Modelling of Dynamic Rock Fracture Process with a Rate-Dependent Combined Continuum Damage-Embedded Discontinuity Model Incorporating Microstructure

NASA Astrophysics Data System (ADS)

Saksala, Timo

2016-10-01

This paper deals with numerical modelling of rock fracture under dynamic loading. For this end, a combined continuum damage-embedded discontinuity model is applied in finite element modelling of crack propagation in rock. In this model, the strong loading rate sensitivity of rock is captured by the rate-dependent continuum scalar damage model that controls the pre-peak nonlinear hardening part of rock behaviour. The post-peak exponential softening part of the rock behaviour is governed by the embedded displacement discontinuity model describing the mode I, mode II and mixed mode fracture of rock. Rock heterogeneity is incorporated in the present approach by random description of the rock mineral texture based on the Voronoi tessellation. The model performance is demonstrated in numerical examples where the uniaxial tension and compression tests on rock are simulated. Finally, the dynamic three-point bending test of a semicircular disc is simulated in order to show that the model correctly predicts the strain rate-dependent tensile strengths as well as the failure modes of rock in this test. Special emphasis is laid on modelling the loading rate sensitivity of tensile strength of Laurentian granite.

Simplifying the complexity of resistance heterogeneity in metastasis

PubMed Central

Lavi, Orit; Greene, James M.; Levy, Doron; Gottesman, Michael M.

2014-01-01

The main goal of treatment regimens for metastasis is to control growth rates, not eradicate all cancer cells. Mathematical models offer methodologies that incorporate high-throughput data with dynamic effects on net growth. The ideal approach would simplify, but not over-simplify, a complex problem into meaningful and manageable estimators that predict a patient’s response to specific treatments. Here, we explore three fundamental approaches with different assumptions concerning resistance mechanisms, in which the cells are categorized into either discrete compartments or described by a continuous range of resistance levels. We argue in favor of modeling resistance as a continuum and demonstrate how integrating cellular growth rates, density-dependent versus exponential growth, and intratumoral heterogeneity improves predictions concerning the resistance heterogeneity of metastases. PMID:24491979

Pore-scale simulation of CO2-water-rock interactions

NASA Astrophysics Data System (ADS)

Deng, H.; Molins, S.; Steefel, C. I.; DePaolo, D. J.

2017-12-01

In Geologic Carbon Storage (GCS) systems, the migration of scCO2 versus CO2-acidifed brine ultimately determines the extent of mineral trapping and caprock integrity, i.e. the long-term storage efficiency and security. While continuum scale multiphase reactive transport models are valuable for large scale investigations, they typically (over-)simplify pore-scale dynamics and cannot capture local heterogeneities that may be important. Therefore, pore-scale models are needed in order to provide mechanistic understanding of how fine scale structural variations and heterogeneous processes influence the transport and geochemistry in the context of multiphase flow, and to inform parameterization of continuum scale modeling. In this study, we investigate the interplay of different processes at pore scale (e.g. diffusion, reactions, and multiphase flow) through the coupling of a well-developed multiphase flow simulator with a sophisticated reactive transport code. The objectives are to understand where brine displaced by scCO2 will reside in a rough pore/fracture, and how the CO2-water-rock interactions may affect the redistribution of different phases. In addition, the coupled code will provide a platform for model testing in pore-scale multiphase reactive transport problems.

Modeling postshock evolution of large electropores

NASA Astrophysics Data System (ADS)

Neu, John C.; Krassowska, Wanda

2003-02-01

The Smoluchowski equation (SE), which describes the evolution of pores created by electric shocks, cannot be applied to modeling large and long-lived pores for two reasons: (1) it does not predict pores of radius above 20 nm without also predicting membrane rupture; (2) it does not predict postshock growth of pores. This study proposes a model in which pores are coupled by membrane tension, resulting in a nonlinear generalization of SE. The predictions of the model are explored using examples of homogeneous (all pore radii r are equal) and heterogeneous (0⩽r⩽rmax) distributions of pores. Pores in a homogeneous population either shrink to zero or assume a stable radius corresponding to the minimum of the bilayer energy. For a heterogeneous population, such a stable radius does not exist. All pores, except rmax, shrink to zero and rmax grows to infinity. However, the unbounded growth of rmax is not physical because the number of pores per cell decreases in time and the continuum model loses validity. When the continuum formulation is replaced by the discrete one, the model predicts the coarsening process: all pores, except rmax, shrink to zero and rmax assumes a stable radius. Thus, the model with tension-coupled pores does not predict membrane rupture and the predicted postshock growth of pores is consistent with experimental evidence.

Multiscale Molecular Dynamics Model for Heterogeneous Charged Systems

NASA Astrophysics Data System (ADS)

Stanton, L. G.; Glosli, J. N.; Murillo, M. S.

2018-04-01

Modeling matter across large length scales and timescales using molecular dynamics simulations poses significant challenges. These challenges are typically addressed through the use of precomputed pair potentials that depend on thermodynamic properties like temperature and density; however, many scenarios of interest involve spatiotemporal variations in these properties, and such variations can violate assumptions made in constructing these potentials, thus precluding their use. In particular, when a system is strongly heterogeneous, most of the usual simplifying assumptions (e.g., spherical potentials) do not apply. Here, we present a multiscale approach to orbital-free density functional theory molecular dynamics (OFDFT-MD) simulations that bridges atomic, interionic, and continuum length scales to allow for variations in hydrodynamic quantities in a consistent way. Our multiscale approach enables simulations on the order of micron length scales and 10's of picosecond timescales, which exceeds current OFDFT-MD simulations by many orders of magnitude. This new capability is then used to study the heterogeneous, nonequilibrium dynamics of a heated interface characteristic of an inertial-confinement-fusion capsule containing a plastic ablator near a fuel layer composed of deuterium-tritium ice. At these scales, fundamental assumptions of continuum models are explored; features such as the separation of the momentum fields among the species and strong hydrogen jetting from the plastic into the fuel region are observed, which had previously not been seen in hydrodynamic simulations.

An Image-based Micro-continuum Pore-scale Model for Gas Transport in Organic-rich Shale

NASA Astrophysics Data System (ADS)

Guo, B.; Tchelepi, H.

2017-12-01

Gas production from unconventional source rocks, such as ultra-tight shales, has increased significantly over the past decade. However, due to the extremely small pores ( 1-100 nm) and the strong material heterogeneity, gas flow in shale is still not well understood and poses challenges for predictive field-scale simulations. In recent years, digital rock analysis has been applied to understand shale gas transport at the pore-scale. An issue with rock images (e.g. FIB-SEM, nano-/micro-CT images) is the so-called "cutoff length", i.e., pores and heterogeneities below the resolution cannot be resolved, which leads to two length scales (resolved features and unresolved sub-resolution features) that are challenging for flow simulations. Here we develop a micro-continuum model, modified from the classic Darcy-Brinkman-Stokes framework, that can naturally couple the resolved pores and the unresolved nano-porous regions. In the resolved pores, gas flow is modeled with Stokes equation. In the unresolved regions where the pore sizes are below the image resolution, we develop an apparent permeability model considering non-Darcy flow at the nanoscale including slip flow, Knudsen diffusion, adsorption/desorption, surface diffusion, and real gas effect. The end result is a micro-continuum pore-scale model that can simulate gas transport in 3D reconstructed shale images. The model has been implemented in the open-source simulation platform OpenFOAM. In this paper, we present case studies to demonstrate the applicability of the model, where we use 3D segmented FIB-SEM and nano-CT shale images that include four material constituents: organic matter, clay, granular mineral, and pore. In addition to the pore structure and the distribution of the material constituents, we populate the model with experimental measurements (e.g. size distribution of the sub-resolution pores from nitrogen adsorption) and parameters from the literature and identify the relative importance of different physics on gas production. Overall, the micro-continuum model provides a novel tool for digital rock analysis of organic-rich shale.

Chimera and modulated drift states in a ring of nonlocally coupled oscillators with heterogeneous phase lags

NASA Astrophysics Data System (ADS)

Choe, Chol-Ung; Kim, Ryong-Son; Ri, Ji-Song

2017-09-01

We consider a ring of phase oscillators with nonlocal coupling strength and heterogeneous phase lags. We analyze the effects of heterogeneity in the phase lags on the existence and stability of a variety of steady states. A nonlocal coupling with heterogeneous phase lags that allows the system to be solved analytically is suggested and the stability of solutions along the Ott-Antonsen invariant manifold is explored. We present a complete bifurcation diagram for stationary patterns including the uniform drift and modulated drift states as well as chimera state, which reveals that the stable modulated drift state and a continuum of metastable drift states could occur due to the heterogeneity of the phase lags. We verify our theoretical results using the direct numerical simulations of the model system.

Bottom-up modeling of damage in heterogeneous quasi-brittle solids

NASA Astrophysics Data System (ADS)

Rinaldi, Antonio

2013-03-01

The theoretical modeling of multisite cracking in quasi-brittle materials is a complex damage problem, hard to model with traditional methods of fracture mechanics due to its multiscale nature and to strain localization induced by microcracks interaction. Macroscale "effective" elastic models can be conveniently applied if a suitable Helmholtz free energy function is identified for a given material scenario. Del Piero and Truskinovsky (Continuum Mech Thermodyn 21:141-171, 2009), among other authors, investigated macroscale continuum solutions capable of matching—in a top-down view—the phenomenology of the damage process for quasi-brittle materials regardless of the microstructure. On the contrary, this paper features a physically based solution method that starts from the direct consideration of the microscale properties and, in a bottom-up view, recovers a continuum elastic description. This procedure is illustrated for a simple one-dimensional problem of this type, a bar modeled stretched by an axial displacement, where the bar is modeled as a 2D random lattice of decohesive spring elements of finite strength. The (microscale) data from simulations are used to identify the "exact" (macro-) damage parameter and to build up the (macro-) Helmholtz function for the equivalent elastic model, bridging the macroscale approach by Del Piero and Truskinovsky. The elastic approach, coupled with microstructural knowledge, becomes a more powerful tool to reproduce a broad class of macroscopic material responses by changing the convexity-concavity of the Helmholtz energy. The analysis points out that mean-field statistics are appropriate prior to damage localization but max-field statistics are better suited in the softening regime up to failure, where microstrain fluctuation needs to be incorporated in the continuum model. This observation is of consequence to revise mean-field damage models from literature and to calibrate Nth gradient continuum models.

Prognostic heterogeneity of diastolic abnormalities along left ventricular remodeling continuum according to survival rates and laser polarimetry of blood

NASA Astrophysics Data System (ADS)

Boychuk, T. M.; Ivashchuk, O. I.; Kolomoiets, M. Y.; Mikhaliev, K. O.; Chursina, T. Y.

2011-09-01

The results of examination of 35 arterial hypertension and coronary heart disease patients are presented. The clinical, paraclinical and echocardiographic examinations were performed, and the parameters of prognosis (survival) according to Seattle Heart Failure Model, as well as the optical (polarimetric) properties of erythrocytic suspension were determined. The group of patients under examination was stratified by patterns of remodeling of left ventricle (LV). It was determined that increasing of anisotropy of erythrocytic suspension along LV remodeling patterns continuum correlates with aggravation of structural and functional state of LV and is associated with unfavorable prognosis.

Is Seismically Determined Q an Intrinsic Material Property?

NASA Astrophysics Data System (ADS)

Langston, C. A.

2003-12-01

The seismic quality factor, Q, has a well-defined physical meaning as an intrinsic material property associated with a visco-elastic or a non-linear stress-strain constitutive relation for a material. Measurement of Q from seismic waves, however, involves interpreting seismic wave amplitude and phase as deviations from some ideal elastic wave propagation model. Thus, assumptions in the elastic wave propagation model become the basis for attributing anelastic properties to the earth continuum. Scientifically, the resulting Q model derived from seismic data is no more than a hypothesis that needs to be verified by other independent experiments concerning the continuum constitutive law and through careful examination of the truth of the assumptions in the wave propagation model. A case in point concerns the anelasticity of Mississippi embayment sediments in the central U.S. that has important implications for evaluation of earthquake strong ground motions. Previous body wave analyses using converted Sp phases have suggested that Qs is ~30 in the sediments based on simple ray theory assumptions. However, detailed modeling of 1D heterogeneity in the sediments shows that Qs cannot be resolved by the Sp data. An independent experiment concerning the amplitude decay of surface waves propagating in the sediments shows that Qs must be generally greater than 80 but is also subject to scattering attenuation. Apparent Q effects seen in direct P and S waves can also be produced by wave tunneling mechanisms in relatively simple 1D heterogeneity. Heterogeneity is a general geophysical attribute of the earth as shown by many high-resolution data sets and should be used as the first litmus test on assumptions made in seismic Q studies before a Q model can be interpreted as an intrinsic material property.

Coarse-grained mechanics of viral shells

NASA Astrophysics Data System (ADS)

Klug, William S.; Gibbons, Melissa M.

2008-03-01

We present an approach for creating three-dimensional finite element models of viral capsids from atomic-level structural data (X-ray or cryo-EM). The models capture heterogeneous geometric features and are used in conjunction with three-dimensional nonlinear continuum elasticity to simulate nanoindentation experiments as performed using atomic force microscopy. The method is extremely flexible; able to capture varying levels of detail in the three-dimensional structure. Nanoindentation simulations are presented for several viruses: Hepatitis B, CCMV, HK97, and φ29. In addition to purely continuum elastic models a multiscale technique is developed that combines finite-element kinematics with MD energetics such that large-scale deformations are facilitated by a reduction in degrees of freedom. Simulations of these capsid deformation experiments provide a testing ground for the techniques, as well as insight into the strength-determining mechanisms of capsid deformation. These methods can be extended as a framework for modeling other proteins and macromolecular structures in cell biology.

Pore-scale and Continuum Simulations of Solute Transport Micromodel Benchmark Experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oostrom, Martinus; Mehmani, Yashar; Romero Gomez, Pedro DJ

Four sets of micromodel nonreactive solute transport experiments were conducted with flow velocity, grain diameter, pore-aspect ratio, and flow focusing heterogeneity as the variables. The data sets were offered to pore-scale modeling groups to test their simulators. Each set consisted of two learning experiments, for which all results was made available, and a challenge experiment, for which only the experimental description and base input parameters were provided. The experimental results showed a nonlinear dependence of the dispersion coefficient on the Peclet number, a negligible effect of the pore-aspect ratio on transverse mixing, and considerably enhanced mixing due to flow focusing.more » Five pore-scale models and one continuum-scale model were used to simulate the experiments. Of the pore-scale models, two used a pore-network (PN) method, two others are based on a lattice-Boltzmann (LB) approach, and one employed a computational fluid dynamics (CFD) technique. The learning experiments were used by the PN models to modify the standard perfect mixing approach in pore bodies into approaches to simulate the observed incomplete mixing. The LB and CFD models used these experiments to appropriately discretize the grid representations. The continuum model use published non-linear relations between transverse dispersion coefficients and Peclet numbers to compute the required dispersivity input values. Comparisons between experimental and numerical results for the four challenge experiments show that all pore-scale models were all able to satisfactorily simulate the experiments. The continuum model underestimated the required dispersivity values and, resulting in less dispersion. The PN models were able to complete the simulations in a few minutes, whereas the direct models needed up to several days on supercomputers to resolve the more complex problems.« less

Net growth rate of continuum heterogeneous biofilms with inhibition kinetics.

PubMed

Gonzo, Elio Emilio; Wuertz, Stefan; Rajal, Veronica B

2018-01-01

Biofilm systems can be modeled using a variety of analytical and numerical approaches, usually by making simplifying assumptions regarding biofilm heterogeneity and activity as well as effective diffusivity. Inhibition kinetics, albeit common in experimental systems, are rarely considered and analytical approaches are either lacking or consider effective diffusivity of the substrate and the biofilm density to remain constant. To address this obvious knowledge gap an analytical procedure to estimate the effectiveness factor (dimensionless substrate mass flux at the biofilm-fluid interface) was developed for a continuum heterogeneous biofilm with multiple limiting-substrate Monod kinetics to different types of inhibition kinetics. The simple perturbation technique, previously validated to quantify biofilm activity, was applied to systems where either the substrate or the inhibitor is the limiting component, and cases where the inhibitor is a reaction product or the substrate also acts as the inhibitor. Explicit analytical equations are presented for the effectiveness factor estimation and, therefore, the calculation of biomass growth rate or limiting substrate/inhibitor consumption rate, for a given biofilm thickness. The robustness of the new biofilm model was tested using kinetic parameters experimentally determined for the growth of Pseudomonas putida CCRC 14365 on phenol. Several additional cases have been analyzed, including examples where the effectiveness factor can reach values greater than unity, characteristic of systems with inhibition kinetics. Criteria to establish when the effectiveness factor can reach values greater than unity in each of the cases studied are also presented.

Transport of Cryptosporidium parvum Oocysts in Charge Heterogeneous Porous Media: Microfluidics Experiment and Numerical Simulation

NASA Astrophysics Data System (ADS)

Liu, Y.; Meng, X.; Guo, Z.; Zhang, C.; Nguyen, T. H.; Hu, D.; Ji, J.; Yang, X.

2017-12-01

Colloidal attachment on charge heterogeneous grains has significant environmental implications for transport of hazardous colloids, such as pathogens, in the aquifer, where iron, manganese, and aluminium oxide minerals are the major source of surface charge heterogeneity of the aquifer grains. A patchwise surface charge model is often used to describe the surface charge heterogeneity of the grains. In the patchwise model, the colloidal attachment efficiency is linearly correlated with the fraction of the favorable patches (θ=λ(θf - θu)+θu). However, our previous microfluidic study showed that the attachment efficiency of oocysts of Cryptosporidium parvum, a waterborne protozoan parasite, was not linear correlated with the fraction of the favorable patches (λ). In this study, we developed a pore scale model to simulate colloidal transport and attachment on charge heterogeneous grains. The flow field was simulated using the LBM method and colloidal transport and attachment were simulated using the Lagrange particle tracking method. The pore scale model was calibrated with experimental results of colloidal and oocyst transport in microfluidic devices and was then used to simulate oocyst transport in charge heterogeneous porous media under a variety of environmental relative conditions, i.e. the fraction of favorable patchwise, ionic strength, and pH. The results of the pore scale simulations were used to evaluate the effect of surface charge heterogeneity on upscaling of oocyst transport from pore to continuum scale and to develop an applicable correlation between colloidal attachment efficiency and the fraction of the favorable patches.

The continuum of monocyte phenotypes: Experimental evidence and prognostic utility in assessing cardiovascular risk.

PubMed

Cignarella, Andrea; Tedesco, Serena; Cappellari, Roberta; Fadini, Gian Paolo

2018-03-30

The monocyte-macrophage cell lineage represents a major player in innate immunity, and is involved in many physiologic and pathologic conditions. Particularly, monocyte-macrophages play a very important role in atherosclerosis and cardiovascular disease. Monocyte heterogeneity is well recognized but the biologic and clinical meaning of the various monocyte subtypes is not entirely understood. Traditionally, monocytes can be divided in classical, intermediate, and nonclassical based on expression of the surface antigens CD14 and CD16. While macrophage diversity is now well recognized to organize as a continuum, monocyte subsets have long been considered as separated entities. However, mounting evidence obtained by tracking the ontology of human monocytes help clarifying that monocytes mature from classical to nonclassical ones, through an intermediate phenotype. This concept is therefore best depicted as a continuum, whereas the subdivision into discrete CD14/CD16 subsets appears an oversimplification. In this review, we discuss the evidence supporting the existence of a monocyte continuum along with the technical challenges of monocyte characterization. In particular, we describe the advantage of considering monocytes along a continuous distribution for the evaluation of cardiovascular risk. We make the point that small transition along the monocyte continuum better reflects cardiovascular risk than a simplified analysis of discrete monocyte subsets. Recognizing the monocyte continuum can be helpful to model other pathophysiologic conditions where these cells are involved. ©2018 Society for Leukocyte Biology.

The Discontinuous Galerkin Method for the Multiscale Modeling of Dynamics of Crystalline Solids

DTIC Science & Technology

2007-08-26

number. 1. REPORT DATE 26 AUG 2007 2 . REPORT TYPE 3. DATES COVERED 00-00-2007 to 00-00-2007 4. TITLE AND SUBTITLE The Discontinuous Galerkin...Dynamics method (MAAD) [ 2 ], the bridging scale method [47], the bridging domain methods [48], the heterogeneous multiscale method (HMM) [23, 36, 24], and...method consists of three components, 1. a macro solver for the continuum model, 2 . a micro solver to equilibrate the atomistic system locally to the appro

Parameterisation of multi-scale continuum perfusion models from discrete vascular networks.

PubMed

Hyde, Eoin R; Michler, Christian; Lee, Jack; Cookson, Andrew N; Chabiniok, Radek; Nordsletten, David A; Smith, Nicolas P

2013-05-01

Experimental data and advanced imaging techniques are increasingly enabling the extraction of detailed vascular anatomy from biological tissues. Incorporation of anatomical data within perfusion models is non-trivial, due to heterogeneous vessel density and disparate radii scales. Furthermore, previous idealised networks have assumed a spatially repeating motif or periodic canonical cell, thereby allowing for a flow solution via homogenisation. However, such periodicity is not observed throughout anatomical networks. In this study, we apply various spatial averaging methods to discrete vascular geometries in order to parameterise a continuum model of perfusion. Specifically, a multi-compartment Darcy model was used to provide vascular scale separation for the fluid flow. Permeability tensor fields were derived from both synthetic and anatomically realistic networks using (1) porosity-scaled isotropic, (2) Huyghe and Van Campen, and (3) projected-PCA methods. The Darcy pressure fields were compared via a root-mean-square error metric to an averaged Poiseuille pressure solution over the same domain. The method of Huyghe and Van Campen performed better than the other two methods in all simulations, even for relatively coarse networks. Furthermore, inter-compartment volumetric flux fields, determined using the spatially averaged discrete flux per unit pressure difference, were shown to be accurate across a range of pressure boundary conditions. This work justifies the application of continuum flow models to characterise perfusion resulting from flow in an underlying vascular network.

Examining variations in health within rural Canada.

PubMed

Lavergne, M Ruth; Kephart, George

2012-01-01

Differences in health between urban and rural areas of Canada are well documented. Canadian rural communities are remarkably heterogeneous in terms of social, economic, and geographic characteristics. There is reason to believe that there is also considerable heterogeneity in health within rural Canada but existing literature has not given this adequate consideration. This article describes heterogeneity in health along the urban-rural continuum, both between and within categories of rural areas. Factors that may explain observed variations are then examined. The study population included all adult (>18 years) respondents on the Canadian Community Health Survey Cycle 1.1, linked to census subdivision-level data from the corresponding Canadian Census. Study areas were classified according to Metropolitan Influenced Zones (MIZ), which group rural areas based on their degree of connectivity with nearby urban areas. Dichotomized Health Utilities Index (HUI) scores were the outcome variable. Random-intercept logistic regression models investigated the associations of HUI with individual and area characteristics. To describe between-area variation in health, the proportion of the total variation accounted for by the area random effect (the intra-class correlation coefficient [ICC]) was estimated. To aid interpretation of the magnitude of the effect of area relative to other variables in the models, the ICC was also expressed as a median odds ratio (MOR), or the median amount by which the probability of disability will change for an individual who moves from one area to another. On a descriptive level, poorer health was observed in more remote rural areas, but the size of estimated effects for categories of rural areas was generally small compared with effects of other individual and area variables, and with the degree of heterogeneity between areas. The composition of rural areas is important in order to understand patterns in health. Individual income, education, and employment, and area characteristics such as Francophone or Aboriginal populations, and migration patterns help explain the gradient in health by MIZ, but considerable heterogeneity in health within categories of MIZ remains. In models stratified by MIZ, significant between-area heterogeneity was observed in all models, with MORs ranging from 1.18 to 1.53. It was observed that heterogeneity in health among rural areas is substantial, and generally larger than the effect of rurality, itself, on health. More attention is needed to understand the characteristics of Canada's heterogeneous rural communities, and the different processes by which disparities in health emerge and persist. The findings suggest that a focus on rurality alone, emphasizing urban versus rural disparities, or even continuum-based approaches like MIZ, may be less informative than finding ways to classify and examine different types of rural areas according to factors relevant to health.

Beyond the continuum: a multi-dimensional phase space for neutral-niche community assembly.

PubMed

Latombe, Guillaume; Hui, Cang; McGeoch, Melodie A

2015-12-22

Neutral and niche processes are generally considered to interact in natural communities along a continuum, exhibiting community patterns bounded by pure neutral and pure niche processes. The continuum concept uses niche separation, an attribute of the community, to test the hypothesis that communities are bounded by pure niche or pure neutral conditions. It does not accommodate interactions via feedback between processes and the environment. By contrast, we introduce the Community Assembly Phase Space (CAPS), a multi-dimensional space that uses community processes (such as dispersal and niche selection) to define the limiting neutral and niche conditions and to test the continuum hypothesis. We compare the outputs of modelled communities in a heterogeneous landscape, assembled by pure neutral, pure niche and composite processes. Differences in patterns under different combinations of processes in CAPS reveal hidden complexity in neutral-niche community dynamics. The neutral-niche continuum only holds for strong dispersal limitation and niche separation. For weaker dispersal limitation and niche separation, neutral and niche processes amplify each other via feedback with the environment. This generates patterns that lie well beyond those predicted by a continuum. Inferences drawn from patterns about community assembly processes can therefore be misguided when based on the continuum perspective. CAPS also demonstrates the complementary information value of different patterns for inferring community processes and captures the complexity of community assembly. It provides a general tool for studying the processes structuring communities and can be applied to address a range of questions in community and metacommunity ecology. © 2015 The Author(s).

Beyond the continuum: a multi-dimensional phase space for neutral–niche community assembly

PubMed Central

Latombe, Guillaume; McGeoch, Melodie A.

2015-01-01

Neutral and niche processes are generally considered to interact in natural communities along a continuum, exhibiting community patterns bounded by pure neutral and pure niche processes. The continuum concept uses niche separation, an attribute of the community, to test the hypothesis that communities are bounded by pure niche or pure neutral conditions. It does not accommodate interactions via feedback between processes and the environment. By contrast, we introduce the Community Assembly Phase Space (CAPS), a multi-dimensional space that uses community processes (such as dispersal and niche selection) to define the limiting neutral and niche conditions and to test the continuum hypothesis. We compare the outputs of modelled communities in a heterogeneous landscape, assembled by pure neutral, pure niche and composite processes. Differences in patterns under different combinations of processes in CAPS reveal hidden complexity in neutral–niche community dynamics. The neutral–niche continuum only holds for strong dispersal limitation and niche separation. For weaker dispersal limitation and niche separation, neutral and niche processes amplify each other via feedback with the environment. This generates patterns that lie well beyond those predicted by a continuum. Inferences drawn from patterns about community assembly processes can therefore be misguided when based on the continuum perspective. CAPS also demonstrates the complementary information value of different patterns for inferring community processes and captures the complexity of community assembly. It provides a general tool for studying the processes structuring communities and can be applied to address a range of questions in community and metacommunity ecology. PMID:26702047

Pore-scale and continuum simulations of solute transport micromodel benchmark experiments

DOE PAGES

Oostrom, M.; Mehmani, Y.; Romero-Gomez, P.; ...

2014-06-18

Four sets of nonreactive solute transport experiments were conducted with micromodels. Three experiments with one variable, i.e., flow velocity, grain diameter, pore-aspect ratio, and flow-focusing heterogeneity were in each set. The data sets were offered to pore-scale modeling groups to test their numerical simulators. Each set consisted of two learning experiments, for which our results were made available, and one challenge experiment, for which only the experimental description and base input parameters were provided. The experimental results showed a nonlinear dependence of the transverse dispersion coefficient on the Peclet number, a negligible effect of the pore-aspect ratio on transverse mixing,more » and considerably enhanced mixing due to flow focusing. Five pore-scale models and one continuum-scale model were used to simulate the experiments. Of the pore-scale models, two used a pore-network (PN) method, two others are based on a lattice Boltzmann (LB) approach, and one used a computational fluid dynamics (CFD) technique. Furthermore, we used the learning experiments, by the PN models, to modify the standard perfect mixing approach in pore bodies into approaches to simulate the observed incomplete mixing. The LB and CFD models used the learning experiments to appropriately discretize the spatial grid representations. For the continuum modeling, the required dispersivity input values were estimated based on published nonlinear relations between transverse dispersion coefficients and Peclet number. Comparisons between experimental and numerical results for the four challenge experiments show that all pore-scale models were all able to satisfactorily simulate the experiments. The continuum model underestimated the required dispersivity values, resulting in reduced dispersion. The PN models were able to complete the simulations in a few minutes, whereas the direct models, which account for the micromodel geometry and underlying flow and transport physics, needed up to several days on supercomputers to resolve the more complex problems.« less

Generalized continuum modeling of scale-dependent crystalline plasticity

NASA Astrophysics Data System (ADS)

Mayeur, Jason R.

The use of metallic material systems (e.g. pure metals, alloys, metal matrix composites) in a wide range of engineering applications from medical devices to electronic components to automobiles continues to motivate the development of improved constitutive models to meet increased performance demands while minimizing cost. Emerging technologies often incorporate materials in which the dominant microstructural features have characteristic dimensions reaching into the submicron and nanometer regime. Metals comprised of such fine microstructures often exhibit unique and size-dependent mechanical response, and classical approaches to constitutive model development at engineering (continuum) scales, being local in nature, are inadequate for describing such behavior. Therefore, traditional modeling frameworks must be augmented and/or reformulated to account for such phenomena. Crystal plasticity constitutive models have proven quite capable of capturing first-order microstructural effects such as grain orientation (elastic/plastic anisotropy), grain morphology, phase distribution, etc. on the deformation behavior of both single and polycrystals, yet suffer from the same limitations as other local continuum theories with regard to capturing scale-dependent mechanical response. This research is focused on the development, numerical implementation, and application of a generalized (nonlocal) theory of single crystal plasticity capable of describing the scale-dependent mechanical response of both single and polycrystalline metals that arises as a result of heterogeneous deformation. This research developed a dislocation-based theory of micropolar single crystal plasticity. The majority of nonlocal crystal plasticity theories are predicated on the connection between gradients of slip and geometrically necessary dislocations. Due to the diversity of existing nonlocal crystal plasticity theories, a review, summary, and comparison of representative model classes is presented in Chapter 2 from a unified dislocation-based perspective. The discussion of the continuum crystal plasticity theories is prefaced by a brief review of discrete dislocation plasticity, which facilitates the comparison of certain model aspects and also serves as a reference for latter segments of the research which make connection to this constitutive description. Chapter 2 has utility not only as a literature review, but also as a synthesis and analysis of competing and alternative nonlocal crystal plasticity modeling strategies from a common viewpoint. The micropolar theory of single crystal plasticity is presented in Chapter 3. Two different types of flow criteria are considered - the so-called single and multicriterion theories, and several variations of the dislocation-based strength models appropriate for each theory are presented and discussed. The numerical implementation of the two-dimensional version of the constitutive theory is given in Chapter 4. A user element subroutine for the implicit commercial finite element code Abaqus/Standard is developed and validated through the solution of initial-boundary value problems with closed-form solutions. Convergent behavior of the subroutine is also demonstrated for an initial-boundary value problem exhibiting strain localization. In Chapter 5, the models are employed to solve several standard initial-boundary value problems for heterogeneously deforming single crystals including simple shearing of a semi-infinite constrained thin film, pure bending of thin films, and simple shearing of a metal matrix composite with elastic inclusions. The simulation results are compared to those obtained from the solution of equivalent boundary value problems using discrete dislocation dynamics and alternative generalized crystal plasticity theories. Comparison and calibration with respect to the former provides guidance in the specification of non-traditional material parameters that arise in the model formulation and demonstrates its effectiveness at capturing the heterogeneous deformation fields and size-dependent mechanical behavior predicted by a finer scale constitutive description. Finally, in Chapter 6, the models are applied to simulate the deformation behavior of small polycrystalline ensembles. Several grain boundary constitutive descriptions are explored and the response characteristics are analyzed with respect to experimental observations as well as results obtained from discrete dislocation dynamics and alternative nonlocal crystal plasticity theories. Particular attention is focused on how the various grain boundary descriptions serve to either locally concentrate or diffuse deformation heterogeneity as a function of grain size.

Nanosecond laser ablation of target Al in a gaseous medium: explosive boiling

NASA Astrophysics Data System (ADS)

Mazhukin, V. I.; Mazhukin, A. V.; Demin, M. M.; Shapranov, A. V.

2018-03-01

An approximate mathematical description of the processes of homogeneous nucleation and homogeneous evaporation (explosive boiling) of a metal target (Al) under the influence of ns laser radiation is proposed in the framework of the hydrodynamic model. Within the continuum approach, a multi-phase, multi-front hydrodynamic model and a computational algorithm are designed to simulate nanosecond laser ablation of the metal targets immersed in gaseous media. The proposed approach is intended for modeling and detailed analysis of the mechanisms of heterogeneous and homogeneous evaporation and their interaction with each other. It is shown that the proposed model and computational algorithm allow modeling of interrelated mechanisms of heterogeneous and homogeneous evaporation of metals, manifested in the form of pulsating explosive boiling. Modeling has shown that explosive evaporation in metals is due to the presence of a near-surface temperature maximum. It has been established that in nanosecond pulsed laser ablation, such exposure regimes can be implemented in which phase explosion is the main mechanism of material removal.

Kinetic limit of heterogeneous melting in metals.

PubMed

Ivanov, Dmitriy S; Zhigilei, Leonid V

2007-05-11

The velocity and nanoscale shape of the melting front are investigated in a model that combines the molecular dynamics method with a continuum description of the electron heat conduction and electron-phonon coupling. The velocity of the melting front is strongly affected by the local drop of the lattice temperature, defined by the kinetic balance between the transfer of thermal energy to the latent heat of melting, the electron heat conduction from the overheated solid, and the electron-phonon coupling. The maximum velocity of the melting front is found to be below 3% of the room temperature speed of sound in the crystal, suggesting a limited contribution of heterogeneous melting under conditions of fast heating.

Frequency Dependent Macro-dispersion Induced by Oscillatory Inputs and Spatial Heterogeneity

NASA Astrophysics Data System (ADS)

Rajabi, F.; Battiato, I.

2017-12-01

Elucidating flow and transport processes at the pore scale is the cornerstone of most hydrologic studies in the subsurface. This becomes even more imperative when the system is subject to a cyclic forcing. Such temporal variations with evolving heterogeneity of time scales spanning from days to years can influence transport phenomena at the pore level, e.g. yearly freeze/thaw in the thin active layer of soil above permafrost zone whose thickness increases throughout the thaw season. Moreover, understanding the interactions of different physical phenomena at the pore scale is key to predict the behavior at the continuum scale. Yet, the connection between periodic inputs at the pore scale and macrotransport is to a great extent unknown. In the spirit of homogenization technique, we derived a macrotime continuum-scale equation as well as expressions for the effective transport coefficients. The macrodispersion arises from contributions of molecular diffusion, spatial heterogeneity and time-dependent fluctuations. Moreover, we have quantified the solute spreading by effective dispersion in terms of dimensionless numbers (Pe, Da, and Strouhal), i.e. expressing the interplay of molecular diffusion, advection, reaction and signal frequency. Yet, as every macroscopic model, spatiotemporally averaged models can breakdown when certain criteria are violated. This makes the continuum scale equation a poor approximation for the processes at the pore scale. To this end, we also provide the conditions under which the space-time averaged equations accurately describe pore-scale processes. In addition, this study gives a robust evidence that transverse mixing can in fact benefit from fluctuating boundary forcing due to the interaction of temporal fluctuations and molecular diffusion. Furthermore, it provides a robust quantitative foundation for designing the desired systems since the interplay of geometry and external forcing has been directly connected to each other in terms of dimensionless (St) number. We compare our theoretical framework with data from an experiment performed on several micro-channels with different geometry and different frequencies of injection at the inlet. The proposed formulation is found to provide remarkably good predictions and correctly explain the experimental mixing dynamics.

Ultra-Long Time Dynamics of Contaminant Plume Mixing Induced by Transient Forcing Factors in Geologic Formations

NASA Astrophysics Data System (ADS)

Rajabi, F.; Battiato, I.

2016-12-01

Long term predictions of the impact of anthropogenic stressors on the environment is essential to reduce the risks associated with processes such as CO2 sequestration and nuclear waste storage in the subsurface. On the other hand, transient forcing factors (e.g. time-varying injection or pumping rate) with evolving heterogeneity of time scales spanning from days to years can influence transport phenomena at the pore scale. A comprehensive spatio-temporal prediction of reactive transport in porous media under time-dependent forcing factors for thousands of years requires the formulation of continuum scale models for time-averages. Yet, as every macroscopic model, time-averaged models can loose predictivity and accuracy when certain conditions are violated. This is true whenever lack of temporal and spatial scale separation occurs and it makes the continuum scale equation a poor assumption for the processes at the pore scale. In this work, we consider mass transport of a dissolved species undergoing a heterogeneous reaction and subject to time-varying boundary conditions in a periodic porous medium. By means of homogenization method and asymptotic expansion technique, we derive a macro-time continuum-scale equation as well as expressions for its effective properties. Our analysis demonstrates that the dynamics at the macro-scale is strongly influenced by the interplay between signal frequency at the boundary and transport processes at the pore level. In addition, we provide the conditions under which the space-time averaged equations accurately describe pore-scale processes. To validate our theoretical predictions, we consider a thin fracture with reacting walls and transient boundary conditions at the inlet. Our analysis shows a good agreement between numerical simulations and theoretical predictions. Furthermore, our numerical experiments show that mixing patterns of the contaminant plumes at the pore level strongly depend on the signal frequency.

Studying the flow dynamics of a karst aquifer system with an equivalent porous medium model.

