Engineering topics

Einstein, Daniel R.

Publications and source records attributed to Einstein, Daniel R..

18 records

DOE OSTI2016

Computational Fluid Dynamics Modeling of Bacillus anthracis Spore Deposition in Rabbit and Human Respiratory Airways

Three-dimensional computational fluid dynamics and Lagrangian particle deposition models were developed to compare the deposition of aerosolized Bacillus anthracis spores in the respiratory airways of a human with that of the rabbit, a species commonly used in the study of anthrax disease. The respiratory airway geometries for each species were derived from computed tomography (CT) or µCT images. Both models encompassed airways that extended from the external nose to the lung with a total of 272 outlets in the human model and 2878 outlets in the rabbit model. All simulations of spore deposition were conducted under transient, inhalation-exhalation breathing conditions using average species-specific minute volumes. The highest exposure concentration was modeled in the rabbit based upon prior acute inhalation studies. For comparison, human simulation was also conducted at the same concentration. Results demonstrated that regional spore deposition patterns were sensitive to airway geometry and ventilation profiles. Due to the complex airway geometries in the rabbit nose, higher spore deposition efficiency was predicted in the upper conducting airways compared to the human at the same air concentration of anthrax spores. As a result, higher particle deposition was predicted in the conducting airways and deep lung of the human compared to the rabbit lung due to differences in airway branching pattern. This information can be used to refine published and ongoing biokinetic models of inhalation anthrax spore exposures, which currently estimate deposited spore concentrations based solely upon exposure concentrations and inhaled doses that do not factor in species-specific anatomy and physiology.

bacillus anthracis↗

DOE OSTI2016

Comparison of realistic and idealized breathing patterns in computational models of airflow and vapor dosimetry in the rodent upper respiratory tract

Abstract Context: Computational fluid dynamics (CFD) simulations of airflows coupled with physiologically based pharmacokinetic (PBPK) modeling of respiratory tissue doses of airborne materials have traditionally used either steady-state inhalation or a sinusoidal approximation of the breathing cycle for airflow simulations despite their differences from normal breathing patterns. Objective: Evaluate the impact of realistic breathing patterns, including sniffing, on predicted nasal tissue concentrations of a reactive vapor that targets the nose in rats as a case study. Materials and methods: Whole-body plethysmography measurements from a free-breathing rat were used to produce profiles of normal breathing, sniffing and combinations of both as flow inputs to CFD/PBPK simulations of acetaldehyde exposure. Results: For the normal measured ventilation profile, modest reductions in time- and tissue depth-dependent areas under the curve (AUC) acetaldehyde concentrations were predicted in the wet squamous, respiratory and transitional epithelium along the main airflow path, while corresponding increases were predicted in the olfactory epithelium, especially the most distal regions of the ethmoid turbinates, versus the idealized profile. The higher amplitude/frequency sniffing profile produced greater AUC increases over the idealized profile in the olfactory epithelium, especially in the posterior region. Conclusions: The differences in tissue AUCs at known lesion-forming regions for acetaldehyde between normal and idealized profiles were minimal, suggesting that sinusoidal profiles may be used for this chemical and exposure concentration. However, depending upon the chemical, exposure system and concentration and the time spent sniffing, the use of realistic breathing profiles, including sniffing, could become an important modulator for local tissue dose predictions.

dosimetry↗

DOE OSTI2016

Development of a Zealand white rabbit deposition model to study inhalation anthrax

Despite using rabbits in several inhalation exposure experiments to study diseases such as anthrax, there is a lack of understanding regarding deposition characteristics and fate of inhaled particles (bio-aerosols and viruses) in the respiratory tracts of rabbits. Such information allows dosimetric extrapolation to humans to inform human outcomes. The lung geometry of the New Zealand white rabbit (referred to simply as rabbits throughout the article) was constructed using recently acquired scanned images of the conducting airways of rabbits and available information on its acinar region. In addition, functional relationships were developed for the lung and breathing parameters of rabbits as a function of body weight. The lung geometry and breathing parameters were used to extend the existing deposition model for humans and several other species to rabbits. Evaluation of the deposition model for rabbits was made by comparing predictions with available measurements in the literature. Deposition predictions in the lungs of rabbits indicated smaller deposition fractions compared to those found in humans across various particle diameter ranges. The application of the deposition model for rabbits was demonstrated by extrapolating deposition predictions in rabbits to find equivalent human exposure concentrations assuming the same dose-response relationship between the two species. Human equivalent exposure concentration levels were found to be much smaller than those for rabbits.

