a parallel finite strain finite element solver. The manifold-based reduced order model is verified using common principles from the machine-learning community. Both homogenization and localization of the multiscale solution are demonstrated on a large three-dimensional example and the local microscopic fields as well as the homogenized macroscopic potential are obtained with acceptable engineering accuracy.
Multiscale Multiphysics and Multidomain Models I: Basic Theory
Wei, Guo-Wei
2013-01-01
This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long
Multiscale Multiphysics and Multidomain Models I: Basic Theory.
Wei, Guo-Wei
2013-12-01
This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long
Kirschner, Denise E; Hunt, C Anthony; Marino, Simeone; Fallahi-Sichani, Mohammad; Linderman, Jennifer J
2014-01-01
The use of multi-scale mathematical and computational models to study complex biological processes is becoming increasingly productive. Multi-scale models span a range of spatial and/or temporal scales and can encompass multi-compartment (e.g., multi-organ) models. Modeling advances are enabling virtual experiments to explore and answer questions that are problematic to address in the wet-lab. Wet-lab experimental technologies now allow scientists to observe, measure, record, and analyze experiments focusing on different system aspects at a variety of biological scales. We need the technical ability to mirror that same flexibility in virtual experiments using multi-scale models. Here we present a new approach, tuneable resolution, which can begin providing that flexibility. Tuneable resolution involves fine- or coarse-graining existing multi-scale models at the user's discretion, allowing adjustment of the level of resolution specific to a question, an experiment, or a scale of interest. Tuneable resolution expands options for revising and validating mechanistic multi-scale models, can extend the longevity of multi-scale models, and may increase computational efficiency. The tuneable resolution approach can be applied to many model types, including differential equation, agent-based, and hybrid models. We demonstrate our tuneable resolution ideas with examples relevant to infectious disease modeling, illustrating key principles at work. WIREs Syst Biol Med 2014, 6:225–245. doi:10.1002/wsbm.1270 How to cite this article: WIREs Syst Biol Med 2014, 6:289–309. doi:10.1002/wsbm.1270 PMID:24810243
Multi-scale modelling of rubber-like materials and soft tissues: an appraisal
Puglisi, G.
2016-01-01
We survey, in a partial way, multi-scale approaches for the modelling of rubber-like and soft tissues and compare them with classical macroscopic phenomenological models. Our aim is to show how it is possible to obtain practical mathematical models for the mechanical behaviour of these materials incorporating mesoscopic (network scale) information. Multi-scale approaches are crucial for the theoretical comprehension and prediction of the complex mechanical response of these materials. Moreover, such models are fundamental in the perspective of the design, through manipulation at the micro- and nano-scales, of new polymeric and bioinspired materials with exceptional macroscopic properties. PMID:27118927
Radiation induced genome instability: multiscale modelling and data analysis
NASA Astrophysics Data System (ADS)
Andreev, Sergey; Eidelman, Yuri
2012-07-01
Genome instability (GI) is thought to be an important step in cancer induction and progression. Radiation induced GI is usually defined as genome alterations in the progeny of irradiated cells. The aim of this report is to demonstrate an opportunity for integrative analysis of radiation induced GI on the basis of multiscale modelling. Integrative, systems level modelling is necessary to assess different pathways resulting in GI in which a variety of genetic and epigenetic processes are involved. The multilevel modelling includes the Monte Carlo based simulation of several key processes involved in GI: DNA double strand breaks (DSBs) generation in cells initially irradiated as well as in descendants of irradiated cells, damage transmission through mitosis. Taking the cell-cycle-dependent generation of DNA/chromosome breakage into account ensures an advantage in estimating the contribution of different DNA damage response pathways to GI, as to nonhomologous vs homologous recombination repair mechanisms, the role of DSBs at telomeres or interstitial chromosomal sites, etc. The preliminary estimates show that both telomeric and non-telomeric DSB interactions are involved in delayed effects of radiation although differentially for different cell types. The computational experiments provide the data on the wide spectrum of GI endpoints (dicentrics, micronuclei, nonclonal translocations, chromatid exchanges, chromosome fragments) similar to those obtained experimentally for various cell lines under various experimental conditions. The modelling based analysis of experimental data demonstrates that radiation induced GI may be viewed as processes of delayed DSB induction/interaction/transmission being a key for quantification of GI. On the other hand, this conclusion is not sufficient to understand GI as a whole because factors of DNA non-damaging origin can also induce GI. Additionally, new data on induced pluripotent stem cells reveal that GI is acquired in normal mature
Jiang, Lijian Li, Xinping
2015-08-01
Stochastic multiscale modeling has become a necessary approach to quantify uncertainty and characterize multiscale phenomena for many practical problems such as flows in stochastic porous media. The numerical treatment of the stochastic multiscale models can be very challengeable as the existence of complex uncertainty and multiple physical scales in the models. To efficiently take care of the difficulty, we construct a computational reduced model. To this end, we propose a multi-element least square high-dimensional model representation (HDMR) method, through which the random domain is adaptively decomposed into a few subdomains, and a local least square HDMR is constructed in each subdomain. These local HDMRs are represented by a finite number of orthogonal basis functions defined in low-dimensional random spaces. The coefficients in the local HDMRs are determined using least square methods. We paste all the local HDMR approximations together to form a global HDMR approximation. To further reduce computational cost, we present a multi-element reduced least-square HDMR, which improves both efficiency and approximation accuracy in certain conditions. To effectively treat heterogeneity properties and multiscale features in the models, we integrate multiscale finite element methods with multi-element least-square HDMR for stochastic multiscale model reduction. This approach significantly reduces the original model's complexity in both the resolution of the physical space and the high-dimensional stochastic space. We analyze the proposed approach, and provide a set of numerical experiments to demonstrate the performance of the presented model reduction techniques. - Highlights: • Multi-element least square HDMR is proposed to treat stochastic models. • Random domain is adaptively decomposed into some subdomains to obtain adaptive multi-element HDMR. • Least-square reduced HDMR is proposed to enhance computation efficiency and approximation accuracy in certain
Intercomparison of Multiscale Modeling Approaches in Simulating Subsurface Flow and Transport
NASA Astrophysics Data System (ADS)
Yang, X.; Mehmani, Y.; Barajas-Solano, D. A.; Song, H. S.; Balhoff, M.; Tartakovsky, A. M.; Scheibe, T. D.
2016-12-01
Hybrid multiscale simulations that couple models across scales are critical to advance predictions of the larger system behavior using understanding of fundamental processes. In the current study, three hybrid multiscale methods are intercompared: multiscale loose-coupling method, multiscale finite volume (MsFV) method and multiscale mortar method. The loose-coupling method enables a parallel workflow structure based on the Swift scripting environment that manages the complex process of executing coupled micro- and macro-scale models without being intrusive to the at-scale simulators. The MsFV method applies microscale and macroscale models over overlapping subdomains of the modeling domain and enforces continuity of concentration and transport fluxes between models via restriction and prolongation operators. The mortar method is a non-overlapping domain decomposition approach capable of coupling all permutations of pore- and continuum-scale models with each other. In doing so, Lagrange multipliers are used at interfaces shared between the subdomains so as to establish continuity of species/fluid mass flux. Subdomain computations can be performed either concurrently or non-concurrently depending on the algorithm used. All the above methods have been proven to be accurate and efficient in studying flow and transport in porous media. However, there has not been any field-scale applications and benchmarking among various hybrid multiscale approaches. To address this challenge, we apply all three hybrid multiscale methods to simulate water flow and transport in a conceptualized 2D modeling domain of the hyporheic zone, where strong interactions between groundwater and surface water exist across multiple scales. In all three multiscale methods, fine-scale simulations are applied to a thin layer of riverbed alluvial sediments while the macroscopic simulations are used for the larger subsurface aquifer domain. Different numerical coupling methods are then applied between
Hybrid continuum-molecular modelling of multiscale internal gas flows
NASA Astrophysics Data System (ADS)
Patronis, Alexander; Lockerby, Duncan A.; Borg, Matthew K.; Reese, Jason M.
2013-12-01
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.
Multiscale Modeling of Chemistry in Water: Are We There Yet?
Bulo, Rosa E; Michel, Carine; Fleurat-Lessard, Paul; Sautet, Philippe
2013-12-10
This paper critically evaluates the state of the art in combined quantum mechanical/molecular mechanical (QM/MM) approaches to the computational description of chemistry in water and supplies guidelines for the setup of customized multiscale simulations of aqueous processes. We differentiate between structural and dynamic performance, since some tasks, e.g., the reproduction of NMR or UV-vis spectra, require only structural accuracy, while others, i.e., reaction mechanisms, require accurate dynamic data as well. As a model system for aqueous solutions in general, the approaches were tested on a QM water cluster in an environment of MM water molecules. The key difficulty is the description of the possible diffusion of QM molecules into the MM region and vice versa. The flexible inner region ensemble separator (FIRES) approach constrains QM solvent molecules within an active (QM) region. Sorted adaptive partitioning (SAP), difference-based adaptive solvation (DAS), and buffered-force (BF) are all adaptive approaches that use a buffer zone in which solvent molecules gradually adapt from QM to MM (or vice versa). The costs of SAP and DAS are relatively high, while BF is fast but sacrifices conservation of both energy and momentum. Simulations in the limit of an infinitely small buffer zone, where DAS and SAP become equivalent, are discussed as well and referred to as ABRUPT. The best structural accuracy is obtained with DAS, BF, and ABRUPT, all three of similar quality. FIRES performs very well for dynamic properties localized deep within the QM region. By means of elimination DAS emerges as the best overall compromise between structural and dynamic performance. Eliminating the buffer zone (ABRUPT) improves efficiency and still leads to surprisingly good results. While none of the many new flavors are perfect, all together this new field already allows accurate description of a wide range of structural and dynamic properties of aqueous solutions.
Modular-based multiscale modeling on viscoelasticity of polymer nanocomposites
NASA Astrophysics Data System (ADS)
Li, Ying; Liu, Zeliang; Jia, Zheng; Liu, Wing Kam; Aldousari, Saad M.; Hedia, Hassan S.; Asiri, Saeed A.
2016-10-01
Polymer nanocomposites have been envisioned as advanced materials for improving the mechanical performance of neat polymers used in aerospace, petrochemical, environment and energy industries. With the filler size approaching the nanoscale, composite materials tend to demonstrate remarkable thermomechanical properties, even with addition of a small amount of fillers. These observations confront the classical composite theories and are usually attributed to the high surface-area-to-volume-ratio of the fillers, which can introduce strong nanoscale interfacial effect and relevant long-range perturbation on polymer chain dynamics. Despite decades of research aimed at understanding interfacial effect and improving the mechanical performance of composite materials, it is not currently possible to accurately predict the mechanical properties of polymer nanocomposites directly from their molecular constituents. To overcome this challenge, different theoretical, experimental and computational schemes will be used to uncover the key physical mechanisms at the relevant spatial and temporal scales for predicting and tuning constitutive behaviors in silico, thereby establishing a bottom-up virtual design principle to achieve unprecedented mechanical performance of nanocomposites. A modular-based multiscale modeling approach for viscoelasticity of polymer nanocomposites has been proposed and discussed in this study, including four modules: (A) neat polymer toolbox; (B) interphase toolbox; (C) microstructural toolbox and (D) homogenization toolbox. Integrating these modules together, macroscopic viscoelasticity of polymer nanocomposites could be directly predicted from their molecular constituents. This will maximize the computational ability to design novel polymer composites with advanced performance. More importantly, elucidating the viscoelasticity of polymer nanocomposites through fundamental studies is a critical step to generate an integrated computational material
Modular-based multiscale modeling on viscoelasticity of polymer nanocomposites
NASA Astrophysics Data System (ADS)
Li, Ying; Liu, Zeliang; Jia, Zheng; Liu, Wing Kam; Aldousari, Saad M.; Hedia, Hassan S.; Asiri, Saeed A.
2017-02-01
Polymer nanocomposites have been envisioned as advanced materials for improving the mechanical performance of neat polymers used in aerospace, petrochemical, environment and energy industries. With the filler size approaching the nanoscale, composite materials tend to demonstrate remarkable thermomechanical properties, even with addition of a small amount of fillers. These observations confront the classical composite theories and are usually attributed to the high surface-area-to-volume-ratio of the fillers, which can introduce strong nanoscale interfacial effect and relevant long-range perturbation on polymer chain dynamics. Despite decades of research aimed at understanding interfacial effect and improving the mechanical performance of composite materials, it is not currently possible to accurately predict the mechanical properties of polymer nanocomposites directly from their molecular constituents. To overcome this challenge, different theoretical, experimental and computational schemes will be used to uncover the key physical mechanisms at the relevant spatial and temporal scales for predicting and tuning constitutive behaviors in silico, thereby establishing a bottom-up virtual design principle to achieve unprecedented mechanical performance of nanocomposites. A modular-based multiscale modeling approach for viscoelasticity of polymer nanocomposites has been proposed and discussed in this study, including four modules: (A) neat polymer toolbox; (B) interphase toolbox; (C) microstructural toolbox and (D) homogenization toolbox. Integrating these modules together, macroscopic viscoelasticity of polymer nanocomposites could be directly predicted from their molecular constituents. This will maximize the computational ability to design novel polymer composites with advanced performance. More importantly, elucidating the viscoelasticity of polymer nanocomposites through fundamental studies is a critical step to generate an integrated computational material
Multiscale modeling of crack initiation and propagation at the nanoscale
NASA Astrophysics Data System (ADS)
Shiari, Behrouz; Miller, Ronald E.