PubMed

Abusaada, Muath; Sauter, Martin

2013-01-01

The modeling of groundwater flow in karst aquifers is a challenge due to the extreme heterogeneity of its hydraulic parameters and the duality in their discharge behavior, that is, rapid response of highly conductive karst conduits and delayed drainage of the low-permeability fractured matrix after recharge events. There are a number of different modeling approaches for the simulation of the karst groundwater dynamics, applicable to different aquifer as well as modeling problem types, ranging from continuum models to double continuum models to discrete and hybrid models. This study presents the application of an equivalent porous model approach (EPM, single continuum model) to construct a steady-state numerical flow model for an important karst aquifer, that is, the Western Mountain Aquifer Basin (WMAB), shared by Israel and the West-Bank, using MODFLOW2000. The WMAB was used as a catchment since it is a well-constrained catchment with well-defined recharge and discharge components and therefore allows a control on the modeling approach, a very rare opportunity for karst aquifer modeling. The model demonstrates the applicability of equivalent porous medium models for the simulation of karst systems, despite their large contrast in hydraulic conductivities. As long as the simulated saturated volume is large enough to average out the local influence of karst conduits and as long as transport velocities are not an issue, EPM models excellently simulate the observed head distribution. The model serves as a starting basis that will be used as a reference for developing a long-term dynamic model for the WMAB, starting from the pre-development period (i.e., 1940s) up to date. © 2012, The Author(s). GroundWater © 2012, National Ground Water Association.

Coupling of a continuum ice sheet model and a discrete element calving model using a scientific workflow system

NASA Astrophysics Data System (ADS)

Memon, Shahbaz; Vallot, Dorothée; Zwinger, Thomas; Neukirchen, Helmut

2017-04-01

Scientific communities generate complex simulations through orchestration of semi-structured analysis pipelines which involves execution of large workflows on multiple, distributed and heterogeneous computing and data resources. Modeling ice dynamics of glaciers requires workflows consisting of many non-trivial, computationally expensive processing tasks which are coupled to each other. From this domain, we present an e-Science use case, a workflow, which requires the execution of a continuum ice flow model and a discrete element based calving model in an iterative manner. Apart from the execution, this workflow also contains data format conversion tasks that support the execution of ice flow and calving by means of transition through sequential, nested and iterative steps. Thus, the management and monitoring of all the processing tasks including data management and transfer of the workflow model becomes more complex. From the implementation perspective, this workflow model was initially developed on a set of scripts using static data input and output references. In the course of application usage when more scripts or modifications introduced as per user requirements, the debugging and validation of results were more cumbersome to achieve. To address these problems, we identified a need to have a high-level scientific workflow tool through which all the above mentioned processes can be achieved in an efficient and usable manner. We decided to make use of the e-Science middleware UNICORE (Uniform Interface to Computing Resources) that allows seamless and automated access to different heterogenous and distributed resources which is supported by a scientific workflow engine. Based on this, we developed a high-level scientific workflow model for coupling of massively parallel High-Performance Computing (HPC) jobs: a continuum ice sheet model (Elmer/Ice) and a discrete element calving and crevassing model (HiDEM). In our talk we present how the use of a high-level scientific workflow middleware enables reproducibility of results more convenient and also provides a reusable and portable workflow template that can be deployed across different computing infrastructures. Acknowledgements This work was kindly supported by NordForsk as part of the Nordic Center of Excellence (NCoE) eSTICC (eScience Tools for Investigating Climate Change at High Northern Latitudes) and the Top-level Research Initiative NCoE SVALI (Stability and Variation of Arctic Land Ice).

Decomposition of heterogeneous organic matterand its long-term stabilization in soils

USGS Publications Warehouse

Sierra, Carlos A.; Harmon, Mark E.; Perakis, Steven S.

2011-01-01

Soil organic matter is a complex mixture of material with heterogeneous biological, physical, and chemical properties. Decomposition models represent this heterogeneity either as a set of discrete pools with different residence times or as a continuum of qualities. It is unclear though, whether these two different approaches yield comparable predictions of organic matter dynamics. Here, we compare predictions from these two different approaches and propose an intermediate approach to study organic matter decomposition based on concepts from continuous models implemented numerically. We found that the disagreement between discrete and continuous approaches can be considerable depending on the degree of nonlinearity of the model and simulation time. The two approaches can diverge substantially for predicting long-term processes in soils. Based on our alternative approach, which is a modification of the continuous quality theory, we explored the temporal patterns that emerge by treating substrate heterogeneity explicitly. The analysis suggests that the pattern of carbon mineralization over time is highly dependent on the degree and form of nonlinearity in the model, mostly expressed as differences in microbial growth and efficiency for different substrates. Moreover, short-term stabilization and destabilization mechanisms operating simultaneously result in long-term accumulation of carbon characterized by low decomposition rates, independent of the characteristics of the incoming litter. We show that representation of heterogeneity in the decomposition process can lead to substantial improvements in our understanding of carbon mineralization and its long-term stability in soils.

Parameterization and prediction of nanoparticle transport in porous media: A reanalysis using artificial neural network

NASA Astrophysics Data System (ADS)

Babakhani, Peyman; Bridge, Jonathan; Doong, Ruey-an; Phenrat, Tanapon

2017-06-01

The continuing rapid expansion of industrial and consumer processes based on nanoparticles (NP) necessitates a robust model for delineating their fate and transport in groundwater. An ability to reliably specify the full parameter set for prediction of NP transport using continuum models is crucial. In this paper we report the reanalysis of a data set of 493 published column experiment outcomes together with their continuum modeling results. Experimental properties were parameterized into 20 factors which are commonly available. They were then used to predict five key continuum model parameters as well as the effluent concentration via artificial neural network (ANN)-based correlations. The Partial Derivatives (PaD) technique and Monte Carlo method were used for the analysis of sensitivities and model-produced uncertainties, respectively. The outcomes shed light on several controversial relationships between the parameters, e.g., it was revealed that the trend of Katt with average pore water velocity was positive. The resulting correlations, despite being developed based on a "black-box" technique (ANN), were able to explain the effects of theoretical parameters such as critical deposition concentration (CDC), even though these parameters were not explicitly considered in the model. Porous media heterogeneity was considered as a parameter for the first time and showed sensitivities higher than those of dispersivity. The model performance was validated well against subsets of the experimental data and was compared with current models. The robustness of the correlation matrices was not completely satisfactory, since they failed to predict the experimental breakthrough curves (BTCs) at extreme values of ionic strengths.

Continuum limit of the vibrational properties of amorphous solids.

PubMed

Mizuno, Hideyuki; Shiba, Hayato; Ikeda, Atsushi

2017-11-14

The low-frequency vibrational and low-temperature thermal properties of amorphous solids are markedly different from those of crystalline solids. This situation is counterintuitive because all solid materials are expected to behave as a homogeneous elastic body in the continuum limit, in which vibrational modes are phonons that follow the Debye law. A number of phenomenological explanations for this situation have been proposed, which assume elastic heterogeneities, soft localized vibrations, and so on. Microscopic mean-field theories have recently been developed to predict the universal non-Debye scaling law. Considering these theoretical arguments, it is absolutely necessary to directly observe the nature of the low-frequency vibrations of amorphous solids and determine the laws that such vibrations obey. Herein, we perform an extremely large-scale vibrational mode analysis of a model amorphous solid. We find that the scaling law predicted by the mean-field theory is violated at low frequency, and in the continuum limit, the vibrational modes converge to a mixture of phonon modes that follow the Debye law and soft localized modes that follow another universal non-Debye scaling law.

Continuum limit of the vibrational properties of amorphous solids

PubMed Central

Mizuno, Hideyuki; Ikeda, Atsushi

2017-01-01

The low-frequency vibrational and low-temperature thermal properties of amorphous solids are markedly different from those of crystalline solids. This situation is counterintuitive because all solid materials are expected to behave as a homogeneous elastic body in the continuum limit, in which vibrational modes are phonons that follow the Debye law. A number of phenomenological explanations for this situation have been proposed, which assume elastic heterogeneities, soft localized vibrations, and so on. Microscopic mean-field theories have recently been developed to predict the universal non-Debye scaling law. Considering these theoretical arguments, it is absolutely necessary to directly observe the nature of the low-frequency vibrations of amorphous solids and determine the laws that such vibrations obey. Herein, we perform an extremely large-scale vibrational mode analysis of a model amorphous solid. We find that the scaling law predicted by the mean-field theory is violated at low frequency, and in the continuum limit, the vibrational modes converge to a mixture of phonon modes that follow the Debye law and soft localized modes that follow another universal non-Debye scaling law. PMID:29087941

Imbedded-Fracture Formulation of THMC Processes in Fractured Media

NASA Astrophysics Data System (ADS)

Yeh, G. T.; Tsai, C. H.; Sung, R.

2016-12-01

Fractured media consist of porous materials and fracture networks. There exist four approaches to mathematically formulating THMC (Thermal-Hydrology-Mechanics-Chemistry) processes models in the system: (1) Equivalent Porous Media, (2) Dual Porosity or Dual Continuum, (3) Heterogeneous Media, and (4) Discrete Fracture Network. The first approach cannot explicitly explore the interactions between porous materials and fracture networks. The second approach introduces too many extra parameters (namely, exchange coefficients) between two media. The third approach may make the problems too stiff because the order of material heterogeneity may be too much. The fourth approach ignore the interaction between porous materials and fracture networks. This talk presents an alternative approach in which fracture networks are modeled with a lower dimension than the surrounding porous materials. Theoretical derivation of mathematical formulations will be given. An example will be illustrated to show the feasibility of this approach.

Deformation behaviors of three-dimensional graphene honeycombs under out-of-plane compression: Atomistic simulations and predictive modeling

NASA Astrophysics Data System (ADS)

Meng, Fanchao; Chen, Cheng; Hu, Dianyin; Song, Jun

2017-12-01

Combining atomistic simulations and continuum modeling, a comprehensive study of the out-of-plane compressive deformation behaviors of equilateral three-dimensional (3D) graphene honeycombs was performed. It was demonstrated that under out-of-plane compression, the honeycomb exhibits two critical deformation events, i.e., elastic mechanical instability (including elastic buckling and structural transformation) and inelastic structural collapse. The above events were shown to be strongly dependent on the honeycomb cell size and affected by the local atomic bonding at the cell junction. By treating the 3D graphene honeycomb as a continuum cellular solid, and accounting for the structural heterogeneity and constraint at the junction, a set of analytical models were developed to accurately predict the threshold stresses corresponding to the onset of those deformation events. The present study elucidates key structure-property relationships of 3D graphene honeycombs under out-of-plane compression, and provides a comprehensive theoretical framework to predictively analyze their deformation responses, and more generally, offers critical new knowledge for the rational bottom-up design of 3D networks of two-dimensional nanomaterials.

A Preprocessor for Modeling Nonpoint Sources in Fractured Media using MODFLOW and MT3D

NASA Astrophysics Data System (ADS)

Mun, Y.; Uchrin, C. G.

2002-05-01

There are a multitude of fractures in the geological structure of fractured media which act as conduits for subsurface fluid flow. The hydraulic properties of this flow are very heterogeneous even within a single unit and this heterogeneity is very localized. As a result, modeling flow in fractured media is difficult due to this heterogeneity. There are two major approaches to simulate the flow and transport of fluid flow in fractured media: the discrete fracture approach and the continuum approach. Precise characteristics such as geometry are required to use the discrete fracture approach. It, however, is difficult to determine the fluid flow through the fractures because of inaccessibility. In the continuum approach, although head distributions can match to well data, chemical concentration distributions are hard to match well sample concentration observations, because some aquifers are dominated by advective transport and others are likely to serve as reservoirs for immobile solutes. The MODFLOW preprocessor described in this paper has been developed and applied to the Cranberry Lake system in Northwestern New Jersey. Cranberry Lake has exhibited eutrophic characteristics for some time by nonpoint sources including surface water runoff, leaching from local septic systems and direct deposition. It has been estimated that 70% of the nutrient loading to the lake flows through fractured media from septic systems. The preprocessor presented in this paper utilizes percolation theory, which is concerned with the existence of ­ropen paths­_. The percolation threshold of a body-centered cubic lattice (3D), a square lattice (2D) and several other percolation numbers are applied to make the model system represent the fractured media. The distribution of hydraulic head within groundwater is simulated by MODFLOW and the advection-dispersion equation of nitrate transport is solved by MT3D. This study also simulates boron transport as an indicator.

Parallel multiscale simulations of a brain aneurysm

PubMed Central

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em

2012-01-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work. PMID:23734066

Parallel multiscale simulations of a brain aneurysm.

PubMed

Grinberg, Leopold; Fedosov, Dmitry A; Karniadakis, George Em

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multi-scale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier-Stokes solver εκ αr . The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers ( εκ αr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

Parallel multiscale simulations of a brain aneurysm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em, E-mail: george_karniadakis@brown.edu

2013-07-01

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm.more » The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.« less

Shock interactions with heterogeneous energetic materials

NASA Astrophysics Data System (ADS)

Yarrington, Cole D.; Wixom, Ryan R.; Damm, David L.

2018-03-01

The complex physical phenomenon of shock wave interaction with material heterogeneities has significant importance and nevertheless remains little understood. In many materials, the observed macroscale response to shock loading is governed by characteristics of the microstructure. Yet, the majority of computational studies aimed at predicting phenomena affected by these processes, such as the initiation and propagation of detonation waves in explosives or shock propagation in geological materials, employ continuum material and reactive burn model treatment. In an effort to highlight the grain-scale processes that underlie the observable effects in an energetic system, a grain-scale model for hexanitrostilbene (HNS) has been developed. The measured microstructures were used to produce synthetic computational representations of the pore structure, and a density functional theory molecular dynamics derived equation of state (EOS) was used for the fully dense HNS matrix. The explicit inclusion of the microstructure along with a fully dense EOS resulted in close agreement with historical shock compression experiments. More recent experiments on the dynamic reaction threshold were also reproduced by inclusion of a global kinetics model. The complete model was shown to reproduce accurately the expected response of this heterogeneous material to shock loading. Mesoscale simulations were shown to provide a clear insight into the nature of threshold behavior and are a way to understand complex physical phenomena.

Shock interactions with heterogeneous energetic materials

DOE PAGES

Yarrington, Cole D.; Wixom, Ryan R.; Damm, David L.

2018-03-14

The complex physical phenomenon of shock wave interaction with material heterogeneities has significant importance and nevertheless remains little understood. In many materials, the observed macroscale response to shock loading is governed by characteristics of the microstructure. Yet the majority of computational studies aimed at predicting phenomena affected by these processes, such as initiation and propagation of detonation waves in explosives, or shock propagation in geological materials, employ continuum material and reactive burn model treatment. In an effort to highlight the grain-scale processes that underlie the observable effects in an energetic system, a grain-scale model for hexanitrostilbene (HNS) has been developed.more » Measured microstructures were used to produce synthetic computational representations of the pore structure, and a density functional theory molecular dynamics (DFT-MD) derived equation of state (EOS) was used for the fully dense HNS matrix. The explicit inclusion of microstructure along with a fully-dense EOS resulted in close agreement with historical shock compression experiments. More recent experiments on dynamic reaction threshold were also reproduced by inclusion of a global kinetics model. The complete model was shown to reproduce accurately the expected response of this heterogeneous material to shock loading. Mesoscale simulations were shown to provide clear insight into the nature of threshold behavior, and are a way to understand complex physical phenomena.« less

Poroelastic finite difference modeling of seismic attenuation and dispersion due to mesoscopic-scale heterogeneity

NASA Astrophysics Data System (ADS)

Masson, Y. J.; Pride, S. R.

2007-03-01

Seismic attenuation and dispersion are numerically determined for computer-generated porous materials that contain arbitrary amounts of mesoscopic-scale heterogeneity in the porous continuum properties. The local equations used to determine the poroelastic response within such materials are those of Biot (1962). Upon applying a step change in stress to samples containing mesoscopic-scale heterogeneity, the poroelastic response is determined using finite difference modeling, and the average strain throughout the sample computed, along with the effective complex and frequency-dependent elastic moduli of the sample. The ratio of the imaginary and real parts of these moduli determines the attenuation as a function of frequency associated with the modes of applied stress (pure compression and pure shear). By having a wide range of heterogeneity present, there exists a wide range of relaxation frequencies in the response with the result that the curves of attenuation as a function of frequency are broader than in existing analytical theories based on a single relaxation frequency. Analytical explanations are given for the various high-frequency and low-frequency asymptotic behavior observed in the numerical simulations. It is also shown that the overall level of attenuation of a given sample is proportional to the square of the incompressibility contrasts locally present.

Multiscale pore structure and constitutive models of fine-grained rocks

NASA Astrophysics Data System (ADS)

Heath, J. E.; Dewers, T. A.; Shields, E. A.; Yoon, H.; Milliken, K. L.

2017-12-01

A foundational concept of continuum poromechanics is the representative elementary volume or REV: an amount of material large enough that pore- or grain-scale fluctuations in relevant properties are dissipated to a definable mean, but smaller than length scales of heterogeneity. We determine 2D-equivalent representative elementary areas (REAs) of pore areal fraction of three major types of mudrocks by applying multi-beam scanning electron microscopy (mSEM) to obtain terapixel image mosaics. Image analysis obtains pore areal fraction and pore size and shape as a function of progressively larger measurement areas. Using backscattering imaging and mSEM data, pores are identified by the components within which they occur, such as in organics or the clastic matrix. We correlate pore areal fraction with nano-indentation, micropillar compression, and axysimmetic testing at multiple length scales on a terrigenous-argillaceous mudrock sample. The combined data set is used to: investigate representative elementary volumes (and areas for the 2D images); determine if scale separation occurs; and determine if transport and mechanical properties at a given length scale can be statistically defined. Clear scale separation occurs between REAs and observable heterogeneity in two of the samples. A highly-laminated sample exhibits fine-scale heterogeneity and an overlapping in scales, in which case typical continuum assumptions on statistical variability may break down. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia LLC, a wholly owned subsidiary of Honeywell International Inc. for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Linking Measures of Adult Nicotine Dependence to a Common Latent Continuum and a Comparison with Adolescent Patterns

PubMed Central

Strong, David R.; Schonbrun, Yael Chatav; Schaffran, Christine; Griesler, Pamela C.; Kandel, Denise

2012-01-01

Background An ongoing debate regarding the nature of Nicotine Dependence (ND) is whether the same instrument can be applied to measure ND among adults and adolescents. Using a hierarchical item response model (IRM), we examined evidence for a common continuum underlying ND symptoms among adults and adolescents. Method The analyses are based on two waves of interviews with subsamples of parents and adolescents from a multi-ethnic longitudinal cohort of 1,039 6th–10th graders from the Chicago Public Schools (CPS). Adults and adolescents who reported smoking cigarettes the last 30 days prior to waves 3 and 5 completed three common instruments measuring ND symptoms and one item measuring loss of autonomy. Results A stable continuum of ND, first identified among adolescents, was replicated among adults. However, some symptoms, such as tolerance and withdrawal, differed markedly across adults and adolescents. The majority of mFTQ items were observed within the highest levels of ND, the NDSS items within the lowest levels, and the DSM-IV items were arrayed in the middle and upper third of the continuum of dependence severity. Loss of Autonomy was positioned at the lower end of the continuum. We propose a ten-symptom measure of ND for adolescents and adults. Conclusions Despite marked differences in the relative severity of specific ND symptoms in each group, common instrumentation of ND can apply to adults and adolescents. The results increase confidence in the ability to describe phenotypic heterogeneity in ND across important developmental periods. PMID:21855236

Identifying variably saturated water-flow patterns in a steep hillslope under intermittent heavy rainfall

USGS Publications Warehouse

El-Kadi, A. I.; Torikai, J.D.

2001-01-01

The objective of this paper is to identify water-flow patterns in part of an active landslide, through the use of numerical simulations and data obtained during a field study. The approaches adopted include measuring rainfall events and pore-pressure responses in both saturated and unsaturated soils at the site. To account for soil variability, the Richards equation is solved within deterministic and stochastic frameworks. The deterministic simulations considered average water-retention data, adjusted retention data to account for stones or cobbles, retention functions for a heterogeneous pore structure, and continuous retention functions for preferential flow. The stochastic simulations applied the Monte Carlo approach which considers statistical distribution and autocorrelation of the saturated conductivity and its cross correlation with the retention function. Although none of the models is capable of accurately predicting field measurements, appreciable improvement in accuracy was attained using stochastic, preferential flow, and heterogeneous pore-structure models. For the current study, continuum-flow models provide reasonable accuracy for practical purposes, although they are expected to be less accurate than multi-domain preferential flow models.

Turbulent Combustion in SDF Explosions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuhl, A L; Bell, J B; Beckner, V E

2009-11-12

A heterogeneous continuum model is proposed to describe the dispersion and combustion of an aluminum particle cloud in an explosion. It combines the gas-dynamic conservation laws for the gas phase with a continuum model for the dispersed phase, as formulated by Nigmatulin. Inter-phase mass, momentum and energy exchange are prescribed by phenomenological models. It incorporates a combustion model based on the mass conservation laws for fuel, air and products; source/sink terms are treated in the fast-chemistry limit appropriate for such gasdynamic fields, along with a model for mass transfer from the particle phase to the gas. The model takes intomore » account both the afterburning of the detonation products of the C-4 booster with air, and the combustion of the Al particles with air. The model equations were integrated by high-order Godunov schemes for both the gas and particle phases. Numerical simulations of the explosion fields from 1.5-g Shock-Dispersed-Fuel (SDF) charge in a 6.6 liter calorimeter were used to validate the combustion model. Then the model was applied to 10-kg Al-SDF explosions in a an unconfined height-of-burst explosion. Computed pressure histories are compared with measured waveforms. Differences are caused by physical-chemical kinetic effects of particle combustion which induce ignition delays in the initial reactive blast wave and quenching of reactions at late times. Current simulations give initial insights into such modeling issues.« less

PACE-90 water and solute transport calculations for 0.01, 0.1, and 0. 5 mm/yr infiltration into Yucca Mountain; Yucca Mountain Site Characterization Project

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dykhuizen, R.C.; Eaton, R.R.; Hopkins, P.L.

1991-12-01

Numerical results are presented for the Performance Assessment Calculational Exercise (PACE-90). One- and two-dimensional water and solute transport are presented for steady infiltration into Yucca Mountain. Evenly distributed infiltration rates of 0.01, 0.1, and 0.5 mm/yr were considered. The calculations of solute transport show that significant amounts of radionuclides can reach the water table over 100,000 yr at the 0.5 mm/yr rate. For time periods less than 10,000 yr or infiltrations less than 0.1 mm/yr very little solute reaches the water table. The numerical simulations clearly demonstrate that multi-dimensional effects can result in significant decreases in the travel time ofmore » solute through the modeled domain. Dual continuum effects are shown to be negligible for the low steady state fluxes considered. However, material heterogeneities may cause local amplification of the flux level in multi-dimensional flows. These higher flux levels may then require modeling of a dual continuum porous medium.« less

CO 2 Leakage Into Shallow Aquifers: Modeling CO 2 Gas Evolution and Accumulation at Interfaces of Heterogeneity

DOE PAGES

Porter, Mark L.; Plampin, Michael; Pawar, Rajesh; ...

2014-12-31

The physicochemical processes associated with CO 2 leakage into shallow aquifer systems are complex and span multiple spatial and time scales. Continuum-scale numerical models that faithfully represent the underlying pore-scale physics are required to predict the long-term behavior and aid in risk analysis regarding regulatory and management decisions. This study focuses on benchmarking the numerical simulator, FEHM, with intermediate-scale column experiments of CO 2 gas evolution in homogeneous and heterogeneous sand configurations. Inverse modeling was conducted to calibrate model parameters and determine model sensitivity to the observed steady-state saturation profiles. It is shown that FEHM is a powerful tool thatmore » is capable of capturing the experimentally observed out ow rates and saturation profiles. Moreover, FEHM captures the transition from single- to multi-phase flow and CO 2 gas accumulation at interfaces separating sands. We also derive a simple expression, based on Darcy's law, for the pressure at which CO 2 free phase gas is observed and show that it reliably predicts the location at which single-phase flow transitions to multi-phase flow.« less

Toughening by crack bridging in heterogeneous ceramics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Curtin, W.A.

1995-05-01

The toughening of a ceramic by crack bridging is considered, including the heterogeneity caused simply by spatial randomness in the bridge locations. The growth of a single planar crack is investigated numerically by representing the microstructure as an array of discrete springs with heterogeneity in the mechanical properties of each spring. The stresses on each microstructural element are determined, for arbitrary configurations of spring properties and heterogeneity, using a lattice Green function technique. For toughening by (heterogeneous) crack bridging for both elastic and Dugdale bridging mechanisms, the following key physical results are found: (1) growing cracks avoid regions which aremore » efficiently bridged, and do not propagate as self-similar penny cracks; (2) crack growth thus proceeds at lower applied stresses in a heterogeneous material than in an ordered material; (3) very little toughening is evident for moderate amounts of crack growth in many cases; and (4) a different R-curve is found for every particular spatial distribution of bridging elements. These results show that material reliability is determined by both the flaw distribution and the ``toughness`` distribution, or local environment, around each flaw. These results also demonstrate that the ``microstructural`` parameters derived from fitting an R-curve to a continuum model may not have an immediate relationship to the actual microstructure; the parameters are ``effective`` parameters that absorb the effects of the heterogeneity. The conceptual issues illuminated by these conclusions must be fully understood and appreciated to further develop microstructure-property relationships in ceramic materials.« less

Incorporating physically-based microstructures in materials modeling: Bridging phase field and crystal plasticity frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lim, Hojun; Abdeljawad, Fadi; Owen, Steven J.

Here, the mechanical properties of materials systems are highly influenced by various features at the microstructural level. The ability to capture these heterogeneities and incorporate them into continuum-scale frameworks of the deformation behavior is considered a key step in the development of complex non-local models of failure. In this study, we present a modeling framework that incorporates physically-based realizations of polycrystalline aggregates from a phase field (PF) model into a crystal plasticity finite element (CP-FE) framework. Simulated annealing via the PF model yields ensembles of materials microstructures with various grain sizes and shapes. With the aid of a novel FEmore » meshing technique, FE discretizations of these microstructures are generated, where several key features, such as conformity to interfaces, and triple junction angles, are preserved. The discretizations are then used in the CP-FE framework to simulate the mechanical response of polycrystalline α-iron. It is shown that the conformal discretization across interfaces reduces artificial stress localization commonly observed in non-conformal FE discretizations. The work presented herein is a first step towards incorporating physically-based microstructures in lieu of the overly simplified representations that are commonly used. In broader terms, the proposed framework provides future avenues to explore bridging models of materials processes, e.g. additive manufacturing and microstructure evolution of multi-phase multi-component systems, into continuum-scale frameworks of the mechanical properties.« less

Incorporating physically-based microstructures in materials modeling: Bridging phase field and crystal plasticity frameworks

DOE PAGES

Lim, Hojun; Abdeljawad, Fadi; Owen, Steven J.; ...

2016-04-25

Here, the mechanical properties of materials systems are highly influenced by various features at the microstructural level. The ability to capture these heterogeneities and incorporate them into continuum-scale frameworks of the deformation behavior is considered a key step in the development of complex non-local models of failure. In this study, we present a modeling framework that incorporates physically-based realizations of polycrystalline aggregates from a phase field (PF) model into a crystal plasticity finite element (CP-FE) framework. Simulated annealing via the PF model yields ensembles of materials microstructures with various grain sizes and shapes. With the aid of a novel FEmore » meshing technique, FE discretizations of these microstructures are generated, where several key features, such as conformity to interfaces, and triple junction angles, are preserved. The discretizations are then used in the CP-FE framework to simulate the mechanical response of polycrystalline α-iron. It is shown that the conformal discretization across interfaces reduces artificial stress localization commonly observed in non-conformal FE discretizations. The work presented herein is a first step towards incorporating physically-based microstructures in lieu of the overly simplified representations that are commonly used. In broader terms, the proposed framework provides future avenues to explore bridging models of materials processes, e.g. additive manufacturing and microstructure evolution of multi-phase multi-component systems, into continuum-scale frameworks of the mechanical properties.« less

Modeling of nanoscale liquid mixture transport by density functional hydrodynamics

NASA Astrophysics Data System (ADS)

Dinariev, Oleg Yu.; Evseev, Nikolay V.

2017-06-01

Modeling of multiphase compositional hydrodynamics at nanoscale is performed by means of density functional hydrodynamics (DFH). DFH is the method based on density functional theory and continuum mechanics. This method has been developed by the authors over 20 years and used for modeling in various multiphase hydrodynamic applications. In this paper, DFH was further extended to encompass phenomena inherent in liquids at nanoscale. The new DFH extension is based on the introduction of external potentials for chemical components. These potentials are localized in the vicinity of solid surfaces and take account of the van der Waals forces. A set of numerical examples, including disjoining pressure, film precursors, anomalous rheology, liquid in contact with heterogeneous surface, capillary condensation, and forward and reverse osmosis, is presented to demonstrate modeling capabilities.

Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats

NASA Astrophysics Data System (ADS)

Stalter, S.; Yelash, L.; Emamy, N.; Statt, A.; Hanke, M.; Lukáčová-Medvid'ová, M.; Virnau, P.

2018-03-01

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations typically pose a computational bottleneck, which we investigate in detail in this study. We find that it is preferable to simulate many small systems as opposed to a few large systems, and that a choice of a simple isokinetic thermostat is typically sufficient while thermostats such as Lowe-Andersen allow for simulations at elevated viscosity. We discuss suitable choices for time steps and finite-size effects which arise in the limit of very small simulation boxes. We also argue that if colloidal systems are considered as opposed to atomistic systems, the gap between microscopic and macroscopic simulations regarding time and length scales is significantly smaller. We propose a novel reduced-order technique for the coupling to the macroscopic solver, which allows us to approximate a non-linear stress-strain relation efficiently and thus further reduce computational effort of microscopic simulations.

Classification of self-injurious behaviour across the continuum of relative environmental-biological influence.

PubMed

Hagopian, L P; Frank-Crawford, M A

2017-10-13

Self-injurious behaviour (SIB) is generally considered to be the product of interactions between dysfunction stemming from the primary developmental disability and experiences that occasion and reinforce SIB. As a result of these complex interactions, SIB presents as a heterogeneous problem. Recent research delineating subtypes of SIB that are nonsocially mediated, including one that is amenable to change and one that is highly invariant, enables classification of SIB across a broader continuum of relative environmental-biological influence. Directly examining how the functional classes of SIB differ has the potential to structure research, will improve our understanding this problem, and lead to more targeted behavioural and pharmacological interventions. Recognising that SIB is not a single entity but is composed of distinct functional classes would better align research with conceptual models that view SIB as the product of interactions between environmental and biological variables. © 2017 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Continuum-based DFN-consistent numerical framework for the simulation of oxygen infiltration into fractured crystalline rocks

NASA Astrophysics Data System (ADS)

Trinchero, Paolo; Puigdomenech, Ignasi; Molinero, Jorge; Ebrahimi, Hedieh; Gylling, Björn; Svensson, Urban; Bosbach, Dirk; Deissmann, Guido

2017-05-01

We present an enhanced continuum-based approach for the modelling of groundwater flow coupled with reactive transport in crystalline fractured rocks. In the proposed formulation, flow, transport and geochemical parameters are represented onto a numerical grid using Discrete Fracture Network (DFN) derived parameters. The geochemical reactions are further constrained by field observations of mineral distribution. To illustrate how the approach can be used to include physical and geochemical complexities into reactive transport calculations, we have analysed the potential ingress of oxygenated glacial-meltwater in a heterogeneous fractured rock using the Forsmark site (Sweden) as an example. The results of high-performance reactive transport calculations show that, after a quick oxygen penetration, steady state conditions are attained where abiotic reactions (i.e. the dissolution of chlorite and the homogeneous oxidation of aqueous iron(II) ions) counterbalance advective oxygen fluxes. The results show that most of the chlorite becomes depleted in the highly conductive deformation zones where higher mineral surface areas are available for reactions.

Non-linear homogenized and heterogeneous FE models for FRCM reinforced masonry walls in diagonal compression

NASA Astrophysics Data System (ADS)

Bertolesi, Elisa; Milani, Gabriele; Poggi, Carlo

2016-12-01

Two FE modeling techniques are presented and critically discussed for the non-linear analysis of tuff masonry panels reinforced with FRCM and subjected to standard diagonal compression tests. The specimens, tested at the University of Naples (Italy), are unreinforced and FRCM retrofitted walls. The extensive characterization of the constituent materials allowed adopting here very sophisticated numerical modeling techniques. In particular, here the results obtained by means of a micro-modeling strategy and homogenization approach are compared. The first modeling technique is a tridimensional heterogeneous micro-modeling where constituent materials (bricks, joints, reinforcing mortar and reinforcing grid) are modeled separately. The second approach is based on a two-step homogenization procedure, previously developed by the authors, where the elementary cell is discretized by means of three-noded plane stress elements and non-linear interfaces. The non-linear structural analyses are performed replacing the homogenized orthotropic continuum with a rigid element and non-linear spring assemblage (RBSM). All the simulations here presented are performed using the commercial software Abaqus. Pros and cons of the two approaches are herein discussed with reference to their reliability in reproducing global force-displacement curves and crack patterns, as well as to the rather different computational effort required by the two strategies.

Development of Continuum-Atomistic Approach for Modeling Metal Irradiation by Heavy Ions

NASA Astrophysics Data System (ADS)

Batgerel, Balt; Dimova, Stefka; Puzynin, Igor; Puzynina, Taisia; Hristov, Ivan; Hristova, Radoslava; Tukhliev, Zafar; Sharipov, Zarif

2018-02-01

Over the last several decades active research in the field of materials irradiation by high-energy heavy ions has been worked out. The experiments in this area are labor-consuming and expensive. Therefore the improvement of the existing mathematical models and the development of new ones based on the experimental data of interaction of high-energy heavy ions with materials are of interest. Presently, two approaches are used for studying these processes: a thermal spike model and molecular dynamics methods. The combination of these two approaches - the continuous-atomistic model - will give the opportunity to investigate more thoroughly the processes of irradiation of materials by high-energy heavy ions. To solve the equations of the continuous-atomistic model, a software package was developed and the block of molecular dynamics software was tested on the heterogeneous cluster HybriLIT.

Application of ERT, Saline Tracer and Numerical Studies to Delineate Preferential Paths in Fractured Granites.

PubMed

Sreeparvathy, Vijay; Kambhammettu, B V N P; Peddinti, Srinivasa Rao; Sarada, P S L

2018-03-22

Accurate quantification of in situ heterogeneity and flow processes through fractured geologic media remains elusive for hydrogeologists due to the complexity in fracture characterization and its multiscale behavior. In this research, we demonstrated the efficacy of tracer-electrical resistivity tomography (ERT) experiments combined with numerical simulations to characterize heterogeneity and delineate preferential flow paths in a fractured granite aquifer. A series of natural gradient saline tracer experiments were conducted from a depth window of 18 to 22 m in an injection well (IW) located inside the Indian Institute of Technology Hyderabad campus. Tracer migration was monitored in a time-lapse mode using two cross-sectional surface ERT profiles placed in the direction of flow gradient. ERT data quality was improved by considering stacking, reciprocal measurements, resolution indicators, and geophysical logs. Dynamic changes in subsurface electrical properties inferred via resistivity anomalies were used to highlight preferential flow paths of the study area. Temporal changes in electrical resistivity and tracer concentration were monitored along the vertical in an observation well located at 48 m to the east of the IW. ERT-derived tracer breakthrough curves were in agreement with geochemical sample measurements. Fracture geometry and hydraulic properties derived from ERT and pumping tests were further used to evaluate two mathematical conceptualizations that are relevant to fractured aquifers. Results of numerical analysis conclude that dual continuum model that combines matrix and fracture systems through a flow exchange term has outperformed equivalent continuum model in reproducing tracer concentrations at the monitoring wells (evident by a decrease in RMSE from 199 to 65 mg/L). A sensitivity analysis on model simulations conclude that spatial variability in hydraulic conductivity, local-scale dispersion, and flow exchange at fracture-matrix interface have a profound effect on model simulations. © 2018, National Ground Water Association.

Continuum modeling of large lattice structures: Status and projections

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Mikulas, Martin M., Jr.

1988-01-01

The status and some recent developments of continuum modeling for large repetitive lattice structures are summarized. Discussion focuses on a number of aspects including definition of an effective substitute continuum; characterization of the continuum model; and the different approaches for generating the properties of the continuum, namely, the constitutive matrix, the matrix of mass densities, and the matrix of thermal coefficients. Also, a simple approach is presented for generating the continuum properties. The approach can be used to generate analytic and/or numerical values of the continuum properties.

Components for Atomistic-to-Continuum Multiscale Modeling of Flow in Micro- and Nanofluidic Systems

DOE PAGES

Adalsteinsson, Helgi; Debusschere, Bert J.; Long, Kevin R.; ...

2008-01-01

Micro- and nanofluidics pose a series of significant challenges for science-based modeling. Key among those are the wide separation of length- and timescales between interface phenomena and bulk flow and the spatially heterogeneous solution properties near solid-liquid interfaces. It is not uncommon for characteristic scales in these systems to span nine orders of magnitude from the atomic motions in particle dynamics up to evolution of mass transport at the macroscale level, making explicit particle models intractable for all but the simplest systems. Recently, atomistic-to-continuum (A2C) multiscale simulations have gained a lot of interest as an approach to rigorously handle particle-levelmore » dynamics while also tracking evolution of large-scale macroscale behavior. While these methods are clearly not applicable to all classes of simulations, they are finding traction in systems in which tight-binding, and physically important, dynamics at system interfaces have complex effects on the slower-evolving large-scale evolution of the surrounding medium. These conditions allow decomposition of the simulation into discrete domains, either spatially or temporally. In this paper, we describe how features of domain decomposed simulation systems can be harnessed to yield flexible and efficient software for multiscale simulations of electric field-driven micro- and nanofluidics.« less

Continuum dislocation-density based models for the dynamic shock response of single-crystal and polycrystalline materials

NASA Astrophysics Data System (ADS)

Luscher, Darby

2017-06-01

The dynamic thermomechanical responses of polycrystalline materials under shock loading are often dominated by the interaction of defects and interfaces. For example, polymer-bonded explosives (PBX) can initiate under weak shock impacts whose energy, if distributed homogeneously throughout the material, translates to temperature increases that are insufficient to drive the rapid chemistry observed. In such cases, heterogeneous thermomechanical interactions at the mesoscale (i.e. between single-crystal and macroscale) lead to the formation of localized hot spots. Within metals, a prescribed deformation associated with a shock wave may be accommodated by crystallographic slip, provided a sufficient population of mobile dislocations is available. However, if the deformation rate is large enough, there may be an insufficient number of freely mobile dislocations. In these cases, additional dislocations may be nucleated, or alternate mechanisms (e.g. twinning, damage) activated in order to accommodate the deformation. Direct numerical simulation at the mesoscale offers insight into these physical processes that can be invaluable to the development of macroscale constitutive theories, if the mesoscale models adequately represent the anisotropic nonlinear thermomechanical response of individual crystals and their interfaces. This talk will briefly outline a continuum mesoscale modeling framework founded upon local and nonlocal variations of dislocation-density based crystal plasticity theory. The nonlocal theory couples continuum dislocation transport with the local theory. In the latter, dislocation transport is modeled by enforcing dislocation conservation at a slip-system level through the solution of advection-diffusion equations. The configuration of geometrically necessary dislocation density gives rise to a back-stress that inhibits or accentuates the flow of dislocations. Development of the local theory and application to modeling the explosive molecular crystal RDX and polycrystalline PBX will be discussed. The talk will also emphasize recent implementation of the coupled nonlocal model into a 3D shock hydrocode and simulation results for the dynamic response of polycrystalline copper in two and three dimensions.