deposition modeling↗

DOE OSTI2015

Respiratory Tract Lung Geometry and Dosimetry Model for Male Sprague-Dawley Rats

While inhalation toxicological studies of various compounds have been conducted using a number of different strains of rats, mechanistic dosimetry models have only had tracheobronchial (TB) structural data for Long-Evans rats, detailed morphometric data on the alveolar region of Sprague-Dawley rats and limited alveolar data on other strains. Based upon CT imaging data for two male Sprague-Dawley rats, a 15-generation, symmetric typical path model was developed for the TB region. Literature data for the alveolar region of Sprague-Dawley rats were analyzed to develop an eight-generation model, and the two regions were joined to provide a complete lower respiratory tract model for Sprague-Dawley rats. The resulting lung model was used to examine particle deposition in Sprague-Dawley rats and to compare these results with predicted deposition in Long-Evans rats. Relationships of various physiologic variables and lung volumes were either developed in this study or extracted from the literature to provide the necessary input data for examining particle deposition. While the lengths, diameters and branching angles of the TB airways differed between the two Sprague-Dawley rats, the predicted deposition patterns in the three major respiratory tract regions were very similar. Between Sprague-Dawley and Long-Evans rats, significant differences in TB and alveolar predicted deposition fractions were observed over a wide range of particle sizes, with TB deposition fractions being up to 3- to 4-fold greater in Sprague-Dawley rats and alveolar deposition being significantly greater in Long-Evans rats. Thus, strain-specific lung geometry models should be used for particle deposition calculations and interspecies dose comparisons.

Miller, Frederick J.↗

DOE OSTI2015

Fluid–Structure Interaction Analysis of Papillary Muscle Forces Using a Comprehensive Mitral Valve Model with 3D Chordal Structure

Numerical models of native heart valves are being used to study valve biomechanics to aid design and development of repair procedures and replacement devices. These models have evolved from simple two-dimensional approximations to complex three-dimensional, fully coupled fluid-structure interaction (FSI) systems. Such simulations are useful for predicting the mechanical and hemodynamic loading on implanted valve devices. A current challenge for improving the accuracy of these predictions is choosing and implementing modeling boundary conditions. In order to address this challenge, we are utilizing an advanced in-vitro system to validate FSI conditions for the mitral valve system. Explanted ovine mitral valves were mounted in an in vitro setup, and structural data for the mitral valve was acquired with *CT. Experimental data from the in-vitro ovine mitral valve system were used to validate the computational model. As the valve closes, the hemodynamic data, high speed lea et dynamics, and force vectors from the in-vitro system were compared to the results of the FSI simulation computational model. The total force of 2.6 N per papillary muscle is matched by the computational model. In vitro and in vivo force measurements are important in validating and adjusting material parameters in computational models. The simulations can then be used to answer questions that are otherwise not possible to investigate experimentally. This work is important to maximize the validity of computational models of not just the mitral valve, but any biomechanical aspect using computational simulation in designing medical devices.

Comprehensive Computational Model↗

DOE OSTI2015

Comparison of CT-derived Ventilation Maps with Deposition Patterns of Inhaled Microspheres in Rats

Purpose: Computer models for inhalation toxicology and drug-aerosol delivery studies rely on ventilation pattern inputs for predictions of particle deposition and vapor uptake. However, changes in lung mechanics due to disease can impact airflow dynamics and model results. It has been demonstrated that non-invasive, in vivo, 4DCT imaging (3D imaging at multiple time points in the breathing cycle) can be used to map heterogeneities in ventilation patterns under healthy and disease conditions. The purpose of this study was to validate ventilation patterns measured from CT imaging by exposing the same rats to an aerosol of fluorescent microspheres (FMS) and examining particle deposition patterns using cryomicrotome imaging. Materials and Methods: Six male Sprague-Dawley rats were intratracheally instilled with elastase to a single lobe to induce a heterogeneous disease. After four weeks, rats were imaged over the breathing cycle by CT then immediately exposed to an aerosol of ~1µm FMS for ~5 minutes. After the exposure, the lungs were excised and prepared for cryomicrotome imaging, where a 3D image of FMS deposition was acquired using serial sectioning. Cryomicrotome images were spatially registered to match the live CT images to facilitate direct quantitative comparisons of FMS signal intensity with the CT-based ventilation maps. Results: Comparisons of fractional ventilation in contiguous, non-overlapping, 3D regions between CT-based ventilation maps and FMS images showed strong correlations in fractional ventilation (r=0.888, p<0.0001). Conclusion: We conclude that ventilation maps derived from CT imaging are predictive of the 1µm aerosol deposition used in ventilation-perfusion heterogeneity inhalation studies.