2016-03-01
Fracture occurs on multiple interacting length scales; atoms separate on the atomic scale while plasticity develops on the microscale. A dynamic multiscale approach (CADD: coupled atomistics and discrete dislocations) is employed to investigate an edge-cracked specimen of single-crystal nickel, Ni, (brittle failure) and aluminum, Al, (ductile failure) subjected to mode-I loading. The dynamic model couples continuum finite elements to a fully atomistic region, with key advantages such as the ability to accommodate discrete dislocations in the continuum region and an algorithm for automatically detecting dislocations as they move from the atomistic region to the continuum region and then correctly "converting" the atomistic dislocations into discrete dislocations, or vice-versa. An ad hoc computational technique is also applied to dissipate localized waves formed during crack advance in the atomistic zone, whereby an embedded damping zone at the atomistic/continuum interface effectively eliminates the spurious reflection of high-frequency phonons, while allowing low-frequency phonons to pass into the continuum region. The simulations accurately capture the essential physics of the crack propagation in a Ni specimen at different temperatures, including the formation of nano-voids and the sudden acceleration of the crack tip to a velocity close to the material Rayleigh wave speed. The nanoscale brittle fracture happens through the crack growth in the form of nano-void nucleation, growth and coalescence ahead of the crack tip, and as such resembles fracture at the microscale. When the crack tip behaves in a ductile manner, the crack does not advance rapidly after the pre-opening process but is blunted by dislocation generation from its tip. The effect of temperature on crack speed is found to be perceptible in both ductile and brittle specimens.
A neotropical Miocene pollen database employing image-based search and semantic modeling1
Han, Jing Ginger; Cao, Hongfei; Barb, Adrian; Punyasena, Surangi W.; Jaramillo, Carlos; Shyu, Chi-Ren
2014-01-01
• Premise of the study: Digital microscopic pollen images are being generated with increasing speed and volume, producing opportunities to develop new computational methods that increase the consistency and efficiency of pollen analysis and provide the palynological community a computational framework for information sharing and knowledge transfer. • Methods: Mathematical methods were used to assign trait semantics (abstract morphological representations) of the images of neotropical Miocene pollen and spores. Advanced database-indexing structures were built to compare and retrieve similar images based on their visual content. A Web-based system was developed to provide novel tools for automatic trait semantic annotation and image retrieval by trait semantics and visual content. • Results: Mathematical models that map visual features to trait semantics can be used to annotate images with morphology semantics and to search image databases with improved reliability and productivity. Images can also be searched by visual content, providing users with customized emphases on traits such as color, shape, and texture. • Discussion: Content- and semantic-based image searches provide a powerful computational platform for pollen and spore identification. The infrastructure outlined provides a framework for building a community-wide palynological resource, streamlining the process of manual identification, analysis, and species discovery. PMID:25202648
NASA Technical Reports Server (NTRS)
Hadden, C. M.; Klimek-McDonald, D. R.; Pineda, E. J.; King, J. A.; Reichanadter, A. M.; Miskioglu, I.; Gowtham, S.; Odegard, G. M.
2015-01-01
Because of the relatively high specific mechanical properties of carbon fiber/epoxy composite materials, they are often used as structural components in aerospace applications. Graphene nanoplatelets (GNPs) can be added to the epoxy matrix to improve the overall mechanical properties of the composite. The resulting GNP/carbon fiber/epoxy hybrid composites have been studied using multiscale modeling to determine the influence of GNP volume fraction, epoxy crosslink density, and GNP dispersion on the mechanical performance. The hierarchical multiscale modeling approach developed herein includes Molecular Dynamics (MD) and micromechanical modeling, and it is validated with experimental testing of the same hybrid composite material system. The results indicate that the multiscale modeling approach is accurate and provides physical insight into the composite mechanical behavior. Also, the results quantify the substantial impact of GNP volume fraction and dispersion on the transverse mechanical properties of the hybrid composite while the effect on the axial properties is shown to be insignificant.
NASA Technical Reports Server (NTRS)
Hadden, C. M.; Klimek-McDonald, D. R.; Pineda, E. J.; King, J. A.; Reichanadter, A. M.; Miskioglu, I.; Gowtham, S.; Odegard, G. M.
2015-01-01
Because of the relatively high specific mechanical properties of carbon fiber/epoxy composite materials, they are often used as structural components in aerospace applications. Graphene nanoplatelets (GNPs) can be added to the epoxy matrix to improve the overall mechanical properties of the composite. The resulting GNP/carbon fiber/epoxy hybrid composites have been studied using multiscale modeling to determine the influence of GNP volume fraction, epoxy crosslink density, and GNP dispersion on the mechanical performance. The hierarchical multiscale modeling approach developed herein includes Molecular Dynamics (MD) and micromechanical modeling, and it is validated with experimental testing of the same hybrid composite material system. The results indicate that the multiscale modeling approach is accurate and provides physical insight into the composite mechanical behavior. Also, the results quantify the substantial impact of GNP volume fraction and dispersion on the transverse mechanical properties of the hybrid composite, while the effect on the axial properties is shown to be insignificant.
NASA Technical Reports Server (NTRS)
Hadden, Cameron M.; Klimek-McDonald, Danielle R.; Pineda, Evan J.; King, Julie A.; Reichanadter, Alex M.; Miskioglu, Ibrahim; Gowtham, S.; Odegard, Gregory M.
2015-01-01
Because of the relatively high specific mechanical properties of carbon fiber/epoxy composite materials, they are often used as structural components in aerospace applications. Graphene nanoplatelets (GNPs) can be added to the epoxy matrix to improve the overall mechanical properties of the composite. The resulting GNP/carbon fiber/epoxy hybrid composites have been studied using multiscale modeling to determine the influence of GNP volume fraction, epoxy crosslink density, and GNP dispersion on the mechanical performance. The hierarchical multiscale modeling approach developed herein includes Molecular Dynamics (MD) and micromechanical modeling, and it is validated with experimental testing of the same hybrid composite material system. The results indicate that the multiscale modeling approach is accurate and provides physical insight into the composite mechanical behavior. Also, the results quantify the substantial impact of GNP volume fraction and dispersion on the transverse mechanical properties of the hybrid composite, while the effect on the axial properties is shown to be insignificant.
Bottom-up model of adsorption and transport in multiscale porous media.
Boţan, Alexandru; Ulm, Franz-Josef; Pellenq, Roland J-M; Coasne, Benoit
2015-03-01
We develop a model of transport in multiscale porous media which accounts for adsorption in the different porosity scales. This model employs statistical mechanics to upscale molecular simulation and describe adsorption and transport at larger time and length scales. Using atom-scale simulations, which capture the changes in adsorption and transport with temperature, pressure, pore size, etc., this approach does not assume any adsorption or flow type. Moreover, by relating the local chemical potential μ(r) and density ρ(r), the present model accounts for adsorption effects and possible changes in the confined fluid state upon transport. This model constitutes a bottom-up framework of adsorption and transport in multiscale materials as it (1) describes the adsorption-transport interplay, (2) accounts for the hydrodynamics breakdown at the nm scale, and (3) is multiscale.
A multiscale modeling study for the convective mass transfer in a subsurface aquifer
NASA Astrophysics Data System (ADS)
Alam, Jahrul M.
2015-09-01
Quantitative and realistic computer simulations of mass transfer associated with disposal in subsurface aquifers is a challenging endeavor. This article has proposed a novel and efficient multiscale modeling framework, and has examined its potential to study the penetrative mass transfer in a plume that migrates in an aquifer. Numerical simulations indicate that the migration of the injected enhances the vorticity generation, and the dissolution of has a strong effect on the natural convection mass transfer. The vorticity decays with the increase of the porosity. The time scale of the vertical migration of a plume is strongly dependent on the rate of dissolution. Comparisons confirm the near optimal performance of the proposed multiscale model. These primary results with an idealized computational model of the migration in an aquifer brings the potential of the proposed multiscale model to the field of heat and mass transfer in the geoscience.
Using Multi-Scale Modeling Systems and Satellite Data to Study the Precipitation Processes
NASA Technical Reports Server (NTRS)
Tao, Wei--Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.
2010-01-01
In recent years, exponentially increasing computer power extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 sq km in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale models can be run in grid size similar to cloud resolving models through nesting technique. 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, W8F). (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 results from using multi-scale modeling systems to study the interactions between clouds, precipitation, and aerosols will be presented. Also how to use the multi-satellite simulator to improve precipitation processes will be discussed.
Microphysics in the Multi-Scale Modeling Systems with Unified Physics
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.
2011-01-01
In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (l) 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-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, the microphysics developments of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the heavy precipitation processes will be presented.
Using Multi-Scale Modeling Systems to Study the Precipitation Processes
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo
2010-01-01
In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. 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 results from using multi-scale modeling system to study the interactions between clouds, precipitation, and aerosols will be presented. Also how to use of the multi-satellite simulator to improve precipitation processes will be discussed.
Using Multi-Scale Modeling Systems to Study the Precipitation Processes
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo
2010-01-01
In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. 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 results from using multi-scale modeling system to study the interactions between clouds, precipitation, and aerosols will be presented. Also how to use of the multi-satellite simulator to improve precipitation processes will be discussed.
Using Multi-Scale Modeling Systems and Satellite Data to Study the Precipitation Processes
NASA Technical Reports Server (NTRS)
Tao, Wei--Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.
2010-01-01
In recent years, exponentially increasing computer power extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 sq km in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale models can be run in grid size similar to cloud resolving models through nesting technique. 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, W8F). (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 results from using multi-scale modeling systems to study the interactions between clouds, precipitation, and aerosols will be presented. Also how to use the multi-satellite simulator to improve precipitation processes will be discussed.
NASA Astrophysics Data System (ADS)
Fwu, Peter Tramyeon
The medical image is very complex by its nature. Modeling built upon the medical image is challenging due to the lack of analytical solution. Finite element method (FEM) is a numerical technique which can be used to solve the partial differential equations. It utilized the transformation from a continuous domain into solvable discrete sub-domains. In three-dimensional space, FEM has the capability dealing with complicated structure and heterogeneous interior. That makes FEM an ideal tool to approach the medical-image based modeling problems. In this study, I will address the three modeling in (1) photon transport inside the human breast by implanting the radiative transfer equation to simulate the diffuse optical spectroscopy imaging (DOSI) in order to measurement the percent density (PD), which has been proven as a cancer risk factor in mammography. Our goal is to use MRI as the ground truth to optimize the DOSI scanning protocol to get a consistent measurement of PD. Our result shows DOSI measurement is position and depth dependent and proper scanning scheme and body configuration are needed; (2) heat flow in the prostate by implementing the Penne's bioheat equation to evaluate the cooling performance of regional hypothermia during the robot assisted radical prostatectomy for the individual patient in order to achieve the optimal cooling setting. Four factors are taken into account during the simulation: blood abundance, artery perfusion, cooling balloon temperature, and the anatomical distance. The result shows that blood abundance, prostate size, and anatomical distance are significant factors to the equilibrium temperature of neurovascular bundle; (3) shape analysis in hippocampus by using the radial distance mapping, and two registration methods to find the correlation between sub-regional change to the age and cognition performance, which might not reveal in the volumetric analysis. The result gives a fundamental knowledge of normal distribution in young
NASA Technical Reports Server (NTRS)
Glaessgen, Edward H.; Saether, Erik; Phillips, Dawn R.; Yamakov, Vesselin
2006-01-01
A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.
Evaluation of the Community Multiscale Air Quality model version 5.1
The Community Multiscale Air Quality model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Atmospheric Modeling and Analysis Division (AMAD) of the U.S. Environment...
The Community Multiscale Air Quality (CMAQ) model is a comprehensive multipollutant air quality modeling system developed and maintained by the US Environmental Protection Agency's (EPA) Office of Research and Development (ORD). Recently, version 5.1 of the CMAQ model (v5.1) was ...
Overview and Evaluation of the Community Multiscale Air Quality (CMAQ) Modeling System Version 5.2
A new version of the Community Multiscale Air Quality (CMAQ) model, version 5.2 (CMAQv5.2), is currently being developed, with a planned release date in 2017. The new model includes numerous updates from the previous version of the model (CMAQv5.1). Specific updates include a new...
Evaluation of the Community Multiscale Air Quality model version 5.1
The Community Multiscale Air Quality model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Atmospheric Modeling and Analysis Division (AMAD) of the U.S. Environment...
Quasi-3D Algorithm in Multi-scale Modeling Framework
NASA Astrophysics Data System (ADS)
Jung, J.; Arakawa, A.
2008-12-01
As discussed in the companion paper by Arakawa and Jung, the Quasi-3D (Q3D) Multi-scale Modeling Framework (MMF) is a 4D estimation/prediction framework that combines a GCM with a 3D anelastic vector vorticity equation model (VVM) applied to a Q3D network of horizontal grid points. This paper presents an outline of the recently revised Q3D algorithm and a highlight of the results obtained by application of the algorithm to an idealized model setting. The Q3D network of grid points consists of two sets of grid-point arrays perpendicular to each other. For a scalar variable, for example, each set consists of three parallel rows of grid points. Principal and supplementary predictions are made on the central and the two adjacent rows, respectively. The supplementary prediction is to allow the principal prediction be three-dimensional at least to the second-order accuracy. To accommodate a higher-order accuracy and to make the supplementary predictions formally three-dimensional, a few rows of ghost points are added at each side of the array. Values at these ghost points are diagnostically determined by a combination of statistical estimation and extrapolation. The basic structure of the estimation algorithm is determined in view of the global stability of Q3D advection. The algorithm is calibrated using the statistics of past data at and near the intersections of the two sets of grid- point arrays. Since the CRM in the Q3D MMF extends beyond individual GCM boxes, the CRM can be a GCM by itself. However, it is better to couple the CRM with the GCM because (1) the CRM is a Q3D CRM based on a highly anisotropic network of grid points and (2) coupling with a GCM makes it more straightforward to inherit our experience with the conventional GCMs. In the coupled system we have selected, prediction of thermdynamic variables is almost entirely done by the Q3D CRM with no direct forcing by the GCM. The coupling of the dynamics between the two components is through mutual
Multi-scale modelling of submarine landslide-generated tsunamis
NASA Astrophysics Data System (ADS)
Hill, J.; Piggott, M. D.; Collins, G. S.; Smith, R. C.; Allison, P. A.