Identification and Simulation of Subsurface Soil patterns using hidden Markov random fields and remote sensing and geophysical EMI data sets

NASA Astrophysics Data System (ADS)

Wang, Hui; Wellmann, Florian; Verweij, Elizabeth; von Hebel, Christian; van der Kruk, Jan

2017-04-01

Lateral and vertical spatial heterogeneity of subsurface properties such as soil texture and structure influences the available water and resource supply for crop growth. High-resolution mapping of subsurface structures using non-invasive geo-referenced geophysical measurements, like electromagnetic induction (EMI), enables a characterization of 3D soil structures, which have shown correlations to remote sensing information of the crop states. The benefit of EMI is that it can return 3D subsurface information, however the spatial dimensions are limited due to the labor intensive measurement procedure. Although active and passive sensors mounted on air- or space-borne platforms return 2D images, they have much larger spatial dimensions. Combining both approaches provides us with a potential pathway to extend the detailed 3D geophysical information to a larger area by using remote sensing information. In this study, we aim at extracting and providing insights into the spatial and statistical correlation of the geophysical and remote sensing observations of the soil/vegetation continuum system. To this end, two key points need to be addressed: 1) how to detect and recognize the geometric patterns (i.e., spatial heterogeneity) from multiple data sets, and 2) how to quantitatively describe the statistical correlation between remote sensing information and geophysical measurements. In the current study, the spatial domain is restricted to shallow depths up to 3 meters, and the geostatistical database contains normalized difference vegetation index (NDVI) derived from RapidEye satellite images and apparent electrical conductivities (ECa) measured from multi-receiver EMI sensors for nine depths of exploration ranging from 0-2.7 m. The integrated data sets are mapped into both the physical space (i.e. the spatial domain) and feature space (i.e. a two-dimensional space framed by the NDVI and the ECa data). Hidden Markov Random Fields (HMRF) are employed to model the underlying heterogeneities in spatial domain and finite Gaussian mixture models are adopted to quantitatively describe the statistical patterns in terms of center vectors and covariance matrices in feature space. A recently developed parallel stochastic clustering algorithm is adopted to implement the HMRF models and the Markov chain Monte Carlo based Bayesian inference. Certain spatial patterns such as buried paleo-river channels covered by shallow sediments are investigated as typical examples. The results indicate that the geometric patterns of the subsurface heterogeneity can be represented and quantitatively characterized by HMRF. Furthermore, the statistical patterns of the NDVI and the EMI data from the soil/vegetation-continuum system can be inferred and analyzed in a quantitative manner.

Modeling Transport of Turbulent Fluxes in a Heterogeneous Urban Canopy Using a Spatially Explicit Energy Balance

NASA Astrophysics Data System (ADS)

Moody, M.; Bailey, B.; Stoll, R., II

2017-12-01

Understanding how changes in the microclimate near individual plants affects the surface energy budget is integral to modeling land-atmosphere interactions and a wide range of near surface atmospheric boundary layer phenomena. In urban areas, the complex geometry of the urban canopy layer results in large spatial deviations of turbulent fluxes further complicating the development of models. Accurately accounting for this heterogeneity in order to model urban energy and water use requires a sub-plant level understanding of microclimate variables. We present analysis of new experimental field data taken in and around two Blue Spruce (Picea pungens) trees at the University of Utah in 2015. The test sites were chosen in order study the effects of heterogeneity in an urban environment. An array of sensors were placed in and around the conifers to quantify transport in the soil-plant-atmosphere continuum: radiative fluxes, temperature, sap fluxes, etc. A spatial array of LEMS (Local Energy Measurement Systems) were deployed to obtain pressure, surrounding air temperature and relative humidity. These quantities are used to calculate the radiative and turbulent fluxes. Relying on measurements alone is insufficient to capture the complexity of microclimate distribution as one reaches sub-plant scales. A spatially-explicit radiation and energy balance model previously developed for deciduous trees was extended to include conifers. The model discretizes the tree into isothermal sub-volumes on which energy balances are performed and utilizes incoming radiation as the primary forcing input. The radiative transfer component of the model yields good agreement between measured and modeled upward longwave and shortwave radiative fluxes. Ultimately, the model was validated through an examination of the full energy budget including radiative and turbulent fluxes through isolated Picea pungens in an urban environment.

Continuum Fatigue Damage Modeling for Use in Life Extending Control

NASA Technical Reports Server (NTRS)

Lorenzo, Carl F.

1994-01-01

This paper develops a simplified continuum (continuous wrp to time, stress, etc.) fatigue damage model for use in Life Extending Controls (LEC) studies. The work is based on zero mean stress local strain cyclic damage modeling. New nonlinear explicit equation forms of cyclic damage in terms of stress amplitude are derived to facilitate the continuum modeling. Stress based continuum models are derived. Extension to plastic strain-strain rate models are also presented. Application of these models to LEC applications is considered. Progress toward a nonzero mean stress based continuum model is presented. Also, new nonlinear explicit equation forms in terms of stress amplitude are also derived for this case.

Electrosensory neural responses to natural electro-communication stimuli are distributed along a continuum

PubMed Central

Sproule, Michael K. J.

2017-01-01

Neural heterogeneities are seen ubiquitously within the brain and greatly complicate classification efforts. Here we tested whether the responses of an anatomically well-characterized sensory neuron population to natural stimuli could be used for functional classification. To do so, we recorded from pyramidal cells within the electrosensory lateral line lobe (ELL) of the weakly electric fish Apteronotus leptorhynchus in response to natural electro-communication stimuli as these cells can be anatomically classified into six different types. We then used two independent methodologies to functionally classify responses: one relies of reducing the dimensionality of a feature space while the other directly compares the responses themselves. Both methodologies gave rise to qualitatively similar results: while ON and OFF-type cells could easily be distinguished from one another, ELL pyramidal neuron responses are actually distributed along a continuum rather than forming distinct clusters due to heterogeneities. We discuss the implications of our results for neural coding and highlight some potential advantages. PMID:28384244

Mesoscale studies of ionic closed membranes with polyhedral geometries

DOE PAGES

Olvera de la Cruz, Monica

2016-06-01

Large crystalline molecular shells buckle spontaneously into icosahedra while multicomponent shells buckle into various polyhedra. Continuum elastic theory explains the buckling of closed shells with one elastic component into icosahedra. A generalized elastic model, on the other hand, describes the spontaneous buckling of inhomogeneous shells into regular and irregular polyhedra. By coassembling water-insoluble anionic (–1) amphiphiles with cationic (3+) amphiphiles, we realized ionic vesicles. Results revealed that surface crystalline domains and the unusual shell shapes observed arise from the competition of ionic correlations with charge-regulation. We explain here the mechanism by which these ionic membranes generate a mechanically heterogeneous vesicle.

AMR Code Simulations of Turbulent Combustion in Confined and Unconfined SDF Explosions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuhl, A L; Bell, J B; Beckner, V

2009-05-29

A heterogeneous continuum model is proposed to describe the dispersion and combustion of an aluminum particle cloud in an explosion. It combines the gas-dynamic conservation laws for the gas phase with a continuum model for the dispersed phase, as formulated by Nigmatulin. Inter-phase mass, momentum and energy exchange are prescribed by phenomenological models. It incorporates a combustion model based on the mass conservation laws for fuel, air and products; source/sink terms are treated in the fast-chemistry limit appropriate for such gas dynamic fields, along with a model for mass transfer from the particle phase to the gas. The model takesmore » into account both the afterburning of the detonation products of the booster with air, and the combustion of the Al particles with air. The model equations were integrated by high-order Godunov schemes for both the gas and particle phases. Numerical simulations of the explosion fields from 1.5-g Shock-Dispersed-Fuel (SDF) charge in a 6.6 liter calorimeter were used to validate the combustion model. Then the model was applied to 10-kg Al-SDF explosions in a vented two-room structure and in an unconfined height-of-burst explosion. Computed pressure histories are in reasonable (but not perfect) agreement with measured waveforms. Differences are caused by physical-chemical kinetic effects of particle combustion which induce ignition delays in the initial reactive blast wave and quenching of reactions at late times. Current simulations give initial insights into such modeling issues.« less

The School Board as Meta-Mediators.

ERIC Educational Resources Information Center

Lutz, Frank W.

School districts are cultural systems that may be classified along a continuum from homogeneous to heterogeneous according to the diversity represented in their cultural composition. School boards are the decision-making system that, given the competitive federal, state, and local demands, decides on the particular educational policies and…

Effects of capillary heterogeneity on vapor-liquid counterflow in porous media

NASA Astrophysics Data System (ADS)

Stubos, A. K.; Satik, C.; Yortsos, Y. C.

1992-06-01

Based on a continuum description, the effect of capillary heterogeneity, induced by variation in permeability, on the steady state, countercurrent, vapor-liquid flow in porous media is analyzed. It is shown that the heterogeneity acts as a body force that may enhance or diminish gravity effects on heat pipes. Selection rules that determine the steady states reached in homogeneous, gravity-driven heat pipes are also formulated. It is shown that the 'infinite' two-phase zone may terminate by a substantial change in the permeability somewhere in the medium. The two possible sequences, liquid-liquid dominated-dry, or liquid-vapor dominated-dry find applications in geothermal systems. Finally, it is shown that although weak heterogeneity affects only gravity controlled flows, stronger variations in permeability can give rise to significant capillary effects.

Addressing the Vaccine Hesitancy Continuum: An Audience Segmentation Analysis of American Adults Who Did Not Receive the 2009 H1N1 Vaccine

PubMed Central

Ramanadhan, Shoba; Galarce, Ezequiel; Xuan, Ziming; Alexander-Molloy, Jaclyn; Viswanath, Kasisomayajula

2015-01-01

Understanding the heterogeneity of groups along the vaccine hesitancy continuum presents an opportunity to tailor and increase the impact of public engagement efforts with these groups. Audience segmentation can support these goals, as demonstrated here in the context of the 2009 H1N1 vaccine. In March 2010, we surveyed 1569 respondents, drawn from a nationally representative sample of American adults, with oversampling of racial/ethnic minorities and persons living below the United States Federal Poverty Level. Guided by the Structural Influence Model, we assessed knowledge, attitudes, and behaviors related to H1N1; communication outcomes; and social determinants. Among those who did not receive the vaccine (n = 1166), cluster analysis identified three vaccine-hesitant subgroups. Disengaged Skeptics (67%) were furthest from vaccine acceptance, with low levels of concern and engagement. The Informed Unconvinced (19%) were sophisticated consumers of media and health information who may not have been reached with information to motivate vaccination. The Open to Persuasion cluster (14%) had the highest levels of concern and motivation and may have required engagement about vaccination broadly. There were significant sociodemographic differences between groups. This analysis highlights the potential to use segmentation techniques to identify subgroups on the vaccine hesitancy continuum and tailor public engagement efforts accordingly. PMID:26350595

Reactive Transport Modeling of CO2-induced Porosity and Permeability Changes in Heterogeneous Carbonate Rocks

NASA Astrophysics Data System (ADS)

Hao, Y.; Smith, M. M.; Mason, H. E.; Carroll, S.

2015-12-01

It has long been appreciated that chemical interactions have a major effect on rock porosity and permeability evolution and may alter the behavior or performance of both natural and engineered reservoir systems. Such reaction-induced permeability evolution is of particular importance for geological CO2 sequestration and storage associated with enhanced oil recovery. In this study we used a three-dimensional Darcy scale reactive transport model to simulate CO2 core flood experiments in which the CO2-equilibrated brine was injected into dolostone cores collected from the Arbuckle carbonate reservoir, Wellington, Kansas. Heterogeneous distributions of macro pores, fractures, and mineral phases inside the cores were obtained from X-ray computed microtomography (XCMT) characterization data, and then used to construct initial model macroscopic properties including porosity, permeability, and mineral compositions. The reactive transport simulations were performed by using the Nonisothermal Unsaturated Flow and Transport (NUFT) code, and their results were compared with experimental data. It was observed both experimentally and numerically that the dissolution fronts became unstable in highly heterogeneous and less permeable formations, leading to the development of highly porous flow paths or wormholes. Our model results indicate that the continuum-scale reactive transport models are able to adequately capture the evolution of distinct dissolution fronts as observed in carbonate rocks at a core scale. The impacts of rock heterogeneity, chemical kinetics and porosity-permeability relationships were also examined in this study. The numerical model developed in this study will not only help improve understanding of coupled physical and chemical processes controlling carbonate dissolution, but also provide a useful basis for upscaling transport and reaction properties from core scale to field scale. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

A model of mudflow propagation downstream from the Grohovo landslide near the city of Rijeka (Croatia)

NASA Astrophysics Data System (ADS)

Žic, E.; Arbanas, Ž.; Bićanić, N.; Ožanić, N.

2014-11-01

Mudflows regularly generate significant human and property losses. Analyzing mudflows is important to assess the risks and to delimit vulnerable areas where mitigation measures are required. In recent decades, modeling of the propagation stage has been largely performed within the framework of continuum mechanics, and a number of new and sophisticated computational models have been developed. Most of the available approaches treat the heterogeneous and multiphase moving mass as a single-phase continuum. The smoothed particle hydrodynamics model (SPH model) adopted here considers, in two phases, a granular skeleton with voids filled with either water or mud. The SPH depth integrated numerical model (Pastor et al., 2009a) used for the present simulations is a 2-D model capable of predicting the runout distance, flow velocity, deposition pattern and the final volume of mudflows. It is based on mathematical and rheological models. In this study, the main characteristics of mudflow processes that have emerged in the past in the area downstream of the Grohovo landslide are examined, and the more relevant parameters and attributes describing the mudflow are presented. Principal equations that form the basis of the SPH depth integrated model are reviewed and applied to analyze the Grohovo landslide and the propagation of the mudflow wave downstream of the landslide. Based on the SPH method, the runout distance, quantities of the deposited materials and the velocity of mudflow progression which occurred in the past at the observed area are analysed and qualitatively compared to the recorded consequences of the actual event.

Continuum-based DFN-consistent numerical framework for the simulation of oxygen infiltration into fractured crystalline rocks.

PubMed

Trinchero, Paolo; Puigdomenech, Ignasi; Molinero, Jorge; Ebrahimi, Hedieh; Gylling, Björn; Svensson, Urban; Bosbach, Dirk; Deissmann, Guido

2017-05-01

We present an enhanced continuum-based approach for the modelling of groundwater flow coupled with reactive transport in crystalline fractured rocks. In the proposed formulation, flow, transport and geochemical parameters are represented onto a numerical grid using Discrete Fracture Network (DFN) derived parameters. The geochemical reactions are further constrained by field observations of mineral distribution. To illustrate how the approach can be used to include physical and geochemical complexities into reactive transport calculations, we have analysed the potential ingress of oxygenated glacial-meltwater in a heterogeneous fractured rock using the Forsmark site (Sweden) as an example. The results of high-performance reactive transport calculations show that, after a quick oxygen penetration, steady state conditions are attained where abiotic reactions (i.e. the dissolution of chlorite and the homogeneous oxidation of aqueous iron(II) ions) counterbalance advective oxygen fluxes. The results show that most of the chlorite becomes depleted in the highly conductive deformation zones where higher mineral surface areas are available for reactions. Copyright © 2017 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yarrington, Cole D.; Wixom, Ryan R.; Damm, David L.

The complex physical phenomenon of shock wave interaction with material heterogeneities has significant importance and nevertheless remains little understood. In many materials, the observed macroscale response to shock loading is governed by characteristics of the microstructure. Yet the majority of computational studies aimed at predicting phenomena affected by these processes, such as initiation and propagation of detonation waves in explosives, or shock propagation in geological materials, employ continuum material and reactive burn model treatment. In an effort to highlight the grain-scale processes that underlie the observable effects in an energetic system, a grain-scale model for hexanitrostilbene (HNS) has been developed.more » Measured microstructures were used to produce synthetic computational representations of the pore structure, and a density functional theory molecular dynamics (DFT-MD) derived equation of state (EOS) was used for the fully dense HNS matrix. The explicit inclusion of microstructure along with a fully-dense EOS resulted in close agreement with historical shock compression experiments. More recent experiments on dynamic reaction threshold were also reproduced by inclusion of a global kinetics model. The complete model was shown to reproduce accurately the expected response of this heterogeneous material to shock loading. Mesoscale simulations were shown to provide clear insight into the nature of threshold behavior, and are a way to understand complex physical phenomena.« less

Equivalent-Continuum Modeling With Application to Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Gates, Thomas S.; Nicholson, Lee M.; Wise, Kristopher E.

2002-01-01

A method has been proposed for developing structure-property relationships of nano-structured materials. This method serves as a link between computational chemistry and solid mechanics by substituting discrete molecular structures with equivalent-continuum models. It has been shown that this substitution may be accomplished by equating the vibrational potential energy of a nano-structured material with the strain energy of representative truss and continuum models. As important examples with direct application to the development and characterization of single-walled carbon nanotubes and the design of nanotube-based devices, the modeling technique has been applied to determine the effective-continuum geometry and bending rigidity of a graphene sheet. A representative volume element of the chemical structure of graphene has been substituted with equivalent-truss and equivalent continuum models. As a result, an effective thickness of the continuum model has been determined. This effective thickness has been shown to be significantly larger than the interatomic spacing of graphite. The effective thickness has been shown to be significantly larger than the inter-planar spacing of graphite. The effective bending rigidity of the equivalent-continuum model of a graphene sheet was determined by equating the vibrational potential energy of the molecular model of a graphene sheet subjected to cylindrical bending with the strain energy of an equivalent continuum plate subjected to cylindrical bending.

Testing a continuum structure of self-determined motivation: A meta-analysis.

PubMed

Howard, Joshua L; Gagné, Marylène; Bureau, Julien S

2017-12-01

Self-determination theory proposes a multidimensional representation of motivation comprised of several factors said to fall along a continuum of relative autonomy. The current meta-analysis examined the relationships between these motivation factors in order to demonstrate how reliably they conformed to a predictable continuum-like pattern. Based on data from 486 samples representing over 205,000 participants who completed 1 of 13 validated motivation scales, the results largely supported a continuum-like structure of motivation and indicate that self-determination is central in explaining human motivation. Further examination of heterogeneity indicated that while regulations were predictably ordered across domains and scales, the exact distance between subscales varied across samples in a way that was not explainable by a set of moderators. Results did not support the inclusion of integrated regulation or the 3 subscales of intrinsic motivation (i.e., intrinsic motivation to know, to experience stimulation, and to achieve) due to excessively high interfactor correlations and overlapping confidence intervals. Recommendations for scale refinements and the scoring of motivation are provided. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Reactive Blast Waves from Composite Charges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuhl, A L; Bell, J B; Beckner, V E

2009-10-16

Investigated here is the performance of composite explosives - measured in terms of the blast wave they drive into the surrounding environment. The composite charge configuration studied here was a spherical booster (1/3 charge mass), surrounded by aluminum (Al) powder (2/3 charge mass) at an initial density of {rho}{sub 0} = 0.604 g/cc. The Al powder acts as a fuel but does not detonate - thereby providing an extreme example of a 'non-ideal' explosive (where 2/3 of the charge does not detonate). Detonation of the booster charge creates a blast wave that disperses the Al powder and ignites the ensuingmore » Al-air mixture - thereby forming a two-phase combustion cloud embedded in the explosion. Afterburning of the booster detonation products with air also enhances and promotes the Al-air combustion process. Pressure waves from such reactive blast waves have been measured in bomb calorimeter experiments. Here we describe numerical simulations of those experiments. A Heterogeneous Continuum Model was used to model the dispersion and combustion of the Al particle cloud. It combines the gasdynamic conservation laws for the gas phase with a dilute continuum model for the dispersed phase, as formulated by Nigmatulin. Inter-phase mass, momentum and energy exchange are prescribed by phenomenological models of Khasainov. It incorporates a combustion model based on mass conservation laws for fuel, air and products; source/sink terms are treated in the fast-chemistry limit appropriate for such gasdynamic fields, along with a model for mass transfer from the particle phase to the gas. The model takes into account both the afterburning of the detonation products of the booster with air, and the combustion of the Al particles with air. The model equations were integrated by high-order Godunov schemes for both the gas and particle phases. Adaptive Mesh Refinement (AMR) was used to capture the energy-bearing scales of the turbulent flow on the computational grid, and to track/resolve reaction zones. Numerical simulations of the explosion fields from 1.5-g and 10-kg composite charges were performed. Computed pressure histories (red curve) are compared with measured waveforms (black curves) in Fig. 1. Comparison of these results with a waveform for a non-combustion case in nitrogen (blue curve) demonstrates that a reactive blast wave was formed. Cross-sectional views of the temperature field at various times are presented in Fig. 2, which shows that the flow is turbulent. Initially, combustion occurs at the fuel-air interface, and the energy release rate is controlled by the rate of turbulent mixing. Eventually, oxidizer becomes distributed throughout the cloud via ballistic mixing of the particles with air; energy release then occurs in a distributed combustion mode, and Al particle kinetics controls the energy release rate. Details of the Heterogeneous Continuum Model and results of the numerical simulations of composite charge explosions will be described in the paper.« less

Reproducing the nonlinear dynamic behavior of a structured beam with a generalized continuum model

NASA Astrophysics Data System (ADS)

Vila, J.; Fernández-Sáez, J.; Zaera, R.

2018-04-01

In this paper we study the coupled axial-transverse nonlinear vibrations of a kind of one dimensional structured solids by application of the so called Inertia Gradient Nonlinear continuum model. To show the accuracy of this axiomatic model, previously proposed by the authors, its predictions are compared with numeric results from a previously defined finite discrete chain of lumped masses and springs, for several number of particles. A continualization of the discrete model equations based on Taylor series allowed us to set equivalent values of the mechanical properties in both discrete and axiomatic continuum models. Contrary to the classical continuum model, the inertia gradient nonlinear continuum model used herein is able to capture scale effects, which arise for modes in which the wavelength is comparable to the characteristic distance of the structured solid. The main conclusion of the work is that the proposed generalized continuum model captures the scale effects in both linear and nonlinear regimes, reproducing the behavior of the 1D nonlinear discrete model adequately.

Linking measures of adolescent nicotine dependence to a common latent continuum.

PubMed

Strong, David R; Kahler, Christopher W; Colby, Suzanne M; Griesler, Pamela C; Kandel, Denise

2009-01-01

Using the theoretical model of nicotine dependence (ND) operationalized within the Diagnostic and Statistical Manual of Mental Disorder, fourth Edition (DSM-IV: American Psychiatric [American Psychiatric Association, 1994. Diagnostic and Statistical Manual of Mental Disorders. 4th ed. American Psychiatric Association, Washington, DC]) as a frame of reference, we used methods based in item response theory to link alternative instruments assessing adolescent nicotine dependence severity to a common latent continuum. A multi-ethnic cohort of 6th-10th graders selected from the Chicago Public Schools (CPS) completed five household interviews over 2 years. Youth who reported at least some cigarette use in the last 30 days prior to the interviews at waves W3-W5 completed measures of DSM-IV ND, the Modified Fagertrom Tolerance Questionnaire (mFTQ: Prokhorov et al., 1998) and the Nicotine Dependence Syndrome Scale (NDSS: Shiffman et al., 2004), yielding samples of 253, 241, and 296 respondents at W3-W5, respectively. Confirmatory factor analysis supported a primary dimension of ND. Each instrument's items had complementary and stable relationships to ND across multiple waves of assessment. By aligning symptoms along a common latent ND continuum, we evaluated the consistency of symptoms from different instruments that target similar content. Further, these methods allowed for the examination of the DSM-IV as a continuous index of ND, evaluation of the degree of heterogeneity in levels of ND within groups above and below diagnostic thresholds, and the utility of using the pattern or particular DSM-IV symptoms that led to each score in further differentiating levels of ND. Finally, we examined concurrent validity of the ND continuum and levels of current of smoking at each wave of assessment.

How does a three-dimensional continuum muscle model affect the kinematics and muscle strains of a finite element neck model compared to a discrete muscle model in rear-end, frontal, and lateral impacts.

PubMed

Hedenstierna, Sofia; Halldin, Peter

2008-04-15

A finite element (FE) model of the human neck with incorporated continuum or discrete muscles was used to simulate experimental impacts in rear, frontal, and lateral directions. The aim of this study was to determine how a continuum muscle model influences the impact behavior of a FE human neck model compared with a discrete muscle model. Most FE neck models used for impact analysis today include a spring element musculature and are limited to discrete geometries and nodal output results. A solid-element muscle model was thought to improve the behavior of the model by adding properties such as tissue inertia and compressive stiffness and by improving the geometry. It would also predict the strain distribution within the continuum elements. A passive continuum muscle model with nonlinear viscoelastic materials was incorporated into the KTH neck model together with active spring muscles and used in impact simulations. The resulting head and vertebral kinematics was compared with the results from a discrete muscle model as well as volunteer corridors. The muscle strain prediction was compared between the 2 muscle models. The head and vertebral kinematics were within the volunteer corridors for both models when activated. The continuum model behaved more stiffly than the discrete model and needed less active force to fit the experimental results. The largest difference was seen in the rear impact. The strain predicted by the continuum model was lower than for the discrete model. The continuum muscle model stiffened the response of the KTH neck model compared with a discrete model, and the strain prediction in the muscles was improved.

Feedback-induced phase transitions in active heterogeneous conductors.

PubMed

Ocko, Samuel A; Mahadevan, L

2015-04-03

An active conducting medium is one where the resistance (conductance) of the medium is modified by the current (flow) and in turn modifies the flow, so that the classical linear laws relating current and resistance, e.g., Ohm's law or Darcy's law, are modified over time as the system itself evolves. We consider a minimal model for this feedback coupling in terms of two parameters that characterize the way in which addition or removal of matter follows a simple local (or nonlocal) feedback rule corresponding to either flow-seeking or flow-avoiding behavior. Using numerical simulations and a continuum mean field theory, we show that flow-avoiding feedback causes an initially uniform system to become strongly heterogeneous via a tunneling (channel-building) phase separation; flow-seeking feedback leads to an immuring (wall-building) phase separation. Our results provide a qualitative explanation for the patterning of active conducting media in natural systems, while suggesting ways to realize complex architectures using simple rules in engineered systems.

Pore scale study of multiphase multicomponent reactive transport during CO 2 dissolution trapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Li; Wang, Mengyi; Kang, Qinjun

Solubility trapping is crucial for permanent CO 2 sequestration in deep saline aquifers. For the first time, a pore-scale numerical method is developed to investigate coupled scCO 2-water two-phase flow, multicomponent (CO 2(aq), H +, HCO 3 –, CO 3 2 – and OH –) mass transport, heterogeneous interfacial dissolution reaction, and homogeneous dissociation reactions. Pore-scale details of evolutions of multiphase distributions and concentration fields are presented and discussed. Time evolutions of several variables including averaged CO 2(aq) concentration, scCO 2 saturation, and pH value are analyzed. Specific interfacial length, an important variable which cannot be determined but is requiredmore » by continuum models, is investigated in detail. Mass transport coefficient or efficient dissolution rate is also evaluated. The pore-scale results show strong non-equilibrium characteristics during solubility trapping due to non-uniform distributions of multiphase as well as slow mass transport process. Complicated coupling mechanisms between multiphase flow, mass transport and chemical reactions are also revealed. Lastly, effects of wettability are also studied. The pore-scale studies provide deep understanding of non-linear non-equilibrium multiple physicochemical processes during CO 2 solubility trapping processes, and also allow to quantitatively predict some important empirical relationships, such as saturation-interfacial surface area, for continuum models.« less

Pore scale study of multiphase multicomponent reactive transport during CO 2 dissolution trapping

DOE PAGES

Chen, Li; Wang, Mengyi; Kang, Qinjun; ...

2018-04-26

Solubility trapping is crucial for permanent CO 2 sequestration in deep saline aquifers. For the first time, a pore-scale numerical method is developed to investigate coupled scCO 2-water two-phase flow, multicomponent (CO 2(aq), H +, HCO 3 –, CO 3 2 – and OH –) mass transport, heterogeneous interfacial dissolution reaction, and homogeneous dissociation reactions. Pore-scale details of evolutions of multiphase distributions and concentration fields are presented and discussed. Time evolutions of several variables including averaged CO 2(aq) concentration, scCO 2 saturation, and pH value are analyzed. Specific interfacial length, an important variable which cannot be determined but is requiredmore » by continuum models, is investigated in detail. Mass transport coefficient or efficient dissolution rate is also evaluated. The pore-scale results show strong non-equilibrium characteristics during solubility trapping due to non-uniform distributions of multiphase as well as slow mass transport process. Complicated coupling mechanisms between multiphase flow, mass transport and chemical reactions are also revealed. Lastly, effects of wettability are also studied. The pore-scale studies provide deep understanding of non-linear non-equilibrium multiple physicochemical processes during CO 2 solubility trapping processes, and also allow to quantitatively predict some important empirical relationships, such as saturation-interfacial surface area, for continuum models.« less

Pore scale study of multiphase multicomponent reactive transport during CO2 dissolution trapping

NASA Astrophysics Data System (ADS)

Chen, Li; Wang, Mengyi; Kang, Qinjun; Tao, Wenquan

2018-06-01

Solubility trapping is crucial for permanent CO2 sequestration in deep saline aquifers. For the first time, a pore-scale numerical method is developed to investigate coupled scCO2-water two-phase flow, multicomponent (CO2(aq), H+, HCO3-, CO32- and OH-) mass transport, heterogeneous interfacial dissolution reaction, and homogeneous dissociation reactions. Pore-scale details of evolutions of multiphase distributions and concentration fields are presented and discussed. Time evolutions of several variables including averaged CO2(aq) concentration, scCO2 saturation, and pH value are analyzed. Specific interfacial length, an important variable which cannot be determined but is required by continuum models, is investigated in detail. Mass transport coefficient or efficient dissolution rate is also evaluated. The pore-scale results show strong non-equilibrium characteristics during solubility trapping due to non-uniform distributions of multiphase as well as slow mass transport process. Complicated coupling mechanisms between multiphase flow, mass transport and chemical reactions are also revealed. Finally, effects of wettability are also studied. The pore-scale studies provide deep understanding of non-linear non-equilibrium multiple physicochemical processes during CO2 solubility trapping processes, and also allow to quantitatively predict some important empirical relationships, such as saturation-interfacial surface area, for continuum models.

Discrete and continuum simulations of near-field ground motion from Source Physics Experiments (SPE) (Invited)

NASA Astrophysics Data System (ADS)

Ezzedine, S. M.; Vorobiev, O.; Herbold, E. B.; Glenn, L. A.; Antoun, T.

2013-12-01

This work is focused on analysis of near-field measurements (up to 100 m from the source) recorded during Source Physics Experiments in a granitic formation. One of the main goals of these experiments is to investigate the possible mechanisms of shear wave generation in the nonlinear source region. SPE experiments revealed significant tangential motion (up to 30 % of the magnitude in the radial direction) at many locations. Furthermore, azimuthal variations in radial velocities were also observed which cannot be generated by a spherical source in isotropic materials. Understanding the nature of this non-radial motion is important for discriminating between the natural seismicity and underground explosions signatures. Possible mechanisms leading to such motion include, but not limited to, heterogeneities in the rock such as joints, faults and geologic layers as well as surface topography and vertical motion at the surface caused by material spall and gravity. We have performed a three dimensional computational studies considering all these effects. Both discrete and continuum methods have been employed to model heterogeneities. In the discrete method, the joints and faults were represented by cohesive contact elements. This enables us to examine various friction laws at the joints which include softening, dilatancy, water saturation and rate-dependent friction. Yet this approach requires the mesh to be aligned with joints, which may present technical difficulties in three dimensions when multiple non-persistent joints are present. In addition, the discrete method is more computationally expensive. The continuum approach assumes that the joints are stiff and the dilatancy and shear softening can be neglected. In this approach, the joints are modeled as weakness planes within the material, which are imbedded into and pass through many finite elements. The advantage of this approach is that it requires neither sophisticated meshing algorithms nor contact detection algorithm. It is also suitable for evaluating the bounds of possible shear motion due to uncertainties in the joints distribution. Details of this uncertainty quantification study are presented in a separate abstract (Vorobiev, et.al). In the present work using both the continuum and the discrete approaches we study the effects of the surface spall, in-situ stress and joint orientation on the observed near-field motion. Three dimensional numerical simulations are performed for different burial depths and yields to investigate scalability of both radial and shear motions. The motion calculated in the near-field is then propagated into a far field. Results of the far field study are presented in an accompanied work (Pitarka, et al). This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Continuum modeling of twinning, amorphization, and fracture: theory and numerical simulations

NASA Astrophysics Data System (ADS)

Clayton, J. D.; Knap, J.

2018-03-01

A continuum mechanical theory is used to model physical mechanisms of twinning, solid-solid phase transformations, and failure by cavitation and shear fracture. Such a sequence of mechanisms has been observed in atomic simulations and/or experiments on the ceramic boron carbide. In the present modeling approach, geometric quantities such as the metric tensor and connection coefficients can depend on one or more director vectors, also called internal state vectors. After development of the general nonlinear theory, a first problem class considers simple shear deformation of a single crystal of this material. For homogeneous fields or stress-free states, algebraic systems or ordinary differential equations are obtained that can be solved by numerical iteration. Results are in general agreement with atomic simulation, without introduction of fitted parameters. The second class of problems addresses the more complex mechanics of heterogeneous deformation and stress states involved in deformation and failure of polycrystals. Finite element calculations, in which individual grains in a three-dimensional polycrystal are fully resolved, invoke a partially linearized version of the theory. Results provide new insight into effects of crystal morphology, activity or inactivity of different inelasticity mechanisms, and imposed deformation histories on strength and failure of the aggregate under compression and shear. The importance of incorporation of inelastic shear deformation in realistic models of amorphization of boron carbide is noted, as is a greater reduction in overall strength of polycrystals containing one or a few dominant flaws rather than many diffusely distributed microcracks.

Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae).

PubMed

Lexer, C; Wüest, R O; Mangili, S; Heuertz, M; Stölting, K N; Pearman, P B; Forest, F; Salamin, N; Zimmermann, N E; Bossolini, E

2014-09-01

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non-neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes. © 2014 John Wiley & Sons Ltd.

Understanding leachate flow in municipal solid waste landfills by combining time-lapse ERT and subsurface flow modelling - Part II: Constraint methodology of hydrodynamic models.

PubMed

Audebert, M; Oxarango, L; Duquennoi, C; Touze-Foltz, N; Forquet, N; Clément, R

2016-09-01

Leachate recirculation is a key process in the operation of municipal solid waste landfills as bioreactors. To ensure optimal water content distribution, bioreactor operators need tools to design leachate injection systems. Prediction of leachate flow by subsurface flow modelling could provide useful information for the design of such systems. However, hydrodynamic models require additional data to constrain them and to assess hydrodynamic parameters. Electrical resistivity tomography (ERT) is a suitable method to study leachate infiltration at the landfill scale. It can provide spatially distributed information which is useful for constraining hydrodynamic models. However, this geophysical method does not allow ERT users to directly measure water content in waste. The MICS (multiple inversions and clustering strategy) methodology was proposed to delineate the infiltration area precisely during time-lapse ERT survey in order to avoid the use of empirical petrophysical relationships, which are not adapted to a heterogeneous medium such as waste. The infiltration shapes and hydrodynamic information extracted with MICS were used to constrain hydrodynamic models in assessing parameters. The constraint methodology developed in this paper was tested on two hydrodynamic models: an equilibrium model where, flow within the waste medium is estimated using a single continuum approach and a non-equilibrium model where flow is estimated using a dual continuum approach. The latter represents leachate flows into fractures. Finally, this methodology provides insight to identify the advantages and limitations of hydrodynamic models. Furthermore, we suggest an explanation for the large volume detected by MICS when a small volume of leachate is injected. Copyright © 2016 Elsevier Ltd. All rights reserved.

Spatial and temporal controls on watershed ecohydrology in the northern Rocky Mountains

Treesearch

Ryan E. Emanuel; Howard E. Epstein; Brian L. McGlynn; Daniel L. Welsch; Daniel J. Muth; Paulo D& #65533; fOdorico

2010-01-01

Vegetation water stress plays an important role in the movement of water through the soil�]plant�]atmosphere continuum. However, the effects of water stress on evapotranspiration (ET) and other hydrological processes at the watershed scale remain poorly understood due in part to spatially and temporally heterogeneous conditions within the...

Predicting colloid transport through saturated porous media: A critical review

NASA Astrophysics Data System (ADS)

Molnar, Ian L.; Johnson, William P.; Gerhard, Jason I.; Willson, Clinton S.; O'Carroll, Denis M.