Jacob, Rick E.↗

DOE OSTI2014

AHF: Array-Based Half-Facet Data Structure for Mixed-Dimensional and Non-Manifold Meshes

We present an Array-based Half-Facet mesh data structure, or AHF, for efficient mesh query and modification operations. The AHF extends the compact array-based half-edge and half-face data structures (T.J. Alumbaugh and X. Jiao, Compact array-based mesh data structures, IMR, 2005) to support mixed-dimensional and non-manifold meshes. The design goals of our data structure include generality to support such meshes, efficiency of neighborhood queries and mesh modification, compactness of memory footprint, and facilitation of interoperability of mesh-based application codes. To accomplish these goals, our data structure uses sibling half-facets as a core abstraction, coupled with other explicit and implicit representations of entities. A unique feature of our data structure is a comprehensive implementation in MATLAB, which allows rapid prototyping, debugging, testing, and deployment of meshing algorithms and other mesh-based numerical methods. We have also developed C++ implementation built on top of MOAB (T.J. Tautges, R. Meyers, and K. Merkley, MOAB: A Mesh-Oriented Database, Sandia National Laboratories, 2004). We present some comparisons of the memory requirements and computational costs, and also demonstrate its effectiveness with a few sample applications.

Dyedov, Volodymyr↗

DOE OSTI2014

Surface Remeshing with Robust High-Order Reconstruction

Remeshing is an important problem in variety of applications, such as finite element methods and geometry processing. Surface remeshing poses some unique challenges, as it must deliver not only good mesh quality but also good geometric accuracy. For applications such as finite elements with high-order elements (quadratic or cubic elements), the geometry must be preserved to high-order (third-order or higher) accuracy, since low-order accuracy may undermine the convergence of numerical computations. The problem is particularly challenging if the CAD model is not available for the underlying geometry, and is even more so if the surface meshes contain some inverted elements. We describe remeshing strategies that can simultaneously produce high-quality triangular meshes, untangling mildly folded triangles and preserve the geometry to high-order of accuracy. Our approach extends our earlier works on high-order surface reconstruction and mesh optimization by enhancing its robustness with a geometric limiter for under-resolved geometries. We also integrate high-order surface reconstruction with surface mesh adaptation techniques, which alter the number of triangles and nodes. We demonstrate the utilization of our method to meshes for high-order finite elements, biomedical image-based surface meshes, and complex interface meshes in fluid simulations.

Ray, Navamita↗

DOE OSTI2013

A Membrane Model from Implicit Elasticity Theory. Application to Visceral Pleura

A Fungean solid is derived for membranous materials as a body defined by isotropic response functions whose mathematical structure is that of a Hookean solid where the elastic constants are replaced by functions of state derived from an implicit, thermodynamic, internal energy function. The theory utilizes Biot’s (Lond Edinb Dublin Philos Mag J Sci 27:468–489, 1939) definitions for stress and strain that, in one-dimension, are the stress/strain measures adopted by Fung (Am J Physiol 28:1532–1544, 1967) when he postulated what is now known as Fung’s law. Our Fungean membrane model is parameterized against a biaxial data set acquired from a porcine pleural membrane subjected to three, sequential, proportional, planar extensions. These data support an isotropic/deviatoric split in the stress and strain-rate hypothesized by our theory. These data also demonstrate that the material response is highly nonlinear but, otherwise, mechanically isotropic. These data are described reasonably well by our otherwise simple, four-parameter, material model.