2013-12-01
Submarine landslides can be far larger than terrestrial landslides and many generate destructive tsunamis. The Storegga Slide, offshore Norway, covers an area larger than Scotland and contains 3,000 km3 of material (enough to cover Scotland to a depth of 80 m). This huge slide occurred at 8.2 ka and extends for 800 km down slope. It produced a tsunami with >20 m run-up around the Norwegian Sea, including the Shetlands, and run-ups were typically 3-4 m along the mainland coast of Scotland. The tsunami propagated as far as East Greenland. Northern Europe faces few, if any, other natural hazards that could cause damage on the scale of a repeat Storegga Slide tsunami. Modelling such vast natural disasters is not straightforward. In order to achieve accurate run-up, high resolution is required near the coastlines, but entire oceans must be modelled to account for the vast distances travelled by the wave. Here, we use the open-source, three-dimensional CFD model, Fluidity, to simulate the Storegga landslide-generated tsunami. Fluidity's unstructured meshing allows resolution to vary by orders of magnitude within a single numerical simulation. We present results from multi-scale simulations that capture fine-scale coastal details and at the same time cover a domain spanning the Arctic ocean to capture run-ups on the East Greenland coast. We also compare the effects of modern vs palaeo-bathymetry, which has been neglected in previous numerical modelling studies. Future work will include assessing other potential landslide sites and how landslide dynamics affect the resulting tsunami wave to be used in hazard assessment for Northern Europe. Close-up of the computational mesh around the UK coast, western Norway and as far east as Iceland. The shift in resolution from 750m at the coast to over 20km in open water is clearly visible. Note the high resolution area to the top left which is the Storegga Landslide region.
Modeling and simulation of high dimensional stochastic multiscale PDE systems at the exascale
Zabaras, Nicolas J.
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.
Multiscale Modeling of Damage Processes in fcc Aluminum: From Atoms to Grains
NASA Technical Reports Server (NTRS)
Glaessgen, E. H.; Saether, E.; Yamakov, V.
2008-01-01
Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, current analysis is limited to small domains and increasing the size of the MD domain quickly presents intractable computational demands. A preferred approach to surmount this computational limitation has been to combine continuum mechanics-based modeling procedures, such as the finite element method (FEM), with MD analyses thereby reducing the region of atomic scale refinement. Such multiscale modeling strategies can be divided into two broad classifications: concurrent multiscale methods that directly incorporate an atomistic domain within a continuum domain and sequential multiscale methods that extract an averaged response from the atomistic simulation for later use as a constitutive model in a continuum analysis.
WE-E-17A-01: Characterization of An Imaging-Based Model of Tumor Angiogenesis
Adhikarla, V; Jeraj, R
2014-06-15
Purpose: Understanding the transient dynamics of tumor oxygenation is important when evaluating tumor-vasculature response to anti-angiogenic therapies. An imaging-based tumor-vasculature model was used to elucidate factors that affect these dynamics. Methods: Tumor growth depends on its doubling time (Td). Hypoxia increases pro-angiogenic factor (VEGF) concentration which is modeled to reduce vessel perfusion, attributing to its effect of increasing vascular permeability. Perfused vessel recruitment depends on the existing perfused vasculature, VEGF concentration and maximum VEGF concentration (VEGFmax) for vessel dysfunction. A convolution-based algorithm couples the tumor to the normal tissue vessel density (VD-nt). The parameters are benchmarked to published pre-clinical data and a sensitivity study evaluating the changes in the peak and time to peak tumor oxygenation characterizes them. The model is used to simulate changes in hypoxia and proliferation PET imaging data obtained using [Cu- 61]Cu-ATSM and [F-18]FLT respectively. Results: Td and VD-nt were found to be the most influential on peak tumor pO2 while VEGFmax was marginally influential. A +20 % change in Td, VD-nt and VEGFmax resulted in +50%, +25% and +5% increase in peak pO2. In contrast, Td was the most influential on the time to peak oxygenation with VD-nt and VEGFmax playing marginal roles. A +20% change in Td, VD-nt and VEGFmax increased the time to peak pO2 by +50%, +5% and +0%. A −20% change in the above parameters resulted in comparable decreases in the peak and time to peak pO2. Model application to the PET data was able to demonstrate the voxel-specific changes in hypoxia of the imaged tumor. Conclusion: Tumor-specific doubling time and vessel density are important parameters to be considered when evaluating hypoxia transients. While the current model simulates the oxygen dynamics of an untreated tumor, incorporation of therapeutic effects can make the model a potent tool for analyzing
Multiscale modelling of nanomechanics and micromechanics: an overview
NASA Astrophysics Data System (ADS)
Ghoniem, Nasr M.; Busso, Esteban P.; Kioussis, Nicholas; Huang, Hanchen
2003-11-01
Recent advances in analytical and computational modelling frameworks to describe the mechanics of materials on scales ranging from the atomistic, through the microstructure or transitional, and up to the continuum are reviewed. It is shown that multiscale modelling of materials approaches relies on a systematic reduction in the degrees of freedom on the natural length scales that can be identified in the material. Connections between such scales are currently achieved either by a parametrization or by a 'zoom-out' or 'coarse-graining' procedure. Issues related to the links between the atomistic scale, nanoscale, microscale and macroscale are discussed, and the parameters required for the information to be transferred between one scale and an upper scale are identified. It is also shown that seamless coupling between length scales has not yet been achieved as a result of two main challenges: firstly, the computational complexity of seamlessly coupled simulations via the coarse-graining approach and, secondly, the inherent difficulty in dealing with system evolution stemming from time scaling, which does not permit coarse graining over temporal events. Starting from the Born-Oppenheimer adiabatic approximation, the problem of solving quantum mechanics equations of motion is first reviewed, with successful applications in the mechanics of nanosystems. Atomic simulation methods (e.g. molecular dynamics, Langevin dynamics and the kinetic Monte Carlo method) and their applications at the nanoscale are then discussed. The role played by dislocation dynamics and statistical mechanics methods in understanding microstructure self-organization, heterogeneous plastic deformation, material instabilities and failure phenomena is also discussed. Finally, we review the main continuum-mechanics-based framework used today to describe the nonlinear deformation behaviour of materials at the local (e.g. single phase or grain level) and macroscopic (e.g. polycrystal) scales. Emphasis is
Multiscale multiphysics and multidomain models--flexibility and rigidity.
Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei
2013-11-21
The emerging complexity of large macromolecules has led to challenges in their full scale theoretical description and computer simulation. Multiscale multiphysics and multidomain models have been introduced to reduce the number of degrees of freedom while maintaining modeling accuracy and achieving computational efficiency. A total energy functional is constructed to put energies for polar and nonpolar solvation, chemical potential, fluid flow, molecular mechanics, and elastic dynamics on an equal footing. The variational principle is utilized to derive coupled governing equations for the above mentioned multiphysical descriptions. Among these governing equations is the Poisson-Boltzmann equation which describes continuum electrostatics with atomic charges. The present work introduces the theory of continuum elasticity with atomic rigidity (CEWAR). The essence of CEWAR is to formulate the shear modulus as a continuous function of atomic rigidity. As a result, the dynamics complexity of a macromolecular system is separated from its static complexity so that the more time-consuming dynamics is handled with continuum elasticity theory, while the less time-consuming static analysis is pursued with atomic approaches. We propose a simple method, flexibility-rigidity index (FRI), to analyze macromolecular flexibility and rigidity in atomic detail. The construction of FRI relies on the fundamental assumption that protein functions, such as flexibility, rigidity, and energy, are entirely determined by the structure of the protein and its environment, although the structure is in turn determined by all the interactions. As such, the FRI measures the topological connectivity of protein atoms or residues and characterizes the geometric compactness of the protein structure. As a consequence, the FRI does not resort to the interaction Hamiltonian and bypasses matrix diagonalization, which underpins most other flexibility analysis methods. FRI's computational complexity is of O
Towards Personalized Cardiology: Multi-Scale Modeling of the Failing Heart
Amr, Ali; Neumann, Dominik; Georgescu, Bogdan; Seegerer, Philipp; Kamen, Ali; Haas, Jan; Frese, Karen S.; Irawati, Maria; Wirsz, Emil; King, Vanessa; Buss, Sebastian; Mereles, Derliz; Zitron, Edgar; Keller, Andreas; Katus, Hugo A.; Comaniciu, Dorin; Meder, Benjamin
2015-01-01
Background Despite modern pharmacotherapy and advanced implantable cardiac devices, overall prognosis and quality of life of HF patients remain poor. This is in part due to insufficient patient stratification and lack of individualized therapy planning, resulting in less effective treatments and a significant number of non-responders. Methods and Results State-of-the-art clinical phenotyping was acquired, including magnetic resonance imaging (MRI) and biomarker assessment. An individualized, multi-scale model of heart function covering cardiac anatomy, electrophysiology, biomechanics and hemodynamics was estimated using a robust framework. The model was computed on n=46 HF patients, showing for the first time that advanced multi-scale models can be fitted consistently on large cohorts. Novel multi-scale parameters derived from the model of all cases were analyzed and compared against clinical parameters, cardiac imaging, lab tests and survival scores to evaluate the explicative power of the model and its potential for better patient stratification. Model validation was pursued by comparing clinical parameters that were not used in the fitting process against model parameters. Conclusion This paper illustrates how advanced multi-scale models can complement cardiovascular imaging and how they could be applied in patient care. Based on obtained results, it becomes conceivable that, after thorough validation, such heart failure models could be applied for patient management and therapy planning in the future, as we illustrate in one patient of our cohort who received CRT-D implantation. PMID:26230546
Multiscale modeling in nanostructures: Physical and biological systems
NASA Astrophysics Data System (ADS)
Dearden, Albert Karcz
With the advent of more powerful computer systems, theoretical modeling of nanoscale systems has quickly become a vital part of scientific research in a multitude of disciplines. From the understanding of semiconductor devices to describing the mechanistic details of protein interactions, theoretical studies on systems of various scales have provided great insight into how nature behaves in each scenario. While at a macroscopic level the differences between biological and non-biological systems are apparent, the underlying principles that dictate their behavior are quite similar. Indeed, modeling these two distinct classes of systems have similar challenges. In both cases, the system sizes typically correspond to nanometer length scales and due to the lack of periodicity in the system, one needs to study a relatively larger number of atoms in simulations in order to represent their behavior. Nonetheless, systems that are much smaller than what exists in experiment may be used to describe specific properties of interest, such as how system stability scales with varying size or describing a reaction process of a large biological structure through the modeling of only the reaction site and not the entire protein. Thus, it is important to be able to correctly and efficiently model various systems at multiple scales in order to provide proper insight and understanding so models and tools developed in one area could be applied to another discipline. Indeed, lessons learned during the process are quite valuable for the general scheme of multiscale modeling in materials. To facilitate this, we have investigated two separate cases involving the efficient use of multiscale modeling through ab initio density functional theory calculations. For the first half of this work, we investigate the effect of size on the net magnetization of zero dimensional graphene based structures with differing edge states. Currently, we have shown that for zigzag edged triangular graphene
Multiscale modeling of nanostructures for electronic and energy-related applications
NASA Astrophysics Data System (ADS)
Kaxiras, Efthimios
2013-03-01
The optimization of materials properties for opto-electronic and energy-related applications is a crucial component in the design of new devices. To this end, multiscale modeling of nanostructures is essential in understanding and predicting materials properties ranging from optical response to the mechanical failure. We present a number of examples where multiscale modeling has yielded useful information concerning the optimal choices for nanostructured device elements. These include the excitation and charge transfer processes in hybrid photovoltaic devices, the tuning of optical and electrical properties of layered materials like graphene and transition-metal-dichalcogenides, and the mechanical response and deformation of silicon-based high-energy-density electrodes.
Xu, Zhiliang; Lioi, Joshua; Mu, Jian; Kamocka, Malgorzata M.; Liu, Xiaomin; Chen, Danny Z.; Rosen, Elliot D.; Alber, Mark
2010-01-01
Abstract A combination of the extended multiscale model, new image processing algorithms, and biological experiments is used for studying the role of Factor VII (FVII) in venous thrombus formation. A detailed submodel of the tissue factor pathway of blood coagulation is introduced within the framework of the multiscale model to provide a detailed description of coagulation cascade. Surface reactions of the extrinsic coagulation pathway on membranes of platelets are studied under different flow conditions. It is shown that low levels of FVII in blood result in a significant delay in thrombin production, demonstrating that FVII plays an active role in promoting thrombus development at an early stage. PMID:20441735
NASA Technical Reports Server (NTRS)
Saether, Erik; Hochhalter, Jacob D.; Glaessgen, Edward H.