2015-09-01

Understanding and predicting colloid transport and retention in water-saturated porous media is important for the protection of human and ecological health. Early applications of colloid transport research before the 1990s included the removal of pathogens in granular drinking water filters. Since then, interest has expanded significantly to include such areas as source zone protection of drinking water systems and injection of nanometals for contaminated site remediation. This review summarizes predictive tools for colloid transport from the pore to field scales. First, we review experimental breakthrough and retention of colloids under favorable and unfavorable colloid/collector interactions (i.e., no significant and significant colloid-surface repulsion, respectively). Second, we review the continuum-scale modeling strategies used to describe observed transport behavior. Third, we review the following two components of colloid filtration theory: (i) mechanistic force/torque balance models of pore-scale colloid trajectories and (ii) approximating correlation equations used to predict colloid retention. The successes and limitations of these approaches for favorable conditions are summarized, as are recent developments to predict colloid retention under the unfavorable conditions particularly relevant to environmental applications. Fourth, we summarize the influences of physical and chemical heterogeneities on colloid transport and avenues for their prediction. Fifth, we review the upscaling of mechanistic model results to rate constants for use in continuum models of colloid behavior at the column and field scales. Overall, this paper clarifies the foundation for existing knowledge of colloid transport and retention, features recent advances in the field, critically assesses where existing approaches are successful and the limits of their application, and highlights outstanding challenges and future research opportunities. These challenges and opportunities include improving mechanistic descriptions, and subsequent correlation equations, for nanoparticle (i.e., Brownian particle) transport through soil, developing mechanistic descriptions of colloid retention in so-called "unfavorable" conditions via methods such as the "discrete heterogeneity" approach, and employing imaging techniques such as X-ray tomography to develop realistic expressions for grain topology and mineral distribution that can aid the development of these mechanistic approaches.

Equivalent-Continuum Modeling of Nano-Structured Materials

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Gates, Thomas S.; Nicholson, Lee M.; Wise, Kristopher E.

2001-01-01

A method has been developed for modeling structure-property relationships of nano-structured materials. This method serves as a link between computational chemistry and solid mechanics by substituting discrete molecular structures with an equivalent-continuum model. It has been shown that this substitution may be accomplished by equating the vibrational potential energy of a nano-structured material with the strain energy of representative truss and continuum models. As an important example with direct application to the development and characterization of single-walled carbon nanotubes, the model has been applied to determine the effective continuum geometry of a graphene sheet. A representative volume element of the equivalent-continuum model has been developed with an effective thickness. This effective thickness has been shown to be similar to, but slightly smaller than, the interatomic spacing of graphite.

Prediction of Size Effects in Notched Laminates Using Continuum Damage Mechanics

NASA Technical Reports Server (NTRS)

Camanho, D. P.; Maimi, P.; Davila, C. G.

2007-01-01

This paper examines the use of a continuum damage model to predict strength and size effects in notched carbon-epoxy laminates. The effects of size and the development of a fracture process zone before final failure are identified in an experimental program. The continuum damage model is described and the resulting predictions of size effects are compared with alternative approaches: the point stress and the inherent flaw models, the Linear-Elastic Fracture Mechanics approach, and the strength of materials approach. The results indicate that the continuum damage model is the most accurate technique to predict size effects in composites. Furthermore, the continuum damage model does not require any calibration and it is applicable to general geometries and boundary conditions.

Effects of continuum breakdown on hypersonic aerothermodynamics for reacting flow

NASA Astrophysics Data System (ADS)

Holman, Timothy D.; Boyd, Iain D.

2011-02-01

This study investigates the effects of continuum breakdown on the surface aerothermodynamic properties (pressure, stress, and heat transfer rate) of a sphere in a Mach 25 flow of reacting air in regimes varying from continuum to a rarefied gas. Results are generated using both continuum [computational fluid dynamics (CFD)] and particle [direct simulation Monte Carlo (DSMC)] approaches. The DSMC method utilizes a chemistry model that calculates the backward rates from an equilibrium constant. A preferential dissociation model is modified in the CFD method to better compare with the vibrationally favored dissociation model that is utilized in the DSMC method. Tests of these models are performed to confirm their validity and to compare the chemistry models in both numerical methods. This study examines the effect of reacting air flow on continuum breakdown and the surface properties of the sphere. As the global Knudsen number increases, the amount of continuum breakdown in the flow and on the surface increases. This increase in continuum breakdown significantly affects the surface properties, causing an increase in the differences between CFD and DSMC. Explanations are provided for the trends observed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kashkooli, Ali Ghorbani; Foreman, Evan; Farhad, Siamak

In this study, synchrotron X-ray computed tomography has been utilized using two different imaging modes, absorption and Zernike phase contrast, to reconstruct the real three-dimensional (3D) morphology of nanostructured Li 4Ti 5O 12 (LTO) electrodes. The morphology of the high atomic number active material has been obtained using the absorption contrast mode, whereas the percolated solid network composed of active material and carbon-doped polymer binder domain (CBD) has been obtained using the Zernike phase contrast mode. The 3D absorption contrast image revealed that some LTO nano-particles tend to agglomerate and form secondary micro-sized particles with varying degrees of sphericity. Themore » tortuosity of electrode’s pore and solid phases were found to have directional dependence, different from Bruggeman’s tortuosity commonly used in macro-homogeneous models. The electrode’s heterogeneous structure was investigated by developing a numerical model to simulate galvanostatic discharge process using the Zernike phase contrast mode. The inclusion of CBD in the Zernike phase contrast results in an integrated percolated network of active material and CBD that is highly suited for continuum modeling. As a result, the simulation results highlight the importance of using the real 3D geometry since the spatial distribution of physical and electrochemical properties have a strong non-uniformity due to microstructural heterogeneities.« less

Revisiting the continuum model of tendon pathology: what is its merit in clinical practice and research?

PubMed Central

Cook, J L; Rio, E; Purdam, C R; Docking, S I

2016-01-01

The pathogenesis of tendinopathy and the primary biological change in the tendon that precipitates pathology have generated several pathoaetiological models in the literature. The continuum model of tendon pathology, proposed in 2009, synthesised clinical and laboratory-based research to guide treatment choices for the clinical presentations of tendinopathy. While the continuum has been cited extensively in the literature, its clinical utility has yet to be fully elucidated. The continuum model proposed a model for staging tendinopathy based on the changes and distribution of disorganisation within the tendon. However, classifying tendinopathy based on structure in what is primarily a pain condition has been challenged. The interplay between structure, pain and function is not yet fully understood, which has partly contributed to the complex clinical picture of tendinopathy. Here we revisit and assess the merit of the continuum model in the context of new evidence. We (1) summarise new evidence in tendinopathy research in the context of the continuum, (2) discuss tendon pain and the relevance of a model based on structure and (3) describe relevant clinical elements (pain, function and structure) to begin to build a better understanding of the condition. Our goal is that the continuum model may help guide targeted treatments and improved patient outcomes. PMID:27127294

NASA Workshop on Distributed Parameter Modeling and Control of Flexible Aerospace Systems

NASA Technical Reports Server (NTRS)

Marks, Virginia B. (Compiler); Keckler, Claude R. (Compiler)

1994-01-01

Although significant advances have been made in modeling and controlling flexible systems, there remains a need for improvements in model accuracy and in control performance. The finite element models of flexible systems are unduly complex and are almost intractable to optimum parameter estimation for refinement using experimental data. Distributed parameter or continuum modeling offers some advantages and some challenges in both modeling and control. Continuum models often result in a significantly reduced number of model parameters, thereby enabling optimum parameter estimation. The dynamic equations of motion of continuum models provide the advantage of allowing the embedding of the control system dynamics, thus forming a complete set of system dynamics. There is also increased insight provided by the continuum model approach.

Optical characterization of multi-scale morphologically complex heterogeneous media - Application to snow with soot impurities

NASA Astrophysics Data System (ADS)

Dai, Xiaoyu; Haussener, Sophia

2018-02-01

A multi-scale methodology for the radiative transfer analysis of heterogeneous media composed of morphologically-complex components on two distinct scales is presented. The methodology incorporates the exact morphology at the various scales and utilizes volume-averaging approaches with the corresponding effective properties to couple the scales. At the continuum level, the volume-averaged coupled radiative transfer equations are solved utilizing (i) effective radiative transport properties obtained by direct Monte Carlo simulations at the pore level, and (ii) averaged bulk material properties obtained at particle level by Lorenz-Mie theory or discrete dipole approximation calculations. This model is applied to a soot-contaminated snow layer, and is experimentally validated with reflectance measurements of such layers. A quantitative and decoupled understanding of the morphological effect on the radiative transport is achieved, and a significant influence of the dual-scale morphology on the macroscopic optical behavior is observed. Our results show that with a small amount of soot particles, of the order of 1ppb in volume fraction, the reduction in reflectance of a snow layer with large ice grains can reach up to 77% (at a wavelength of 0.3 μm). Soot impurities modeled as compact agglomerates yield 2-3% lower reduction of the reflectance in a thick show layer compared to snow with soot impurities modeled as chain-like agglomerates. Soot impurities modeled as equivalent spherical particles underestimate the reflectance reduction by 2-8%. This study implies that the morphology of the heterogeneities in a media significantly affects the macroscopic optical behavior and, specifically for the soot-contaminated snow, indicates the non-negligible role of soot on the absorption behavior of snow layers. It can be equally used in technical applications for the assessment and optimization of optical performance in multi-scale media.

Individual Differences in the Severely Retarded Child in Acquisition, Stimulus Generalization, and Extinction in Go-No-Go Discrimination Learning

ERIC Educational Resources Information Center

Evans, P. L. C.; Hogg, J. H.

1975-01-01

This study relates excitatory and inhibitory personality variables of a heterogeneous group of severely retarded children to performance on a discrete trial, successive go-no-go intradimensional discrimination learning problem, which was followed by stimulus generalization tests on a color hue continuum and extinction trials. (GO)

Inclusive Education for Children with Specific Learning Difficulties: Analysis of Opportunities and Barriers in Inclusive Education in Slovenia

ERIC Educational Resources Information Center

Kavkler, Marija; Babuder, Milena Košak; Magajna, Lidija

2015-01-01

Inclusive education allows for universal inclusion, participation and achievement of all children, including children with specific learning difficulties (SpLD). Children with SpLD form a heterogeneous group with diverse cognitive deficits, special educational needs (SEN) and strengths, and have a legislated right to the continuum of both…

DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma

PubMed Central

Sheffield, Nathan C; Pierron, Gaelle; Klughammer, Johanna; Datlinger, Paul; Schönegger, Andreas; Schuster, Michael; Hadler, Johanna; Surdez, Didier; Guillemot, Delphine; Lapouble, Eve; Freneaux, Paul; Champigneulle, Jacqueline; Bouvier, Raymonde; Walder, Diana; Ambros, Ingeborg M; Hutter, Caroline; Sorz, Eva; Amaral, Ana T; de Álava, Enrique; Schallmoser, Katharina; Strunk, Dirk; Rinner, Beate; Liegl-Atzwanger, Bernadette; Huppertz, Berthold; Leithner, Andreas; de Pinieux, Gonzague; Terrier, Philippe; Laurence, Valérie; Michon, Jean; Ladenstein, Ruth; Holter, Wolfgang; Windhager, Reinhard; Dirksen, Uta; Ambros, Peter F; Delattre, Olivier; Kovar, Heinrich; Bock, Christoph; Tomazou, Eleni M

2018-01-01

Developmental tumors in children and young adults carry few genetic alterations, yet they have diverse clinical presentation. Focusing on Ewing sarcoma, we sought to establish the prevalence and characteristics of epigenetic heterogeneity in genetically homogeneous cancers. We performed genome-scale DNA methylation sequencing for a large cohort of Ewing sarcoma tumors and analyzed epigenetic heterogeneity on three levels: between cancers, between tumors, and within tumors. We observed consistent DNA hypomethylation at enhancers regulated by the disease-defining EWS-FLI1 fusion protein, thus establishing epigenomic enhancer reprogramming as a ubiquitous and characteristic feature of Ewing sarcoma. DNA methylation differences between tumors identified a continuous disease spectrum underlying Ewing sarcoma, which reflected the strength of an EWS-FLI1 regulatory signature and a continuum between mesenchymal and stem cell signatures. There was substantial epigenetic heterogeneity within tumors, particularly in patients with metastatic disease. In summary, our study provides a comprehensive assessment of epigenetic heterogeneity in Ewing sarcoma and thereby highlights the importance of considering nongenetic aspects of tumor heterogeneity in the context of cancer biology and personalized medicine. PMID:28134926

Finite Dimensional Approximations for Continuum Multiscale Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berlyand, Leonid

2017-01-24

The completed research project concerns the development of novel computational techniques for modeling nonlinear multiscale physical and biological phenomena. Specifically, it addresses the theoretical development and applications of the homogenization theory (coarse graining) approach to calculation of the effective properties of highly heterogenous biological and bio-inspired materials with many spatial scales and nonlinear behavior. This theory studies properties of strongly heterogeneous media in problems arising in materials science, geoscience, biology, etc. Modeling of such media raises fundamental mathematical questions, primarily in partial differential equations (PDEs) and calculus of variations, the subject of the PI’s research. The focus of completed researchmore » was on mathematical models of biological and bio-inspired materials with the common theme of multiscale analysis and coarse grain computational techniques. Biological and bio-inspired materials offer the unique ability to create environmentally clean functional materials used for energy conversion and storage. These materials are intrinsically complex, with hierarchical organization occurring on many nested length and time scales. The potential to rationally design and tailor the properties of these materials for broad energy applications has been hampered by the lack of computational techniques, which are able to bridge from the molecular to the macroscopic scale. The project addressed the challenge of computational treatments of such complex materials by the development of a synergistic approach that combines innovative multiscale modeling/analysis techniques with high performance computing.« less

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.

The significance of turbulent flow representation in single-continuum models

USGS Publications Warehouse

Reimann, T.; Rehrl, C.; Shoemaker, W.B.; Geyer, T.; Birk, S.

2011-01-01

Karst aquifers exhibit highly conductive features caused from rock dissolution processes. Flow within these structures can become turbulent and therefore can be expressed by nonlinear gradient functions. One way to account for these effects is by coupling a continuum model with a conduit network. Alternatively, turbulent flow can be considered by adapting the hydraulic conductivity within the continuum model. Consequently, the significance of turbulent flow on the dynamic behavior of karst springs is investigated by an enhanced single-continuum model that results in conduit-type flow in continuum cells (CTFC). The single-continuum approach CTFC represents laminar and turbulent flow as well as more complex hybrid models that require additional programming and numerical efforts. A parameter study is conducted to investigate the effects of turbulent flow on the response of karst springs to recharge events using the new CTFC approach, existing hybrid models, and MODFLOW-2005. Results reflect the importance of representing (1) turbulent flow in karst conduits and (2) the exchange between conduits and continuum cells. More specifically, laminar models overestimate maximum spring discharge and underestimate hydraulic gradients within the conduit. It follows that aquifer properties inferred from spring hydrographs are potentially impaired by ignoring flow effects due to turbulence. The exchange factor used for hybrid models is necessary to account for the scale dependency between hydraulic properties of the matrix continuum and conduits. This functionality, which is not included in CTFC, can be mimicked by appropriate use of the Horizontal Flow Barrier package for MODFLOW. Copyright 2011 by the American Geophysical Union.

Neurobiology of fibromyalgia and chronic widespread pain.

PubMed

Sluka, Kathleen A; Clauw, Daniel J

2016-12-03

Fibromyalgia is the current term for chronic widespread musculoskeletal pain for which no alternative cause can be identified. The underlying mechanisms, in both human and animal studies, for the continued pain in individuals with fibromyalgia will be explored in this review. There is a substantial amount of support for alterations of central nervous system nociceptive processing in people with fibromyalgia, and that psychological factors such as stress can enhance the pain experience. Emerging evidence has begun exploring other potential mechanisms including a peripheral nervous system component to the generation of pain and the role of systemic inflammation. We will explore the data and neurobiology related to the role of the CNS in nociceptive processing, followed by a short review of studies examining potential peripheral nervous system changes and cytokine involvement. We will not only explore the data from human subjects with fibromyalgia but will relate this to findings from animal models of fibromyalgia. We conclude that fibromyalgia and related disorders are heterogenous conditions with a complicated pathobiology with patients falling along a continuum with one end a purely peripherally driven painful condition and the other end of the continuum is when pain is purely centrally driven. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

Application of Mortar Coupling in Multiscale Modelling of Coupled Flow, Transport, and Biofilm Growth in Porous Media

NASA Astrophysics Data System (ADS)

Laleian, A.; Valocchi, A. J.; Werth, C. J.

2017-12-01

Multiscale models of reactive transport in porous media are capable of capturing complex pore-scale processes while leveraging the efficiency of continuum-scale models. In particular, porosity changes caused by biofilm development yield complex feedbacks between transport and reaction that are difficult to quantify at the continuum scale. Pore-scale models, needed to accurately resolve these dynamics, are often impractical for applications due to their computational cost. To address this challenge, we are developing a multiscale model of biofilm growth in which non-overlapping regions at pore and continuum spatial scales are coupled with a mortar method providing continuity at interfaces. We explore two decompositions of coupled pore-scale and continuum-scale regions to study biofilm growth in a transverse mixing zone. In the first decomposition, all reaction is confined to a pore-scale region extending the transverse mixing zone length. Only solute transport occurs in the surrounding continuum-scale regions. Relative to a fully pore-scale result, we find the multiscale model with this decomposition has a reduced run time and consistent result in terms of biofilm growth and solute utilization. In the second decomposition, reaction occurs in both an up-gradient pore-scale region and a down-gradient continuum-scale region. To quantify clogging, the continuum-scale model implements empirical relations between porosity and continuum-scale parameters, such as permeability and the transverse dispersion coefficient. Solutes are sufficiently mixed at the end of the pore-scale region, such that the initial reaction rate is accurately computed using averaged concentrations in the continuum-scale region. Relative to a fully pore-scale result, we find accuracy of biomass growth in the multiscale model with this decomposition improves as the interface between pore-scale and continuum-scale regions moves downgradient where transverse mixing is more fully developed. Also, this decomposition poses additional challenges with respect to mortar coupling. We explore these challenges and potential solutions. While recent work has demonstrated growing interest in multiscale models, further development is needed for their application to field-scale subsurface contaminant transport and remediation.

Coupling discrete and continuum concentration particle models for multiscale and hybrid molecular-continuum simulations

NASA Astrophysics Data System (ADS)

Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott

2017-12-01

Hybrid molecular-continuum simulation techniques afford a number of advantages for problems in the rapidly burgeoning area of nanoscale engineering and technology, though they are typically quite complex to implement and limited to single-component fluid systems. We describe an approach for modeling multicomponent hydrodynamic problems spanning multiple length scales when using particle-based descriptions for both the finely resolved (e.g., molecular dynamics) and coarse-grained (e.g., continuum) subregions within an overall simulation domain. This technique is based on the multiscale methodology previously developed for mesoscale binary fluids [N. D. Petsev, L. G. Leal, and M. S. Shell, J. Chem. Phys. 144, 084115 (2016)], simulated using a particle-based continuum method known as smoothed dissipative particle dynamics. An important application of this approach is the ability to perform coupled molecular dynamics (MD) and continuum modeling of molecularly miscible binary mixtures. In order to validate this technique, we investigate multicomponent hybrid MD-continuum simulations at equilibrium, as well as non-equilibrium cases featuring concentration gradients.

Applicability of the Continuum-Shell Theories to the Mechanics of Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Harik, V. M.; Gates, T. S.; Nemeth, M. P.

2002-01-01

Validity of the assumptions relating the applicability of continuum shell theories to the global mechanical behavior of carbon nanotubes is examined. The present study focuses on providing a basis that can be used to qualitatively assess the appropriateness of continuum-shell models for nanotubes. To address the effect of nanotube structure on their deformation, all nanotube geometries are divided into four major classes that require distinct models. Criteria for the applicability of continuum models are presented. The key parameters that control the buckling strains and deformation modes of these classes of nanotubes are determined. In an analogy with continuum mechanics, mechanical laws of geometric similitude are presented. A parametric map is constructed for a variety of nanotube geometries as a guide for the applicability of different models. The continuum assumptions made in representing a nanotube as a homogeneous thin shell are analyzed to identify possible limitations of applying shell theories and using their bifurcation-buckling equations at the nano-scale.

A detailed study of CO 2-brine capillary trapping mechanisms as applied to geologic carbon storage. Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wildenschild, Dorthe

2017-04-06

The proposed research focuses on improved fundamental understanding of the efficiency of physical trapping mechanisms, and as such will provide the basis for subsequent upscaling efforts. The overarching hypothesis of the proposed research is that capillary pressure plays a significant role in capillary trapping of CO 2, especially during the water imbibition stage of the sequestration process. We posit that the relevant physics of the sequestration process is more complex than is currently captured in relative permeability models, which are often based on so-called trapping models to represent relative permeability hysteresis. Our 4 main questions, guiding the 4 main tasksmore » of the proposed research, are as follows: (1) What is the morphology of capillary trapped CO 2 at the pore scale as a function of temperature, pressure, brine concentration, interfacial tension, and pore-space morphology under injection and subsequent imbibition? (2) Is it possible to describe the capillary trapping process using formation-dependent, but otherwise unique continuum-scale functions in permeability-capillary pressure, interfacial area and saturation space, rather than hysteretic functions in permeability-saturation or capillary pressure-saturation space? (3) How do continuum-scale relationships between kr-Pc-S-Anw developed based on pore-scale observations compare with traditional models incorporating relative permeability hysteresis (such as Land’s and other models,) and with observations at the core (5-10cm) scale? (4) How can trapped CO 2 volume be optimized via engineered injection and sweep strategies, and as a function of formation type (incl. heterogeneity)?« less

Considerations for the Development of a Substance-Related Care and Prevention Continuum Model

PubMed Central

Perlman, David C.; Jordan, Ashly E.

2017-01-01

There are significant gaps in the identification and engagement in care and prevention services of people who use illicit substances. Care continuum models have proven to be useful tools in the evaluation of care for HIV and other conditions; numerous issues in substance-related care and prevention resemble those identified in other continua models. Systems of care for substance misuse and substance use disorders (SUDs) can be viewed as consisting of a prevention and care continuum, reflecting incidence and prevalence of substance misuse and SUDs, screening and identification, medical and psychosocial evaluation for treatment, engagement in evidence-based treatment, treatment retention, relapse prevention, timeliness of step completion, and measures of overall and substance use-related specific morbidity and mortality. Care and prevention continuum models could potentially be applied at program, local, regional, state, and national levels. We discuss important lessons that can be drawn from applications of continuum models in other fields. The development and use of a substance-related care and prevention continuum may yield significant patient care, program evaluation and improvement, and population-level benefits. PMID:28770195

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perdikaris, Paris, E-mail: parisp@mit.edu; Grinberg, Leopold, E-mail: leopoldgrinberg@us.ibm.com; Karniadakis, George Em, E-mail: george-karniadakis@brown.edu

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 takingmore » 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.« less

Momentum and Heat Transfer Models for Detonation in Nitromethane with Metal Particles

NASA Astrophysics Data System (ADS)

Ripley, Robert; Zhang, Fan; Lien, Fue-Sang

2009-06-01

Models for momentum and heat exchange have been derived from the results of previous 3D mesoscale simulations of detonation in packed aluminum particles saturated with nitromethane, where the shock interaction timescale was resolved. In these models, particle acceleration and heating within the shock and detonation zone have been expressed in terms of velocity and temperature transmission factors, which are a function of metal to explosive density ratio, metal volume fraction and ratio of particle size to detonation zone thickness. These models are incorporated as source terms in the governing equations for continuum dense two-phase flow and macroscopic simulation is then applied to detonation of nitromethane/aluminum in lightly-cased cylinders. Heterogeneous detonation features such as velocity deficit, enhanced pressure, and critical diameter effects are reproduced. Various spherical particle diameters from 3 -- 30 μm are utilized where most of the particles react in the expanding detonation products. Results for detonation velocity, pressure history, failure and U-shaped critical diameter behavior are compared to the existing experiments.

Momentum and Heat Transfer Models for Detonation in Nitromethane with Metal Particles

NASA Astrophysics Data System (ADS)

Ripley, R. C.; Zhang, F.; Lien, F.-S.

2009-12-01

Models for momentum and heat exchange have been derived from the results of previous 3D mesoscale simulations of detonation in packed aluminum particles saturated with nitromethane, where the shock interaction timescale was resolved. In these models, particle acceleration and heating within the shock and detonation zone are expressed in terms of velocity and temperature transmission factors, which are a function of the metal to explosive density ratio, solid volume fraction and ratio of particle size to detonation zone thickness. These models are incorporated as source terms in the governing equations for continuum dense two-phase flow, and then applied to macroscopic simulation of detonation of nitromethane/aluminum in lightly-cased cylinders. Heterogeneous detonation features such as velocity deficit, enhanced pressure, and critical diameter effects are demonstrated. Various spherical particle diameters from 3-350 μm are utilized where most of the particles react in the expanding detonation products. Results for detonation velocity, pressure history, failure and U-shaped critical diameter behavior are compared to existing experiments.

Realistic Gamow shell model for resonance and continuum in atomic nuclei

NASA Astrophysics Data System (ADS)

Xu, F. R.; Sun, Z. H.; Wu, Q.; Hu, B. S.; Dai, S. J.

2018-02-01

The Gamow shell model can describe resonance and continuum for atomic nuclei. The model is established in the complex-moment (complex-k) plane of the Berggren coordinates in which bound, resonant and continuum states are treated on equal footing self-consistently. In the present work, the realistic nuclear force, CD Bonn, has been used. We have developed the full \\hat{Q}-box folded-diagram method to derive the realistic effective interaction in the model space which is nondegenerate and contains resonance and continuum channels. The CD-Bonn potential is renormalized using the V low-k method. With choosing 16O as the inert core, we have applied the Gamow shell model to oxygen isotopes.

Hybrid plasma modeling.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hopkins, Matthew Morgan; DeChant, Lawrence Justin.; Piekos, Edward Stanley

2009-02-01

This report summarizes the work completed during FY2007 and FY2008 for the LDRD project ''Hybrid Plasma Modeling''. The goal of this project was to develop hybrid methods to model plasmas across the non-continuum-to-continuum collisionality spectrum. The primary methodology to span these regimes was to couple a kinetic method (e.g., Particle-In-Cell) in the non-continuum regions to a continuum PDE-based method (e.g., finite differences) in continuum regions. The interface between the two would be adjusted dynamically ased on statistical sampling of the kinetic results. Although originally a three-year project, it became clear during the second year (FY2008) that there were not sufficientmore » resources to complete the project and it was terminated mid-year.« less

Discrete-to-continuum modelling of weakly interacting incommensurate two-dimensional lattices.

PubMed

Español, Malena I; Golovaty, Dmitry; Wilber, J Patrick

2018-01-01

In this paper, we derive a continuum variational model for a two-dimensional deformable lattice of atoms interacting with a two-dimensional rigid lattice. The starting point is a discrete atomistic model for the two lattices which are assumed to have slightly different lattice parameters and, possibly, a small relative rotation. This is a prototypical example of a three-dimensional system consisting of a graphene sheet suspended over a substrate. We use a discrete-to-continuum procedure to obtain the continuum model which recovers both qualitatively and quantitatively the behaviour observed in the corresponding discrete model. The continuum model predicts that the deformable lattice develops a network of domain walls characterized by large shearing, stretching and bending deformation that accommodates the misalignment and/or mismatch between the deformable and rigid lattices. Two integer-valued parameters, which can be identified with the components of a Burgers vector, describe the mismatch between the lattices and determine the geometry and the details of the deformation associated with the domain walls.

Peridynamic Multiscale Finite Element Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Costa, Timothy; Bond, Stephen D.; Littlewood, David John

The problem of computing quantum-accurate design-scale solutions to mechanics problems is rich with applications and serves as the background to modern multiscale science research. The prob- lem can be broken into component problems comprised of communicating across adjacent scales, which when strung together create a pipeline for information to travel from quantum scales to design scales. Traditionally, this involves connections between a) quantum electronic structure calculations and molecular dynamics and between b) molecular dynamics and local partial differ- ential equation models at the design scale. The second step, b), is particularly challenging since the appropriate scales of molecular dynamic andmore » local partial differential equation models do not overlap. The peridynamic model for continuum mechanics provides an advantage in this endeavor, as the basic equations of peridynamics are valid at a wide range of scales limiting from the classical partial differential equation models valid at the design scale to the scale of molecular dynamics. In this work we focus on the development of multiscale finite element methods for the peridynamic model, in an effort to create a mathematically consistent channel for microscale information to travel from the upper limits of the molecular dynamics scale to the design scale. In particular, we first develop a Nonlocal Multiscale Finite Element Method which solves the peridynamic model at multiple scales to include microscale information at the coarse-scale. We then consider a method that solves a fine-scale peridynamic model to build element-support basis functions for a coarse- scale local partial differential equation model, called the Mixed Locality Multiscale Finite Element Method. Given decades of research and development into finite element codes for the local partial differential equation models of continuum mechanics there is a strong desire to couple local and nonlocal models to leverage the speed and state of the art of local models with the flexibility and accuracy of the nonlocal peridynamic model. In the mixed locality method this coupling occurs across scales, so that the nonlocal model can be used to communicate material heterogeneity at scales inappropriate to local partial differential equation models. Additionally, the computational burden of the weak form of the peridynamic model is reduced dramatically by only requiring that the model be solved on local patches of the simulation domain which may be computed in parallel, taking advantage of the heterogeneous nature of next generation computing platforms. Addition- ally, we present a novel Galerkin framework, the 'Ambulant Galerkin Method', which represents a first step towards a unified mathematical analysis of local and nonlocal multiscale finite element methods, and whose future extension will allow the analysis of multiscale finite element methods that mix models across scales under certain assumptions of the consistency of those models.« less

Applications of Artificial Neural Networks in Structural Engineering with Emphasis on Continuum Models

NASA Technical Reports Server (NTRS)

Kapania, Rakesh K.; Liu, Youhua

1998-01-01

The use of continuum models for the analysis of discrete built-up complex aerospace structures is an attractive idea especially at the conceptual and preliminary design stages. But the diversity of available continuum models and hard-to-use qualities of these models have prevented them from finding wide applications. In this regard, Artificial Neural Networks (ANN or NN) may have a great potential as these networks are universal approximators that can realize any continuous mapping, and can provide general mechanisms for building models from data whose input-output relationship can be highly nonlinear. The ultimate aim of the present work is to be able to build high fidelity continuum models for complex aerospace structures using the ANN. As a first step, the concepts and features of ANN are familiarized through the MATLAB NN Toolbox by simulating some representative mapping examples, including some problems in structural engineering. Then some further aspects and lessons learned about the NN training are discussed, including the performances of Feed-Forward and Radial Basis Function NN when dealing with noise-polluted data and the technique of cross-validation. Finally, as an example of using NN in continuum models, a lattice structure with repeating cells is represented by a continuum beam whose properties are provided by neural networks.

[Hypochondria sine materia as a psychosomatic problem: a model of hypochondriac disorders realized in the cutaneous sphere].

PubMed

Smulevich, A B; Dorozhenok, I Iu; Romanov, D V; L'vov, A N

2012-01-01

Hypochondria sine materia is a disorder with physical complains corresponding to no any somatic diagnosis. Hypochondria sine materia is a more complicated psychopathological condition compared to hypochondria cum materia. Hypochondria sine materia could be diagnosed not only in psychiatry, but mainly in general medicine. It is especially prevalent in dermatology. As a result of analysis of hypochondriac disorders involving cutaneous sphere in patients without dermatological diseases, a binary model of psychodermatological syndromes presenting with hypochondria sine materia in dermatology was developed. The binary structure of the psychodermatological syndromes includes secondary psychiatric symptoms based on primary coenesthesiopathic phenomena. The heterogeneous psychodermatological syndromes (cutaneous organ neurosis, impulsive excoriations syndrome, circumscripta hypochondria, coenesthesiopathic paranoia) could be arranged in a continuum of consecutively worsening conditions from neurotic to psychotic severity register. The syndromes differ in clinical and social prognosis requiring different approach to diagnosis and treatment.

Mesoscale modeling of vacancy-mediated Si segregation near an edge dislocation in Ni under irradiation

NASA Astrophysics Data System (ADS)

Li, Zebo; Trinkle, Dallas R.

2017-04-01

We use a continuum method informed by transport coefficients computed using self-consistent mean field theory to model vacancy-mediated diffusion of substitutional Si solutes in FCC Ni near an a/2 [1 1 ¯0 ] (111 ) edge dislocation. We perform two sequential simulations: first under equilibrium boundary conditions and then under irradiation. The strain field around the dislocation induces heterogeneity and anisotropy in the defect transport properties and determines the steady-state vacancy and Si distributions. At equilibrium both vacancies and Si solutes diffuse to form Cottrell atmospheres with vacancies accumulating in the compressive region above the dislocation core while Si segregates to the tensile region below the core. Irradiation raises the bulk vacancy concentration, driving vacancies to flow into the dislocation core. The out-of-equilibrium vacancy fluxes drag Si atoms towards the core, causing segregation to the compressive region, despite Si being an oversized solute in Ni.

Fundamental analysis of the failure of polymer-based fiber reinforced composites

NASA Technical Reports Server (NTRS)

Kanninen, M. F.; Rybicki, E. F.; Griffith, W. I.; Broek, D.

1975-01-01

A mathematical model predicting the strength of unidirectional fiber reinforced composites containing known flaws and with linear elastic-brittle material behavior was developed. The approach was to imbed a local heterogeneous region surrounding the crack tip into an anisotropic elastic continuum. This (1) permits an explicit analysis of the micromechanical processes involved in the fracture, and (2) remains simple enough to be useful in practical computations. Computations for arbitrary flaw size and orientation under arbitrary applied loads were performed. The mechanical properties were those of graphite epoxy. With the rupture properties arbitrarily varied to test the capabilities of the model to reflect real fracture modes, it was shown that fiber breakage, matrix crazing, crack bridging, matrix-fiber debonding, and axial splitting can all occur during a period of (gradually) increasing load prior to catastrophic failure. The calculations also reveal the sequential nature of the stable crack growth process proceding fracture.

A Public-Private Partnership Develops and Externally Validates a 30-Day Hospital Readmission Risk Prediction Model

PubMed Central

Choudhry, Shahid A.; Li, Jing; Davis, Darcy; Erdmann, Cole; Sikka, Rishi; Sutariya, Bharat

2013-01-01

Introduction: Preventing the occurrence of hospital readmissions is needed to improve quality of care and foster population health across the care continuum. Hospitals are being held accountable for improving transitions of care to avert unnecessary readmissions. Advocate Health Care in Chicago and Cerner (ACC) collaborated to develop all-cause, 30-day hospital readmission risk prediction models to identify patients that need interventional resources. Ideally, prediction models should encompass several qualities: they should have high predictive ability; use reliable and clinically relevant data; use vigorous performance metrics to assess the models; be validated in populations where they are applied; and be scalable in heterogeneous populations. However, a systematic review of prediction models for hospital readmission risk determined that most performed poorly (average C-statistic of 0.66) and efforts to improve their performance are needed for widespread usage. Methods: The ACC team incorporated electronic health record data, utilized a mixed-method approach to evaluate risk factors, and externally validated their prediction models for generalizability. Inclusion and exclusion criteria were applied on the patient cohort and then split for derivation and internal validation. Stepwise logistic regression was performed to develop two predictive models: one for admission and one for discharge. The prediction models were assessed for discrimination ability, calibration, overall performance, and then externally validated. Results: The ACC Admission and Discharge Models demonstrated modest discrimination ability during derivation, internal and external validation post-recalibration (C-statistic of 0.76 and 0.78, respectively), and reasonable model fit during external validation for utility in heterogeneous populations. Conclusions: The ACC Admission and Discharge Models embody the design qualities of ideal prediction models. The ACC plans to continue its partnership to further improve and develop valuable clinical models. PMID:24224068

Morphological and Electrochemical Characterization of Nanostructured Li 4Ti 5O 12 Electrodes Using Multiple Imaging Mode Synchrotron X-ray Computed Tomography

DOE PAGES

Kashkooli, Ali Ghorbani; Foreman, Evan; Farhad, Siamak; ...

2017-09-21

In this study, synchrotron X-ray computed tomography has been utilized using two different imaging modes, absorption and Zernike phase contrast, to reconstruct the real three-dimensional (3D) morphology of nanostructured Li 4Ti 5O 12 (LTO) electrodes. The morphology of the high atomic number active material has been obtained using the absorption contrast mode, whereas the percolated solid network composed of active material and carbon-doped polymer binder domain (CBD) has been obtained using the Zernike phase contrast mode. The 3D absorption contrast image revealed that some LTO nano-particles tend to agglomerate and form secondary micro-sized particles with varying degrees of sphericity. Themore » tortuosity of electrode’s pore and solid phases were found to have directional dependence, different from Bruggeman’s tortuosity commonly used in macro-homogeneous models. The electrode’s heterogeneous structure was investigated by developing a numerical model to simulate galvanostatic discharge process using the Zernike phase contrast mode. The inclusion of CBD in the Zernike phase contrast results in an integrated percolated network of active material and CBD that is highly suited for continuum modeling. As a result, the simulation results highlight the importance of using the real 3D geometry since the spatial distribution of physical and electrochemical properties have a strong non-uniformity due to microstructural heterogeneities.« less

Nonlinear modeling of crystal system transition of black phosphorus using continuum-DFT model.

PubMed

Setoodeh, A R; Farahmand, H

2018-01-24

In this paper, the nonlinear behavior of black phosphorus crystals is investigated in tandem with dispersion-corrected density functional theory (DFT-D) analysis under uniaxial loadings. From the identified anisotropic behavior of black phosphorus due to its morphological anisotropy, a hyperelastic anisotropic (HA) model named continuum-DFT is established to predict the nonlinear behavior of the material. In this respect, uniaxial Cauchy stresses are employed on both the DFT-D and HA models along the zig-zag and armchair directions. Simultaneously, the transition of the crystal system is recognized at about 4.5 GPa of the applied uniaxial tensile stress along the zig-zag direction on the DFT-D simulation in the nonlinear region. In order to develop the nonlinear continuum model, unknown constants are surveyed with the optimized least square technique. In this regard, the continuum model is obtained to reproduce the Cauchy stress-stretch and density of strain-stretch results of the DFT-D simulation. Consequently, the modified HA model is introduced to characterize the nonlinear behavior of black phosphorus along the zig-zag direction. More importantly, the specific transition of the crystal system is successfully predicted in the new modified continuum-DFT model. The results reveal that the multiscale continuum-DFT model is well defined to replicate the nonlinear behavior of black phosphorus along the zig-zag and armchair directions.