36 MATERIALS SCIENCE↗

DOE OSTI2013

In Situ Casting and Imaging of the Rat Airway Tree for Accurate 3D Reconstruction

The use of anatomically accurate, animal-specific airway geometries is important for understanding and modeling the physiology of the respiratory system. One approach for acquiring detailed airway architecture is to create a bronchial cast of the conducting airways. However, typical casting procedures either do not faithfully preserve the in vivo branching angles, or produce rigid casts that when removed for imaging are fragile and thus easily damaged. We address these problems by creating an in situ bronchial cast of the conducting airways in rats that can be subsequently imaged in situ using 3D micro-CT imaging. We also demonstrate that deformations in airway branch angles resulting from the casting procedure are small, and that these angle deformations can be reversed through an interactive adjustment of the segmented cast geometry. Animal work was approved by the Institutional Animal Care and Use Committee of Pacific Northwest National Laboratory.

Jacob, Rick E.↗

DOE OSTI2013

A bidirectional coupling procedure applied to multiscale respiratory modeling

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 pressure applied to the multiple sets of ODEs. In both the simplified geometry and in the imaging-based geometry, the performance of the method was comparable to that of monolithic schemes, in most cases requiring only a single CFD evaluation per time step. Thus, this new accelerator allows us to begin combining pulmonary CFD models with lower-dimensional models of pulmonary mechanics with little computational overhead. Moreover, because the CFD and lower-dimensional models are totally separate, this framework affords great flexibility in terms of the type and breadth of the adopted lower-dimensional model, allowing the biomedical researcher to appropriately focus on model design. Research funded by the National Heart and Blood Institute Award 1RO1HL073598.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2013

Dynamic Multiscale Boundary Conditions for 4D CT Images of Healthy and Emphysematous Rat

Changes in the shape of the lung during breathing determine the movement of airways and alveoli, and thus impact airflow dynamics. Modeling airflow dynamics in health and disease is a key goal for predictive multiscale models of respiration. Past efforts to model changes in lung shape during breathing have measured shape at multiple breath-holds. However, breath-holds do not capture hysteretic differences between inspiration and expiration resulting from the additional energy required for inspiration. Alternatively, imaging dynamically – without breath-holds – allows measurement of hysteretic differences. In this study, we acquire multiple micro-CT images per breath (4DCT) in live rats, and from these images we develop, for the first time, dynamic volume maps. These maps show changes in local volume across the entire lung throughout the breathing cycle and accurately predict the global pressure-volume (PV) hysteresis.

Jacob, Rick E.↗

DOE OSTI2013

Velo and REXAN - Integrated Data Management and High Speed Analysis for Experimental Facilities

The Chemical Imaging Initiative at the Pacific Northwest National Laboratory (PNNL) is creating a ‘Rapid Experimental Analysis’ (REXAN) Framework, based on the concept of reusable component libraries. REXAN allows developers to quickly compose and customize high throughput analysis pipelines for a range of experiments, as well as supporting the creation of multi-modal analysis pipelines. In addition, PNNL has coupled REXAN with its collaborative data management and analysis environment Velo to create an easy to use data management and analysis environments for experimental facilities. This paper will discuss the benefits of Velo and REXAN in the context of three examples: PNNL High Resolution Mass Spectrometry - reducing analysis times from hours to seconds, and enabling the analysis of much larger data samples (100KB to 40GB) at the same time · ALS X-Ray tomography - reducing analysis times of combined STXM and EM data collected at the ALS from weeks to minutes, decreasing manual work and increasing data volumes that can be analysed in a single step ·Multi-modal nano-scale analysis of STXM and TEM data - providing a semi automated process for particle detection The creation of REXAN has significantly shortened the development time for these analysis pipelines. The integration of Velo and REXAN has significantly increased the scientific productivity of the instruments and their users by creating easy to use data management and analysis environments with greatly reduced analysis times and improved analysis capabilities.

Kleese van Dam, Kerstin↗

DOE OSTI2013

An Efficient Algorithm for Mapping Imaging Data to 3D Unstructured Grids in Computational Biomechanics

Geometries for organ scale and multiscale simulations of organ function are now routinely derived from imaging data. However, medical images may also contain spatially heterogeneous information other than geometry that are relevant to such simulations either as initial conditions or in the form of model parameters. In this manuscript, we present an algorithm for the efficient and robust mapping of such data to imaging based unstructured polyhedral grids in parallel. We then illustrate the application of our mapping algorithm to three different mapping problems: 1) the mapping of MRI diffusion tensor data to an unstuctured ventricular grid; 2) the mapping of serial cyro-section histology data to an unstructured mouse brain grid; and 3) the mapping of CT-derived volumetric strain data to an unstructured multiscale lung grid. Execution times and parallel performance are reported for each case.