2012-01-01
A multiscale modeling methodology that combines the predictive capability of discrete dislocation plasticity and the computational efficiency of continuum crystal plasticity is developed. Single crystal configurations of different grain sizes modeled with periodic boundary conditions are analyzed using discrete dislocation plasticity (DD) to obtain grain size-dependent stress-strain predictions. These relationships are mapped into crystal plasticity parameters to develop a multiscale DD/CP model for continuum level simulations. A polycrystal model of a structurally-graded microstructure is developed, analyzed and used as a benchmark for comparison between the multiscale DD/CP model and the DD predictions. The multiscale DD/CP model follows the DD predictions closely up to an initial peak stress and then follows a strain hardening path that is parallel but somewhat offset from the DD predictions. The difference is believed to be from a combination of the strain rate in the DD simulation and the inability of the DD/CP model to represent non-monotonic material response.
Wavelet-based multiscale performance analysis: An approach to assess and improve hydrological models
NASA Astrophysics Data System (ADS)
Rathinasamy, Maheswaran; Khosa, Rakesh; Adamowski, Jan; ch, Sudheer; Partheepan, G.; Anand, Jatin; Narsimlu, Boini
2014-12-01
The temporal dynamics of hydrological processes are spread across different time scales and, as such, the performance of hydrological models cannot be estimated reliably from global performance measures that assign a single number to the fit of a simulated time series to an observed reference series. Accordingly, it is important to analyze model performance at different time scales. Wavelets have been used extensively in the area of hydrological modeling for multiscale analysis, and have been shown to be very reliable and useful in understanding dynamics across time scales and as these evolve in time. In this paper, a wavelet-based multiscale performance measure for hydrological models is proposed and tested (i.e., Multiscale Nash-Sutcliffe Criteria and Multiscale Normalized Root Mean Square Error). The main advantage of this method is that it provides a quantitative measure of model performance across different time scales. In the proposed approach, model and observed time series are decomposed using the Discrete Wavelet Transform (known as the à trous wavelet transform), and performance measures of the model are obtained at each time scale. The applicability of the proposed method was explored using various case studies--both real as well as synthetic. The synthetic case studies included various kinds of errors (e.g., timing error, under and over prediction of high and low flows) in outputs from a hydrologic model. The real time case studies investigated in this study included simulation results of both the process-based Soil Water Assessment Tool (SWAT) model, as well as statistical models, namely the Coupled Wavelet-Volterra (WVC), Artificial Neural Network (ANN), and Auto Regressive Moving Average (ARMA) methods. For the SWAT model, data from Wainganga and Sind Basin (India) were used, while for the Wavelet Volterra, ANN and ARMA models, data from the Cauvery River Basin (India) and Fraser River (Canada) were used. The study also explored the effect of the
COMMUNITY MULTISCALE AIR QUALITY ( CMAQ ) MODEL - QUALITY ASSURANCE AND VERSION CONTROL
This presentation will be given to the EPA Exposure Modeling Workgroup on January 24, 2006. The quality assurance and version control procedures for the Community Multiscale Air Quality (CMAQ) Model are presented. A brief background of CMAQ is given, then issues related to qual...
Evaluation of the Community Multi-scale Air Quality (CMAQ) Model Version 5.2
The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...
Evaluation of the Community Multi-scale Air Quality Model Version 5.2
The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...
Evaluation of the Community Multi-scale Air Quality Model Version 5.2
The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...
Evaluation of the Community Multi-scale Air Quality (CMAQ) Model Version 5.2
The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...
Evaluation of the Community Multiscale Air Quality (CMAQ) Model Version 5.2
The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...
Evaluation of the Community Multi-scale Air Quality (CMAQ) Model Version 5.1
The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...
Incremental Testing of the Community Multiscale Air Quality (CMAQ) Modeling System Version 4.7
This paper describes the scientific and structural updates to the latest release of the Community Multiscale Air Quality (CMAQ) modeling system version 4.7 (v4.7) and points the reader to additional resources for further details. The model updates were evaluated relative to obse...
Evaluation of the Community Multi-scale Air Quality (CMAQ) Model Version 5.1
The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...
2005-01-01
The objective of the project was to develop a multiscale computational model capable of predicting the evolution of matrix cracking, delamination...currently under development by the author. The cohesive zone model for predicting damage evolution in laminated composite plates is cast within a...three dimensional continuum finite element algorithm capable of simulating the evolution of matrix, fiber, and delamination cracking in composite
Overview and Evaluation of the Community Multiscale Air Quality Model Version 5.2
The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...
Overview and Evaluation of the Community Multiscale Air Quality Model Version 5.2
The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Pr...
Hayenga, Heather N; Thorne, Bryan C; Peirce, Shayn M; Humphrey, Jay D
2011-11-01
There is a need to develop multiscale models of vascular adaptations to understand tissue-level manifestations of cellular level mechanisms. Continuum-based biomechanical models are well suited for relating blood pressures and flows to stress-mediated changes in geometry and properties, but less so for describing underlying mechanobiological processes. Discrete stochastic agent-based models are well suited for representing biological processes at a cellular level, but not for describing tissue-level mechanical changes. We present here a conceptually new approach to facilitate the coupling of continuum and agent-based models. Because of ubiquitous limitations in both the tissue- and cell-level data from which one derives constitutive relations for continuum models and rule-sets for agent-based models, we suggest that model verification should enforce congruency across scales. That is, multiscale model parameters initially determined from data sets representing different scales should be refined, when possible, to ensure that common outputs are consistent. Potential advantages of this approach are illustrated by comparing simulated aortic responses to a sustained increase in blood pressure predicted by continuum and agent-based models both before and after instituting a genetic algorithm to refine 16 objectively bounded model parameters. We show that congruency-based parameter refinement not only yielded increased consistency across scales, it also yielded predictions that are closer to in vivo observations.
Multiscale computational modeling of defects in uranium dioxide
NASA Astrophysics Data System (ADS)
Goyal, Anuj
Manufacturing, extreme operation conditions, and storage introduce large variety of defects into uranium dioxide (UO2) nuclear fuel, which have diverse effects on fuel properties. In this study, a multiscale computational approach to model defect behavior in UO2 is presented, by passing information in stages from electronic structure and atomistic calculations to a stochastic kinetic method. Understanding the interaction of fission products with dislocations is critical to interpret their interaction with fuel microstructure. Atomistic simulations are employed to predict the segregation of ruthenium and cesium, both fission products, to edge and screw dislocations. Dislocation loops of different shapes and sizes are simulated to investigate their atomic structure. To understand the segregation behavior, comparisons are made between atomistic simulations and continuum-elastic based results. Segregation behavior is found to be directly related to the elastic strain field around the dislocation core and is affected by the orientation of dislocation and electrostatic interactions at the atomic defect site. A detailed mechanism of, and the effect of homogeneous strains on, the migration of uranium vacancies in UO2 is presented. Migration pathways and barriers are identified using density functional theory and the effect of strain fields are accounted for using a dipole tensor approach. This information is then passed to the kinetic Monte Carlo simulations, to compute the diffusivities in the presence of external strain fields. We report complex migration pathways for uranium vacancy and show under homogeneous strain, only the dipole tensor of the saddle with respect to the minimum is required to correctly predict the change in energy barrier between the strained and the unstrained case. Homogeneous strains as small as 2% have considerable effect on diffusivity of both single and di-vacancies, with the effect of strain more pronounced for single vacancies than di
Advanced computational workflow for the multi-scale modeling of the bone metabolic processes.
Dao, Tien Tuan
2016-09-16
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.
Pope, Bernard J; Fitch, Blake G; Pitman, Michael C; Rice, John J; Reumann, Matthias
2011-10-01
Future multiscale and multiphysics models that support research into human disease, translational medical science, and treatment can utilize the power of high-performance computing (HPC) systems. We anticipate that computationally efficient multiscale models will require the use of sophisticated hybrid programming models, mixing distributed message-passing processes [e.g., the message-passing interface (MPI)] with multithreading (e.g., OpenMP, Pthreads). The objective of this study is to compare the performance of such hybrid programming models when applied to the simulation of a realistic physiological multiscale model of the heart. Our results show that the hybrid models perform favorably when compared to an implementation using only the MPI and, furthermore, that OpenMP in combination with the MPI provides a satisfactory compromise between performance and code complexity. Having the ability to use threads within MPI processes enables the sophisticated use of all processor cores for both computation and communication phases. Considering that HPC systems in 2012 will have two orders of magnitude more cores than what was used in this study, we believe that faster than real-time multiscale cardiac simulations can be achieved on these systems.
Modeling Framework for Fracture in Multiscale Cement-Based Material Structures
Qian, Zhiwei; Schlangen, Erik; Ye, Guang; van Breugel, Klaas
2017-01-01
Multiscale modeling for cement-based materials, such as concrete, is a relatively young subject, but there are already a number of different approaches to study different aspects of these classical materials. In this paper, the parameter-passing multiscale modeling scheme is established and applied to address the multiscale modeling problem for the integrated system of cement paste, mortar, and concrete. The block-by-block technique is employed to solve the length scale overlap challenge between the mortar level (0.1–10 mm) and the concrete level (1–40 mm). The microstructures of cement paste are simulated by the HYMOSTRUC3D model, and the material structures of mortar and concrete are simulated by the Anm material model. Afterwards the 3D lattice fracture model is used to evaluate their mechanical performance by simulating a uniaxial tensile test. The simulated output properties at a lower scale are passed to the next higher scale to serve as input local properties. A three-level multiscale lattice fracture analysis is demonstrated, including cement paste at the micrometer scale, mortar at the millimeter scale, and concrete at centimeter scale. PMID:28772948
Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success.
Yankeelov, Thomas E; An, Gary; Saut, Oliver; Luebeck, E Georg; Popel, Aleksander S; Ribba, Benjamin; Vicini, Paolo; Zhou, Xiaobo; Weis, Jared A; Ye, Kaiming; Genin, Guy M
2016-09-01
Hierarchical processes spanning several orders of magnitude of both space and time underlie nearly all cancers. Multi-scale statistical, mathematical, and computational modeling methods are central to designing, implementing and assessing treatment strategies that account for these hierarchies. The basic science underlying these modeling efforts is maturing into a new discipline that is close to influencing and facilitating clinical successes. The purpose of this review is to capture the state-of-the-art as well as the key barriers to success for multi-scale modeling in clinical oncology. We begin with a summary of the long-envisioned promise of multi-scale modeling in clinical oncology, including the synthesis of disparate data types into models that reveal underlying mechanisms and allow for experimental testing of hypotheses. We then evaluate the mathematical techniques employed most widely and present several examples illustrating their application as well as the current gap between pre-clinical and clinical applications. We conclude with a discussion of what we view to be the key challenges and opportunities for multi-scale modeling in clinical oncology.
Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success
Yankeelov, Thomas E.; An, Gary; Saut, Oliver; Luebeck, E. Georg; Popel, Aleksander S.; Ribba, Benjamin; Vicini, Paolo; Zhou, Xiaobo; Weis, Jared A.; Ye, Kaiming; Genin, Guy M.
2016-01-01
Hierarchical processes spanning several orders of magnitude of both space and time underlie nearly all cancers. Multi-scale statistical, mathematical, and computational modeling methods are central to designing, implementing and assessing treatment strategies that account for these hierarchies. The basic science underlying these modeling efforts is maturing into a new discipline that is close to influencing and facilitating clinical successes. The purpose of this review is to capture the state-of-the-art as well as the key barriers to success for multi-scale modeling in clinical oncology. We begin with a summary of the long-envisioned promise of multi-scale modeling in clinical oncology, including the synthesis of disparate data types into models that reveal underlying mechanisms and allow for experimental testing of hypotheses. We then evaluate the mathematical techniques employed most widely and present several examples illustrating their application as well as the current gap between pre-clinical and clinical applications. We conclude with a discussion of what we view to be the key challenges and opportunities for multi-scale modeling in clinical oncology. PMID:27384942
A second gradient theoretical framework for hierarchical multiscale modeling of materials
Luscher, Darby J; Bronkhorst, Curt A; Mc Dowell, David L
2009-01-01
A theoretical framework for the hierarchical multiscale modeling of inelastic response of heterogeneous materials has been presented. Within this multiscale framework, the second gradient is used as a non local kinematic link between the response of a material point at the coarse scale and the response of a neighborhood of material points at the fine scale. Kinematic consistency between these scales results in specific requirements for constraints on the fluctuation field. The wryness tensor serves as a second-order measure of strain. The nature of the second-order strain induces anti-symmetry in the first order stress at the coarse scale. The multiscale ISV constitutive theory is couched in the coarse scale intermediate configuration, from which an important new concept in scale transitions emerges, namely scale invariance of dissipation. Finally, a strategy for developing meaningful kinematic ISVs and the proper free energy functions and evolution kinetics is presented.
Luscher, Darby J.
2010-04-01
All materials are heterogeneous at various scales of observation. The influence of material heterogeneity on nonuniform response and microstructure evolution can have profound impact on continuum thermomechanical response at macroscopic “engineering” scales. In many cases, it is necessary to treat this behavior as a multiscale process thus integrating the physical understanding of material behavior at various physical (length and time) scales in order to more accurately predict the thermomechanical response of materials as their microstructure evolves. The intent of the dissertation is to provide a formal framework for multiscale hierarchical homogenization to be used in developing constitutive models.
A Stochastic Multiscale Model for Microstructure Model Reduction
2011-12-19
methods. In [4, 5] the principle of maximum entropy ( MaxEnt ) was used to describe the microstructure topology of binary and polycrystalline materials. A...such MaxEnt distribution and interrogated using appropriate physical model, e.g. a crystal plasticity finite element method (CPFEM) [6] for polycrystals
A nonlocal multiscale discrete-continuum digital rock physics model at pendular regime
NASA Astrophysics Data System (ADS)
Sun, W.; Liu, Y.; Yuan, Z.; Fish, J.