Coupling discrete and continuum concentration particle models for multiscale and hybrid molecular-continuum simulations

DOE PAGES

Petsev, Nikolai Dimitrov; Leal, L. Gary; Shell, M. Scott

2017-12-21

Hybrid molecular-continuum simulation techniques afford a number of advantages for problems in the rapidly burgeoning area of nanoscale engineering and technology, though they are typically quite complex to implement and limited to single-component fluid systems. We describe an approach for modeling multicomponent hydrodynamic problems spanning multiple length scales when using particle-based descriptions for both the finely-resolved (e.g. molecular dynamics) and coarse-grained (e.g. continuum) subregions within an overall simulation domain. This technique is based on the multiscale methodology previously developed for mesoscale binary fluids [N. D. Petsev, L. G. Leal, and M. S. Shell, J. Chem. Phys. 144, 84115 (2016)], simulatedmore » using a particle-based continuum method known as smoothed dissipative particle dynamics (SDPD). An important application of this approach is the ability to perform coupled molecular dynamics (MD) and continuum modeling of molecularly miscible binary mixtures. In order to validate this technique, we investigate multicomponent hybrid MD-continuum simulations at equilibrium, as well as non-equilibrium cases featuring concentration gradients.« less

Coupling discrete and continuum concentration particle models for multiscale and hybrid molecular-continuum simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petsev, Nikolai Dimitrov; Leal, L. Gary; Shell, M. Scott

Hybrid molecular-continuum simulation techniques afford a number of advantages for problems in the rapidly burgeoning area of nanoscale engineering and technology, though they are typically quite complex to implement and limited to single-component fluid systems. We describe an approach for modeling multicomponent hydrodynamic problems spanning multiple length scales when using particle-based descriptions for both the finely-resolved (e.g. molecular dynamics) and coarse-grained (e.g. continuum) subregions within an overall simulation domain. This technique is based on the multiscale methodology previously developed for mesoscale binary fluids [N. D. Petsev, L. G. Leal, and M. S. Shell, J. Chem. Phys. 144, 84115 (2016)], simulatedmore » using a particle-based continuum method known as smoothed dissipative particle dynamics (SDPD). An important application of this approach is the ability to perform coupled molecular dynamics (MD) and continuum modeling of molecularly miscible binary mixtures. In order to validate this technique, we investigate multicomponent hybrid MD-continuum simulations at equilibrium, as well as non-equilibrium cases featuring concentration gradients.« less

On the origin of the water vapor continuum absorption within rotational and fundamental vibrational bands

NASA Astrophysics Data System (ADS)

Serov, E. A.; Odintsova, T. A.; Tretyakov, M. Yu.; Semenov, V. E.

2017-05-01

Analysis of the continuum absorption in water vapor at room temperature within the purely rotational and fundamental ro-vibrational bands shows that a significant part (up to a half) of the observed absorption cannot be explained within the framework of the existing concepts of the continuum. Neither of the two most prominent mechanisms of continuum originating, namely, the far wings of monomer lines and the dimers, cannot reproduce the currently available experimental data adequately. We propose a new approach to developing a physically based model of the continuum. It is demonstrated that water dimers and wings of monomer lines may contribute equally to the continuum within the bands, and their contribution should be taken into account in the continuum model. We propose a physical mechanism giving missing justification for the super-Lorentzian behavior of the intermediate line wing. The qualitative validation of the proposed approach is given on the basis of a simple empirical model. The obtained results are directly indicative of the necessity to reconsider the existing line wing theory and can guide this consideration.

Hybrid Multiscale Finite Volume Method for Advection-Diffusion Equations Subject to Heterogeneous Reactive Boundary Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barajas-Solano, David A.; Tartakovsky, A. M.

2016-10-13

We present a hybrid scheme for the coupling of macro and microscale continuum models for reactive contaminant transport in fractured and porous media. The transport model considered is the advection-dispersion equation, subject to linear heterogeneous reactive boundary conditions. The Multiscale Finite Volume method (MsFV) is employed to define an approximation to the microscale concentration field defined in terms of macroscopic or \\emph{global} degrees of freedom, together with local interpolator and corrector functions capturing microscopic spatial variability. The macroscopic mass balance relations for the MsFV global degrees of freedom are coupled with the macroscopic model, resulting in a global problem for the simultaneous time-stepping of all macroscopic degrees of freedom throughout the domain. In order to perform the hybrid coupling, the micro and macroscale models are applied over overlapping subdomains of the simulation domain, with the overlap denoted as the handshake subdomainmore » $$\\Omega^{hs}$$, over which continuity of concentration and transport fluxes between models is enforced. Continuity of concentration is enforced by posing a restriction relation between models over $$\\Omega^{hs}$$. Continuity of fluxes is enforced by prolongating the macroscopic model fluxes across the boundary of $$\\Omega^{hs}$$ to microscopic resolution. The microscopic interpolator and corrector functions are solutions to local microscopic advection-diffusion problems decoupled from the global degrees of freedom and from each other by virtue of the MsFV decoupling ansatz. The error introduced by the decoupling ansatz is reduced iteratively by the preconditioned GMRES algorithm, with the hybrid MsFV operator serving as the preconditioner.« less

Formulation and validation of a reduced order model of 2D materials exhibiting a two-phase microstructure as applied to graphene oxide

NASA Astrophysics Data System (ADS)

Benedetti, Ivano; Nguyen, Hoang; Soler-Crespo, Rafael A.; Gao, Wei; Mao, Lily; Ghasemi, Arman; Wen, Jianguo; Nguyen, SonBinh; Espinosa, Horacio D.

2018-03-01

Novel 2D materials, e.g., graphene oxide (GO), are attractive building blocks in the design of advanced materials due to their reactive chemistry, which can enhance interfacial interactions while providing good in-plane mechanical properties. Recent studies have hypothesized that the randomly distributed two-phase microstructure of GO, which arises due to its oxidized chemistry, leads to differences in nano- vs meso-scale mechanical responses. However, this effect has not been carefully studied using molecular dynamics due to computational limitations. Herein, a continuum mechanics model, formulated based on density functional based tight binding (DFTB) constitutive results for GO nano-flakes, is establish for capturing the effect of oxidation patterns on the material mechanical properties. GO is idealized as a continuum heterogeneous two-phase material, where the mechanical response of each phase, graphitic and oxidized, is informed from DFTB simulations. A finite element implementation of the model is validated via MD simulations and then used to investigate the existence of GO representative volume elements (RVE). We find that for the studied GO, an RVE behavior arises for monolayer sizes in excess to 40 nm. Moreover, we reveal that the response of monolayers with two main different functional chemistries, epoxide-rich and hydroxyl-rich, present distinct differences in mechanical behavior. In addition, we explored the role of defect density in GO, and validate the applicability of the model to larger length scales by predicting membrane deflection behavior, in close agreement with previous experimental and theoretical observations. As such the work presents a reduced order modeling framework applicable in the study of mechanical properties and deformation mechanisms in 2D multiphase materials.

A continuum theory for multicomponent chromatography modeling.

PubMed

Pfister, David; Morbidelli, Massimo; Nicoud, Roger-Marc

2016-05-13

A continuum theory is proposed for modeling multicomponent chromatographic systems under linear conditions. The model is based on the description of complex mixtures, possibly involving tens or hundreds of solutes, by a continuum. The present approach is shown to be very efficient when dealing with a large number of similar components presenting close elution behaviors and whose individual analytical characterization is impossible. Moreover, approximating complex mixtures by continuous distributions of solutes reduces the required number of model parameters to the few ones specific to the characterization of the selected continuous distributions. Therefore, in the frame of the continuum theory, the simulation of large multicomponent systems gets simplified and the computational effectiveness of the chromatographic model is thus dramatically improved. Copyright © 2016 Elsevier B.V. All rights reserved.

A CONTINUUM HARD-SPHERE MODEL OF PROTEIN ADSORPTION

PubMed Central

Finch, Craig; Clarke, Thomas; Hickman, James J.

2012-01-01

Protein adsorption plays a significant role in biological phenomena such as cell-surface interactions and the coagulation of blood. Two-dimensional random sequential adsorption (RSA) models are widely used to model the adsorption of proteins on solid surfaces. Continuum equations have been developed so that the results of RSA simulations can be used to predict the kinetics of adsorption. Recently, Brownian dynamics simulations have become popular for modeling protein adsorption. In this work a continuum model was developed to allow the results from a Brownian dynamics simulation to be used as the boundary condition in a computational fluid dynamics (CFD) simulation. Brownian dynamics simulations were used to model the diffusive transport of hard-sphere particles in a liquid and the adsorption of the particles onto a solid surface. The configuration of the adsorbed particles was analyzed to quantify the chemical potential near the surface, which was found to be a function of the distance from the surface and the fractional surface coverage. The near-surface chemical potential was used to derive a continuum model of adsorption that incorporates the results from the Brownian dynamics simulations. The equations of the continuum model were discretized and coupled to a CFD simulation of diffusive transport to the surface. The kinetics of adsorption predicted by the continuum model closely matched the results from the Brownian dynamics simulation. This new model allows the results from mesoscale simulations to be incorporated into micro- or macro-scale CFD transport simulations of protein adsorption in practical devices. PMID:23729843

Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities

PubMed Central

Bardhan, Jaydeep P.

2014-01-01

In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics. PMID:25505358

Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities.

PubMed

Bardhan, Jaydeep P

2013-12-01

In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

Gradient models in molecular biophysics: progress, challenges, opportunities

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.

2013-12-01

In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g., molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding nonlocal dielectric response. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain, and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost 40 years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The review concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

Progress toward bridging from atomistic to continuum modeling to predict nuclear waste glass dissolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zapol, Peter; Bourg, Ian; Criscenti, Louise Jacqueline

2011-10-01

This report summarizes research performed for the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Subcontinuum and Upscaling Task. The work conducted focused on developing a roadmap to include molecular scale, mechanistic information in continuum-scale models of nuclear waste glass dissolution. This information is derived from molecular-scale modeling efforts that are validated through comparison with experimental data. In addition to developing a master plan to incorporate a subcontinuum mechanistic understanding of glass dissolution into continuum models, methods were developed to generate constitutive dissolution rate expressions from quantum calculations, force field models were selected to generate multicomponent glass structures and gel layers,more » classical molecular modeling was used to study diffusion through nanopores analogous to those in the interfacial gel layer, and a micro-continuum model (K{mu}C) was developed to study coupled diffusion and reaction at the glass-gel-solution interface.« less

Analysis of an optimization-based atomistic-to-continuum coupling method for point defects

DOE PAGES

Olson, Derek; Shapeev, Alexander V.; Bochev, Pavel B.; ...

2015-11-16

Here, we formulate and analyze an optimization-based Atomistic-to-Continuum (AtC) coupling method for problems with point defects. Application of a potential-based atomistic model near the defect core enables accurate simulation of the defect. Away from the core, where site energies become nearly independent of the lattice position, the method switches to a more efficient continuum model. The two models are merged by minimizing the mismatch of their states on an overlap region, subject to the atomistic and continuum force balance equations acting independently in their domains. We prove that the optimization problem is well-posed and establish error estimates.

Nanoindentation of virus capsids in a molecular model

NASA Astrophysics Data System (ADS)

Cieplak, Marek; Robbins, Mark O.

2010-01-01

A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that constitute the capsids and is described in terms of the Cα atoms. Nanoindentation by a large tip is modeled as compression between parallel plates. Plots of the compressive force versus plate separation for CCMV are qualitatively consistent with continuum models and experiments, showing an elastic region followed by an irreversible drop in force. The mechanical response of CPMV has not been studied, but the molecular model predicts an order of magnitude higher stiffness and a much shorter elastic region than for CCMV. These large changes result from small structural changes that increase the number of bonds by only 30% and would be difficult to capture in continuum models. Direct comparison of local deformations in continuum and molecular models of CCMV shows that the molecular model undergoes a gradual symmetry breaking rotation and accommodates more strain near the walls than the continuum model. The irreversible drop in force at small separations is associated with rupturing nearly all of the bonds between capsid proteins in the molecular model, while a buckling transition is observed in continuum models.

Continuum model of tensile fracture of metal melts and its application to a problem of high-current electron irradiation of metals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayer, Alexander E., E-mail: mayer@csu.ru, E-mail: mayer.al.evg@gmail.com; Mayer, Polina N.

2015-07-21

A continuum model of the metal melt fracture is formulated on the basis of the continuum mechanics and theory of metastable liquid. A character of temperature and strain rate dependences of the tensile strength that is predicted by the continuum model is verified, and parameters of the model are fitted with the use of the results of the molecular dynamics simulations for ultra-high strain rates (≥1–10/ns). A comparison with experimental data from literature is also presented for Al and Ni melts. Using the continuum model, the dynamic tensile strength of initially uniform melts of Al, Cu, Ni, Fe, Ti, andmore » Pb within a wide range of strain rates (from 1–10/ms to 100/ns) and temperatures (from melting temperature up to 70–80% of critical temperature) is calculated. The model is applied to numerical investigation of a problem of the high-current electron irradiation of Al, Cu, and Fe targets.« less

Modeling stock price dynamics by continuum percolation system and relevant complex systems analysis

NASA Astrophysics Data System (ADS)

Xiao, Di; Wang, Jun

2012-10-01

The continuum percolation system is developed to model a random stock price process in this work. Recent empirical research has demonstrated various statistical features of stock price changes, the financial model aiming at understanding price fluctuations needs to define a mechanism for the formation of the price, in an attempt to reproduce and explain this set of empirical facts. The continuum percolation model is usually referred to as a random coverage process or a Boolean model, the local interaction or influence among traders is constructed by the continuum percolation, and a cluster of continuum percolation is applied to define the cluster of traders sharing the same opinion about the market. We investigate and analyze the statistical behaviors of normalized returns of the price model by some analysis methods, including power-law tail distribution analysis, chaotic behavior analysis and Zipf analysis. Moreover, we consider the daily returns of Shanghai Stock Exchange Composite Index from January 1997 to July 2011, and the comparisons of return behaviors between the actual data and the simulation data are exhibited.

Numerical simulation of freshwater/seawater interaction in a dual-permeability karst system with conduits: the development of discrete-continuum VDFST-CFP model

NASA Astrophysics Data System (ADS)

Xu, Zexuan; Hu, Bill

2016-04-01

Dual-permeability karst aquifers of porous media and conduit networks with significant different hydrological characteristics are widely distributed in the world. Discrete-continuum numerical models, such as MODFLOW-CFP and CFPv2, have been verified as appropriate approaches to simulate groundwater flow and solute transport in numerical modeling of karst hydrogeology. On the other hand, seawater intrusion associated with fresh groundwater resources contamination has been observed and investigated in numbers of coastal aquifers, especially under conditions of sea level rise. Density-dependent numerical models including SEAWAT are able to quantitatively evaluate the seawater/freshwater interaction processes. A numerical model of variable-density flow and solute transport - conduit flow process (VDFST-CFP) is developed to provide a better description of seawater intrusion and submarine groundwater discharge in a coastal karst aquifer with conduits. The coupling discrete-continuum VDFST-CFP model applies Darcy-Weisbach equation to simulate non-laminar groundwater flow in the conduit system in which is conceptualized and discretized as pipes, while Darcy equation is still used in continuum porous media. Density-dependent groundwater flow and solute transport equations with appropriate density terms in both conduit and porous media systems are derived and numerically solved using standard finite difference method with an implicit iteration procedure. Synthetic horizontal and vertical benchmarks are created to validate the newly developed VDFST-CFP model by comparing with other numerical models such as variable density SEAWAT, couplings of constant density groundwater flow and solute transport MODFLOW/MT3DMS and discrete-continuum CFPv2/UMT3D models. VDFST-CFP model improves the simulation of density dependent seawater/freshwater mixing processes and exchanges between conduit and matrix. Continuum numerical models greatly overestimated the flow rate under turbulent flow condition but discrete-continuum models provide more accurate results. Parameters sensitivities analysis indicates that conduit diameter and friction factor, matrix hydraulic conductivity and porosity are important parameters that significantly affect variable-density flow and solute transport simulation. The pros and cons of model assumptions, conceptual simplifications and numerical techniques in VDFST-CFP are discussed. In general, the development of VDFST-CFP model is an innovation in numerical modeling methodology and could be applied to quantitatively evaluate the seawater/freshwater interaction in coastal karst aquifers. Keywords: Discrete-continuum numerical model; Variable density flow and transport; Coastal karst aquifer; Non-laminar flow

Translational research: understanding the continuum from bench to bedside.

PubMed

Drolet, Brian C; Lorenzi, Nancy M

2011-01-01

The process of translating basic scientific discoveries to clinical applications, and ultimately to public health improvements, has emerged as an important, but difficult, objective in biomedical research. The process is best described as a "translation continuum" because various resources and actions are involved in this progression of knowledge, which advances discoveries from the bench to the bedside. The current model of this continuum focuses primarily on translational research, which is merely one component of the overall translation process. This approach is ineffective. A revised model to address the entire continuum would provide a methodology to identify and describe all translational activities (eg, implementation, adoption translational research, etc) as well their place within the continuum. This manuscript reviews and synthesizes the literature to provide an overview of the current terminology and model for translation. A modification of the existing model is proposed to create a framework called the Biomedical Research Translation Continuum, which defines the translation process and describes the progression of knowledge from laboratory to health gains. This framework clarifies translation for readers who have not followed the evolving and complicated models currently described. Authors and researchers may use the continuum to understand and describe their research better as well as the translational activities within a conceptual framework. Additionally, the framework may increase the advancement of knowledge by refining discussions of translation and allowing more precise identification of barriers to progress. Copyright © 2011 Mosby, Inc. All rights reserved.

A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores

PubMed Central

Yoo, Jejoong; Jackson, Meyer B.; Cui, Qiang

2013-01-01

To establish the validity of continuum mechanics models quantitatively for the analysis of membrane remodeling processes, we compare the shape and energies of the membrane fusion pore predicted by coarse-grained (MARTINI) and continuum mechanics models. The results at these distinct levels of resolution give surprisingly consistent descriptions for the shape of the fusion pore, and the deviation between the continuum and coarse-grained models becomes notable only when the radius of curvature approaches the thickness of a monolayer. Although slow relaxation beyond microseconds is observed in different perturbative simulations, the key structural features (e.g., dimension and shape of the fusion pore near the pore center) are consistent among independent simulations. These observations provide solid support for the use of coarse-grained and continuum models in the analysis of membrane remodeling. The combined coarse-grained and continuum analysis confirms the recent prediction of continuum models that the fusion pore is a metastable structure and that its optimal shape is neither toroidal nor catenoidal. Moreover, our results help reveal a new, to our knowledge, bowing feature in which the bilayers close to the pore axis separate more from one another than those at greater distances from the pore axis; bowing helps reduce the curvature and therefore stabilizes the fusion pore structure. The spread of the bilayer deformations over distances of hundreds of nanometers and the substantial reduction in energy of fusion pore formation provided by this spread indicate that membrane fusion can be enhanced by allowing a larger area of membrane to participate and be deformed. PMID:23442963

Stochastic Ground Water Flow Simulation with a Fracture Zone Continuum Model

USGS Publications Warehouse

Langevin, C.D.

2003-01-01

A method is presented for incorporating the hydraulic effects of vertical fracture zones into two-dimensional cell-based continuum models of ground water flow and particle tracking. High hydraulic conductivity features are used in the model to represent fracture zones. For fracture zones that are not coincident with model rows or columns, an adjustment is required for the hydraulic conductivity value entered into the model cells to compensate for the longer flowpath through the model grid. A similar adjustment is also required for simulated travel times through model cells. A travel time error of less than 8% can occur for particles moving through fractures with certain orientations. The fracture zone continuum model uses stochastically generated fracture zone networks and Monte Carlo analysis to quantify uncertainties with simulated advective travel times. An approach is also presented for converting an equivalent continuum model into a fracture zone continuum model by establishing the contribution of matrix block transmissivity to the bulk transmissivity of the aquifer. The methods are used for a case study in west-central Florida to quantify advective travel times from a potential wetland rehydration site to a municipal supply wellfield. Uncertainties in advective travel times are assumed to result from the presence of vertical fracture zones, commonly observed on aerial photographs as photolineaments.

Cells competition in tumor growth poroelasticity

NASA Astrophysics Data System (ADS)

Fraldi, Massimiliano; Carotenuto, Angelo R.

2018-03-01

Growth of biological tissues has been recently treated within the framework of Continuum Mechanics, by adopting heterogeneous poroelastic models where the interaction between soft matrix and interstitial fluid flow is coupled with inelastic effects ad hoc introduced to simulate the macroscopic volumetric growth determined by cells division, cells growth and extracellular matrix changes occurring at the micro-scale level. These continuum models seem to overcome some limitations intrinsically associated to other alternative approaches based on mass balances in multiphase systems, because the crucial role played by residual stresses accompanying growth and nutrients walkway is preserved. Nevertheless, when these strategies are applied to analyze solid tumors, mass growth is usually assigned in a prescribed form that essentially copies the in vitro measured intrinsic growth rates of the cell species. As a consequence, some important cell-cell dynamics governing mass evolution and invasion rates of cancer cells, as well as their coupling with feedback mechanisms associated to in situ stresses, are inevitably lost and thus the spatial distribution and the evolution with time of the growth inside the tumor -which would be results rather than inputs- are forced to enter in the model simply as data. In order to solve this paradox, it is here proposed an enhanced multi-scale poroelastic model undergoing large deformations and embodying inelastic growth, where the net growth terms directly result from the "interspecific" predator-prey (Volterra/Lotka-like) competition occurring at the micro-scale level between healthy and abnormal cell species. In this way, a system of fully-coupled non-linear PDEs is derived to describe how the fight among cell species to grab the available common resources, stress field, pressure gradients, interstitial fluid flows driving nutrients and inhomogeneous growth all simultaneously interact to decide the tumor fate.

Safety and feasibility of an exercise prescription approach to rehabilitation across the continuum of care for survivors of critical illness.

PubMed

Berney, Sue; Haines, Kimberley; Skinner, Elizabeth H; Denehy, Linda

2012-12-01

Survivors of critical illness can experience long-standing functional limitations that negatively affect their health-related quality of life. To date, no model of rehabilitation has demonstrated sustained improvements in physical function for survivors of critical illness beyond hospital discharge. The aims of this study were: (1) to describe a model of rehabilitation for survivors of critical illness, (2) to compare the model to local standard care, and (3) to report the safety and feasibility of the program. This was a cohort study. As part of a larger randomized controlled trial, 74 participants were randomly assigned, 5 days following admission to the intensive care unit (ICU), to a protocolized rehabilitation program that commenced in the ICU and continued on the acute care ward and for a further 8 weeks following hospital discharge as an outpatient program. Exercise training was prescribed based on quantitative outcome measures to achieve a physiological training response. During acute hospitalization, 60% of exercise sessions were able to be delivered. The most frequently occurring barriers to exercise were patient safety and patient refusal due to fatigue. Point prevalence data showed patients were mobilized more often and for longer periods compared with standard care. Outpatient classes were poorly attended, with only 41% of the patients completing more than 70% of outpatient classes. No adverse events occurred. Limitations included patient heterogeneity and delayed commencement of exercise in the ICU due to issues of consent and recruitment. Exercise training that commences in the ICU and continues through to an outpatient program is safe and feasible for survivors of critical illness. Models of care that maximize patient participation across the continuum of care warrant further investigation.

Ranges of Applicability for the Continuum-beam Model in the Constitutive Analysis of Carbon Nanotubes: Nanotubes or Nano-beams?

NASA Technical Reports Server (NTRS)

Harik, Vasyl Michael; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

Ranges of validity for the continuum-beam model, the length-scale effects and continuum assumptions are analyzed in the framework of scaling analysis of NT structure. Two coupled criteria for the applicability of the continuum model are presented. Scaling analysis of NT buckling and geometric parameters (e.g., diameter and length) is carried out to determine the key non-dimensional parameters that control the buckling strains and modes of NT buckling. A model applicability map, which represents two classes of NTs, is constructed in the space of non-dimensional parameters. In an analogy with continuum mechanics, a mechanical law of geometric similitude is presented for two classes of beam-like NTs having different geometries. Expressions for the critical buckling loads and strains are tailored for the distinct groups of NTs and compared with the data provided by the molecular dynamics simulations. Implications for molecular dynamics simulations and the NT-based scanning probes are discussed.

A Micro-Mechanism-Based Continuum Corrosion Fatigue Damage Model for Steels

NASA Astrophysics Data System (ADS)

Sun, Bin; Li, Zhaoxia

2018-05-01

A micro-mechanism-based corrosion fatigue damage model is developed for studying the high-cycle corrosion fatigue of steel from multi-scale viewpoint. The developed physical corrosion fatigue damage model establishes micro-macro relationships between macroscopic continuum damage evolution and collective evolution behavior of microscopic pits and cracks, which can be used to describe the multi-scale corrosion fatigue process of steel. As a case study, the model is used to predict continuum damage evolution and number density of the corrosion pit and short crack of steel component in 5% NaCl water under constant stress amplitude at 20 kHz, and the numerical results are compared with experimental results. It shows that the model is effective and can be used to evaluate the continuum macroscopic corrosion fatigue damage and study microscopic corrosion fatigue mechanisms of steel.

A Micro-Mechanism-Based Continuum Corrosion Fatigue Damage Model for Steels

NASA Astrophysics Data System (ADS)

Sun, Bin; Li, Zhaoxia

2018-04-01

A micro-mechanism-based corrosion fatigue damage model is developed for studying the high-cycle corrosion fatigue of steel from multi-scale viewpoint. The developed physical corrosion fatigue damage model establishes micro-macro relationships between macroscopic continuum damage evolution and collective evolution behavior of microscopic pits and cracks, which can be used to describe the multi-scale corrosion fatigue process of steel. As a case study, the model is used to predict continuum damage evolution and number density of the corrosion pit and short crack of steel component in 5% NaCl water under constant stress amplitude at 20 kHz, and the numerical results are compared with experimental results. It shows that the model is effective and can be used to evaluate the continuum macroscopic corrosion fatigue damage and study microscopic corrosion fatigue mechanisms of steel.

Micropolar continuum modelling of bi-dimensional tetrachiral lattices

PubMed Central

Chen, Y.; Liu, X. N.; Hu, G. K.; Sun, Q. P.; Zheng, Q. S.

2014-01-01

The in-plane behaviour of tetrachiral lattices should be characterized by bi-dimensional orthotropic material owing to the existence of two orthogonal axes of rotational symmetry. Moreover, the constitutive model must also represent the chirality inherent in the lattices. To this end, a bi-dimensional orthotropic chiral micropolar model is developed based on the theory of irreducible orthogonal tensor decomposition. The obtained constitutive tensors display a hierarchy structure depending on the symmetry of the underlying microstructure. Eight additional material constants, in addition to five for the hemitropic case, are introduced to characterize the anisotropy under Z2 invariance. The developed continuum model is then applied to a tetrachiral lattice, and the material constants of the continuum model are analytically derived by a homogenization process. By comparing with numerical simulations for the discrete lattice, it is found that the proposed continuum model can correctly characterize the static and wave properties of the tetrachiral lattice. PMID:24808754

A continuum model for pressure-flow relationship in human pulmonary circulation.

PubMed

Huang, Wei; Zhou, Qinlian; Gao, Jian; Yen, R T

2011-06-01

A continuum model was introduced to analyze the pressure-flow relationship for steady flow in human pulmonary circulation. The continuum approach was based on the principles of continuum mechanics in conjunction with detailed measurement of vascular geometry, vascular elasticity and blood rheology. The pulmonary arteries and veins were considered as elastic tubes and the "fifth-power law" was used to describe the pressure-flow relationship. For pulmonary capillaries, the "sheet-flow" theory was employed and the pressure-flow relationship was represented by the "fourth-power law". In this paper, the pressure-flow relationship for the whole pulmonary circulation and the longitudinal pressure distribution along the streamlines were studied. Our computed data showed general agreement with the experimental data for the normal subjects and the patients with mitral stenosis and chronic bronchitis in the literature. In conclusion, our continuum model can be used to predict the changes of steady flow in human pulmonary circulation.

Dynamical discrete/continuum linear response shells theory of solvation: convergence test for NH4+ and OH- ions in water solution using DFT and DFTB methods.

PubMed

de Lima, Guilherme Ferreira; Duarte, Hélio Anderson; Pliego, Josefredo R

2010-12-09

A new dynamical discrete/continuum solvation model was tested for NH(4)(+) and OH(-) ions in water solvent. The method is similar to continuum solvation models in a sense that the linear response approximation is used. However, different from pure continuum models, explicit solvent molecules are included in the inner shell, which allows adequate treatment of specific solute-solvent interactions present in the first solvation shell, the main drawback of continuum models. Molecular dynamics calculations coupled with SCC-DFTB method are used to generate the configurations of the solute in a box with 64 water molecules, while the interaction energies are calculated at the DFT level. We have tested the convergence of the method using a variable number of explicit water molecules and it was found that even a small number of waters (as low as 14) are able to produce converged values. Our results also point out that the Born model, often used for long-range correction, is not reliable and our method should be applied for more accurate calculations.

Mathematics for understanding disease.

PubMed

Bies, R R; Gastonguay, M R; Schwartz, S L

2008-06-01

The application of mathematical models to reflect the organization and activity of biological systems can be viewed as a continuum of purpose. The far left of the continuum is solely the prediction of biological parameter values, wherein an understanding of the underlying biological processes is irrelevant to the purpose. At the far right of the continuum are mathematical models, the purposes of which are a precise understanding of those biological processes. No models in present use fall at either end of the continuum. Without question, however, the emphasis in regards to purpose has been on prediction, e.g., clinical trial simulation and empirical disease progression modeling. Clearly the model that ultimately incorporates a universal understanding of biological organization will also precisely predict biological events, giving the continuum the logical form of a tautology. Currently that goal lies at an immeasurable distance. Nonetheless, the motive here is to urge movement in the direction of that goal. The distance traveled toward understanding naturally depends upon the nature of the scientific question posed with respect to comprehending and/or predicting a particular disease process. A move toward mathematical models implies a move away from static empirical modeling and toward models that focus on systems biology, wherein modeling entails the systematic study of the complex pattern of organization inherent in biological systems.

Moving Contact Lines: Linking Molecular Dynamics and Continuum-Scale Modeling.

PubMed

Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

2018-05-17

Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide a link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which governs the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modeling and highlight the opportunities for future developments in this area.

Solar radio continuum storms and a breathing magnetic field model

NASA Technical Reports Server (NTRS)

1975-01-01

Radio noise continuum emissions observed in metric and decametric wave frequencies are, in general, associated with actively varying sunspot groups accompanied by the S-component of microwave radio emissions. These continuum emission sources, often called type I storm sources, are often associated with type III burst storm activity from metric to hectometric wave frequencies. This storm activity is, therefore, closely connected with the development of these continuum emission sources. It is shown that the S-component emission in microwave frequencies generally precedes, by several days, the emission of these noise continuum storms of lower frequencies. In order for these storms to develop, the growth of sunspot groups into complex types is very important in addition to the increase of the average magnetic field intensity and area of these groups. After giving a review on the theory of these noise continuum storm emissions, a model is briefly considered to explain the relation of the emissions to the storms.

Ensuring congruency in multiscale modeling: towards linking agent based and continuum biomechanical models of arterial adaptation.

PubMed

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.

Models of collective cell spreading with variable cell aspect ratio: a motivation for degenerate diffusion models.

PubMed

Simpson, Matthew J; Baker, Ruth E; McCue, Scott W

2011-02-01

Continuum diffusion models are often used to represent the collective motion of cell populations. Most previous studies have simply used linear diffusion to represent collective cell spreading, while others found that degenerate nonlinear diffusion provides a better match to experimental cell density profiles. In the cell modeling literature there is no guidance available with regard to which approach is more appropriate for representing the spreading of cell populations. Furthermore, there is no knowledge of particular experimental measurements that can be made to distinguish between situations where these two models are appropriate. Here we provide a link between individual-based and continuum models using a multiscale approach in which we analyze the collective motion of a population of interacting agents in a generalized lattice-based exclusion process. For round agents that occupy a single lattice site, we find that the relevant continuum description of the system is a linear diffusion equation, whereas for elongated rod-shaped agents that occupy L adjacent lattice sites we find that the relevant continuum description is connected to the porous media equation (PME). The exponent in the nonlinear diffusivity function is related to the aspect ratio of the agents. Our work provides a physical connection between modeling collective cell spreading and the use of either the linear diffusion equation or the PME to represent cell density profiles. Results suggest that when using continuum models to represent cell population spreading, we should take care to account for variations in the cell aspect ratio because different aspect ratios lead to different continuum models.

Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

NASA Astrophysics Data System (ADS)

Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kibaek

2017-01-01

We describe the ignition of an explosive crystal of gamma-phase RDX due to a thermal hot spot with reactive molecular dynamics (RMD), with first-principles trained, reactive force field based molecular potentials that represents an extremely complex reaction network. The RMD simulation is analyzed by sorting molecular product fragments into high and low molecular weight groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation has a single temperature and stress state for the mixture. The continuum simulation that mirrors the atomistic simulation allows us to study the atomistic simulation in the familiar physical chemistry framework and provides an essential, continuum/atomistic link.

The role of pragmatism in explaining heterogeneity in meta-analyses of randomised trials: a protocol for a cross-sectional methodological review.

PubMed

Aves, Theresa; Allan, Katherine S; Lawson, Daeria; Nieuwlaat, Robby; Beyene, Joseph; Mbuagbaw, Lawrence

2017-09-03

There has been increasing interest in pragmatic trials methodology. As a result, tools such as the Pragmatic-Explanatory Continuum Indicator Summary-2 (PRECIS-2) are being used prospectively to help researchers design randomised controlled trials (RCTs) within the pragmatic-explanatory continuum. There may be value in applying the PRECIS-2 tool retrospectively in a systematic review setting as it could provide important information about how to pool data based on the degree of pragmatism. To investigate the role of pragmatism as a source of heterogeneity in systematic reviews by (1) identifying systematic reviews with meta-analyses of RCTs that have moderate to high heterogeneity, (2) applying PRECIS-2 to RCTs of systematic reviews, (3) evaluating the inter-rater reliability of PRECIS-2, (4) determining how much of this heterogeneity may be explained by pragmatism. A cross-sectional methodological review will be conducted on systematic reviews of RCTs published in the Cochrane Library from 1 January 2014 to 1 January 2017. Included systematic reviews will have a minimum of 10 RCTs in the meta-analysis of the primary outcome and moderate to substantial heterogeneity (I 2 ≥50%). Of the eligible systematic reviews, a random selection of 10 will be included for quantitative evaluation. In each systematic review, RCTs will be scored using the PRECIS-2 tool, in duplicate. Agreement between raters will be measured using the intraclass correlation coefficient. Subgroup analyses and meta-regression will be used to evaluate how much variability in the primary outcome may be due to pragmatism. This review will be among the first to evaluate the PRECIS-2 tool in a systematic review setting. Results from this research will provide inter-rater reliability information about PRECIS-2 and may be used to provide methodological guidance when dealing with pragmatism in systematic reviews and subgroup considerations. On completion, this review will be submitted to a peer-reviewed journal for publication. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Reply to "Comment on 'Hydrodynamics of fractal continuum flow' and 'Map of fluid flow in fractal porous medium into fractal continuum flow'".

PubMed

Balankin, Alexander S; Elizarraraz, Benjamin Espinoza

2013-11-01

The aim of this Reply is to elucidate the difference between the fractal continuum models used in the preceding Comment and the models of fractal continuum flow which were put forward in our previous articles [Phys. Rev. E 85, 025302(R) (2012); 85, 056314 (2012)]. In this way, some drawbacks of the former models are highlighted. Specifically, inconsistencies in the definitions of the fractal derivative, the Jacobian of transformation, the displacement vector, and angular momentum are revealed. The proper forms of the Reynolds' transport theorem and angular momentum principle for the fractal continuum are reaffirmed in a more illustrative manner. Consequently, we emphasize that in the absence of any internal angular momentum, body couples, and couple stresses, the Cauchy stress tensor in the fractal continuum should be symmetric. Furthermore, we stress that the approach based on the Cartesian product measured and used in the preceding Comment cannot be employed to study the path-connected fractals, such as a flow in a fractally permeable medium. Thus, all statements of our previous works remain unchallenged.

Time-Resolved Properties and Global Trends in dMe Flares from Simultaneous Photometry and Spectra

NASA Astrophysics Data System (ADS)

Kowalski, Adam F.