Einstein, Daniel R.↗

DOE OSTI2012

Development of a rhesus monkey lung geometry model and application to particle deposition in comparison to humans

The exposure-dose-response characterization of an inhalation hazard established in an animal species needs to be translated to an equivalent characterization in humans relative to comparable doses or exposure scenarios. Here, the first geometry model of the conducting airways for rhesus monkeys is developed based upon CT images of the conducting airways of a 6-month-old male, rhesus monkey. An algorithm was developed for adding the alveolar region airways using published rhesus morphometric data. The resultant lung geometry model can be used in mechanistic particle or gaseous dosimetry models. Such dosimetry models require estimates of the upper respiratory tract volume of the animal and the functional residual capacity, as well as of the tidal volume and breathing frequency of the animal. The relationship of these variables to rhesus monkeys of differing body weights was established by synthesizing and modeling published data as well as modeling pulmonary function measurements on 121 rhesus control animals. Deposition patterns of particles up to 10 µm in size were examined for endotracheal and and up to 5 µm for spontaneous breathing in infant and young adult monkeys and compared to those for humans. Deposition fraction of respirable size particles was found to be higher in the conducting airways of infant and young adult rhesus monkeys compared to humans. Due to the filtering effect of the conducting airways, pulmonary deposition in rhesus monkeys was lower than that in humans. Finally, future research areas are identified that would either allow replacing assumptions or improving the newly developed lung model.

Asgharian, Bahman↗

DOE OSTI2012

Branch-Based Model for the Diameters of the Pulmonary Airways: Accounting for Departures From Self-Consistency and Registration Errors

We examine a previously published branch-based approach to modeling airway diameters that is predicated on the assumption of self-consistency across all levels of the tree. We mathematically formulate this assumption, propose a method to test it and develop a more general model to be used when the assumption is violated. We discuss the effect of measurement error on the estimated models and propose methods that account for it. The methods are illustrated on data from MRI and CT images of silicone casts of two rats, two normal monkeys and one ozone-exposed monkey. Our results showed substantial departures from self-consistency in all five subjects. When departures from selfconsistency exist we do not recommend using the self-consistency model, even as an approximation, as we have shown that it may likely lead to an incorrect representation of the diameter geometry. Measurement error has an important impact on the estimated morphometry models and needs to be accounted for in the analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Viscoelastic Model for Lung Parenchyma for Multi-Scale Modeling of Respiratory System - Phase II: Dodecahedral Micro-Model

In the first year of this contractual effort a hypo-elastic constitutive model was developed and shown to have great potential in modeling the elastic response of parenchyma. This model resides at the macroscopic level of the continuum. In this, the second year of our support, an isotropic dodecahedron is employed as an alveolar model. This is a microscopic model for parenchyma. A hopeful outcome is that the linkage between these two scales of modeling will be a source of insight and inspiration that will aid us in the final year's activity: creating a viscoelastic model for parenchyma.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2004

Invariant Theory for Dispersed Transverse Isotropy: An Efficient Means for Modeling Fiber Splay

Most soft tissues possess an oriented architecture of collagen fiber bundles, conferring both anisotropy and nonlinearity to their elastic behavior. Transverse isotropy has often been assumed for a subset of these tissues that have a single macroscopically-identifiable preferred fiber direction. Micro-structural studies, however, suggest that, in some tissues, collagen fibers are approximately normally distributed about a mean preferred fiber direction. Structural constitutive equations that account for this dispersion of fibers have been shown to capture the mechanical complexity of these tissues quite well. Such descriptions, however, are computationally cumbersome for two-dimensional (2D) fiber distributions, let alone for fully three-dimensional (3D) fiber populations. In this paper, we develop a new constitutive law for such tissues, based on a novel invariant theory for dispersed transverse isotropy. The invariant theory is based on a novel closed-form splay invariant that can easily handle 3D fiber populations, and that only requires a single parameter in the 2D case. The model is polyconvex and fits biaxial data for aortic valve tissue as accurately as the standard structural model. Modification of the fiber stress-strain law requires no re-formulation of the constitutive tangent matrix, making the model flexible for different types of soft tissues. Most importantly, the model is computationally expedient in a finite-element analysis.

Freed, alan D.↗