2014-12-01
We propose a nonlocal multiscale framework that couples grain-scale micro-structural simulations of porous media with a macroscopic continuum-based finite element model at pendular regime. The upshot of this nonlocal coupling model is that it retains the simplicity and efficiency of the continuum-based finite element model, while possessing the original length scale of the microstructure. In particular, the collective mechanical responses of grains at material points are homogenized via a staggered nonlocal operator applied on local regions such that the multiscale simulations exhibit no pathological mesh dependence. Since granular materials may appear to be incompressible at critical state, we employ a one-point quadrature integration rule to relax the solution, while using hourglass control to eliminate the zero-energy modes. Numerical examples are used to analyze the onset and propagation of shear bands in granular materials. Finally, the robustness and accuracy of the proposed multiscale model are verified in comparisons with single-scale benchmark microstructural simulations. The nonlocal multiscale coupling scheme is able to capture the plastic dilatancy and pressure-sensitive frictional responses commonly observed inside dilatant shear bands, and replicate the anisotropy induced by the liquid-bridge and contact fabrics, without employing any phenomenological plasticity model or water-retention curve at macroscopic level.
Chiverton, John P; Ige, Olubisi; Barnett, Stephanie J; Parry, Tony
2017-11-01
This paper is concerned with the modeling and analysis of the orientation and distance between steel fibers in X-ray micro-tomography data. The advantage of combining both orientation and separation in a model is that it helps provide a detailed understanding of how the steel fibers are arranged, which is easy to compare. The developed models are designed to summarize the randomness of the orientation distribution of the steel fibers both locally and across an entire volume based on multiscale entropy. Theoretical modeling, simulation, and application to real imaging data are shown here. The theoretical modeling of multiscale entropy for orientation includes a proof showing the final form of the multiscale taken over a linear range of scales. A series of image processing operations are also included to overcome interslice connectivity issues to help derive the statistical descriptions of the orientation distributions of the steel fibers. The results demonstrate that multiscale entropy provides unique insights into both simulated and real imaging data of steel fiber reinforced concrete.
NASA Astrophysics Data System (ADS)
Iacobellis, Vincent
Composite and nanocomposite materials exhibit behaviour which is inherently multiscale, extending from the atomistic to continuum levels. In composites, damage growth tends to occur at the nano and microstructural scale by means of crack growth and fibre-matrix debonding. Concurrent multiscale modeling provides a means of efficiently solving such localized phenomena, however its use in this application has been limited due to a number of existing issues in the multiscale field. These include the seamless transfer of information between continuum and atomistic domains, the small timesteps required for dynamic simulation, and limited research into concurrent multiscale modeling of amorphous polymeric materials. The objective of this thesis is thus twofold: to formulate a generalized approach to solving a coupled atomistic-to-continuum system that addresses these issues and to extend the application space of concurrent multiscale modeling to damage modeling in composite microstructures. To achieve these objectives, a finite element based multiscale technique termed the Bridging Cell Method (BCM), has been formulated with a focus on crystalline material systems. Case studies are then presented that show the effectiveness of the developed technique with respect to full atomistic simulations. The BCM is also demonstrated for applications of stress around a nanovoid, nanoindentation, and crack growth due to monotonic and cyclic loading. Next, the BCM is extended to modeling amorphous polymeric material systems where an adaptive solver and a two-step iterative solution algorithm are introduced. Finally, the amorphous and crystalline BCM is applied to modeling a polymer-graphite interface. This interface model is used to obtain cohesive zone parameters which are used in a cohesive zone model of fibre-matrix interfacial cracking in a composite microstructure. This allows for an investigation of the temperature dependent damage mechanics from the nano to microscale within
Image-based flow modeling in a two-chamber model of the left heart
NASA Astrophysics Data System (ADS)
Vedula, Vijay; Seo, Jung-Hee; Shoele, Kourosh; George, Richard; Younes, Laurent; Mittal, Rajat
2014-11-01
Computational modeling of cardiac flows has been an active topic of discussion over the past decade. Modeling approaches have been consistently improved by inclusion of additional complexities and these continue to provide new insights into the dynamics of blood flow in health and disease. The vast majority of cardiac models have been single-chamber models, which have typically focused on the left or right ventricles, and in these models, the atria are modeled in highly simplistic ways. However, the left atrium acts as a mixing chamber and works with the left ventricle in a highly coordinated fashion to move the blood from the pulmonary veins to the aorta. The flow dynamics associated with this two-chamber interaction is not well understood. In addition, the flow in the left atrium has by itself significant clinical implications and our understanding of this is far less than that of the left ventricle. In the current study, we use 4D CT to create a physiological heart model that is functionally normal and use an experimentally validated sharp-interface immersed boundary flow solver to explore the atrio-ventricular interaction and develop insights into some of the questions addressed above. This research is supported by the U.S. National Science Foundation through NSF Grants IOS-1124804 and IIS-1344772. Computational resources are provided in part through the NSF XSEDE grants TG-CTS100002 and TG-CTS130064.
Optimization of Focused Ultrasound and Image Based Modeling in Image Guided Interventions
NASA Astrophysics Data System (ADS)
Almekkawy, Mohamed Khaled Ibrahim
Image-guided high intensity focused ultrasound (HIFU) is becoming increasingly accepted as a form of noninvasive ablative therapy for the treatment of prostate cancer, uterine fibroids and other tissue abnormalities. In principle, HIFU beams can be focused within small volumes which results in forming precise lesions within the target volume (e.g. tumor, atherosclerotic plaque) while sparing the intervening tissue. With this precision, HIFU offers the promise of noninvasive tumor therapy. The goal of this thesis is to develop an image-guidance mode with an interactive image-based computational modeling of tissue response to HIFU. This model could be used in treatment planning and post-treatment retrospective evaluation of treatment outcome(s). Within the context of treatment planning, the challenge of using HIFU to target tumors in organs partially obscured by the rib cage are addressed. Ribs distort HIFU beams in a manner that reduces the focusing gain at the target (tumor) and could cause a treatment-limiting collateral damage. We present a refocusing algorithms to efficiently steer higher power towards the target while limiting power deposition on the ribs, improving the safety and efficacy of tumor ablation. Our approach is based on an approximation of a non-convex to a convex optimization known as the semidefinite relaxation (SDR) technique. An important advantage of the SDR method over previously proposed optimization methods is the explicit control of the sidelobes in the focal plane. A finite-difference time domain (FDTD) heterogeneous propagation model of a 1-MHz concave phased array was used to model the acoustic propagation and temperature simulations in different tissues including ribs. The numerical methods developed for the refocusing problem are also used for retrospective analysis of targeting of atherosclerotic plaques using HIFU. Cases were simulated where seven adjacent HIFU shots (5000 W/cm2, 2 sec exposure time) were focused at the plaque
Recent Enhancements to the Community Multiscale Air Quality Modeling System (CMAQ)
EPA’s Office of Research and Development, Computational Exposure Division held a webinar on January 31, 2017 to present the recent scientific and computational updates made by EPA to the Community Multi-Scale Air Quality Model (CMAQ). Topics covered included: (1) Improveme...
Multi-scale habitat selection modeling: A review and outlook
Kevin McGarigal; Ho Yi Wan; Kathy A. Zeller; Brad C. Timm; Samuel A. Cushman
2016-01-01
Scale is the lens that focuses ecological relationships. Organisms select habitat at multiple hierarchical levels and at different spatial and/or temporal scales within each level. Failure to properly address scale dependence can result in incorrect inferences in multi-scale habitat selection modeling studies.
Updating sea spray aerosol emissions in the Community Multiscale Air Quality (CMAQ) model
Sea spray aerosols (SSA) impact the particle mass concentration and gas-particle partitioning in coastal environments, with implications for human and ecosystem health. In this study, the Community Multiscale Air Quality (CMAQ) model is updated to enhance fine mode SSA emissions,...
The Industrial Process System Assessment (IPSA) methodology is a multiple step allocation approach for connecting information from the production line level up to the facility level and vice versa using a multiscale model of process systems. The allocation procedure assigns inpu...
Updating sea spray aerosol emissions in the Community Multiscale Air Quality (CMAQ) model
Sea spray aerosols (SSA) impact the particle mass concentration and gas-particle partitioning in coastal environments, with implications for human and ecosystem health. In this study, the Community Multiscale Air Quality (CMAQ) model is updated to enhance fine mode SSA emissions,...
NASA Technical Reports Server (NTRS)
Vlachos, Dion G.
2002-01-01
The focus of this presentation is on multiscale modeling in order to link processing, microstructure, and properties of materials. Overview of problems we study includes: Growth mechanisms in chemical and physical vapor epitaxy; thin films of zeolites for separation and sensing; thin Pd films for hydrogen separation and pattern formation by self-regulation routes.
Recent Enhancements to the Community Multiscale Air Quality Modeling System (CMAQ)
EPA’s Office of Research and Development, Computational Exposure Division held a webinar on January 31, 2017 to present the recent scientific and computational updates made by EPA to the Community Multi-Scale Air Quality Model (CMAQ). Topics covered included: (1) Improveme...
The Industrial Process System Assessment (IPSA) methodology is a multiple step allocation approach for connecting information from the production line level up to the facility level and vice versa using a multiscale model of process systems. The allocation procedure assigns inpu...
NASA Technical Reports Server (NTRS)
Vlachos, Dion G.
2002-01-01
The focus of this presentation is on multiscale modeling in order to link processing, microstructure, and properties of materials. Overview of problems we study includes: Growth mechanisms in chemical and physical vapor epitaxy; thin films of zeolites for separation and sensing; thin Pd films for hydrogen separation and pattern formation by self-regulation routes.
1999-08-24
Page 1 Center for Auditory and Acoustic Research Sound Classification and Localization Based on Biology Hearing Models and Multiscale Vector...Quantization John S. Baras Center for Auditory and Acoustic Research Electrical and Computer Engineering Department and the Institute for Systems... Acoustic Microsensors Workshop held on August 24 and 25, 1999 in Crystal City, VA., The original document contains color images. 14. ABSTRACT 15
The Role of Continuity in Residual-Based Variational Multiscale Modeling of Turbulence
2007-05-01
incompressible flows , finite elements, NURBS, Navier - Stokes equations, boundary layers, turbulent channel flows , residual-based turbulence modeling...upwind / Petrov-Galerkin for- mulations for convection dominated flows with particular emphasis on the incompressible Navier - Stokes equations. Computer...incompressible Navier - Stokes (INS) equations at the continuous level. In Sec- tion 3, we give the semi-discrete, residual-based variational multiscale
Modeling of Multiscale and Multiphase Phenomena in Materials Processing
NASA Astrophysics Data System (ADS)
Ludwig, Andreas; Kharicha, Abdellah; Wu, Menghuai
2013-03-01
In order to demonstrate how CFD can help scientists and engineers to better understand the fundamentals of engineering processes, a number of examples are shown and discussed. The paper covers (i) special aspects of continuous casting of steel including turbulence, motion and entrapment of non-metallic inclusions, and impact of soft reduction; (ii) multiple flow phenomena and multiscale aspects during casting of large ingots including flow-induced columnar-to-equiaxed transition and 3D formation of channel segregation; (iii) multiphase magneto-hydrodynamics during electro-slag remelting; and (iv) melt flow and solidification of thin but large centrifugal castings.
Multiscale Modeling of Polymer Membranes for Soldiers Protective Clothing
2006-11-01
of polymer multiscale simulations (Yip et al., 2005) (Fig. 1): (i) quantum mechanical solutions of Schrodinger equation providing electronic... equations : δρI /δt = M ∇ρI ∇µI + η where µI is the intrinsic chemical potential that is derived from the differentiation of the free energy with...using mesoscale results distance t i m e QM MD MESO MACRO Mathematical Homogenization Solution of an elliptic partial differential equations y D y D y
Multiscale musculoskeletal modelling, data-model fusion and electromyography-informed modelling.
Fernandez, J; Zhang, J; Heidlauf, T; Sartori, M; Besier, T; Röhrle, O; Lloyd, D
2016-04-06
This paper proposes methods and technologies that advance the state of the art for modelling the musculoskeletal system across the spatial and temporal scales; and storing these using efficient ontologies and tools. We present population-based modelling as an efficient method to rapidly generate individual morphology from only a few measurements and to learn from the ever-increasing supply of imaging data available. We present multiscale methods for continuum muscle and bone models; and efficient mechanostatistical methods, both continuum and particle-based, to bridge the scales. Finally, we examine both the importance that muscles play in bone remodelling stimuli and the latest muscle force prediction methods that use electromyography-assisted modelling techniques to compute musculoskeletal forces that best reflect the underlying neuromuscular activity. Our proposal is that, in order to have a clinically relevant virtual physiological human, (i) bone and muscle mechanics must be considered together; (ii) models should be trained on population data to permit rapid generation and use underlying principal modes that describe both muscle patterns and morphology; and (iii) these tools need to be available in an open-source repository so that the scientific community may use, personalize and contribute to the database of models.
Multiscale musculoskeletal modelling, data–model fusion and electromyography-informed modelling
Zhang, J.; Heidlauf, T.; Sartori, M.; Besier, T.; Röhrle, O.; Lloyd, D.