We present a homogeneous survey of near-ultraviolet (NUV) /optical line and continuum emission during twenty M dwarf flares with simultaneous, high cadence photometry and spectra. These data were obtained to study the white-light continuum components to the blue and red of the Balmer jump to break the degeneracy with fitting emission mechanisms to broadband colors and to provide constraints for radiative-hydrodynamic flare models that seek to reproduce the white-light flare emission. The main results from the continuum analysis are the following: 1) the detection of Balmer continuum (in emission) that is present during all flares, with a wide range of relative contribution to the continuum flux in the NUV; 2) a blue continuum at the peak of the photometry that is linear with wavelength from λ = 4000 - 4800Å, matched by the spectral shape of hot, blackbody emission with typical temperatures of 10 000 - 12 000 K; 3) a redder continuum apparent at wavelengths longer than Hβ; this continuum becomes relatively more important to the energy budget during the late gradual phase. The hot blackbody component and redder continuum component (which we call "the conundruum") have been detected in previous UBVR colorimetry studies of flares. With spectra, one can compare the properties and detailed timings of all three components. Using time-resolved spectra during the rise phase of three flares, we calculate the speed of an expanding flare region assuming a simple geometry; the speeds are found to be ~5- 10 km s-1 and 50 - 120 km s -1, which are strikingly consistent with the speeds at which two-ribbon flares develop on the Sun. The main results from the emission line analysis are 1) the presentation of the "time-decrement", a relation between the timescales of the Balmer series; 2) a Neupert-like relation between Ca \\pcy K and the blackbody continuum, and 3) the detection of absorption wings in the Hydrogen Balmer lines during times of peak continuum emission, indicative of hot-star spectra forming during the flare. A byproduct of this study is a new method for deriving absolute fluxes during M dwarf flare observations obtained from narrow-slit spectra or during variable weather conditions. This technique allows us to analyze the spectra and photometry independently of one another, in order to connect the spectral properties to the rise, peak, and decay phases of broadband light curve morphology. We classify the light curve morphology according to an "impulsiveness index" and find that the fast (impulsive) flares have less Balmer continuum at peak emission than the slow (gradual) flares. In the gradual phase, the energy budget of the flare spectrum during almost all flares has a larger contribution from the Hydrogen Balmer component than in the impulsive phase, suggesting that the heating and cooling processes evolve over the course of a flare. We find that, in general, the evolution of the hot blackbody is rapid, and that the blackbody temperature decreases to ~8000 K in the gradual phase. The Balmer continuum evolves more slowly than the blackbody ¨C similar to the higher order Balmer lines but faster than the lower order Balmer lines. The height of the Balmer jump increases during the gradual decay phase. We model the Balmer continuum emission using the RHD F11 model spectrum from Allred et al. (2006), but we discuss several important systematic uncertainties in relating the apparent amount of Balmer continuum to a given RHD beam model. Good fits to the shape of the RHD F11 model spectrum are not obtained at peak times, in contrast to the gradual phase. We model the blackbody component using model hot star atmospheres from Castelli & Kurucz (2004) in order to account for the effects of flux redistribution in the flare atmosphere. This modeling is motivated by observations during a secondary flare in the decay phase of a megaflare, when the newly formed flare spectrum resembled that of Vega with the Balmer continuum and lines in absorption. We model this continuum phenomenologically with the RH code using hot spots placed at high column mass in the M dwarf quiescent atmosphere; a superposition of hot spot models and the RHD model are used to explain the anti-correlation in the apparent amount of Balmer continuum in emission and the U-band light curve. We attempt to reproduce the blackbody component in self-consistent 1D radiative hydrodynamic flare models using the RADYN code. We simulate the flare using a solar-type nonthermal electron beam heating function with a total energy flux of 1012 ergs cm-2 s-1 (F12) for a duration of 5 seconds and a subsequent gradual phase. Although there is a larger amount of NUV backwarming at log mc/(1g cm-2)~0 than in the F11 model, the resulting flare continuum shape is similar to the F11 model spectrum with a larger Balmer jump and a much redder spectral shape than is seen in the observations. We do not find evidence of white-light emitting chromospheric condensations, in contrast to the previous F12 model of Livshits et al. (1981). We discuss future avenues for RHD modeling in order to produce a hot blackbody component, including the treatment of nonthermal protons in M dwarf flares.

Pore-scale simulation of liquid CO2 displacement of water using a two-phase lattice Boltzmann model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Haihu; Valocchi, Albert J.; Werth, Charles J.

A lattice Boltzmann color-fluid model, which was recently proposed by Liu et al. [H. Liu, A.J. Valocchi, and Q. Kang. Three-dimensional lattice Boltzmann model for immiscible two-phase flow simulations. Phys. Rev. E, 85:046309, 2012.] based on a concept of continuum surface force, is improved to simulate immiscible two-phase flows in porous media. The new improvements allow the model to account for different kinematic viscosities of both fluids and to model fluid-solid interactions. The capability and accuracy of this model is first validated by two benchmark tests: a layered two-phase flow with a viscosity ratio, and a dynamic capillary intrusion. Thismore » model is then used to simulate liquid CO2 (LCO2) displacing water in a dual-permeability pore network. The extent and behavior of LCO2 preferential flow (i.e., fingering) is found to depend on the capillary number (Ca), and three different displacement patterns observed in previous micromodel experiments are reproduced. The predicted variation of LCO2 saturation with Ca, as well as variation of specific interfacial length with LCO2 saturation, are both in good agreement with the experimental observations. To understand the effect of heterogeneity on pore-scale displacement, we also simulate LCO2 displacing water in a randomly heterogeneous pore network, which has the same size and porosity as the dual-permeability pore network. In comparison to the dual-permeability case, the transition from capillary fingering to viscous fingering occurs at a higher Ca, and LCO2 saturation is higher at low Ca but lower at high Ca. In either pore network, the LCO2-water specific interfacial length is found to obey a power-law dependence on LCO2 saturation.« less

THE BINARY BLACK HOLE MODEL FOR MRK 231 BITES THE DUST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leighly, Karen M.; Terndrup, Donald M.; Gallagher, Sarah C.

2016-09-20

Mrk 231 is a nearby quasar with an unusually red near-UV-to-optical continuum, generally explained as heavy reddening by dust. Yan et al. proposed that Mrk 231 is a milliparsec black hole binary with little intrinsic reddening. We show that if the observed FUV continuum is intrinsic, as assumed by Yan et al., it fails by a factor of about 100 in powering the observed strength of the near-infrared emission lines and the thermal near and mid-infrared continuum. In contrast, the line and continuum strengths are typical for a reddened AGN spectral energy distribution (SED). We find that the He i*/Pmore » β ratio is sensitive to the SED for a one-zone model. If this sensitivity is maintained in general broadline region models, then this ratio may prove a useful diagnostic for heavily reddened quasars. Analysis of archival Hubble Space Telescope STIS and Faint Object Camera data revealed evidence that the far-UV continuum emission is resolved on size scales of ∼40 pc. The lack of broad absorption lines in the far-UV continuum might be explained if it were not coincident with the central engine. One possibility is that it is the central engine continuum reflected from the receding wind on the far side of the quasar.« less

Multiscale volatility duration characteristics on financial multi-continuum percolation dynamics

NASA Astrophysics Data System (ADS)

Wang, Min; Wang, Jun

A random stock price model based on the multi-continuum percolation system is developed to investigate the nonlinear dynamics of stock price volatility duration, in an attempt to explain various statistical facts found in financial data, and have a deeper understanding of mechanisms in the financial market. The continuum percolation system is usually referred to be a random coverage process or a Boolean model, it is a member of a class of statistical physics systems. In this paper, the multi-continuum percolation (with different values of radius) is employed to model and reproduce the dispersal of information among the investors. To testify the rationality of the proposed model, the nonlinear analyses of return volatility duration series are preformed by multifractal detrending moving average analysis and Zipf analysis. The comparison empirical results indicate the similar nonlinear behaviors for the proposed model and the actual Chinese stock market.

Bipotential continuum models for granular mechanics

NASA Astrophysics Data System (ADS)

Goddard, Joe

2014-03-01

Most currently popular continuum models for granular media are special cases of a generalized Maxwell fluid model, which describes the evolution of stress and internal variables such as granular particle fraction and fabric,in terms of imposed strain rate. It is shown how such models can be obtained from two scalar potentials, a standard elastic free energy and a ``dissipation potential'' given rigorously by the mathematical theory of Edelen. This allows for a relatively easy derivation of properly invariant continuum models for granular media and fluid-particle suspensions within a thermodynamically consistent framework. The resulting continuum models encompass all the prominent regimes of granular flow, ranging from the quasi-static to rapidly sheared, and are readily extended to include higher-gradient or Cosserat effects. Models involving stress diffusion, such as that proposed recently by Kamrin and Koval (PRL 108 178301), provide an alternative approach that is mentioned in passing. This paper provides a brief overview of a forthcoming review articles by the speaker (The Princeton Companion to Applied Mathematics, and Appl. Mech. Rev.,in the press, 2013).

Improvements in continuum modeling for biomolecular systems

NASA Astrophysics Data System (ADS)

Yu, Qiao; Ben-Zhuo, Lu

2016-01-01

Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson- Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress. Project supported by the National Natural Science Foundation of China (Grant No. 91230106) and the Chinese Academy of Sciences Program for Cross & Cooperative Team of the Science & Technology Innovation.

A note on the discrete approach for generalized continuum models

NASA Astrophysics Data System (ADS)

Kalampakas, Antonios; Aifantis, Elias C.

2014-12-01

Generalized continuum theories for materials and processes have been introduced in order to account in a phenomenological manner for microstructural effects. Their drawback mainly rests in the determination of the extra phenomenological coefficients through experiments and simulations. It is shown here that a graphical representation of the local topology describing deformation models can be used to deduce restrictions on the phenomenological coefficients of the gradient elasticity continuum theories.

Modified Continuum Mechanics Modeling on Size-Dependent Properties of Piezoelectric Nanomaterials: A Review

PubMed Central

Yan, Zhi; Jiang, Liying

2017-01-01

Piezoelectric nanomaterials (PNs) are attractive for applications including sensing, actuating, energy harvesting, among others in nano-electro-mechanical-systems (NEMS) because of their excellent electromechanical coupling, mechanical and physical properties. However, the properties of PNs do not coincide with their bulk counterparts and depend on the particular size. A large amount of efforts have been devoted to studying the size-dependent properties of PNs by using experimental characterization, atomistic simulation and continuum mechanics modeling with the consideration of the scale features of the nanomaterials. This paper reviews the recent progresses and achievements in the research on the continuum mechanics modeling of the size-dependent mechanical and physical properties of PNs. We start from the fundamentals of the modified continuum mechanics models for PNs, including the theories of surface piezoelectricity, flexoelectricity and non-local piezoelectricity, with the introduction of the modified piezoelectric beam and plate models particularly for nanostructured piezoelectric materials with certain configurations. Then, we give a review on the investigation of the size-dependent properties of PNs by using the modified continuum mechanics models, such as the electromechanical coupling, bending, vibration, buckling, wave propagation and dynamic characteristics. Finally, analytical modeling and analysis of nanoscale actuators and energy harvesters based on piezoelectric nanostructures are presented. PMID:28336861

Modified Continuum Mechanics Modeling on Size-Dependent Properties of Piezoelectric Nanomaterials: A Review.

PubMed

Yan, Zhi; Jiang, Liying

2017-01-26

Piezoelectric nanomaterials (PNs) are attractive for applications including sensing, actuating, energy harvesting, among others in nano-electro-mechanical-systems (NEMS) because of their excellent electromechanical coupling, mechanical and physical properties. However, the properties of PNs do not coincide with their bulk counterparts and depend on the particular size. A large amount of efforts have been devoted to studying the size-dependent properties of PNs by using experimental characterization, atomistic simulation and continuum mechanics modeling with the consideration of the scale features of the nanomaterials. This paper reviews the recent progresses and achievements in the research on the continuum mechanics modeling of the size-dependent mechanical and physical properties of PNs. We start from the fundamentals of the modified continuum mechanics models for PNs, including the theories of surface piezoelectricity, flexoelectricity and non-local piezoelectricity, with the introduction of the modified piezoelectric beam and plate models particularly for nanostructured piezoelectric materials with certain configurations. Then, we give a review on the investigation of the size-dependent properties of PNs by using the modified continuum mechanics models, such as the electromechanical coupling, bending, vibration, buckling, wave propagation and dynamic characteristics. Finally, analytical modeling and analysis of nanoscale actuators and energy harvesters based on piezoelectric nanostructures are presented.

Peridynamics with LAMMPS : a user guide.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehoucq, Richard B.; Silling, Stewart Andrew; Seleson, Pablo

Peridynamics is a nonlocal extension of classical continuum mechanics. The discrete peridynamic model has the same computational structure as a molecular dynamics model. This document provides a brief overview of the peridynamic model of a continuum, then discusses how the peridynamic model is discretized within LAMMPS. An example problem is also included.

Outdoor Program Models: Placing Cooperative Adventure and Adventure Education Models on the Continuum.

ERIC Educational Resources Information Center

Guthrie, Steven P.

In two articles on outdoor programming models, Watters distinguished four models on a continuum ranging from the common adventure model, with minimal organizational structure and leadership control, to the guide service model, in which leaders are autocratic and trips are highly structured. Club programs and instructional programs were in between,…

Simulation and theory of spontaneous TAE frequency sweeping

NASA Astrophysics Data System (ADS)

Wang, Ge; Berk, H. L.

2012-09-01

A simulation model, based on the linear tip model of Rosenbluth, Berk and Van Dam (RBV), is developed to study frequency sweeping of toroidal Alfvén eigenmodes (TAEs). The time response of the background wave in the RBV model is given by a Volterra integral equation. This model captures the properties of TAE waves both in the gap and in the continuum. The simulation shows that phase space structures form spontaneously at frequencies close to the linearly predicted frequency, due to resonant particle-wave interactions and background dissipation. The frequency sweeping signals are found to chirp towards the upper and lower continua. However, the chirping signals penetrate only the lower continuum, whereupon the frequency chirps and mode amplitude increases in synchronism to produce an explosive solution. An adiabatic theory describing the evolution of a chirping signal is developed which replicates the chirping dynamics of the simulation in the lower continuum. This theory predicts that a decaying chirping signal will terminate at the upper continuum though in the numerical simulation the hole disintegrates before the upper continuum is reached.

Pore and Continuum Scale Study of the Effect of Subgrid Transport Heterogeneity on Redox Reaction Rates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Yuanyuan; Liu, Chongxuan; Zhang, Changyong

2015-08-01

A micromodel system with a pore structure for heterogeneous flow and transport was used to investigate the effect of subgrid transport heterogeneity on redox reaction rates. Hematite reductive dissolution by injecting a reduced form of flavin mononucleotide (FMNH2) at variable flow rates was used as an example to probe the variations of redox reaction rates in different subgrid transport domains. Experiments, pore-scale simulations, and macroscopic modeling were performed to measure and simulate in-situ hematite reduction and to evaluate the scaling behavior of the redox reaction rates from the pore to macroscopic scales. The results indicated that the measured pore-scale ratesmore » of hematite reduction were consistent with the predictions from a pore scale reactive transport model. A general trend is that hematite reduction followed reductant transport pathways, starting from the advection-dominated pores toward the interior of diffusion-dominated domains. Two types of diffusion domains were considered in the micromodel: a micropore diffusion domain, which locates inside solid grains or aggregates where reactant transport is limited by diffusion; and a macropore diffusion domain, which locates at wedged, dead-end pore spaces created by the grain-grain contacts. The rate of hematite reduction in the advection-dominated domain was faster than those in the diffusion-controlled domains, and the rate in the macropore diffusion domain was faster than that in the micropore domain. The reduction rates in the advection and macropore diffusion domains increased with increasing flow rate, but were affected by different mechanisms. The rate increase in the advection domain was controlled by the mass action effect as a faster flow supplied more reactants, and the rate increase in the macropore domain was more affected by the rate of mass exchange with the advection domain, which increased with increasing flow rate. The hematite reduction rate in the micropore domain was, however, not affected by the flow rate because molecular diffusion limits reductant supply to the micropore domain interior. Domain-based macroscopic models were evaluated to scale redox reaction rates from the pore to macroscopic scales. A single domain model, which ignores subgrid transport heterogeneity deviated significantly from the pore-scale results. Further analysis revealed that the rate expression for hematite reduction was not scalable from the pore to porous media using the single domain model. A three-domain model, which effectively considers subgrid reactive diffusion in the micropore and macropore domains, significantly improved model description. Overall this study revealed the importance of subgrid transport heterogeneity in the manifestation of redox reaction rates in porous media and in scaling reactions from the pore to porous media. The research also supported that the domain-based scaling approach can be used to directly scale redox reactions in porous media with subgrid transport heterogeneity.« less

Spin waves, vortices, fermions, and duality in the Ising and Baxter models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogilvie, M.C.

1981-10-15

Field-theoretic methods are applied to a number of two-dimensional lattice models with Abelian symmetry groups. It is shown, using a vortex+spin-wave decomposition, that the Z/sub p/-Villain models are related to a class of continuum field theories with analogous duality properties. Fermion operators for these field theories are discussed. In the case of the Ising model, the vortices and spin-waves conspire to produce a free, massive Majorana field theory in the continuum limit. The continuum limit of the Baxter model is also studied, and the recent results of Kadanoff and Brown are rederived and extended.

Modeling of Continuum Manipulators Using Pythagorean Hodograph Curves.

PubMed

Singh, Inderjeet; Amara, Yacine; Melingui, Achille; Mani Pathak, Pushparaj; Merzouki, Rochdi

2018-05-10

Research on continuum manipulators is increasingly developing in the context of bionic robotics because of their many advantages over conventional rigid manipulators. Due to their soft structure, they have inherent flexibility, which makes it a huge challenge to control them with high performances. Before elaborating a control strategy of such robots, it is essential to reconstruct first the behavior of the robot through development of an approximate behavioral model. This can be kinematic or dynamic depending on the conditions of operation of the robot itself. Kinematically, two types of modeling methods exist to describe the robot behavior; quantitative methods describe a model-based method, and qualitative methods describe a learning-based method. In kinematic modeling of continuum manipulator, the assumption of constant curvature is often considered to simplify the model formulation. In this work, a quantitative modeling method is proposed, based on the Pythagorean hodograph (PH) curves. The aim is to obtain a three-dimensional reconstruction of the shape of the continuum manipulator with variable curvature, allowing the calculation of its inverse kinematic model (IKM). It is noticed that the performances of the PH-based kinematic modeling of continuum manipulators are considerable regarding position accuracy, shape reconstruction, and time/cost of the model calculation, than other kinematic modeling methods, for two cases: free load manipulation and variable load manipulation. This modeling method is applied to the compact bionic handling assistant (CBHA) manipulator for validation. The results are compared with other IKMs developed in case of CBHA manipulator.

On the physically based modeling of surface tension and moving contact lines with dynamic contact angles on the continuum scale

NASA Astrophysics Data System (ADS)

Huber, M.; Keller, F.; Säckel, W.; Hirschler, M.; Kunz, P.; Hassanizadeh, S. M.; Nieken, U.

2016-04-01

The description of wetting phenomena is a challenging problem on every considerable length-scale. The behavior of interfaces and contact lines on the continuum scale is caused by intermolecular interactions like the Van der Waals forces. Therefore, to describe surface tension and the resulting dynamics of interfaces and contact lines on the continuum scale, appropriate formulations must be developed. While the Continuum Surface Force (CSF) model is well-engineered for the description of interfaces, there is still a lack of treatment of contact lines, which are defined by the intersection of an ending fluid interface and a solid boundary surface. In our approach we use a balance equation for the contact line and extend the Navier-Stokes equations in analogy to the extension of a two-phase interface in the CSF model. Since this model depicts a physically motivated approach on the continuum scale, no fitting parameters are introduced and the deterministic description leads to a dynamical evolution of the system. As verification of our theory, we show a Smoothed Particle Hydrodynamics (SPH) model and simulate the evolution of droplet shapes and their corresponding contact angles.

Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes.

PubMed Central

Ashbaugh, H S; Kaler, E W; Paulaitis, M E

1998-01-01

We consider whether the continuum model of hydration optimized to reproduce vacuum-to-water transfer free energies simultaneously describes the hydration free energy contributions to conformational equilibria of the same solutes in water. To this end, transfer and conformational free energies of idealized hydrophobic and amphiphilic solutes in water are calculated from explicit water simulations and compared to continuum model predictions. As benchmark hydrophobic solutes, we examine the hydration of linear alkanes from methane through hexane. Amphiphilic solutes were created by adding a charge of +/-1e to a terminal methyl group of butane. We find that phenomenological continuum parameters fit to transfer free energies are significantly different from those fit to conformational free energies of our model solutes. This difference is attributed to continuum model parameters that depend on solute conformation in water, and leads to effective values for the free energy/surface area coefficient and Born radii that best describe conformational equilibrium. In light of these results, we believe that continuum models of hydration optimized to fit transfer free energies do not accurately capture the balance between hydrophobic and electrostatic contributions that determines the solute conformational state in aqueous solution. PMID:9675177

Passing waves from atomistic to continuum

NASA Astrophysics Data System (ADS)

Chen, Xiang; Diaz, Adrian; Xiong, Liming; McDowell, David L.; Chen, Youping

2018-02-01

Progress in the development of coupled atomistic-continuum methods for simulations of critical dynamic material behavior has been hampered by a spurious wave reflection problem at the atomistic-continuum interface. This problem is mainly caused by the difference in material descriptions between the atomistic and continuum models, which results in a mismatch in phonon dispersion relations. In this work, we introduce a new method based on atomistic dynamics of lattice coupled with a concurrent atomistic-continuum method to enable a full phonon representation in the continuum description. This permits the passage of short-wavelength, high-frequency phonon waves from the atomistic to continuum regions. The benchmark examples presented in this work demonstrate that the new scheme enables the passage of all allowable phonons through the atomistic-continuum interface; it also preserves the wave coherency and energy conservation after phonons transport across multiple atomistic-continuum interfaces. This work is the first step towards developing a concurrent atomistic-continuum simulation tool for non-equilibrium phonon-mediated thermal transport in materials with microstructural complexity.

Explicitly Representing the Solvation Shell in Continuum Solvent Calculations

PubMed Central

Svendsen, Hallvard F.; Merz, Kenneth M.

2009-01-01

A method is presented to explicitly represent the first solvation shell in continuum solvation calculations. Initial solvation shell geometries were generated with classical molecular dynamics simulations. Clusters consisting of solute and 5 solvent molecules were fully relaxed in quantum mechanical calculations. The free energy of solvation of the solute was calculated from the free energy of formation of the cluster and the solvation free energy of the cluster calculated with continuum solvation models. The method has been implemented with two continuum solvation models, a Poisson-Boltzmann model and the IEF-PCM model. Calculations were carried out for a set of 60 ionic species. Implemented with the Poisson-Boltzmann model the method gave an unsigned average error of 2.1 kcal/mol and a RMSD of 2.6 kcal/mol for anions, for cations the unsigned average error was 2.8 kcal/mol and the RMSD 3.9 kcal/mol. Similar results were obtained with the IEF-PCM model. PMID:19425558

Mirrored continuum and molecular scale simulations of the ignition of gamma phase RDX

NASA Astrophysics Data System (ADS)

Stewart, D. Scott; Chaudhuri, Santanu; Joshi, Kaushik; Lee, Kiabek

2015-06-01

We consider the ignition of a high-pressure gamma-phase of an explosive crystal of RDX which forms during overdriven shock initiation. Molecular dynamics (MD), with first-principles based or reactive force field based molecular potentials, provides a description of the chemistry as an extremely complex reaction network. The results of the molecular simulation is analyzed by sorting molecular product fragments into high and low molecular groups, to represent identifiable components that can be interpreted by a continuum model. A continuum model based on a Gibbs formulation, that has a single temperature and stress state for the mixture is used to represent the same RDX material and its chemistry. Each component in the continuum model has a corresponding Gibbs continuum potential, that are in turn inferred from molecular MD informed equation of state libraries such as CHEETAH, or are directly simulated by Monte Carlo MD simulations. Information about transport, kinetic rates and diffusion are derived from the MD simulation and the growth of a reactive hot spot in the RDX is studied with both simulations that mirror the other results to provide an essential, continuum/atomistic link. Supported by N000014-12-1-0555, subaward-36561937 (ONR).

Reducing Actuator Requirements in Continuum Robots Through Optimized Cable Routing.

PubMed

Case, Jennifer C; White, Edward L; SunSpiral, Vytas; Kramer-Bottiglio, Rebecca

2018-02-01

Continuum manipulators offer many advantages compared to their rigid-linked counterparts, such as increased degrees of freedom and workspace volume. Inspired by biological systems, such as elephant trunks and octopus tentacles, many continuum manipulators are made of multiple segments that allow large-scale deformations to be distributed throughout the body. Most continuum manipulators currently control each segment individually. For example, a planar cable-driven system is typically controlled by a pair of cables for each segment, which implies two actuators per segment. In this article, we demonstrate how highly coupled crossing cable configurations can reduce both actuator count and actuator torque requirements in a planar continuum manipulator, while maintaining workspace reachability and manipulability. We achieve highly coupled actuation by allowing cables to cross through the manipulator to create new cable configurations. We further derive an analytical model to predict the underactuated manipulator workspace and experimentally verify the model accuracy with a physical system. We use this model to compare crossing cable configurations to the traditional cable configuration using workspace performance metrics. Our work here focuses on a simplified planar robot, both in simulation and in hardware, with the goal of extending this to spiraling-cable configurations on full 3D continuum robots in future work.

Discrete and continuum modelling of soil cutting

NASA Astrophysics Data System (ADS)

Coetzee, C. J.

2014-12-01

Both continuum and discrete methods are used to investigate the soil cutting process. The Discrete Element Method ( dem) is used for the discrete modelling and the Material-Point Method ( mpm) is used for continuum modelling. M pmis a so-called particle method or meshless finite element method. Standard finite element methods have difficulty in modelling the entire cutting process due to large displacements and deformation of the mesh. The use of meshless methods overcomes this problem. M pm can model large deformations, frictional contact at the soil-tool interface, and dynamic effects (inertia forces). In granular materials the discreteness of the system is often important and rotational degrees of freedom are active, which might require enhanced theoretical approaches like polar continua. In polar continuum theories, the material points are considered to possess orientations. A material point has three degrees-of-freedom for rigid rotations, in addition to the three classic translational degrees-of-freedom. The Cosserat continuum is the most transparent and straightforward extension of the nonpolar (classic) continuum. Two-dimensional dem and mpm (polar and nonpolar) simulations of the cutting problem are compared to experiments. The drag force and flow patterns are compared using cohesionless corn grains as material. The corn macro (continuum) and micro ( dem) properties were obtained from shear and oedometer tests. Results show that the dilatancy angle plays a significant role in the flow of material but has less of an influence on the draft force. Nonpolar mpm is the most accurate in predicting blade forces, blade-soil interface stresses and the position and orientation of shear bands. Polar mpm fails in predicting the orientation of the shear band, but is less sensitive to mesh size and mesh orientation compared to nonpolar mpm. dem simulations show less material dilation than observed during experiments.

Emerging Methods in Sub Core-Scale Imaging and Characterization of the Influence of Heterogeneity on Flow in Rocks (Invited)

NASA Astrophysics Data System (ADS)

Benson, S. M.; Hingerl, F.; Pini, R.

2013-12-01

New imaging techniques and approaches are providing unparalleled insight into the influence of sub-core scale heterogeneities on single and multiphase flows. Quantification of sub core-scale porosity, permeability, and even capillary pressure curves at a spatial scale of about 1-10 cubic millimeters is now possible. This scale provides a critical link in the continuum of spatial scales needed to link pore-scale processes to core-scale and field scale flow and transport. Data from such studies can be used to directly test the veracity of models for flow and transport in heterogeneous rocks, provide data for multi-stage upscaling, and reveal insights about physical/chemical processes heretofore neglected. Here we present data from three emerging techniques capable of imaging and quantifying transport properties and phenomena at the sub-core scale: magnetic resonance imaging (MRI); positron emission tomography (PET); and X-Ray CT scanning. Direct imaging of spatially resolved fluid velocities and porosity is possible with MRI (Romanenko et al., 2012). These data can be inverted to provide permeability and porosity maps at a spatial scale of ~10 cubic millimeter. PET imaging can be used to track movement of a radioactive tracer through a rock and simultaneously measure effluent tracer concentrations at a similar resolution (Boutchko et al., 2012). X-ray CT scanning of multiphase flow experiments can be used to measure capillary pressure curves and through scaling relationships, to calculate permeability at a scale of about 1 cubic millimeters(Krause et al., 2011; Pini et al., 2013). Strengths and shortcomings of these techniques are discussed--along with the benefits of combining them. Together these techniques provide a new platform from which to probe more deeply the ubiquitous influence of heterogeneity on subsurface flow and transport processes, and ultimately improve predictions of subsurface transport. Boutchk et al., 2012. Imaging and modeling of flow in porous media using clinical nuclear emission tomography systems and computational fluid dynamics. Journal of Applied geophysics, 76, 74-81. Krause, M.H., J.C. Perrin, and S.M. Benson, 2011. Modeling permeability distributions in a sandstone core for history matching core flood experiments, SPE Journal, 16, 768-777. Pini R. and Benson S., Characterization and scaling of meso-scale heterogeneities in sandstones. Geophysical Research Letters, 2013, 40. Romanenko, K., and Balscom, Permeability mapping in naturally heterogeneous sandstone cores with magnetization prepared SPRITE, 2012, 58, 3916-3926.

Mirrored continuum and molecular scale simulations of the ignition of high-pressure phases of RDX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Kibaek; Stewart, D. Scott, E-mail: santc@illinois.edu, E-mail: dss@illinois.edu; Joshi, Kaushik

2016-05-14

We present a mirrored atomistic and continuum framework that is used to describe the ignition of energetic materials, and a high-pressure phase of RDX in particular. The continuum formulation uses meaningful averages of thermodynamic properties obtained from the atomistic simulation and a simplification of enormously complex reaction kinetics. In particular, components are identified based on molecular weight bin averages and our methodology assumes that both the averaged atomistic and continuum simulations are represented on the same time and length scales. The atomistic simulations of thermally initiated ignition of RDX are performed using reactive molecular dynamics (RMD). The continuum model ismore » based on multi-component thermodynamics and uses a kinetics scheme that describes observed chemical changes of the averaged atomistic simulations. Thus the mirrored continuum simulations mimic the rapid change in pressure, temperature, and average molecular weight of species in the reactive mixture. This mirroring enables a new technique to simplify the chemistry obtained from reactive MD simulations while retaining the observed features and spatial and temporal scales from both the RMD and continuum model. The primary benefit of this approach is a potentially powerful, but familiar way to interpret the atomistic simulations and understand the chemical events and reaction rates. The approach is quite general and thus can provide a way to model chemistry based on atomistic simulations and extend the reach of those simulations.« less

Kinematics and the implementation of an elephant's trunk manipulator and other continuum style robots.

PubMed

Hannan, Michael W; Walker, Ian D

2003-02-01

Traditionally, robot manipulators have been a simple arrangement of a small number of serially connected links and actuated joints. Though these manipulators prove to be very effective for many tasks, they are not without their limitations, due mainly to their lack of maneuverability or total degrees of freedom. Continuum style (i.e., continuous "back-bone") robots, on the other hand, exhibit a wide range of maneuverability, and can have a large number of degrees of freedom. The motion of continuum style robots is generated through the bending of the robot over a given section; unlike traditional robots where the motion occurs in discrete locations, i.e., joints. The motion of continuum manipulators is often compared to that of biological manipulators such as trunks and tentacles. These continuum style robots can achieve motions that could only be obtainable by a conventionally designed robot with many more degrees of freedom. In this paper we present a detailed formulation and explanation of a novel kinematic model for continuum style robots. The design, construction, and implementation of our continuum style robot called the elephant trunk manipulator is presented. Experimental results are then provided to verify the legitimacy of our model when applied to our physical manipulator. We also provide a set of obstacle avoidance experiments that help to exhibit the practical implementation of both our manipulator and our kinematic model. c2003 Wiley Periodicals, Inc.

Kinematics and the implementation of an elephant's trunk manipulator and other continuum style robots

NASA Technical Reports Server (NTRS)

Hannan, Michael W.; Walker, Ian D.

2003-01-01

Traditionally, robot manipulators have been a simple arrangement of a small number of serially connected links and actuated joints. Though these manipulators prove to be very effective for many tasks, they are not without their limitations, due mainly to their lack of maneuverability or total degrees of freedom. Continuum style (i.e., continuous "back-bone") robots, on the other hand, exhibit a wide range of maneuverability, and can have a large number of degrees of freedom. The motion of continuum style robots is generated through the bending of the robot over a given section; unlike traditional robots where the motion occurs in discrete locations, i.e., joints. The motion of continuum manipulators is often compared to that of biological manipulators such as trunks and tentacles. These continuum style robots can achieve motions that could only be obtainable by a conventionally designed robot with many more degrees of freedom. In this paper we present a detailed formulation and explanation of a novel kinematic model for continuum style robots. The design, construction, and implementation of our continuum style robot called the elephant trunk manipulator is presented. Experimental results are then provided to verify the legitimacy of our model when applied to our physical manipulator. We also provide a set of obstacle avoidance experiments that help to exhibit the practical implementation of both our manipulator and our kinematic model. c2003 Wiley Periodicals, Inc.

Pathophysiological Progression Model for Selected Toxicological Endpoints

EPA Science Inventory

The existing continuum paradigms are effective models to organize toxicological data associated with endpoints used in human health assessments. A compendium of endpoints characterized along a pathophysiological continuum would serve to: weigh the relative importance of effects o...

Continuum Modeling and Control of Large Nonuniform Wireless Networks via Nonlinear Partial Differential Equations

DOE PAGES

Zhang, Yang; Chong, Edwin K. P.; Hannig, Jan; ...

2013-01-01

We inmore » troduce a continuum modeling method to approximate a class of large wireless networks by nonlinear partial differential equations (PDEs). This method is based on the convergence of a sequence of underlying Markov chains of the network indexed by N , the number of nodes in the network. As N goes to infinity, the sequence converges to a continuum limit, which is the solution of a certain nonlinear PDE. We first describe PDE models for networks with uniformly located nodes and then generalize to networks with nonuniformly located, and possibly mobile, nodes. Based on the PDE models, we develop a method to control the transmissions in nonuniform networks so that the continuum limit is invariant under perturbations in node locations. This enables the networks to maintain stable global characteristics in the presence of varying node locations.« less

On the influence of pseudoelastic material behaviour in planar shape-memory tubular continuum structures

NASA Astrophysics Data System (ADS)

Greiner-Petter, Christoph; Sattel, Thomas

2017-12-01

For planar tubular continuum structures based on precurved shape memory alloy tubes a beam model with respect to the pseudoelastic material behaviour of NiTi is derived. Thereunto a constitutive material law respecting tension-compression asymmetry as well as hysteresis is used. The beam model is then employed to calculate equilibrium curvatures of concentric tube assemblies without clearance between the tubes. In a second step, the influence of clearance is approximated to account for non-concentric tube assemblies. These elastokinematic results are integrated into a purely kinematic model to describe the cannula path under the presence of material hysteresis and clearance. Finally a photogrammetric measurement system is used to track the path of an exemplary two-tube continuum structure to examine the accuracy of the proposed model. It is shown that material hysteresis leads to a hysteresis phenomena in the path of the tubular continuum structure.

Nonlinear waves in solids with slow dynamics: an internal-variable model.

PubMed

Berjamin, H; Favrie, N; Lombard, B; Chiavassa, G

2017-05-01

In heterogeneous solids such as rocks and concrete, the speed of sound diminishes with the strain amplitude of a dynamic loading (softening). This decrease, known as 'slow dynamics', occurs at time scales larger than the period of the forcing. Also, hysteresis is observed in the steady-state response. The phenomenological model by Vakhnenko et al. (2004 Phys. Rev. E 70, 015602. (doi:10.1103/PhysRevE.70.015602)) is based on a variable that describes the softening of the material. However, this model is one dimensional and it is not thermodynamically admissible. In the present article, a three-dimensional model is derived in the framework of the finite-strain theory. An internal variable that describes the softening of the material is introduced, as well as an expression of the specific internal energy. A mechanical constitutive law is deduced from the Clausius-Duhem inequality. Moreover, a family of evolution equations for the internal variable is proposed. Here, an evolution equation with one relaxation time is chosen. By construction, this new model of the continuum is thermodynamically admissible and dissipative (inelastic). In the case of small uniaxial deformations, it is shown analytically that the model reproduces qualitatively the main features of real experiments.

Microenvironmental independence associated with tumor progression.

PubMed

Anderson, Alexander R A; Hassanein, Mohamed; Branch, Kevin M; Lu, Jenny; Lobdell, Nichole A; Maier, Julie; Basanta, David; Weidow, Brandy; Narasanna, Archana; Arteaga, Carlos L; Reynolds, Albert B; Quaranta, Vito; Estrada, Lourdes; Weaver, Alissa M

2009-11-15

Tumor-microenvironment interactions are increasingly recognized to influence tumor progression. To understand the competitive dynamics of tumor cells in diverse microenvironments, we experimentally parameterized a hybrid discrete-continuum mathematical model with phenotypic trait data from a set of related mammary cell lines with normal, transformed, or tumorigenic properties. Surprisingly, in a resource-rich microenvironment, with few limitations on proliferation or migration, transformed (but not tumorigenic) cells were most successful and outcompeted other cell types in heterogeneous tumor simulations. Conversely, constrained microenvironments with limitations on space and/or growth factors gave a selective advantage to phenotypes derived from tumorigenic cell lines. Analysis of the relative performance of each phenotype in constrained versus unconstrained microenvironments revealed that, although all cell types grew more slowly in resource-constrained microenvironments, the most aggressive cells were least affected by microenvironmental constraints. A game theory model testing the relationship between microenvironment resource availability and competitive cellular dynamics supports the concept that microenvironmental independence is an advantageous cellular trait in resource-limited microenvironments.

The assessment of medical competencies.

PubMed

Sureda-Demeulemeester, E; Ramis-Palmer, C; Sesé-Abad, A

2017-12-01

To describe the most widely used tools in the assessment of medical competencies, analyse their prevalence of use, their advantages and disadvantages and propose an appropriate model for our context. We conducted a narrative review of articles from MEDLINE, following the PRISM protocol, and analysed a total of 62 articles. The assessment of competencies is heterogeneous, especially in the educational and professional settings. The specific and technical competencies acquired during university education are mainly assessed using the objective structured clinical assessment. In the professional setting, core competencies are assessed using the 360° technique. We need a rigorous empiric comparison of the efficiency of the tools according to the type of competency. We propose a competency management model for the «undergraduate/graduate/active professional» continuum, whose goal is to improve training and professional practice and thereby increase the quality of patient care. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Medicina Interna (SEMI). All rights reserved.

Modes of interconnected lattice trusses using continuum models, part 1

NASA Technical Reports Server (NTRS)

Balakrishnan, A. V.

1991-01-01

This represents a continuing systematic attempt to explore the use of continuum models--in contrast to the Finite Element Models currently universally in use--to develop feedback control laws for stability enhancement of structures, particularly large structures, for deployment in space. We shall show that for the control objective, continuum models do offer unique advantages. It must be admitted of course that developing continuum models for arbitrary structures is no easy task. In this paper we take advantage of the special nature of current Large Space Structures--typified by the NASA-LaRC Evolutionary Model which will be our main concern--which consists of interconnected orthogonal lattice trusses each with identical bays. Using an equivalent one-dimensional Timoshenko beam model, we develop an almost complete continuum model for the evolutionary structure. We do this in stages, beginning only with the main bus as flexible and then going on to make all the appendages also flexible-except for the antenna structure. Based on these models we proceed to develop formulas for mode frequencies and shapes. These are shown to be the roots of the determinant of a matrix of small dimension compared with mode calculations using Finite Element Models, even though the matrix involves transcendental functions. The formulas allow us to study asymptotic properties of the modes and how they evolve as we increase the number of bodies which are treated as flexible. The asymptotics, in fact, become simpler.