2016-01-01
This paper proposes methods and technologies that advance the state of the art for modelling the musculoskeletal system across the spatial and temporal scales; and storing these using efficient ontologies and tools. We present population-based modelling as an efficient method to rapidly generate individual morphology from only a few measurements and to learn from the ever-increasing supply of imaging data available. We present multiscale methods for continuum muscle and bone models; and efficient mechanostatistical methods, both continuum and particle-based, to bridge the scales. Finally, we examine both the importance that muscles play in bone remodelling stimuli and the latest muscle force prediction methods that use electromyography-assisted modelling techniques to compute musculoskeletal forces that best reflect the underlying neuromuscular activity. Our proposal is that, in order to have a clinically relevant virtual physiological human, (i) bone and muscle mechanics must be considered together; (ii) models should be trained on population data to permit rapid generation and use underlying principal modes that describe both muscle patterns and morphology; and (iii) these tools need to be available in an open-source repository so that the scientific community may use, personalize and contribute to the database of models. PMID:27051510
Castro, Marcelo A; Ahumada Olivares, María C; Putman, Christopher M; Cebral, Juan R
2014-10-01
The aim of this work was to determine whether or not Newtonian rheology assumption in image-based patient-specific computational fluid dynamics (CFD) cerebrovascular models harboring cerebral aneurysms may affect the hemodynamics characteristics, which have been previously associated with aneurysm progression and rupture. Ten patients with cerebral aneurysms with lobulations were considered. CFD models were reconstructed from 3DRA and 4DCTA images by means of region growing, deformable models, and an advancing front technique. Patient-specific FEM blood flow simulations were performed under Newtonian and Casson rheological models. Wall shear stress (WSS) maps were created and distributions were compared at the end diastole. Regions of lower WSS (lobulation) and higher WSS (neck) were identified. WSS changes in time were analyzed. Maximum, minimum and time-averaged values were calculated and statistically compared. WSS characterization remained unchanged. At high WSS regions, Casson rheology systematically produced higher WSS minimum, maximum and time-averaged values. However, those differences were not statistically significant. At low WSS regions, when averaging over all cases, the Casson model produced higher stresses, although in some cases the Newtonian model did. However, those differences were not significant either. There is no evidence that Newtonian model overestimates WSS. Differences are not statistically significant.
Multiscale Interactions in a 3D Model of the Contracting Ventricle.
Amar, Ani; Zlochiver, Sharon; Barnea, Ofer
2015-12-01
A biophysical detailed multiscale model of the myocardium is presented. The model was used to study the contribution of interrelated cellular mechanisms to global myocardial function. The multiscale model integrates cellular electrophysiology, excitation propagation dynamics and force development models into a geometrical fiber based model of the ventricle. The description of the cellular electrophysiology in this study was based on the Ten Tusscher-Noble-Noble-Panfilov heterogeneous model for human ventricular myocytes. A four-state model of the sarcomeric control of contraction developed by Negroni and Lascano was employed to model the intracellular mechanism of force generation. The propagation of electrical excitation was described by a reaction-diffusion equation. The 3D geometrical model of the ventricle, based on single fiber contraction was used as a platform for the evaluation of proposed models. The model represents the myocardium as an anatomically oriented array of contracting fibers with individual fiber parameters such as size, spatial location, orientation and mechanical properties. Moreover, the contracting ventricle model interacts with intraventricular blood elements linking the contractile elements to the heart's preload and afterload, thereby producing the corresponding pressure-volume loop. The results show that the multiscale ventricle model is capable of simulating mechanical contraction, pressure generation and load interactions as well as demonstrating the individual contribution of each ion current.
Hierarchical Multiscale Modeling of Macromolecules and their Assemblies
Ortoleva, P.; Singharoy, A.; Pankavich, S.
2013-01-01
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character of such systems often makes traditional molecular dynamics simulation impractical, a multiscale approach has been presented that allows for long-time simulation with atomic detail based on the co-evolution of slowly-varying order parameters (OPs) with the quasi-equilibrium probability density of atomic configurations. However, this approach breaks down when the structural change is extreme, or when nearest-neighbor connectivity of atoms is not maintained. In the current study, a self-consistent approach is presented wherein OPs and a reference structure co-evolve slowly to yield long-time simulation for dynamical soft-matter phenomena such as structural transitions and self-assembly. The development begins with the Liouville equation for N classical atoms and an ansatz on the form of the associated N-atom probability density. Multiscale techniques are used to derive Langevin equations for the coupled OP-configurational dynamics. The net result is a set of equations for the coupled stochastic dynamics of the OPs and centers of mass of the subsystems that constitute a soft material body. The theory is based on an all-atom methodology and an interatomic force field, and therefore enables calibration-free simulations of soft matter, such as macromolecular assemblies. PMID:23671457
Multiscale modeling and simulation of soft adhesion and contact of stem cells.
Zeng, Xiaowei; Li, Shaofan
2011-02-01
Recently, we have developed a multiscale soft matter model for stem cells or primitive cells in general, aiming at improving the understanding of mechanotransduction mechanism of cells that is responsible for information exchange between cells and their extracellular environment. In this paper, we report the preliminary results of our research on multiscale modeling and simulation of soft contact and adhesion of cells. The proposed multiscale soft matter cell model may be used to model soft contact and adhesion between cells and their extracellular substrates. This model is a generalization of the Fluid Mosaic Model (Singer and Nicolson, 1972), or an extension of Helfrich's liquid crystal membrane model (Helfrich, 1973). To the best of the authors' knowledge, this may be the first time that a soft matter model is developed for cell contact and adhesion. Moreover we have developed and implemented a Lagrange type meshfree Galerkin formulation and the computational algorithm for the proposed cell model. Comparison study with experimental data has been conducted to validate the parameters of the model. By using the soft matter cell model, we have simulated the soft adhesive contact process between cells and their extracellular substrates. The simulation shows that the cell can sense substrate elasticity by responding in different manners from cell spreading motion to cell contact configurations.
On the multiscale modeling of heart valve biomechanics in health and disease.
Weinberg, Eli J; Shahmirzadi, Danial; Mofrad, Mohammad Reza Kaazempur
2010-08-01
Theoretical models of the human heart valves are useful tools for understanding and characterizing the dynamics of healthy and diseased valves. Enabled by advances in numerical modeling and in a range of disciplines within experimental biomechanics, recent models of the heart valves have become increasingly comprehensive and accurate. In this paper, we first review the fundamentals of native heart valve physiology, composition and mechanics in health and disease. We will then furnish an overview of the development of theoretical and experimental methods in modeling heart valve biomechanics over the past three decades. Next, we will emphasize the necessity of using multiscale modeling approaches in order to provide a comprehensive description of heart valve biomechanics able to capture general heart valve behavior. Finally, we will offer an outlook for the future of valve multiscale modeling, the potential directions for further developments and the challenges involved.
2011-03-01
couples different models to each other, and the domain decomposition method ( DDM ) divides a flow domain into many subdomains, each of which is...assigned to an individual model. Combining HM and DDM is one of the most promising currently available techniques to bridge the scales and overcome...recent work in modeling of multiscale and multiphysics hydrodynamics phenomena using HM and DDM . We also discuss related sediment transport, with
The deep crust beneath the Trans-European Suture Zone from a multiscale magnetic model
NASA Astrophysics Data System (ADS)
Milano, Maurizio; Fedi, Maurizio; Fairhead, J. Derek
2016-09-01
We present a 3-D interpretation of the deep magnetic sources beneath the main geological structure of central-eastern Europe, the "Trans-European Suture Zone" (TESZ). We used a multiscale analysis of aeromagnetic data, based on a multiscale data set generated by upward continuation of the European and Mediterranean Magnetic Project data set from 5 to 100 km altitude. We also computed the multiscale total gradient |∇T| of the multiscale field. Both of the multiscale data sets allow us to discriminate the main crustal contributions to the field at various scales, and we showed that at large altitudes the field is dominated by the sole effect of the TESZ. The multiridge geometric method was very useful in studying the complex features of the main crustal interfaces, either shallow or deep. The interpreted interfaces are largely agreement with geological models based on seismic surveys and, in some cases, complete the models out of the analyzed region. In order to estimate the deepest source depths in the TESZ region, we applied the multiridge method to the large scales (50-100 km altitude), obtaining a set of singular points at depths ranging between 35 and 40 km. Considering the heat flow trend and the geological models around the TESZ area, we found a meaningful correspondence among the location of the estimated singular points and the most abrupt variations and complex morphology features of the Moho boundary. The multiridge estimates are consistent with known structural information and can be used for a 3-D representation of the Moho depth along the TESZ.
A multiscale approach to model hydrogen bonding: The case of polyamide
Gowers, Richard J. Carbone, Paola
2015-06-14
We present a simple multiscale model for polymer chains in which it is possible to selectively remove degrees of freedom. The model integrates all-atom and coarse-grained potentials in a simple and systematic way and allows a fast sampling of the complex conformational energy surface typical of polymers whilst maintaining a realistic description of selected atomistic interactions. In particular, we show that it is possible to simultaneously reproduce the structure of highly directional non-bonded interactions such as hydrogen bonds and efficiently explore the large number of conformations accessible to the polymer chain. We apply the method to a melt of polyamide removing from the model only the degrees of freedom associated to the aliphatic segments and keeping at atomistic resolution the amide groups involved in the formation of the hydrogen bonds. The results show that the multiscale model produces structural properties that are comparable with the fully atomistic model despite being five times faster to simulate.
Band, Leah R; Fozard, John A; Godin, Christophe; Jensen, Oliver E; Pridmore, Tony; Bennett, Malcolm J; King, John R
2012-10-01
Over recent decades, we have gained detailed knowledge of many processes involved in root growth and development. However, with this knowledge come increasing complexity and an increasing need for mechanistic modeling to understand how those individual processes interact. One major challenge is in relating genotypes to phenotypes, requiring us to move beyond the network and cellular scales, to use multiscale modeling to predict emergent dynamics at the tissue and organ levels. In this review, we highlight recent developments in multiscale modeling, illustrating how these are generating new mechanistic insights into the regulation of root growth and development. We consider how these models are motivating new biological data analysis and explore directions for future research. This modeling progress will be crucial as we move from a qualitative to an increasingly quantitative understanding of root biology, generating predictive tools that accelerate the development of improved crop varieties.
Band, Leah R.; Fozard, John A.; Godin, Christophe; Jensen, Oliver E.; Pridmore, Tony; Bennett, Malcolm J.; King, John R.
2012-01-01
Over recent decades, we have gained detailed knowledge of many processes involved in root growth and development. However, with this knowledge come increasing complexity and an increasing need for mechanistic modeling to understand how those individual processes interact. One major challenge is in relating genotypes to phenotypes, requiring us to move beyond the network and cellular scales, to use multiscale modeling to predict emergent dynamics at the tissue and organ levels. In this review, we highlight recent developments in multiscale modeling, illustrating how these are generating new mechanistic insights into the regulation of root growth and development. We consider how these models are motivating new biological data analysis and explore directions for future research. This modeling progress will be crucial as we move from a qualitative to an increasingly quantitative understanding of root biology, generating predictive tools that accelerate the development of improved crop varieties. PMID:23110897
Using Multi-Scale Modeling Systems and Satellite Data to Study the Precipitation Processes
NASA Technical Reports Server (NTRS)
Tao, Wei-Kuo; Chern, J.; Lamg, S.; Matsui, T.; Shen, B.; Zeng, X.; Shi, R.
2011-01-01
In recent years, exponentially increasing computer power has extended Cloud Resolving Model (CRM) integrations from hours to months, the number of computational grid points from less than a thousand to close to ten million. Three-dimensional models are now more prevalent. Much attention is devoted to precipitating cloud systems where the crucial 1-km scales are resolved in horizontal domains as large as 10,000 km in two-dimensions, and 1,000 x 1,000 km2 in three-dimensions. Cloud resolving models now provide statistical information useful for developing more realistic physically based parameterizations for climate models and numerical weather prediction models. It is also expected that NWP and mesoscale model can be run in grid size similar to cloud resolving model through nesting technique. Recently, a multi-scale modeling system with unified physics was developed at NASA Goddard. It consists of (l) 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, the recent developments and applications of the multi-scale modeling system will be presented. In particular, the results from using multi-scale modeling system to study the precipitating systems and hurricanes/typhoons will be presented. The high-resolution spatial and temporal visualization will be utilized to show the evolution of precipitation processes. Also how to
Multiscale modelling of plastic flow localization in irradiated materials
NASA Astrophysics Data System (ADS)
Diaz de la Rubia, Tomas; Zbib, Hussein M.; Khraishi, Tariq A.; Wirth, Brian D.; Victoria, Max; Caturla, Maria Jose
2000-08-01
The irradiation of metals by energetic particles causes significant degradation of the mechanical properties, most notably an increased yield stress and decreased ductility, often accompanied by plastic flow localization. Such effects limit the lifetime of pressure vessels in nuclear power plants, and constrain the choice of materials for fusion-based alternative energy sources. Although these phenomena have been known for many years, the underlying fundamental mechanisms and their relation to the irradiation field have not been clearly demonstrated. Here we use three-dimensional multiscale simulations of irradiated metals to reveal the mechanisms underlying plastic flow localization in defect-free channels. We observe dislocation pinning by irradiation-induced clusters of defects, subsequent unpinning as defects are absorbed by the dislocations, and cross-slip of the latter as the stress is increased. The width of the plastic flow channels is limited by the interaction among opposing dislocation dipole segments and the remaining defect clusters.
Multiscale modeling of turbulent channel flow over porous walls
NASA Astrophysics Data System (ADS)
Yogaraj, Sudhakar; Lacis, Ugis; Bagheri, Shervin
2016-11-01
We perform direct numerical simulations of fully developed turbulent flow through a channel coated with a porous material. The Navier-stokes equations governing the fluid domain and the Darcy equations of the porous medium are coupled using an iterative partitioned scheme. At the interface between the two media, boundary conditions derived using a multiscale homogenization approach are enforced. The main feature of this approach is that the anisotropic micro-structural pore features are directly taken into consideration to derive the constitutive coefficients of the porous media as well as of the interface. The focus of the present work is to study the influence of micro-structure pore geometry on the dynamics of turbulent flows. Detailed turbulence statistics and instantaneous flow field are presented. For comparison, flow through impermeable channel flows are included. Supported by the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant agreement No 708281.
Simulation of Left Atrial Function Using a Multi-Scale Model of the Cardiovascular System
Pironet, Antoine; Dauby, Pierre C.; Paeme, Sabine; Kosta, Sarah; Chase, J. Geoffrey; Desaive, Thomas
2013-01-01
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. PMID:23755183
Stochastic multiscale modelling of cortical bone elasticity based on high-resolution imaging.
Sansalone, Vittorio; Gagliardi, Davide; Desceliers, Christophe; Bousson, Valérie; Laredo, Jean-Denis; Peyrin, Françoise; Haïat, Guillaume; Naili, Salah
2016-02-01
Accurate and reliable assessment of bone quality requires predictive methods which could probe bone microstructure and provide information on bone mechanical properties. Multiscale modelling and simulation represent a fast and powerful way to predict bone mechanical properties based on experimental information on bone microstructure as obtained through X-ray-based methods. However, technical limitations of experimental devices used to inspect bone microstructure may produce blurry data, especially in in vivo conditions. Uncertainties affecting the experimental data (input) may question the reliability of the results predicted by the model (output). Since input data are uncertain, deterministic approaches are limited and new modelling paradigms are required. In this paper, a novel stochastic multiscale model is developed to estimate the elastic properties of bone while taking into account uncertainties on bone composition. Effective elastic properties of cortical bone tissue were computed using a multiscale model based on continuum micromechanics. Volume fractions of bone components (collagen, mineral, and water) were considered as random variables whose probabilistic description was built using the maximum entropy principle. The relevance of this approach was proved by analysing a human bone sample taken from the inferior femoral neck. The sample was imaged using synchrotron radiation micro-computed tomography. 3-D distributions of Haversian porosity and tissue mineral density extracted from these images supplied the experimental information needed to build the stochastic models of the volume fractions. Thus, the stochastic multiscale model provided reliable statistical information (such as mean values and confidence intervals) on bone elastic properties at the tissue scale. Moreover, the existence of a simpler "nominal model", accounting for the main features of the stochastic model, was investigated. It was shown that such a model does exist, and its relevance
Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform.
Marshall-Colon, Amy; Long, Stephen P; Allen, Douglas K; Allen, Gabrielle; Beard, Daniel A; Benes, Bedrich; von Caemmerer, Susanne; Christensen, A J; Cox, Donna J; Hart, John C; Hirst, Peter M; Kannan, Kavya; Katz, Daniel S; Lynch, Jonathan P; Millar, Andrew J; Panneerselvam, Balaji; Price, Nathan D; Prusinkiewicz, Przemyslaw; Raila, David; Shekar, Rachel G; Shrivastava, Stuti; Shukla, Diwakar; Srinivasan, Venkatraman; Stitt, Mark; Turk, Matthew J; Voit, Eberhard O; Wang, Yu; Yin, Xinyou; Zhu, Xin-Guang
2017-01-01
Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop.
Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform
Marshall-Colon, Amy; Long, Stephen P.; Allen, Douglas K.; Allen, Gabrielle; Beard, Daniel A.; Benes, Bedrich; von Caemmerer, Susanne; Christensen, A. J.; Cox, Donna J.; Hart, John C.; Hirst, Peter M.; Kannan, Kavya; Katz, Daniel S.; Lynch, Jonathan P.; Millar, Andrew J.; Panneerselvam, Balaji; Price, Nathan D.; Prusinkiewicz, Przemyslaw; Raila, David; Shekar, Rachel G.; Shrivastava, Stuti; Shukla, Diwakar; Srinivasan, Venkatraman; Stitt, Mark; Turk, Matthew J.; Voit, Eberhard O.; Wang, Yu; Yin, Xinyou; Zhu, Xin-Guang
2017-01-01
Multi-scale models can facilitate whole plant simulations by linking gene networks, protein synthesis, metabolic pathways, physiology, and growth. Whole plant models can be further integrated with ecosystem, weather, and climate models to predict how various interactions respond to environmental perturbations. These models have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts. Outcomes will potentially accelerate improvement of crop yield, sustainability, and increase future food security. It is time for a paradigm shift in plant modeling, from largely isolated efforts to a connected community that takes advantage of advances in high performance computing and mechanistic understanding of plant processes. Tools for guiding future crop breeding and engineering, understanding the implications of discoveries at the molecular level for whole plant behavior, and improved prediction of plant and ecosystem responses to the environment are urgently needed. The purpose of this perspective is to introduce Crops in silico (cropsinsilico.org), an integrative and multi-scale modeling platform, as one solution that combines isolated modeling efforts toward the generation of virtual crops, which is open and accessible to the entire plant biology community. The major challenges involved both in the development and deployment of a shared, multi-scale modeling platform, which are summarized in this prospectus, were recently identified during the first Crops in silico Symposium and Workshop. PMID:28555150
A multi-scale modeling framework for instabilities of film/substrate systems
NASA Astrophysics Data System (ADS)
Xu, Fan; Potier-Ferry, Michel
2016-01-01
Spatial pattern formation in stiff thin films on soft substrates is investigated from a multi-scale point of view based on a technique of slowly varying Fourier coefficients. A general macroscopic modeling framework is developed and then a simplified macroscopic model is derived. The model incorporates Asymptotic Numerical Method (ANM) as a robust path-following technique to trace the post-buckling evolution path and to predict secondary bifurcations. The proposed multi-scale finite element framework allows sinusoidal and square checkerboard patterns as well as their bifurcation portraits to be described from a quantitative standpoint. Moreover, it provides an efficient way to compute large-scale instability problems with a significant reduction of computational cost compared to full models.
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.
Multiscale Modeling of Transport Phenomena and Dendritic Growth in Laser Cladding Processes
NASA Astrophysics Data System (ADS)
Tan, Wenda; Wen, Shaoyi; Bailey, Neil; Shin, Yung C.
2011-12-01
A multiscale model is developed in this article to investigate the transport phenomena and dendrite growth in the diode-laser-cladding process. A transient model with an improved level-set method is built to simulate the heat/mass transport and the dynamic evolution of the molten pool surface on the macroscale. A novel model integrating the cellular automata (CA) and phase field (PF) methods is used to simulate the dendritic growth of multicomponent alloys in the mushy zone. The multiscale model is validated against the experiments, and the predicted geometry of clad tracks and the predicted dendrite arm spacing of microstructure match reasonably well with the experimental results. The effects of the processing parameters on the track geometry and microstructure are also investigated.
A multiscale modelling approach for the regulation of the cell cycle by the circadian clock.
El Cheikh, Raouf; Bernard, Samuel; El Khatib, Nader
2017-08-07
We present a multiscale mathematical model for the regulation of the cell cycle by the circadian clock. Biologically, the model describes the proliferation of a population of heterogeneous cells connected to each other. The model consists of a high dimensional transport equation structured by molecular contents of the cell cycle-circadian clock coupled oscillator. We propose a computational method for resolution adapted from the concept of particle methods. We study the impact of molecular dynamics on cell proliferation and show an example where discordance of division rhythms between population and single cell levels is observed. This highlights the importance of multiscale modeling where such results cannot be inferred from considering solely one biological level. Copyright © 2017 Elsevier Ltd. All rights reserved.
Asynchronous coupling of hybrid models for efficient simulation of multiscale systems
NASA Astrophysics Data System (ADS)
Lockerby, Duncan A.; Patronis, Alexander; Borg, Matthew K.; Reese, Jason M.
2015-03-01
We present a new coupling approach for the time advancement of multi-physics models of multiscale systems. This extends the method of E et al. (2009) [5] to deal with an arbitrary number of models. Coupling is performed asynchronously, with each model being assigned its own timestep size. This enables accurate long timescale predictions to be made at the computational cost of the short timescale simulation. We propose a method for selecting appropriate timestep sizes based on the degree of scale separation that exists between models. A number of example applications are used for testing and benchmarking, including a comparison with experimental data of a thermally driven rarefied gas flow in a micro capillary. The multiscale simulation results are in very close agreement with the experimental data, but are produced almost 50,000 times faster than from a conventionally-coupled simulation.
Voluntary EMG-to-force estimation with a multi-scale physiological muscle model.
Hayashibe, Mitsuhiro; Guiraud, David
2013-09-04
EMG-to-force estimation based on muscle models, for voluntary contraction has many applications in human motion analysis. The so-called Hill model is recognized as a standard model for this practical use. However, it is a phenomenological model whereby muscle activation, force-length and force-velocity properties are considered independently. Perreault reported Hill modeling errors were large for different firing frequencies, level of activation and speed of contraction. It may be due to the lack of coupling between activation and force-velocity properties. In this paper, we discuss EMG-force estimation with a multi-scale physiology based model, which has a link to underlying crossbridge dynamics. Differently from the Hill model, the proposed method provides dual dynamics of recruitment and calcium activation. The ankle torque was measured for the plantar flexion along with EMG measurements of the medial gastrocnemius (GAS) and soleus (SOL). In addition to Hill representation of the passive elements, three models of the contractile parts have been compared. Using common EMG signals during isometric contraction in four able-bodied subjects, torque was estimated by the linear Hill model, the nonlinear Hill model and the multi-scale physiological model that refers to Huxley theory. The comparison was made in normalized scale versus the case in maximum voluntary contraction. The estimation results obtained with the multi-scale model showed the best performances both in fast-short and slow-long term contraction in randomized tests for all the four subjects. The RMS errors were improved with the nonlinear Hill model compared to linear Hill, however it showed limitations to account for the different speed of contractions. Average error was 16.9% with the linear Hill model, 9.3% with the modified Hill model. In contrast, the error in the multi-scale model was 6.1% while maintaining a uniform estimation performance in both fast and slow contractions schemes. We introduced a
Wirth, B; Asoka-Kumar, P; Denison, A; Glade, S; Howell, R; Marian, J; Odette, G; Sterne, P
2004-04-06
The objective of this work is to determine the chemical composition of nanometer precipitates responsible for irradiation hardening and embrittlement of reactor pressure vessel steels, which threaten to limit the operating lifetime of nuclear power plants worldwide. The scientific approach incorporates computational multiscale modeling of radiation damage and microstructural evolution in Fe-Cu-Ni-Mn alloys, and experimental characterization by positron annihilation spectroscopy and small angle neutron scattering. The modeling and experimental results are
Multiscale Modeling for the Analysis for Grain-Scale Fracture Within Aluminum Microstructures
NASA Technical Reports Server (NTRS)
Glaessgen, Edward H.; Phillips, Dawn R.; Yamakov, Vesselin; Saether, Erik
2005-01-01
Multiscale modeling methods for the analysis of metallic microstructures are discussed. Both molecular dynamics and the finite element method are used to analyze crack propagation and stress distribution in a nanoscale aluminum bicrystal model subjected to hydrostatic loading. Quantitative similarity is observed between the results from the two very different analysis methods. A bilinear traction-displacement relationship that may be embedded into cohesive zone finite elements is extracted from the nanoscale molecular dynamics results.
On unified modeling, theory, and method for solving multi-scale global optimization problems
NASA Astrophysics Data System (ADS)
Gao, David Yang
2016-10-01
A unified model is proposed for general optimization problems in multi-scale complex systems. Based on this model and necessary assumptions in physics, the canonical duality theory is presented in a precise way to include traditional duality theories and popular methods as special applications. Two conjectures on NP-hardness are proposed, which should play important roles for correctly understanding and efficiently solving challenging real-world problems. Applications are illustrated for both nonconvex continuous optimization and mixed integer nonlinear programming.
Multiscale modeling approach for calculating grain-boundary energies from first principles
Shenderova, O.A.; Brenner, D.W.; Nazarov, A.A.; Romanov, A.E.; Yang, L.H.
1998-02-01
A multiscale modeling approach is proposed for calculating energies of tilt-grain boundaries in covalent materials from first principles over an entire misorientation range for given tilt axes. The method uses energies from density-functional calculations for a few key structures as input into a disclination structural-units model. This approach is demonstrated by calculating energies of {l_angle}001{r_angle}-symmetrical tilt-grain boundaries in diamond. {copyright} {ital 1998} {ital The American Physical Society}
The Models 3 / Community Multiscale Model for Air Quality (CMAQ) has been designed for one-atmosphere assessments for multiple pollutants including ozone (O3), particulate matter (PM10, PM2.5), and acid / nutrient deposition. In this paper we report initial results of our evalu...
The Models-3 Community Multi-scale Air Quality (CMAQ) model, first released by the USEPA in 1999 (Byun and Ching. 1999), continues to be developed and evaluated. The principal components of the CMAQ system include a comprehensive emission processor known as the Sparse Matrix O...
The Models 3 / Community Multiscale Model for Air Quality (CMAQ) has been designed for one-atmosphere assessments for multiple pollutants including ozone (O3), particulate matter (PM10, PM2.5), and acid / nutrient deposition. In this paper we report initial results of our evalu...
The development of an episode selection and aggregation approach, designed to support distributional estimation of use with the Models-3 Community Multiscale Air Quality (CMAQ) model, is described. The approach utilized cluster analysis of the 700-hPa east-west and north-south...
The adaptation of the Community Multiscale Air Quality (CMAQ) modeling system to simulate O_{3}, particulate matter, and related precursor distributions over the northern hemisphere is presented. Hemispheric simulations with CMAQ and the Weather Research and Forecasting (...