Continuum Thinking and the Contexts of Personal Information Management

ERIC Educational Resources Information Center

Huvila, Isto; Eriksen, Jon; Häusner, Eva-Maria; Jansson, Ina-Maria

2014-01-01

Introduction: Recent personal information management literature has underlined the significance of the contextuality of personal information and its use. The present article discusses the applicability of the records continuum model and its generalisation, continuum thinking, as a theoretical framework for explicating the overlap and evolution of…

A new computational approach to simulate pattern formation in Paenibacillus dendritiformis bacterial colonies

NASA Astrophysics Data System (ADS)

Tucker, Laura Jane

Under the harsh conditions of limited nutrient and hard growth surface, Paenibacillus dendritiformis in agar plates form two classes of patterns (morphotypes). The first class, called the dendritic morphotype, has radially directed branches. The second class, called the chiral morphotype, exhibits uniform handedness. The dendritic morphotype has been modeled successfully using a continuum model on a regular lattice; however, a suitable computational approach was not known to solve a continuum chiral model. This work details a new computational approach to solving the chiral continuum model of pattern formation in P. dendritiformis. The approach utilizes a random computational lattice and new methods for calculating certain derivative terms found in the model.

Landau-Zener transitions and Dykhne formula in a simple continuum model

NASA Astrophysics Data System (ADS)

Dunham, Yujin; Garmon, Savannah

The Landau-Zener model describing the interaction between two linearly driven discrete levels is useful in describing many simple dynamical systems; however, no system is completely isolated from the surrounding environment. Here we examine a generalizations of the original Landau-Zener model to study simple environmental influences. We consider a model in which one of the discrete levels is replaced with a energy continuum, in which we find that the survival probability for the initially occupied diabatic level is unaffected by the presence of the continuum. This result can be predicted by assuming that each step in the evolution for the diabatic state evolves independently according to the Landau-Zener formula, even in the continuum limit. We also show that, at least for the simplest model, this result can also be predicted with the natural generalization of the Dykhne formula for open systems. We also observe dissipation as the non-escape probability from the discrete levels is no longer equal to one.

Continuum mesoscopic framework for multiple interacting species and processes on multiple site types and/or crystallographic planes.

PubMed

Chatterjee, Abhijit; Vlachos, Dionisios G

2007-07-21

While recently derived continuum mesoscopic equations successfully bridge the gap between microscopic and macroscopic physics, so far they have been derived only for simple lattice models. In this paper, general deterministic continuum mesoscopic equations are derived rigorously via nonequilibrium statistical mechanics to account for multiple interacting surface species and multiple processes on multiple site types and/or different crystallographic planes. Adsorption, desorption, reaction, and surface diffusion are modeled. It is demonstrated that contrary to conventional phenomenological continuum models, microscopic physics, such as the interaction potential, determines the final form of the mesoscopic equation. Models of single component diffusion and binary diffusion of interacting particles on single-type site lattice and of single component diffusion on complex microporous materials' lattices consisting of two types of sites are derived, as illustrations of the mesoscopic framework. Simplification of the diffusion mesoscopic model illustrates the relation to phenomenological models, such as the Fickian and Maxwell-Stefan transport models. It is demonstrated that the mesoscopic equations are in good agreement with lattice kinetic Monte Carlo simulations for several prototype examples studied.

Kinematics optimization and static analysis of a modular continuum robot used for minimally invasive surgery.

PubMed

Qi, Fei; Ju, Feng; Bai, Dong Ming; Chen, Bai

2018-02-01

For the outstanding compliance and dexterity of continuum robot, it is increasingly used in minimally invasive surgery. The wide workspace, high dexterity and strong payload capacity are essential to the continuum robot. In this article, we investigate the workspace of a cable-driven continuum robot that we proposed. The influence of section number on the workspace is discussed when robot is operated in narrow environment. Meanwhile, the structural parameters of this continuum robot are optimized to achieve better kinematic performance. Moreover, an indicator based on the dexterous solid angle for evaluating the dexterity of robot is introduced and the distal end dexterity is compared for the three-section continuum robot with different range of variables. Results imply that the wider range of variables achieve the better dexterity. Finally, the static model of robot based on the principle of virtual work is derived to analyze the relationship between the bending shape deformation and the driven force. The simulations and experiments for plane and spatial motions are conducted to validate the feasibility of model, respectively. Results of this article can contribute to the real-time control and movement and can be a design reference for cable-driven continuum robot.

Finite-temperature stress calculations in atomic models using moments of position.

PubMed

Parthasarathy, Ranganathan; Misra, Anil; Ouyang, Lizhi

2018-07-04

Continuum modeling of finite temperature mechanical behavior of atomic systems requires refined description of atomic motions. In this paper, we identify additional kinematical quantities that are relevant for a more accurate continuum description as the system is subjected to step-wise loading. The presented formalism avoids the necessity for atomic trajectory mapping with deformation, provides the definitions of the kinematic variables and their conjugates in real space, and simplifies local work conjugacy. The total work done on an atom under deformation is decomposed into the work corresponding to changing its equilibrium position and work corresponding to changing its second moment about equilibrium position. Correspondingly, we define two kinematic variables: a deformation gradient tensor and a vibration tensor, and derive their stress conjugates, termed here as static and vibration stresses, respectively. The proposed approach is validated using MD simulation in NVT ensembles for fcc aluminum subjected to uniaxial extension. The observed evolution of second moments in the MD simulation with macroscopic deformation is not directly related to the transformation of atomic trajectories through the deformation gradient using generator functions. However, it is noteworthy that deformation leads to a change in the second moment of the trajectories. Correspondingly, the vibration part of the Piola stress becomes particularly significant at high temperature and high tensile strain as the crystal approaches the softening limit. In contrast to the eigenvectors of the deformation gradient, the eigenvectors of the vibration tensor show strong spatial heterogeneity in the vicinity of softening. More importantly, the elliptic distribution of local atomic density transitions to a dumbbell shape, before significant non-affinity in equilibrium positions has occurred.

Finite-temperature stress calculations in atomic models using moments of position

NASA Astrophysics Data System (ADS)

Parthasarathy, Ranganathan; Misra, Anil; Ouyang, Lizhi

2018-07-01

Continuum modeling of finite temperature mechanical behavior of atomic systems requires refined description of atomic motions. In this paper, we identify additional kinematical quantities that are relevant for a more accurate continuum description as the system is subjected to step-wise loading. The presented formalism avoids the necessity for atomic trajectory mapping with deformation, provides the definitions of the kinematic variables and their conjugates in real space, and simplifies local work conjugacy. The total work done on an atom under deformation is decomposed into the work corresponding to changing its equilibrium position and work corresponding to changing its second moment about equilibrium position. Correspondingly, we define two kinematic variables: a deformation gradient tensor and a vibration tensor, and derive their stress conjugates, termed here as static and vibration stresses, respectively. The proposed approach is validated using MD simulation in NVT ensembles for fcc aluminum subjected to uniaxial extension. The observed evolution of second moments in the MD simulation with macroscopic deformation is not directly related to the transformation of atomic trajectories through the deformation gradient using generator functions. However, it is noteworthy that deformation leads to a change in the second moment of the trajectories. Correspondingly, the vibration part of the Piola stress becomes particularly significant at high temperature and high tensile strain as the crystal approaches the softening limit. In contrast to the eigenvectors of the deformation gradient, the eigenvectors of the vibration tensor show strong spatial heterogeneity in the vicinity of softening. More importantly, the elliptic distribution of local atomic density transitions to a dumbbell shape, before significant non-affinity in equilibrium positions has occurred.

Soil compaction: Evaluation of stress transmission and resulting soil structure

NASA Astrophysics Data System (ADS)

Naveed, Muhammad; Schjønning, Per; Keller, Thomas; Lamande, Mathieu

2016-04-01

Accurate estimation of stress transmission and resultant deformation in soil profiles is a prerequisite for the development of predictive models and decision support tools for preventing soil compaction. Numerous studies have been carried out on the effects of soil compaction, whilst relatively few studies have focused on the cause (mode of stress transmission in the soil). We have coupled both cause and effects together in the present study by carrying out partially confined compression tests on (1) wet aggregates, (2) air dry aggregates, and (3) intact soils to quantify stress transmission and compaction-resulted soil structure at the same time. Stress transmission was quantified using both X-ray CT and Tactilus sensor mat, and soil-pore structure was quantified using X-ray CT. Our results imply that stress transmission through soil highly depends on the magnitude of applied load and aggregate strength. As soon as the applied load is lower than the aggregate strength, the mode of stress transmission is discrete as stresses were mainly transmitted through chain of aggregates. With increasing applied load soil aggregates start deforming that transformed heterogeneous soil into homogenous, as a result stress transmission mode was shifted from discrete towards more like a continuum. Continuum-like stress transmission mode was better simulated with Boussinesq (1885) model based on theory of elasticity compared to discrete. The soil-pore structure was greatly affected by increasing applied stresses. Total porosity was reduced 5-16% and macroporosity 50-85% at 620 kPa applied stress for the intact soils. Similarly, significant changes in the morphological indices of the macropore space were also observed with increasing applied stresses.

Mathematical and Computational Aspects of Multiscale Materials Modeling, Mathematics-Numerical analysis, Section II.A.a.3.4, Conference and symposia organization II.A.2.a

DTIC Science & Technology

2015-02-04

dislocation dynamics models ( DDD ), continuum representations). Coupling of these models is difficult. Coupling of atomistics and DDD models has been...explored to some extent, but the coupling between DDD and continuum models of the evolution of large populations of dislocations is essentially unexplored

Continuum theory of edge states of topological insulators: variational principle and boundary conditions.

PubMed

Medhi, Amal; Shenoy, Vijay B

2012-09-05

We develop a continuum theory to model low energy excitations of a generic four-band time reversal invariant electronic system with boundaries. We propose a variational energy functional for the wavefunctions which allows us to derive natural boundary conditions valid for such systems. Our formulation is particularly suited for developing a continuum theory of the protected edge/surface excitations of topological insulators both in two and three dimensions. By a detailed comparison of our analytical formulation with tight binding calculations of ribbons of topological insulators modelled by the Bernevig-Hughes-Zhang (BHZ) Hamiltonian, we show that the continuum theory with a natural boundary condition provides an appropriate description of the low energy physics.

Modeling plasticity by non-continuous deformation

NASA Astrophysics Data System (ADS)

Ben-Shmuel, Yaron; Altus, Eli

2017-10-01

Plasticity and failure theories are still subjects of intense research. Engineering constitutive models on the macroscale which are based on micro characteristics are very much in need. This study is motivated by the observation that continuum assumptions in plasticity in which neighbour material elements are inseparable at all-time are physically impossible, since local detachments, slips and neighbour switching must operate, i.e. non-continuous deformation. Material microstructure is modelled herein by a set of point elements (particles) interacting with their neighbours. Each particle can detach from and/or attach with its neighbours during deformation. Simulations on two- dimensional configurations subjected to uniaxial compression cycle are conducted. Stochastic heterogeneity is controlled by a single "disorder" parameter. It was found that (a) macro response resembles typical elasto-plastic behaviour; (b) plastic energy is proportional to the number of detachments; (c) residual plastic strain is proportional to the number of attachments, and (d) volume is preserved, which is consistent with macro plastic deformation. Rigid body displacements of local groups of elements are also observed. Higher disorder decreases the macro elastic moduli and increases plastic energy. Evolution of anisotropic effects is obtained with no additional parameters.

Nonlinear force propagation, anisotropic stiffening and non-affine relaxation in a model cytoskeleton

NASA Astrophysics Data System (ADS)

Mizuno, Daisuke; Head, David; Ikebe, Emi; Nakamasu, Akiko; Kinoshita, Suguru; Peijuan, Zhang; Ando, Shoji

2013-03-01

Forces are generated heterogeneously in living cells and transmitted through cytoskeletal networks that respond highly non-linearly. Here, we carry out high-bandwidth passive microrheology on vimentin networks reconstituted in vitro, and observe the nonlinear mechanical response due to forces propagating from a local source applied by an optical tweezer. Since the applied force is constant, the gel becomes equilibrated and the fluctuation-dissipation theorem can be employed to deduce the viscoelasticity of the local environment from the thermal fluctuations of colloidal probes. Our experiments unequivocally demonstrate the anisotropic stiffening of the cytoskeletal network behind the applied force, with greater stiffening in the parallel direction. Quantitative agreement with an affine continuum model is obtained, but only for the response at certain frequency ~ 10-1000 Hz which separates the high-frequency power law and low-frequency elastic behavior of the network. We argue that the failure of the model at lower frequencies is due to the presence of non-affinity, and observe that zero-frequency changes in particle separation can be fitted when an independently-measured, empirical nonaffinity factor is applied.

Fundamental analysis of the failure of polymer-based fiber reinforced composites

NASA Technical Reports Server (NTRS)

Kanninen, M. F.; Rybicki, E. F.; Griffith, W. I.; Broek, D.

1976-01-01

A mathematical model is described which will permit predictions of the strength of fiber reinforced composites containing known flaws to be made from the basic properties of their constituents. The approach was to embed a local heterogeneous region (LHR) surrounding the crack tip into an anisotropic elastic continuum. The model should (1) permit an explicit analysis of the micromechanical processes involved in the fracture process, and (2) remain simple enough to be useful in practical computations. Computations for arbitrary flaw size and orientation under arbitrary applied load combinations were performed from unidirectional composites with linear elastic-brittle constituent behavior. The mechanical properties were nominally those of graphite epoxy. With the rupture properties arbitrarily varied to test the capability of the model to reflect real fracture modes in fiber composites, it was shown that fiber breakage, matrix crazing, crack bridging, matrix-fiber debonding, and axial splitting can all occur during a period of (gradually) increasing load prior to catastrophic fracture. The computations reveal qualitatively the sequential nature of the stable crack process that precedes fracture.

Water vapour foreign-continuum absorption in near-infrared windows from laboratory measurements.

PubMed

Ptashnik, Igor V; McPheat, Robert A; Shine, Keith P; Smith, Kevin M; Williams, R Gary

2012-06-13

For a long time, it has been believed that atmospheric absorption of radiation within wavelength regions of relatively high infrared transmittance (so-called 'windows') was dominated by the water vapour self-continuum, that is, spectrally smooth absorption caused by H(2)O--H(2)O pair interaction. Absorption due to the foreign continuum (i.e. caused mostly by H(2)O--N(2) bimolecular absorption in the Earth's atmosphere) was considered to be negligible in the windows. We report new retrievals of the water vapour foreign continuum from high-resolution laboratory measurements at temperatures between 350 and 430 K in four near-infrared windows between 1.1 and 5 μm (9000-2000 cm(-1)). Our results indicate that the foreign continuum in these windows has a very weak temperature dependence and is typically between one and two orders of magnitude stronger than that given in representations of the continuum currently used in many climate and weather prediction models. This indicates that absorption owing to the foreign continuum may be comparable to the self-continuum under atmospheric conditions in the investigated windows. The calculated global-average clear-sky atmospheric absorption of solar radiation is increased by approximately 0.46 W m(-2) (or 0.6% of the total clear-sky absorption) by using these new measurements when compared with calculations applying the widely used MTCKD (Mlawer-Tobin-Clough-Kneizys-Davies) foreign-continuum model.

Quantifying sampling noise and parametric uncertainty in atomistic-to-continuum simulations using surrogate models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salloum, Maher N.; Sargsyan, Khachik; Jones, Reese E.

2015-08-11

We present a methodology to assess the predictive fidelity of multiscale simulations by incorporating uncertainty in the information exchanged between the components of an atomistic-to-continuum simulation. We account for both the uncertainty due to finite sampling in molecular dynamics (MD) simulations and the uncertainty in the physical parameters of the model. Using Bayesian inference, we represent the expensive atomistic component by a surrogate model that relates the long-term output of the atomistic simulation to its uncertain inputs. We then present algorithms to solve for the variables exchanged across the atomistic-continuum interface in terms of polynomial chaos expansions (PCEs). We alsomore » consider a simple Couette flow where velocities are exchanged between the atomistic and continuum components, while accounting for uncertainty in the atomistic model parameters and the continuum boundary conditions. Results show convergence of the coupling algorithm at a reasonable number of iterations. As a result, the uncertainty in the obtained variables significantly depends on the amount of data sampled from the MD simulations and on the width of the time averaging window used in the MD simulations.« less

A comparison of FE beam and continuum elements for typical nitinol stent geometries

NASA Astrophysics Data System (ADS)

Ballew, Wesley; Seelecke, Stefan

2009-03-01

With interest in improved efficiency and a more complete description of the SMA material, this paper compares finite element (FE) simulations of typical stent geometries using two different constitutive models and two different element types. Typically, continuum elements are used for the simulation of stents, for example the commercial FE software ANSYS offers a continuum element based on Auricchio's SMA model. Almost every stent geometry, however, is made up of long and slender components and can be modeled more efficiently, in the computational sense, with beam elements. Using the ANSYS user programmable material feature, we implement the free energy based SMA model developed by Mueller and Seelecke into the ANSYS beam element 188. Convergence behavior for both, beam and continuum formulations, is studied in terms of element and layer number, respectively. This is systematically illustrated first for the case of a straight cantilever beam under end loading, and subsequently for a section of a z-bend wire, a typical stent sub-geometry. It is shown that the computation times for the beam element are reduced to only one third of those of the continuum element, while both formulations display a comparable force/displacement response.

The influence of ligament modelling strategies on the predictive capability of finite element models of the human knee joint.

PubMed

Naghibi Beidokhti, Hamid; Janssen, Dennis; van de Groes, Sebastiaan; Hazrati, Javad; Van den Boogaard, Ton; Verdonschot, Nico

2017-12-08

In finite element (FE) models knee ligaments can represented either by a group of one-dimensional springs, or by three-dimensional continuum elements based on segmentations. Continuum models closer approximate the anatomy, and facilitate ligament wrapping, while spring models are computationally less expensive. The mechanical properties of ligaments can be based on literature, or adjusted specifically for the subject. In the current study we investigated the effect of ligament modelling strategy on the predictive capability of FE models of the human knee joint. The effect of literature-based versus specimen-specific optimized material parameters was evaluated. Experiments were performed on three human cadaver knees, which were modelled in FE models with ligaments represented either using springs, or using continuum representations. In spring representation collateral ligaments were each modelled with three and cruciate ligaments with two single-element bundles. Stiffness parameters and pre-strains were optimized based on laxity tests for both approaches. Validation experiments were conducted to evaluate the outcomes of the FE models. Models (both spring and continuum) with subject-specific properties improved the predicted kinematics and contact outcome parameters. Models incorporating literature-based parameters, and particularly the spring models (with the representations implemented in this study), led to relatively high errors in kinematics and contact pressures. Using a continuum modelling approach resulted in more accurate contact outcome variables than the spring representation with two (cruciate ligaments) and three (collateral ligaments) single-element-bundle representations. However, when the prediction of joint kinematics is of main interest, spring ligament models provide a faster option with acceptable outcome. Copyright © 2017 Elsevier Ltd. All rights reserved.

Roughness Versus Charge Contributions to Representative Discrete Heterogeneity Underlying Mechanistic Prediction of Colloid Attachment, Detachment and Breakthrough-Elution Behavior Under Environmental Conditions.

NASA Astrophysics Data System (ADS)

Johnson, William; Farnsworth, Anna; Vanness, Kurt; Hilpert, Markus

2017-04-01

The key element of a mechanistic theory to predict colloid attachment in porous media under environmental conditions where colloid-collector repulsion exists (unfavorable conditions for attachment) is representation of the nano-scale surface heterogeneity (herein called discrete heterogeneity) that drives colloid attachment under unfavorable conditions. The observed modes of colloid attachment under unfavorable conditions emerge from simulations that incorporate discrete heterogeneity. Quantitative prediction of attachment (and detachment) requires capturing the sizes, spatial frequencies, and other properties of roughness asperities and charge heterodomains in discrete heterogeneity representations of different surfaces. The fact that a given discrete heterogeneity representation will interact differently with different-sized colloids as well as different ionic strengths for a given sized colloid allows backing out representative discrete heterogeneity via comparison of simulations to experiments performed across a range of colloid size, solution IS, and fluid velocity. This has been achieved on unfavorable smooth surfaces yielding quantitative prediction of attachment, and qualitative prediction of detachment in response to ionic strength or flow perturbations. Extending this treatment to rough surfaces, and representing the contributions of nanoscale roughness as well as charge heterogeneity is a focus of this talk. Another focus of this talk is the upscaling the pore scale simulations to produce contrasting breakthrough-elution behaviors at the continuum (column) scale that are observed, for example, for different-sized colloids, or same-sized colloids under different ionic strength conditions. The outcome of mechanistic pore scale simulations incorporating discrete heterogeneity and subsequent upscaling is that temporal processes such as blocking and ripening will emerge organically from these simulations, since these processes fundamentally stem from the limited sites available for attachment as represented in discrete heterogeneity.

Development of a multiaxial viscoelastoplastic continuum damage model for asphalt mixtures.

DOT National Transportation Integrated Search

2009-09-01

This report highlights findings from the FHWA DTFH61-05-H-00019 project, which focused on the development of the multiaxial viscoelastoplastic continuum damage model for asphalt concrete in both compression and tension. Asphalt concrete pavement, one...

Sensitivity of the Properties of Ruthenium “Blue Dimer” to Method, Basis Set, and Continuum Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozkanlar, Abdullah; Clark, Aurora E.

2012-05-23

The ruthenium “blue dimer” [(bpy)2RuIIIOH2]2O4+ is best known as the first well-defined molecular catalyst for water oxidation. It has been subject to numerous computational studies primarily employing density functional theory. However, those studies have been limited in the functionals, basis sets, and continuum models employed. The controversy in the calculated electronic structure and the reaction energetics of this catalyst highlights the necessity of benchmark calculations that explore the role of density functionals, basis sets, and continuum models upon the essential features of blue-dimer reactivity. In this paper, we report Kohn-Sham complete basis set (KS-CBS) limit extrapolations of the electronic structuremore » of “blue dimer” using GGA (BPW91 and BP86), hybrid-GGA (B3LYP), and meta-GGA (M06-L) density functionals. The dependence of solvation free energy corrections on the different cavity types (UFF, UA0, UAHF, UAKS, Bondi, and Pauling) within polarizable and conductor-like polarizable continuum model has also been investigated. The most common basis sets of double-zeta quality are shown to yield results close to the KS-CBS limit; however, large variations are observed in the reaction energetics as a function of density functional and continuum cavity model employed.« less

Modal kinematics for multisection continuum arms.

PubMed

Godage, Isuru S; Medrano-Cerda, Gustavo A; Branson, David T; Guglielmino, Emanuele; Caldwell, Darwin G

2015-05-13

This paper presents a novel spatial kinematic model for multisection continuum arms based on mode shape functions (MSF). Modal methods have been used in many disciplines from finite element methods to structural analysis to approximate complex and nonlinear parametric variations with simple mathematical functions. Given certain constraints and required accuracy, this helps to simplify complex phenomena with numerically efficient implementations leading to fast computations. A successful application of the modal approximation techniques to develop a new modal kinematic model for general variable length multisection continuum arms is discussed. The proposed method solves the limitations associated with previous models and introduces a new approach for readily deriving exact, singularity-free and unique MSF's that simplifies the approach and avoids mode switching. The model is able to simulate spatial bending as well as straight arm motions (i.e., pure elongation/contraction), and introduces inverse position and orientation kinematics for multisection continuum arms. A kinematic decoupling feature, splitting position and orientation inverse kinematics is introduced. This type of decoupling has not been presented for these types of robotic arms before. The model also carefully accounts for physical constraints in the joint space to provide enhanced insight into practical mechanics and impose actuator mechanical limitations onto the kinematics thus generating fully realizable results. The proposed method is easily applicable to a broad spectrum of continuum arm designs.

Persistent Homology fingerprinting of microstructural controls on larger-scale fluid flow in porous media

NASA Astrophysics Data System (ADS)

Moon, C.; Mitchell, S. A.; Callor, N.; Dewers, T. A.; Heath, J. E.; Yoon, H.; Conner, G. R.

2017-12-01

Traditional subsurface continuum multiphysics models include useful yet limiting geometrical assumptions: penny- or disc-shaped cracks, spherical or elliptical pores, bundles of capillary tubes, cubic law fracture permeability, etc. Each physics (flow, transport, mechanics) uses constitutive models with an increasing number of fit parameters that pertain to the microporous structure of the rock, but bear no inter-physics relationships or self-consistency. Recent advances in digital rock physics and pore-scale modeling link complex physics to detailed pore-level geometries, but measures for upscaling are somewhat unsatisfactory and come at a high computational cost. Continuum mechanics rely on a separation between small scale pore fluctuations and larger scale heterogeneity (and perhaps anisotropy), but this can break down (particularly for shales). Algebraic topology offers powerful mathematical tools for describing a local-to-global structure of shapes. Persistent homology, in particular, analyzes the dynamics of topological features and summarizes into numeric values. It offers a roadmap to both "fingerprint" topologies of pore structure and multiscale connectedness as well as links pore structure to physical behavior, thus potentially providing a means to relate the dependence of constitutive behaviors of pore structures in a self-consistent way. We present a persistence homology (PH) analysis framework of 3D image sets including a focused ion beam-scanning electron microscopy data set of the Selma Chalk. We extract structural characteristics of sampling volumes via persistence homology and fit a statistical model using the summarized values to estimate porosity, permeability, and connectivity—Lattice Boltzmann methods for single phase flow modeling are used to obtain the relationships. These PH methods allow for prediction of geophysical properties based on the geometry and connectivity in a computationally efficient way. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia LLC, a wholly owned subsidiary of Honeywell International Inc. for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Modeling the elastic energy of alloys: Potential pitfalls of continuum treatments.

PubMed

Baskaran, Arvind; Ratsch, Christian; Smereka, Peter

2015-12-01

Some issues that arise when modeling elastic energy for binary alloys are discussed within the context of a Keating model and density-functional calculations. The Keating model is a simplified atomistic formulation based on modeling elastic interactions of a binary alloy with harmonic springs whose equilibrium length is species dependent. It is demonstrated that the continuum limit for the strain field are the usual equations of linear elasticity for alloys and that they correctly capture the coarse-grained behavior of the displacement field. In addition, it is established that Euler-Lagrange equation of the continuum limit of the elastic energy will yield the same strain field equation. This is the same energy functional that is often used to model elastic effects in binary alloys. However, a direct calculation of the elastic energy atomistic model reveals that the continuum expression for the elastic energy is both qualitatively and quantitatively incorrect. This is because it does not take atomistic scale compositional nonuniformity into account. Importantly, this result also shows that finely mixed alloys tend to have more elastic energy than segregated systems, which is the exact opposite of predictions made by some continuum theories. It is also shown that for strained thin films the traditionally used effective misfit for alloys systematically underestimate the strain energy. In some models, this drawback is handled by including an elastic contribution to the enthalpy of mixing, which is characterized in terms of the continuum concentration. The direct calculation of the atomistic model reveals that this approach suffers serious difficulties. It is demonstrated that elastic contribution to the enthalpy of mixing is nonisotropic and scale dependent. It is also shown that such effects are present in density-functional theory calculations for the Si-Ge system. This work demonstrates that it is critical to include the microscopic arrangements in any elastic model to achieve even qualitatively correct behavior.

Mind the Gap: A Semicontinuum Model for Discrete Electrical Propagation in Cardiac Tissue.

PubMed

Costa, Caroline Mendonca; Silva, Pedro Andre Arroyo; dos Santos, Rodrigo Weber

2016-04-01

Electrical propagation in cardiac tissue is a discrete or discontinuous phenomenon that reflects the complexity of the anatomical structures and their organization in the heart, such as myocytes, gap junctions, microvessels, and extracellular matrix, just to name a few. Discrete models or microscopic and discontinuous models are, so far, the best options to accurately study how structural properties of cardiac tissue influence electrical propagation. These models are, however, inappropriate in the context of large scale simulations, which have been traditionally performed by the use of continuum and macroscopic models, such as the monodomain and the bidomain models. However, continuum models may fail to reproduce many important physiological and physiopathological aspects of cardiac electrophysiology, for instance, those related to slow conduction. In this study, we develop a new mathematical model that combines characteristics of both continuum and discrete models. The new model was evaluated in scenarios of low gap-junctional coupling, where slow conduction is observed, and was able to reproduce conduction block, increase of the maximum upstroke velocity and of the repolarization dispersion. None of these features can be captured by continuum models. In addition, the model overcomes a great disadvantage of discrete models, as it allows variation of the spatial resolution within a certain range.

Monolayers of hard rods on planar substrates. II. Growth

NASA Astrophysics Data System (ADS)

Klopotek, M.; Hansen-Goos, H.; Dixit, M.; Schilling, T.; Schreiber, F.; Oettel, M.

2017-02-01

Growth of hard-rod monolayers via deposition is studied in a lattice model using rods with discrete orientations and in a continuum model with hard spherocylinders. The lattice model is treated with kinetic Monte Carlo simulations and dynamic density functional theory while the continuum model is studied by dynamic Monte Carlo simulations equivalent to diffusive dynamics. The evolution of nematic order (excess of upright particles, "standing-up" transition) is an entropic effect and is mainly governed by the equilibrium solution, rendering a continuous transition [Paper I, M. Oettel et al., J. Chem. Phys. 145, 074902 (2016)]. Strong non-equilibrium effects (e.g., a noticeable dependence on the ratio of rates for translational and rotational moves) are found for attractive substrate potentials favoring lying rods. Results from the lattice and the continuum models agree qualitatively if the relevant characteristic times for diffusion, relaxation of nematic order, and deposition are matched properly. Applicability of these monolayer results to multilayer growth is discussed for a continuum-model realization in three dimensions where spherocylinders are deposited continuously onto a substrate via diffusion.

Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model

PubMed Central

Sharma, Ity; Kaminski, George A.

2012-01-01

We have computed pKa values for eleven substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We have also reproduced pKa values of propanoic and butanoic acids within ca. 0.1 pH units from the experimental values by fitting the solvation parameters for carboxylate ion carbon and oxygen atoms. The FB model combines two distinguishing features. First, it limits the amount of noise which is common in numerical treatment of continuum solvation models by using fixed-position grid points. Second, it employs either second- or first-order approximation for the solvent polarization, depending on a particular implementation. These approximations are similar to those used for solute and explicit solvent fast polarization treatment which we developed previously. This article describes results of employing the first-order technique. This approximation places the presented methodology between the Generalized Born and Poisson-Boltzmann continuum solvation models with respect to their accuracy of reproducing the many-body effects in modeling a continuum solvent. PMID:22815192

Dynamics of electrical double layer formation in room-temperature ionic liquids under constant-current charging conditions

NASA Astrophysics Data System (ADS)

Jiang, Xikai; Huang, Jingsong; Zhao, Hui; Sumpter, Bobby G.; Qiao, Rui

2014-07-01

We report detailed simulation results on the formation dynamics of an electrical double layer (EDL) inside an electrochemical cell featuring room-temperature ionic liquids (RTILs) enclosed between two planar electrodes. Under relatively small charging currents, the evolution of cell potential from molecular dynamics (MD) simulations during charging can be suitably predicted by the Landau-Ginzburg-type continuum model proposed recently (Bazant et al 2011 Phys. Rev. Lett. 106 046102). Under very large charging currents, the cell potential from MD simulations shows pronounced oscillation during the initial stage of charging, a feature not captured by the continuum model. Such oscillation originates from the sequential growth of the ionic space charge layers near the electrode surface. This allows the evolution of EDLs in RTILs with time, an atomistic process difficult to visualize experimentally, to be studied by analyzing the cell potential under constant-current charging conditions. While the continuum model cannot predict the potential oscillation under such far-from-equilibrium charging conditions, it can nevertheless qualitatively capture the growth of cell potential during the later stage of charging. Improving the continuum model by introducing frequency-dependent dielectric constant and density-dependent ion diffusion coefficients may help to further extend the applicability of the model. The evolution of ion density profiles is also compared between the MD and the continuum model, showing good agreement.

Dynamics of electrical double layer formation in room-temperature ionic liquids under constant-current charging conditions.

PubMed

Jiang, Xikai; Huang, Jingsong; Zhao, Hui; Sumpter, Bobby G; Qiao, Rui

2014-07-16

We report detailed simulation results on the formation dynamics of an electrical double layer (EDL) inside an electrochemical cell featuring room-temperature ionic liquids (RTILs) enclosed between two planar electrodes. Under relatively small charging currents, the evolution of cell potential from molecular dynamics (MD) simulations during charging can be suitably predicted by the Landau-Ginzburg-type continuum model proposed recently (Bazant et al 2011 Phys. Rev. Lett. 106 046102). Under very large charging currents, the cell potential from MD simulations shows pronounced oscillation during the initial stage of charging, a feature not captured by the continuum model. Such oscillation originates from the sequential growth of the ionic space charge layers near the electrode surface. This allows the evolution of EDLs in RTILs with time, an atomistic process difficult to visualize experimentally, to be studied by analyzing the cell potential under constant-current charging conditions. While the continuum model cannot predict the potential oscillation under such far-from-equilibrium charging conditions, it can nevertheless qualitatively capture the growth of cell potential during the later stage of charging. Improving the continuum model by introducing frequency-dependent dielectric constant and density-dependent ion diffusion coefficients may help to further extend the applicability of the model. The evolution of ion density profiles is also compared between the MD and the continuum model, showing good agreement.

Creating a Simple Single Computational Approach to Modeling Rarefied and Continuum Flow About Aerospace Vehicles

NASA Technical Reports Server (NTRS)

Goldstein, David B.; Varghese, Philip L.

1997-01-01

We proposed to create a single computational code incorporating methods that can model both rarefied and continuum flow to enable the efficient simulation of flow about space craft and high altitude hypersonic aerospace vehicles. The code was to use a single grid structure that permits a smooth transition between the continuum and rarefied portions of the flow. Developing an appropriate computational boundary between the two regions represented a major challenge. The primary approach chosen involves coupling a four-speed Lattice Boltzmann model for the continuum flow with the DSMC method in the rarefied regime. We also explored the possibility of using a standard finite difference Navier Stokes solver for the continuum flow. With the resulting code we will ultimately investigate three-dimensional plume impingement effects, a subject of critical importance to NASA and related to the work of Drs. Forrest Lumpkin, Steve Fitzgerald and Jay Le Beau at Johnson Space Center. Below is a brief background on the project and a summary of the results as of the end of the grant.

Development and calibration of a reactive transport model for carbonate reservoir porosity and permeability changes based on CO 2 core-flood experiments

DOE PAGES

Smith, Megan M.; Hao, Y.; Carroll, S. A.

2017-01-02

Here, beneficial pore space and permeability enhancements are likely to occur as CO 2-charged fluids partially dissolve carbonate minerals in carbonate reservoir formations used for geologic CO 2 storage. The ability to forecast the extent and impact of changes in porosity and permeability will aid geologic CO 2 storage operations and lower uncertainty in estimates of long-term storage capacity. Our work is directed toward developing calibrated reactive transport models that more accurately capture the chemical impacts of CO 2-fluid-rock interactions and their effects on porosity and permeability by matching pressure, fluid chemistry, and dissolution features that developed as a resultmore » of reaction with CO 2-acidified brines at representative reservoir conditions. We present new results from experiments conducted on seven core samples from the Arbuckle Dolostone (near Wellington, Kansas, USA, recovered as part of the South-Central Kansas CO 2 Demonstration). Cores were obtained from both target reservoir and lower-permeability baffle zones, and together these samples span over 3–4 orders of magnitude of permeability according to downhole measurements. Core samples were nondestructively imaged by X-ray computed tomography and the resulting characterization data were mapped onto a continuum domain to further develop a reactive transport model for a range of mineral and physical heterogeneity. We combine these new results with those from previous experimental studies to more fully constrain the governing equations used in reactive transport models to better estimate the transition of enhanced oil recovery operations to long-term geology CO 2 storage. Calcite and dolomite kinetic rate constants (mol m –2 s –1) derived by fitting the results from core-flood experiments range from k calcite,25C = 10 –6.8 to 10 –4.6, and k dolomite,25C = 10 –7.5 to 10 –5.3. The power law-based porosity-permeability relationship is sensitive to the overall pore space heterogeneity of each core. Stable dissolution fronts observed in the more homogeneous dolostones could be accurately simulated using an exponential value of n = 3. Furthermore, unstable dissolution fronts consisting of preferential flowpaths could be simulated using an exponential value of n = 3 for heterogeneous dolostones, and larger values ( n = 6–8) for heterogeneous limestones.« less

Development and calibration of a reactive transport model for carbonate reservoir porosity and permeability changes based on CO 2 core-flood experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Megan M.; Hao, Y.; Carroll, S. A.

Here, beneficial pore space and permeability enhancements are likely to occur as CO 2-charged fluids partially dissolve carbonate minerals in carbonate reservoir formations used for geologic CO 2 storage. The ability to forecast the extent and impact of changes in porosity and permeability will aid geologic CO 2 storage operations and lower uncertainty in estimates of long-term storage capacity. Our work is directed toward developing calibrated reactive transport models that more accurately capture the chemical impacts of CO 2-fluid-rock interactions and their effects on porosity and permeability by matching pressure, fluid chemistry, and dissolution features that developed as a resultmore » of reaction with CO 2-acidified brines at representative reservoir conditions. We present new results from experiments conducted on seven core samples from the Arbuckle Dolostone (near Wellington, Kansas, USA, recovered as part of the South-Central Kansas CO 2 Demonstration). Cores were obtained from both target reservoir and lower-permeability baffle zones, and together these samples span over 3–4 orders of magnitude of permeability according to downhole measurements. Core samples were nondestructively imaged by X-ray computed tomography and the resulting characterization data were mapped onto a continuum domain to further develop a reactive transport model for a range of mineral and physical heterogeneity. We combine these new results with those from previous experimental studies to more fully constrain the governing equations used in reactive transport models to better estimate the transition of enhanced oil recovery operations to long-term geology CO 2 storage. Calcite and dolomite kinetic rate constants (mol m –2 s –1) derived by fitting the results from core-flood experiments range from k calcite,25C = 10 –6.8 to 10 –4.6, and k dolomite,25C = 10 –7.5 to 10 –5.3. The power law-based porosity-permeability relationship is sensitive to the overall pore space heterogeneity of each core. Stable dissolution fronts observed in the more homogeneous dolostones could be accurately simulated using an exponential value of n = 3. Furthermore, unstable dissolution fronts consisting of preferential flowpaths could be simulated using an exponential value of n = 3 for heterogeneous dolostones, and larger values ( n = 6–8) for heterogeneous limestones.« less

On the continuum mechanics approach for the analysis of single walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Chaudhry, M. S.; Czekanski, A.