The adaptation of the Community Multiscale Air Quality (CMAQ) modeling system to simulate O_{3}, particulate matter, and related precursor distributions over the northern hemisphere is presented. Hemispheric simulations with CMAQ and the Weather Research and Forecasting (...
Thomas, Michael S C; Forrester, Neil A; Ronald, Angelica
2016-01-01
In the multidisciplinary field of developmental cognitive neuroscience, statistical associations between levels of description play an increasingly important role. One example of such associations is the observation of correlations between relatively common gene variants and individual differences in behavior. It is perhaps surprising that such associations can be detected despite the remoteness of these levels of description, and the fact that behavior is the outcome of an extended developmental process involving interaction of the whole organism with a variable environment. Given that they have been detected, how do such associations inform cognitive-level theories? To investigate this question, we employed a multiscale computational model of development, using a sample domain drawn from the field of language acquisition. The model comprised an artificial neural network model of past-tense acquisition trained using the backpropagation learning algorithm, extended to incorporate population modeling and genetic algorithms. It included five levels of description-four internal: genetic, network, neurocomputation, behavior; and one external: environment. Since the mechanistic assumptions of the model were known and its operation was relatively transparent, we could evaluate whether cross-level associations gave an accurate picture of causal processes. We established that associations could be detected between artificial genes and behavioral variation, even under polygenic assumptions of a many-to-one relationship between genes and neurocomputational parameters, and when an experience-dependent developmental process interceded between the action of genes and the emergence of behavior. We evaluated these associations with respect to their specificity (to different behaviors, to function vs. structure), to their developmental stability, and to their replicability, as well as considering issues of missing heritability and gene-environment interactions. We argue that gene
A multi-scale urban atmospheric dispersion model for emergency management
NASA Astrophysics Data System (ADS)
Miao, Yucong; Liu, Shuhua; Zheng, Hui; Zheng, Yijia; Chen, Bicheng; Wang, Shu
2014-11-01
To assist emergency management planning and prevention in case of hazardous chemical release into the atmosphere, especially in densely built-up regions with large populations, a multi-scale urban atmospheric dispersion model was established. Three numerical dispersion experiments, at horizontal resolutions of 10 m, 50 m and 3000 m, were performed to estimate the adverse effects of toxic chemical release in densely built-up areas. The multi-scale atmospheric dispersion model is composed of the Weather Forecasting and Research (WRF) model, the Open Source Field Operation and Manipulation software package, and a Lagrangian dispersion model. Quantification of the adverse health effects of these chemical release events are given by referring to the U.S. Environmental Protection Agency's Acute Exposure Guideline Levels. The wind fields of the urban-scale case, with 3 km horizontal resolution, were simulated by the Beijing Rapid Update Cycle system, which were utilized by the WRF model. The sub-domain-scale cases took advantage of the computational fluid dynamics method to explicitly consider the effects of buildings. It was found that the multi-scale atmospheric dispersion model is capable of simulating the flow pattern and concentration distribution on different scales, ranging from several meters to kilometers, and can therefore be used to improve the planning of prevention and response programs.
A multi-scale approach to mass segmentation using active contour models
NASA Astrophysics Data System (ADS)
Yu, Hongwei; Li, Lihua; Xu, Weidong; Liu, Wei
2010-03-01
As an important step of mass classification, mass segmentation plays an important role in computer-aided diagnosis (CAD). In this paper, we propose a novel scheme for breast mass segmentation in mammograms, which is based on level set method and multi-scale analysis. Mammogram is firstly decomposed by Gaussian pyramid into a sequence of images from fine to coarse, the C-V model is then applied at the coarse scale, and the obtained rough contour is used as the initial contour for segmentation at the fine scale. A local active contour (LAC) model based on image local information is utilized to refine the rough contour locally at the fine scale. In addition, the feature of area and gray level extracted from coarse segmentation is used to set the parameters of LAC model automatically to improve the adaptivity of our method. The results show the higher accuracy and robustness of the proposed multi-scale segmentation method than the conventional ones.
Multiscale Modeling, Simulation and Visualization and Their Potential for Future Aerospace Systems
NASA Technical Reports Server (NTRS)
Noor, Ahmed K. (Compiler)
2002-01-01
This document contains the proceedings of the Training Workshop on Multiscale Modeling, Simulation and Visualization and Their Potential for Future Aerospace Systems held at NASA Langley Research Center, Hampton, Virginia, March 5 - 6, 2002. The workshop was jointly sponsored by Old Dominion University's Center for Advanced Engineering Environments and NASA. Workshop attendees were from NASA, other government agencies, industry, and universities. The objectives of the workshop were to give overviews of the diverse activities in hierarchical approach to material modeling from continuum to atomistics; applications of multiscale modeling to advanced and improved material synthesis; defects, dislocations, and material deformation; fracture and friction; thin-film growth; characterization at nano and micro scales; and, verification and validation of numerical simulations, and to identify their potential for future aerospace systems.
Multiscale modeling of membrane rearrangement, drainage, and rupture in evolving foams.
Saye, Robert I; Sethian, James A
2013-05-10
Modeling the physics of foams and foamlike materials, such as soapy froths, fire retardants, and lightweight crash-absorbent structures, presents challenges, because of the vastly different time and space scales involved. By separating and coupling these disparate scales, we have designed a multiscale framework to model dry foam dynamics. This leads to a predictive and flexible computational methodology linking, with a few simplifying assumptions, foam drainage, rupture, and topological rearrangement, to coupled interface-fluid motion under surface tension, gravity, and incompressible fluid dynamics. Our computed results match theoretical analyses and experimentally observed physical effects, including thin-film drainage and interference, and are used to study bubble rupture cascades and macroscopic rearrangement. The developed multiscale model allows quantitative computation of complex foam evolution phenomena.
Stress and strain localization in stretched collagenous tissues via a multiscale modelling approach.
Marino, Michele; Vairo, Giuseppe
2014-01-01
Mechanobiology of cells in soft collagenous tissues is highly affected by both tissue response at the macroscale and stress/strain localization mechanisms due to features at lower scales. In this paper, the macroscale mechanical behaviour of soft collagenous tissues is modelled by a three-level multiscale approach, based on a multi-step homogenisation technique from nanoscale up to the macroscale. Nanoscale effects, related to both intermolecular cross-links and collagen mechanics, are accounted for, together with geometric nonlinearities at the microscale. Moreover, an effective submodelling procedure is conceived in order to evaluate the local stress and strain fields at the microscale, which is around and within cells. Numerical results, obtained by using an incremental finite element formulation and addressing stretched tendinous tissues, prove consistency and accuracy of the model at both macroscale and microscale, confirming also the effectiveness of the multiscale modelling concept for successfully analysing physiopathological processes in biological tissues.
Zhang, Le; Jiang, Beini; Wu, Yukun; Strouthos, Costas; Sun, Phillip Zhe; Su, Jing; Zhou, Xiaobo
2011-12-16
Multiscale agent-based modeling (MABM) has been widely used to simulate Glioblastoma Multiforme (GBM) and its progression. At the intracellular level, the MABM approach employs a system of ordinary differential equations to describe quantitatively specific intracellular molecular pathways that determine phenotypic switches among cells (e.g. from migration to proliferation and vice versa). At the intercellular level, MABM describes cell-cell interactions by a discrete module. At the tissue level, partial differential equations are employed to model the diffusion of chemoattractants, which are the input factors of the intracellular molecular pathway. Moreover, multiscale analysis makes it possible to explore the molecules that play important roles in determining the cellular phenotypic switches that in turn drive the whole GBM expansion. However, owing to limited computational resources, MABM is currently a theoretical biological model that uses relatively coarse grids to simulate a few cancer cells in a small slice of brain cancer tissue. In order to improve this theoretical model to simulate and predict actual GBM cancer progression in real time, a graphics processing unit (GPU)-based parallel computing algorithm was developed and combined with the multi-resolution design to speed up the MABM. The simulated results demonstrated that the GPU-based, multi-resolution and multiscale approach can accelerate the previous MABM around 30-fold with relatively fine grids in a large extracellular matrix. Therefore, the new model has great potential for simulating and predicting real-time GBM progression, if real experimental data are incorporated.
Lefkimmiatis, Stamatios; Maragos, Petros; Papandreou, George
2009-08-01
We present an improved statistical model for analyzing Poisson processes, with applications to photon-limited imaging. We build on previous work, adopting a multiscale representation of the Poisson process in which the ratios of the underlying Poisson intensities (rates) in adjacent scales are modeled as mixtures of conjugate parametric distributions. Our main contributions include: 1) a rigorous and robust regularized expectation-maximization (EM) algorithm for maximum-likelihood estimation of the rate-ratio density parameters directly from the noisy observed Poisson data (counts); 2) extension of the method to work under a multiscale hidden Markov tree model (HMT) which couples the mixture label assignments in consecutive scales, thus modeling interscale coefficient dependencies in the vicinity of image edges; 3) exploration of a 2-D recursive quad-tree image representation, involving Dirichlet-mixture rate-ratio densities, instead of the conventional separable binary-tree image representation involving beta-mixture rate-ratio densities; and 4) a novel multiscale image representation, which we term Poisson-Haar decomposition, that better models the image edge structure, thus yielding improved performance. Experimental results on standard images with artificially simulated Poisson noise and on real photon-limited images demonstrate the effectiveness of the proposed techniques.
Developing a multiscale, multi-resolution agent-based brain tumor model by graphics processing units
2011-01-01
Multiscale agent-based modeling (MABM) has been widely used to simulate Glioblastoma Multiforme (GBM) and its progression. At the intracellular level, the MABM approach employs a system of ordinary differential equations to describe quantitatively specific intracellular molecular pathways that determine phenotypic switches among cells (e.g. from migration to proliferation and vice versa). At the intercellular level, MABM describes cell-cell interactions by a discrete module. At the tissue level, partial differential equations are employed to model the diffusion of chemoattractants, which are the input factors of the intracellular molecular pathway. Moreover, multiscale analysis makes it possible to explore the molecules that play important roles in determining the cellular phenotypic switches that in turn drive the whole GBM expansion. However, owing to limited computational resources, MABM is currently a theoretical biological model that uses relatively coarse grids to simulate a few cancer cells in a small slice of brain cancer tissue. In order to improve this theoretical model to simulate and predict actual GBM cancer progression in real time, a graphics processing unit (GPU)-based parallel computing algorithm was developed and combined with the multi-resolution design to speed up the MABM. The simulated results demonstrated that the GPU-based, multi-resolution and multiscale approach can accelerate the previous MABM around 30-fold with relatively fine grids in a large extracellular matrix. Therefore, the new model has great potential for simulating and predicting real-time GBM progression, if real experimental data are incorporated. PMID:22176732
Daily reservoir inflow forecasting using multiscale deep feature learning with hybrid models
NASA Astrophysics Data System (ADS)
Bai, Yun; Chen, Zhiqiang; Xie, Jingjing; Li, Chuan
2016-01-01
Inflow forecasting applies data supports for the operations and managements of reservoirs. A multiscale deep feature learning (MDFL) method with hybrid models is proposed in this paper to deal with the daily reservoir inflow forecasting. Ensemble empirical mode decomposition and Fourier spectrum are first employed to extract multiscale (trend, period and random) features, which are then represented by three deep belief networks (DBNs), respectively. The weights of each DBN are subsequently applied to initialize a neural network (D-NN). The outputs of the three-scale D-NNs are finally reconstructed using a sum-up strategy toward the forecasting results. A historical daily inflow series (from 1/1/2000 to 31/12/2012) of the Three Gorges reservoir, China, is investigated by the proposed MDFL with hybrid models. For comparison, four peer models are adopted for the same task. The results show that, the present model overwhelms all the peer models in terms of mean absolute percentage error (MAPE = 11.2896%), normalized root-mean-square error (NRMSE = 0.2292), determination coefficient criteria (R2 = 0.8905), and peak percent threshold statistics (PPTS(5) = 10.0229%). The addressed method integrates the deep framework with multiscale and hybrid observations, and therefore being good at exploring sophisticated natures in the reservoir inflow forecasting.
Toward multiscale modelings of grain-fluid systems
NASA Astrophysics Data System (ADS)
Chareyre, Bruno; Yuan, Chao; Montella, Eduard P.; Salager, Simon
2017-06-01
Computationally efficient methods have been developed for simulating partially saturated granular materials in the pendular regime. In contrast, one hardly avoid expensive direct resolutions of 2-phase fluid dynamics problem for mixed pendular-funicular situations or even saturated regimes. Following previous developments for single-phase flow, a pore-network approach of the coupling problems is described. The geometry and movements of phases and interfaces are described on the basis of a tetrahedrization of the pore space, introducing elementary objects such as bridge, meniscus, pore body and pore throat, together with local rules of evolution. As firmly established local rules are still missing on some aspects (entry capillary pressure and pore-scale pressure-saturation relations, forces on the grains, or kinetics of transfers in mixed situations) a multi-scale numerical framework is introduced, enhancing the pore-network approach with the help of direct simulations. Small subsets of a granular system are extracted, in which multiphase scenario are solved using the Lattice-Boltzman method (LBM). In turns, a global problem is assembled and solved at the network scale, as illustrated by a simulated primary drainage.
Multi-scale modelling of uranyl chloride solutions
Nguyen, Thanh-Nghi; Duvail, Magali Villard, Arnaud; Dufrêche, Jean-François; Molina, John Jairo; Guilbaud, Philippe
2015-01-14
Classical molecular dynamics simulations with explicit polarization have been successfully used to determine the structural and thermodynamic properties of binary aqueous solutions of uranyl chloride (UO{sub 2}Cl{sub 2}). Concentrated aqueous solutions of uranyl chloride have been studied to determine the hydration properties and the ion-ion intera