2016-04-01

Today carbon nanotubes have found various applications in structural, thermal and almost every field of engineering. Carbon nanotubes provide great strength, stiffness resilience properties. Evaluating the structural behavior of nanoscale materials is an important task. In order to understand the materialistic behavior of nanotubes, atomistic models provide a basis for continuum mechanics modelling. Although the properties of bulk materials are consistent with the size and depends mainly on the material but the properties when we are in Nano-range, continuously change with the size. Such models start from the modelling of interatomic interaction. Modelling and simulation has advantage of cost saving when compared with the experiments. So in this project our aim is to use a continuum mechanics model of carbon nanotubes from atomistic perspective and analyses some structural behaviors of nanotubes. It is generally recognized that mechanical properties of nanotubes are dependent upon their structural details. The properties of nanotubes vary with the varying with the interatomic distance, angular orientation, radius of the tube and many such parameters. Based on such models one can analyses the variation of young's modulus, strength, deformation behavior, vibration behavior and thermal behavior. In this study some of the structural behaviors of the nanotubes are analyzed with the help of continuum mechanics models. Using the properties derived from the molecular mechanics model a Finite Element Analysis of carbon nanotubes is performed and results are verified. This study provides the insight on continuum mechanics modelling of nanotubes and hence the scope to study the effect of various parameters on some structural behavior of nanotubes.

Post-injection Multiphase Flow Modeling and Risk Assessments for Subsurface CO2 Storage in Naturally Fractured Reservoirs

NASA Astrophysics Data System (ADS)

Jin, G.

2015-12-01

Subsurface storage of carbon dioxide in geological formations is widely regarded as a promising tool for reducing global atmospheric CO2 emissions. Successful geologic storage for sequestrated carbon dioxides must prove to be safe by means of risk assessments including post-injection analysis of injected CO2 plumes. Because fractured reservoirs exhibit a higher degree of heterogeneity, it is imperative to conduct such simulation studies in order to reliably predict the geometric evolution of plumes and risk assessment of post CO2injection. The research has addressed the pressure footprint of CO2 plumes through the development of new techniques which combine discrete fracture network and stochastic continuum modeling of multiphase flow in fractured geologic formations. A subsequent permeability tensor map in 3-D, derived from our preciously developed method, can accurately describe the heterogeneity of fracture reservoirs. A comprehensive workflow integrating the fracture permeability characterization and multiphase flow modeling has been developed to simulate the CO2plume migration and risk assessments. A simulated fractured reservoir model based on high-priority geological carbon sinks in central Alabama has been employed for preliminary study. Discrete fracture networks were generated with an NE-oriented regional fracture set and orthogonal NW-fractures. Fracture permeability characterization revealed high permeability heterogeneity with an order of magnitude of up to three. A multiphase flow model composed of supercritical CO2 and saline water was then applied to predict CO2 plume volume, geometry, pressure footprint, and containment during and post injection. Injection simulation reveals significant permeability anisotropy that favors development of northeast-elongate CO2 plumes, which are aligned with systematic fractures. The diffusive spreading front of the CO2 plume shows strong viscous fingering effects. Post-injection simulation indicates significant upward lateral spreading of CO2 resulting in accumulation of CO2 directly under the seal unit because of its buoyancy and strata-bound vertical fractures. Risk assessment shows that lateral movement of CO2 along interconnected fractures requires widespread seals with high integrity to confine the injected CO2.

A nonmonotonic dependence of standard rate constant on reorganization energy for heterogeneous electron transfer processes on electrode surface

NASA Astrophysics Data System (ADS)

Xu, Weilin; Li, Songtao; Zhou, Xiaochun; Xing, Wei; Huang, Mingyou; Lu, Tianhong; Liu, Changpeng

2006-05-01

In the present work a nonmonotonic dependence of standard rate constant (k0) on reorganization energy (λ) was discovered qualitatively from electron transfer (Marcus-Hush-Levich) theory for heterogeneous electron transfer processes on electrode surface. It was found that the nonmonotonic dependence of k0 on λ is another result, besides the disappearance of the famous Marcus inverted region, coming from the continuum of electronic states in electrode: with the increase of λ, the states for both Process I and Process II ET processes all vary from nonadiabatic to adiabatic state continuously, and the λ dependence of k0 for Process I is monotonic thoroughly, while for Process II on electrode surface the λ dependence of k0 could show a nonmonotonicity.

Inequality spectra

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2017-03-01

Inequality indices are widely applied in economics and in the social sciences as quantitative measures of the socioeconomic inequality of human societies. The application of inequality indices extends to size-distributions at large, where these indices can be used as general gauges of statistical heterogeneity. Moreover, as inequality indices are plentiful, arrays of such indices facilitate high-detail quantification of statistical heterogeneity. In this paper we elevate from arrays of inequality indices to inequality spectra: continuums of inequality indices that are parameterized by a single control parameter. We present a general methodology of constructing Lorenz-based inequality spectra, apply the general methodology to establish four sets of inequality spectra, investigate the properties of these sets, and show how these sets generalize known inequality gauges such as: the Gini index, the extended Gini index, the Rényi index, and hill curves.

All Elder Abuse Perpetrators Are Not Alike: The Heterogeneity of Elder Abuse Perpetrators and Implications for Intervention.

PubMed

Jackson, Shelly L

2016-02-01

The tendency to label all elder abuse perpetrators as the "bad guys" has diminished our ability to respond effectively. A review of the literature demonstrates that elder abuse perpetrators are in fact heterogeneous with important differences across types of abuse. A reformulation of perpetrator interventions away from a singular emphasis on prosecution to meaningful alternatives that utilize criminal justice and/or therapeutic approaches tailored to the needs of the case is needed. These interventions must incorporate the needs of both victims and perpetrators, take into consideration the type of abuse involved, acknowledge the variations in perpetrator culpability, and recognize the continuum of complexity among these cases. Without addressing these nuances, intervention and prevention efforts will be futile if not harmful. © The Author(s) 2014.

Airborne and satellite remote sensing of the mid-infrared water vapour continuum.

PubMed

Newman, Stuart M; Green, Paul D; Ptashnik, Igor V; Gardiner, Tom D; Coleman, Marc D; McPheat, Robert A; Smith, Kevin M

2012-06-13

Remote sensing of the atmosphere from space plays an increasingly important role in weather forecasting. Exploiting observations from the latest generation of weather satellites relies on an accurate knowledge of fundamental spectroscopy, including the water vapour continuum absorption. Field campaigns involving the Facility for Airborne Atmospheric Measurements research aircraft have collected a comprehensive dataset, comprising remotely sensed infrared radiance observations collocated with accurate measurements of the temperature and humidity structure of the atmosphere. These field measurements have been used to validate the strength of the infrared water vapour continuum in comparison with the latest laboratory measurements. The recent substantial changes to self-continuum coefficients in the widely used MT_CKD (Mlawer-Tobin-Clough-Kneizys-Davies) model between 2400 and 3200 cm(-1) are shown to be appropriate and in agreement with field measurements. Results for the foreign continuum in the 1300-2000 cm(-1) band suggest a weak temperature dependence that is not currently included in atmospheric models. A one-dimensional variational retrieval experiment is performed that shows a small positive benefit from using new laboratory-derived continuum coefficients for humidity retrievals.

Continuum-Kinetic Models and Numerical Methods for Multiphase Applications

NASA Astrophysics Data System (ADS)

Nault, Isaac Michael

This thesis presents a continuum-kinetic approach for modeling general problems in multiphase solid mechanics. In this context, a continuum model refers to any model, typically on the macro-scale, in which continuous state variables are used to capture the most important physics: conservation of mass, momentum, and energy. A kinetic model refers to any model, typically on the meso-scale, which captures the statistical motion and evolution of microscopic entitites. Multiphase phenomena usually involve non-negligible micro or meso-scopic effects at the interfaces between phases. The approach developed in the thesis attempts to combine the computational performance benefits of a continuum model with the physical accuracy of a kinetic model when applied to a multiphase problem. The approach is applied to modeling a single particle impact in Cold Spray, an engineering process that intimately involves the interaction of crystal grains with high-magnitude elastic waves. Such a situation could be classified a multiphase application due to the discrete nature of grains on the spatial scale of the problem. For this application, a hyper elasto-plastic model is solved by a finite volume method with approximate Riemann solver. The results of this model are compared for two types of plastic closure: a phenomenological macro-scale constitutive law, and a physics-based meso-scale Crystal Plasticity model.

Simple Estimators for the Simple Latent Class Mastery Testing Model. Twente Educational Memorandum No. 19.

ERIC Educational Resources Information Center

van der Linden, Wim J.

Latent class models for mastery testing differ from continuum models in that they do not postulate a latent mastery continuum but conceive mastery and non-mastery as two latent classes, each characterized by different probabilities of success. Several researchers use a simple latent class model that is basically a simultaneous application of the…

Polarizable Force Fields and Polarizable Continuum Model: A Fluctuating Charges/PCM Approach. 1. Theory and Implementation.

PubMed

Lipparini, Filippo; Barone, Vincenzo

2011-11-08

We present a combined fluctuating charges-polarizable continuum model approach to describe molecules in solution. Both static and dynamic approaches are discussed: analytical first and second derivatives are shown as well as an extended lagrangian for molecular dynamics simluations. In particular, we use the polarizable continuum model to provide nonperiodic boundary conditions for molecular dynamics simulations of aqueous solutions. The extended lagrangian method is extensively discussed, with specific reference to the fluctuating charge model, from a numerical point of view by means of several examples, and a rationalization of the behavior found is presented. Several prototypical applications are shown, especially regarding solvation of ions and polar molecules in water.

Heterogeneous structure and surface tension effects on mechanical response in pulmonary acinus: A finite element analysis.

PubMed

Koshiyama, Kenichiro; Nishimoto, Keisuke; Ii, Satoshi; Sera, Toshihiro; Wada, Shigeo

2018-01-20

The pulmonary acinus is a dead-end microstructure that consists of ducts and alveoli. High-resolution micro-CT imaging has recently provided detailed anatomical information of a complete in vivo acinus, but relating its mechanical response with its detailed acinar structure remains challenging. This study aimed to investigate the mechanical response of acinar tissue in a whole acinus for static inflation using computational approaches. We performed finite element analysis of a whole acinus for static inflation. The acinar structure model was generated based on micro-CT images of an intact acinus. A continuum mechanics model of the lung parenchyma was used for acinar tissue material model, and surface tension effects were explicitly included. An anisotropic mechanical field analysis based on a stretch tensor was combined with a curvature-based local structure analysis. The airspace of the acinus exhibited nonspherical deformation as a result of the anisotropic deformation of acinar tissue. A strain hotspot occurred at the ridge-shaped region caused by a rod-like deformation of acinar tissue on the ridge. The local structure becomes bowl-shaped for inflation and, without surface tension effects, the surface of the bowl-shaped region primarily experiences isotropic deformation. Surface tension effects suppressed the increase in airspace volume and inner surface area, while facilitating anisotropic deformation on the alveolar surface. In the lungs, the heterogeneous acinar structure and surface tension induce anisotropic deformation at the acinar and alveolar scales. Further research is needed on structural variation of acini, inter-acini connectivity, or dynamic behavior to understand multiscale lung mechanics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Modeling Soft Tissue Damage and Failure Using a Combined Particle/Continuum Approach.

PubMed

Rausch, M K; Karniadakis, G E; Humphrey, J D

2017-02-01

Biological soft tissues experience damage and failure as a result of injury, disease, or simply age; examples include torn ligaments and arterial dissections. Given the complexity of tissue geometry and material behavior, computational models are often essential for studying both damage and failure. Yet, because of the need to account for discontinuous phenomena such as crazing, tearing, and rupturing, continuum methods are limited. Therefore, we model soft tissue damage and failure using a particle/continuum approach. Specifically, we combine continuum damage theory with Smoothed Particle Hydrodynamics (SPH). Because SPH is a meshless particle method, and particle connectivity is determined solely through a neighbor list, discontinuities can be readily modeled by modifying this list. We show, for the first time, that an anisotropic hyperelastic constitutive model commonly employed for modeling soft tissue can be conveniently implemented within a SPH framework and that SPH results show excellent agreement with analytical solutions for uniaxial and biaxial extension as well as finite element solutions for clamped uniaxial extension in 2D and 3D. We further develop a simple algorithm that automatically detects damaged particles and disconnects the spatial domain along rupture lines in 2D and rupture surfaces in 3D. We demonstrate the utility of this approach by simulating damage and failure under clamped uniaxial extension and in a peeling experiment of virtual soft tissue samples. In conclusion, SPH in combination with continuum damage theory may provide an accurate and efficient framework for modeling damage and failure in soft tissues.

Modeling Soft Tissue Damage and Failure Using a Combined Particle/Continuum Approach

PubMed Central

Rausch, M. K.; Karniadakis, G. E.; Humphrey, J. D.

2016-01-01

Biological soft tissues experience damage and failure as a result of injury, disease, or simply age; examples include torn ligaments and arterial dissections. Given the complexity of tissue geometry and material behavior, computational models are often essential for studying both damage and failure. Yet, because of the need to account for discontinuous phenomena such as crazing, tearing, and rupturing, continuum methods are limited. Therefore, we model soft tissue damage and failure using a particle/continuum approach. Specifically, we combine continuum damage theory with Smoothed Particle Hydrodynamics (SPH). Because SPH is a meshless particle method, and particle connectivity is determined solely through a neighbor list, discontinuities can be readily modeled by modifying this list. We show, for the first time, that an anisotropic hyperelastic constitutive model commonly employed for modeling soft tissue can be conveniently implemented within a SPH framework and that SPH results show excellent agreement with analytical solutions for uniaxial and biaxial extension as well as finite element solutions for clamped uniaxial extension in 2D and 3D. We further develop a simple algorithm that automatically detects damaged particles and disconnects the spatial domain along rupture lines in 2D and rupture surfaces in 3D. We demonstrate the utility of this approach by simulating damage and failure under clamped uniaxial extension and in a peeling experiment of virtual soft tissue samples. In conclusion, SPH in combination with continuum damage theory may provide an accurate and efficient framework for modeling damage and failure in soft tissues. PMID:27538848

Continuum of Medical Education in Obstetrics and Gynecology.

ERIC Educational Resources Information Center

Dohner, Charles W.; Hunter, Charles A., Jr.

1980-01-01

Over the past eight years the obstetric and gynecology specialty has applied a system model of instructional planning to the continuum of medical education. The systems model of needs identification, preassessment, instructional objectives, instructional materials, learning experiences; and evaluation techniques directly related to objectives was…

Issues and Methods for Standard-Setting.

ERIC Educational Resources Information Center

Hambleton, Ronald K.; And Others

Issues involved in standard setting along with methods for standard setting are reviewed, with specific reference to their relevance for criterion referenced testing. Definitions are given of continuum and state models, and traditional and normative standard setting procedures. Since continuum models are considered more appropriate for criterion…

Quantum mechanical/molecular mechanical/continuum style solvation model: linear response theory, variational treatment, and nuclear gradients.

PubMed

Li, Hui

2009-11-14

Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S(0)-->S(1) excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.

Experimental verification of a progressive damage model for composite laminates based on continuum damage mechanics. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Coats, Timothy William

1994-01-01

Progressive failure is a crucial concern when using laminated composites in structural design. Therefore the ability to model damage and predict the life of laminated composites is vital. The purpose of this research was to experimentally verify the application of the continuum damage model, a progressive failure theory utilizing continuum damage mechanics, to a toughened material system. Damage due to tension-tension fatigue was documented for the IM7/5260 composite laminates. Crack density and delamination surface area were used to calculate matrix cracking and delamination internal state variables, respectively, to predict stiffness loss. A damage dependent finite element code qualitatively predicted trends in transverse matrix cracking, axial splits and local stress-strain distributions for notched quasi-isotropic laminates. The predictions were similar to the experimental data and it was concluded that the continuum damage model provided a good prediction of stiffness loss while qualitatively predicting damage growth in notched laminates.

Self-consistent continuum solvation for optical absorption of complex molecular systems in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Timrov, Iurii; Biancardi, Alessandro; Andreussi, Oliviero

2015-01-21

We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem andmore » a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the QUANTUM ESPRESSO distribution of open-source codes.« less

Continuum Mean-Field Theories for Molecular Fluids, and Their Validity at the Nanoscale

NASA Astrophysics Data System (ADS)

Hanna, C. B.; Peyronel, F.; MacDougall, C.; Marangoni, A.; Pink, D. A.; AFMNet-NCE Collaboration

2011-03-01

We present a calculation of the physical properties of solid triglyceride particles dispersed in an oil phase, using atomic- scale molecular dynamics. Significant equilibrium density oscillations in the oil appear when the interparticle distance, d , becomes sufficiently small, with a global minimum in the free energy found at d ~ 1.4 nm. We compare the simulation values of the Hamaker coefficient with those of models which assume that the oil is a homogeneous continuum: (i) Lifshitz theory, (ii) the Fractal Model, and (iii) a Lennard-Jones 6-12 potential model. The last-named yields a minimum in the free energy at d ~ 0.26 nm. We conclude that, at the nanoscale, continuum Lifshitz theory and other continuum mean-field theories based on the assumption of homogeneous fluid density can lead to erroneous conclusions. CBH supported by NSF DMR-0906618. DAP supported by NSERC. This work supported by AFMNet-NCE.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Onić, D.; Urošević, D.; Leahy, D., E-mail: donic@matf.bg.ac.rs

Recent observations of the microwave sky, by space telescopes such as the Wilkinson Microwave Anisotropy Probe and Planck , have opened a new window into the analysis of continuum emission from supernova remnants (SNRs). In this paper, different emission models that can explain the characteristic shape of currently known integrated radio/microwave continuum spectrum of the Galactic SNR IC 443 are tested and discussed. In particular, the possibility is emphasized that the slight bump in the integrated continuum of this remnant around 20–70 GHz is genuine and that it can be explained by the contribution of an additional emission mechanism suchmore » as spinning dust. We find that adding a spinning dust component to the emission model improves the fit of the integrated spectrum of this SNR while at the same time preserving the physically probable parameter values. Finally, models that include the high-frequency synchrotron bending of the IC 443 radio to microwave continuum are favored.« less

A Commodity Computing Cluster

NASA Astrophysics Data System (ADS)

Teuben, P. J.; Wolfire, M. G.; Pound, M. W.; Mundy, L. G.

We have assembled a cluster of Intel-Pentium based PCs running Linux to compute a large set of Photodissociation Region (PDR) and Dust Continuum models. For various reasons the cluster is heterogeneous, currently ranging from a single Pentium-II 333 MHz to dual Pentium-III 450 MHz CPU machines. Although this will be sufficient for our ``embarrassingly parallelizable problem'' it may present some challenges for as yet unplanned future use. In addition the cluster was used to construct a MIRIAD benchmark, and compared to equivalent Ultra-Sparc based workstations. Currently the cluster consists of 8 machines, 14 CPUs, 50GB of disk-space, and a total peak speed of 5.83 GHz, or about 1.5 Gflops. The total cost of this cluster has been about $12,000, including all cabling, networking equipment, rack, and a CD-R backup system. The URL for this project is http://dustem.astro.umd.edu.

An upscaled two-equation model of transport in porous media through unsteady-state closure of volume averaged formulations

NASA Astrophysics Data System (ADS)

Chaynikov, S.; Porta, G.; Riva, M.; Guadagnini, A.

2012-04-01

We focus on a theoretical analysis of nonreactive solute transport in porous media through the volume averaging technique. Darcy-scale transport models based on continuum formulations typically include large scale dispersive processes which are embedded in a pore-scale advection diffusion equation through a Fickian analogy. This formulation has been extensively questioned in the literature due to its inability to depict observed solute breakthrough curves in diverse settings, ranging from the laboratory to the field scales. The heterogeneity of the pore-scale velocity field is one of the key sources of uncertainties giving rise to anomalous (non-Fickian) dispersion in macro-scale porous systems. Some of the models which are employed to interpret observed non-Fickian solute behavior make use of a continuum formulation of the porous system which assumes a two-region description and includes a bimodal velocity distribution. A first class of these models comprises the so-called ''mobile-immobile'' conceptualization, where convective and dispersive transport mechanisms are considered to dominate within a high velocity region (mobile zone), while convective effects are neglected in a low velocity region (immobile zone). The mass exchange between these two regions is assumed to be controlled by a diffusive process and is macroscopically described by a first-order kinetic. An extension of these ideas is the two equation ''mobile-mobile'' model, where both transport mechanisms are taken into account in each region and a first-order mass exchange between regions is employed. Here, we provide an analytical derivation of two region "mobile-mobile" meso-scale models through a rigorous upscaling of the pore-scale advection diffusion equation. Among the available upscaling methodologies, we employ the Volume Averaging technique. In this approach, the heterogeneous porous medium is supposed to be pseudo-periodic, and can be represented through a (spatially) periodic unit cell. Consistently with the two-region model working hypotheses, we subdivide the pore space into two volumes, which we select according to the features of the local micro-scale velocity field. Assuming separation of the scales, the mathematical development associated with the averaging method in the two volumes leads to a generalized two-equation model. The final (upscaled) formulation includes the standard first order mass exchange term together with additional terms, which we discuss. Our developments allow to identify the assumptions which are usually implicitly embedded in the usual adoption of a two region mobile-mobile model. All macro-scale properties introduced in this model can be determined explicitly from the pore-scale geometry and hydrodynamics through the solution of a set of closure equations. We pursue here an unsteady closure of the problem, leading to the occurrence of nonlocal (in time) terms in the upscaled system of equations. We provide the solution of the closure problems for a simple application documenting the time dependent and the asymptotic behavior of the system.

A continuum-based structural modeling approach for cellulose nanocrystals (CNCs)

Treesearch

Mehdi Shishehbor; Fernando L. Dri; Robert J. Moon; Pablo D. Zavattieri

2018-01-01

We present a continuum-based structural model to study the mechanical behavior of cel- lulose nanocrystals (CNCs), and analyze the effect of bonded and non-bonded interactions on the mechanical properties under various loading conditions. In particular, this model assumes the uncoupling between the bonded and non-bonded interactions and their be- havior is obtained...

Peridynamics with LAMMPS : a user guide.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehoucq, Richard B.; Silling, Stewart Andrew; Plimpton, Steven James

2008-01-01

Peridynamics is a nonlocal formulation of continuum mechanics. The discrete peridynamic model has the same computational structure as a molecular dynamic model. This document details the implementation of a discrete peridynamic model within the LAMMPS molecular dynamic code. This document provides a brief overview of the peridynamic model of a continuum, then discusses how the peridynamic model is discretized, and overviews the LAMMPS implementation. A nontrivial example problem is also included.

Applications of discrete element method in modeling of grain postharvest operations

USDA-ARS?s Scientific Manuscript database

Grain kernels are finite and discrete materials. Although flowing grain can behave like a continuum fluid at times, the discontinuous behavior exhibited by grain kernels cannot be simulated solely with conventional continuum-based computer modeling such as finite-element or finite-difference methods...

The morphological heterogeneity of cricket flow-sensing hairs conveys the complex flow signature of predator attacks.

PubMed

Steinmann, Thomas; Casas, Jérôme

2017-06-01

Arthropod flow-sensing hair length ranges over more than an order of magnitude, from 0.1 to 5 mm. Previous studies repeatedly identified the longest hairs as the most sensitive, but recent studies identified the shortest hairs as the most responsive. We resolved this apparent conflict by proposing a new model, taking into account both the initial and long-term aspects of the flow pattern produced by a lunging predator. After the estimation of the mechanical parameters of hairs, we measured the flow produced by predator mimics and compared the predicted and observed values of hair displacements in this flow. Short and long hairs respond over different time scales during the course of an attack. By harbouring a canopy of hairs of different lengths, forming a continuum, the insect can fractionize these moments. Short hairs are more agile, but are less able to harvest energy from the air. This may result in longer hairs firing their neurons earlier, despite their slower deflection. The complex interplay between hair agility and sensitivity is also modulated by the predator distance and the attack speed, characteristics defining flow properties. We conclude that the morphological heterogeneity of the hair canopy mirrors the flow complexity of an entire attack, from launch to grasp. © 2017 The Author(s).

Geometric effects in microfluidics on heterogeneous cell stress using an Eulerian-Lagrangian approach.

PubMed

Warren, K M; Mpagazehe, J N; LeDuc, P R; Higgs, C F

2016-02-07

The response of individual cells at the micro-scale in cell mechanics is important in understanding how they are affected by changing environments. To control cell stresses, microfluidics can be implemented since there is tremendous control over the geometry of the devices. Designing microfluidic devices to induce and manipulate stress levels on biological cells can be aided by computational modeling approaches. Such approaches serve as an efficient precursor to fabricating various microfluidic geometries that induce predictable levels of stress on biological cells, based on their mechanical properties. Here, a three-dimensional, multiphase computational fluid dynamics (CFD) modeling approach was implemented for soft biological materials. The computational model incorporates the physics of the particle dynamics, fluid dynamics and solid mechanics, which allows us to study how stresses affect the cells. By using an Eulerian-Lagrangian approach to treat the fluid domain as a continuum in the microfluidics, we are conducting studies of the cells' movement and the stresses applied to the cell. As a result of our studies, we were able to determine that a channel with periodically alternating columns of obstacles was capable of stressing cells at the highest rate, and that microfluidic systems can be engineered to impose heterogenous cell stresses through geometric configuring. We found that when using controlled geometries of the microfluidics channels with staggered obstructions, we could increase the maximum cell stress by nearly 200 times over cells flowing through microfluidic channels with no obstructions. Incorporating computational modeling in the design of microfluidic configurations for controllable cell stressing could help in the design of microfludic devices for stressing cells such as cell homogenizers.

Investigation of Coupled model of Pore network and Continuum in shale gas

NASA Astrophysics Data System (ADS)

Cao, G.; Lin, M.

2016-12-01

Flow in shale spanning over many scales, makes the majority of conventional treatment methods disabled. For effectively simulating, a coupled model of pore-scale and continuum-scale was proposed in this paper. Based on the SEM image, we decompose organic-rich-shale into two subdomains: kerogen and inorganic matrix. In kerogen, the nanoscale pore-network is the main storage space and migration pathway so that the molecular phenomena (slip and diffusive transport) is significant. Whereas, inorganic matrix, with relatively large pores and micro fractures, the flow is approximate to Darcy. We use pore-scale network models (PNM) to represent kerogen and continuum-scale models (FVM or FEM) to represent matrix. Finite element mortars are employed to couple pore- and continuum-scale models by enforcing continuity of pressures and fluxes at shared boundary interfaces. In our method, the process in the coupled model is described by pressure square equation, and uses Dirichlet boundary conditions. We discuss several problems: the optimal element number of mortar faces, two categories boundary faces of pore network, the difference between 2D and 3D models, and the difference between continuum models FVM and FEM in mortars. We conclude that: (1) too coarse mesh in mortars will decrease the accuracy, while too fine mesh will lead to an ill-condition even singular system, the optimal element number is depended on boundary pores and nodes number. (2) pore network models are adjacent to two different mortar faces (PNM to PNM, PNM to continuum model), incidental repeated mortar nodes must be deleted. (3) 3D models can be replaced by 2D models under certain condition. (4) FVM is more convenient than FEM, for its simplicity in assigning interface nodes pressure and calculating interface fluxes. This work is supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB10020302), the 973 Program (2014CB239004), the Key Instrument Developing Project of the CAS (ZDYZ2012-1-08-02), the National Natural Science Foundation of China (41574129).

Strain gradient drives shear banding in metallic glasses

NASA Astrophysics Data System (ADS)

Tian, Zhi-Li; Wang, Yun-Jiang; Chen, Yan; Dai, Lan-Hong

2017-09-01

Shear banding is a nucleation-controlled process in metallic glasses (MGs) involving multiple temporal-spatial scales, which hinders a concrete understanding of its structural origin down to the atomic scale. Here, inspired by the morphology of composite materials, we propose a different perspective of MGs as a hard particle-reinforced material based on atomic-scale structural heterogeneity. The local stable structures indicated by a high level of local fivefold symmetry (L5FS) act as hard "particles" which are embedded in the relatively soft matrix. We demonstrate this concept by performing atomistic simulations of shear banding in CuZr MG. A shear band is prone to form in a sample with a high degree of L5FS which is slowly quenched from the liquid. An atomic-scale analysis on strain and the structural evolution reveals that it is the strain gradient effect that has originated from structural heterogeneity that facilitates shear transformation zones (STZs) to mature shear bands. An artificial composite model with a high degree of strain gradient, generated by inserting hard MG strips into a soft MG matrix, demonstrates a great propensity for shear banding. It therefore confirms the critical role strain gradient plays in shear banding. The strain gradient effect on shear banding is further quantified with a continuum model and a mechanical instability analysis. These physical insights might highlight the strain gradient as the hidden driving force in transforming STZs into shear bands in MGs.

Fundamentals of continuum mechanics – classical approaches and new trends

NASA Astrophysics Data System (ADS)

Altenbach, H.

2018-04-01

Continuum mechanics is a branch of mechanics that deals with the analysis of the mechanical behavior of materials modeled as a continuous manifold. Continuum mechanics models begin mostly by introducing of three-dimensional Euclidean space. The points within this region are defined as material points with prescribed properties. Each material point is characterized by a position vector which is continuous in time. Thus, the body changes in a way which is realistic, globally invertible at all times and orientation-preserving, so that the body cannot intersect itself and as transformations which produce mirror reflections are not possible in nature. For the mathematical formulation of the model it is also assumed to be twice continuously differentiable, so that differential equations describing the motion may be formulated. Finally, the kinematical relations, the balance equations, the constitutive and evolution equations and the boundary and/or initial conditions should be defined. If the physical fields are non-smooth jump conditions must be taken into account. The basic equations of continuum mechanics are presented following a short introduction. Additionally, some examples of solid deformable continua will be discussed within the presentation. Finally, advanced models of continuum mechanics will be introduced. The paper is dedicated to Alexander Manzhirov’s 60th birthday.

Rupture Propagation for Stochastic Fault Models

NASA Astrophysics Data System (ADS)

Favreau, P.; Lavallee, D.; Archuleta, R.

2003-12-01

The inversion of strong motion data of large earhquakes give the spatial distribution of pre-stress on the ruptured faults and it can be partially reproduced by stochastic models, but a fundamental question remains: how rupture propagates, constrained by the presence of spatial heterogeneity? For this purpose we investigate how the underlying random variables, that control the pre-stress spatial variability, condition the propagation of the rupture. Two stochastic models of prestress distributions are considered, respectively based on Cauchy and Gaussian random variables. The parameters of the two stochastic models have values corresponding to the slip distribution of the 1979 Imperial Valley earthquake. We use a finite difference code to simulate the spontaneous propagation of shear rupture on a flat fault in a 3D continuum elastic body. The friction law is the slip dependent friction law. The simulations show that the propagation of the rupture front is more complex, incoherent or snake-like for a prestress distribution based on Cauchy random variables. This may be related to the presence of a higher number of asperities in this case. These simulations suggest that directivity is stronger in the Cauchy scenario, compared to the smoother rupture of the Gauss scenario.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leitherer, Claus; Lee, Janice C.; Hernandez, Svea

We report on the detection of Lyman continuum radiation in two nearby starburst galaxies. Tol 0440-381, Tol 1247-232, and Mrk 54 were observed with the Cosmic Origins Spectrograph on board the Hubble Space Telescope . The three galaxies have radial velocities of ∼13,000 km s{sup −1}, permitting a ∼35 Å window on the restframe Lyman continuum shortward of the Milky Way Lyman edge at 912 Å. The chosen instrument configuration using the G140L grating covers the spectral range from 912 to 2000 Å. We developed a dedicated background subtraction method to account for the temporal and spatial background variations ofmore » the detector, which is crucial at the low flux levels around 912 Å. This modified pipeline allowed us to significantly improve the statistical and systematic detector noise and will be made available to the community. We detect Lyman continuum in all three galaxies. However, we conservatively interpret the emission in Tol 0440-381 as an upper limit due to possible contamination by geocoronal Lyman series lines. We determined the current star formation properties from the far-ultraviolet continuum and spectral lines and used synthesis models to predict the Lyman continuum radiation emitted by the current population of hot stars. We discuss various model uncertainties such as, among others, atmospheres and evolution models. Lyman continuum escape fractions were derived from a comparison between the observed and predicted Lyman continuum fluxes. Tol 1247-232, Mrk 54, and Tol 0440-381 have absolute escape fractions of (4.5 ± 1.2)%, (2.5 ± 0.72)%, and <(7.1 ± 1.1)%, respectively.« less

Airborne spectrophotometry of SN 1987A from 1.7 to 12.6 microns - Time history of the dust continuum and line emission

NASA Technical Reports Server (NTRS)

Wooden, Diane H.; Rank, David M.; Bregman, Jesse D.; Witteborn, Fred C.; Tielens, A. G. G. M.; Cohen, Martin; Pinto, Philip A.; Axelrod, Timothy S.

1993-01-01

Spectrophotometric observations of SN 1987A from the Kuiper Airborne Observatory are presented for five epochs at 60, 260, 415, 615, and 775 days after the explosion. The low-resolution (lambda/Delta lambda = 50-100) spectra of SN 1987A are combined with data from other wavelengths to model the continuum, subtract the continuum from the spectra to determine line strengths and reveal molecular bands, separate the atomic continuum radiation from the dust continuum, and derive constraints on the grain temperatures and optical depths. A scenario for the evolution of SN 1987A and that of the ejecta from which it arises is obtained on the basis of the analysis of the continuum emission.

A comparison of the lattice discrete particle method to the finite-element method and the K&C material model for simulating the static and dynamic response of concrete.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Jovanca J.; Bishop, Joseph E.

2013-11-01

This report summarizes the work performed by the graduate student Jovanca Smith during a summer internship in the summer of 2012 with the aid of mentor Joe Bishop. The projects were a two-part endeavor that focused on the use of the numerical model called the Lattice Discrete Particle Model (LDPM). The LDPM is a discrete meso-scale model currently used at Northwestern University and the ERDC to model the heterogeneous quasi-brittle material, concrete. In the first part of the project, LDPM was compared to the Karagozian and Case Concrete Model (K&C) used in Presto, an explicit dynamics finite-element code, developed atmore » Sandia National Laboratories. In order to make this comparison, a series of quasi-static numerical experiments were performed, namely unconfined uniaxial compression tests on four varied cube specimen sizes, three-point bending notched experiments on three proportional specimen sizes, and six triaxial compression tests on a cylindrical specimen. The second part of this project focused on the application of LDPM to simulate projectile perforation on an ultra high performance concrete called CORTUF. This application illustrates the strengths of LDPM over traditional continuum models.« less

The Multiple Continuum Components in the White-Light Flare of 16 January 2009 on the dM4.5e Star YZ CMi

NASA Astrophysics Data System (ADS)

Kowalski, A. F.; Hawley, S. L.; Holtzman, J. A.; Wisniewski, J. P.; Hilton, E. J.

2012-03-01

The white light during M dwarf flares has long been known to exhibit the broadband shape of a T≈10 000 K blackbody, and the white light in solar-flares is thought to arise primarily from hydrogen recombination. Yet, a current lack of broad-wavelength coverage solar flare spectra in the optical/near-UV region prohibits a direct comparison of the continuum properties to determine if they are indeed so different. New spectroscopic observations of a secondary flare during the decay of a megaflare on the dM4.5e star YZ CMi have revealed multiple components in the white-light continuum of stellar flares, including both a blackbody-like spectrum and a hydrogen-recombination spectrum. One of the most surprising findings is that these two components are anti-correlated in their temporal evolution. We combine initial phenomenological modeling of the continuum components with spectra from radiative hydrodynamic models to show that continuum veiling causes the measured anti-correlation. This modeling allows us to use the components' inferred properties to predict how a similar spatially resolved, multiple-component, white-light continuum might appear using analogies to several solar-flare phenomena. We also compare the properties of the optical stellar flare white light to Ellerman bombs on the Sun.

Determining spatially discretized surface flow and baseflow in the context of climate change and water quality management

NASA Astrophysics Data System (ADS)

Raimonet, M.; Oudin, L.; Rabouille, C.; Garnier, J.; Silvestre, M.; Vautard, R.; Thieu, V.

2016-12-01

Water quality management of fresh and marine aquatic systems requires modelling tools along the land-ocean continuum in order to evaluate the effect of climate change on nutrient transfer and on potential ecosystem dysfonctioning (e.g. eutrophication, anoxia). In addition to direct effects of climate change on water temperature, it is essential to consider indirect effects of precipitation and temperature changes on hydrology since nutrient transfers are particularly sensitive to the partition of streamflow between surface flow and baseflow. Yet, the determination of surface flow and baseflow, their spatial repartition on drainage basins, and their relative potential evolution under climate change remains challenging. In this study, we developed a generic approach to determine 10-day surface flow and baseflow using a regionalized hydrological model applied at a high spatial resolution (unitary catchments of area circa 10km²). Streamflow data at gauged basins were used to calibrate hydrological model parameters that were then applied on neighbor ungauged basins to estimate streamflow at the scale of the French territory. The proposed methodology allowed representing spatialized surface flow and baseflow that are consistent with climatic and geomorphological settings. The methodology was then used to determine the effect of climate change on the spatial repartition of surface flow and baseflow on the Seine drainage bassin. Results showed large discrepancies of both the amount and the spatial repartition of changes of surface flow and baseflow according to the several GCM and RCM used to derive projected climatic forcing. Consequently, it is expected that the impact of climate change on nutrient transfer might also be quite heterogeneous for the Seine River. This methodology could be applied in any drainage basin where at least several gauged hydrometric stations are available. The estimated surface flow and baseflow can then be used in hydro-ecological models in order to evaluate direct and indirect impacts of climate change on nutrient transfers and potential ecosystem dysfunctioning along the land-ocean continuum.

Families with burn injury: application in the clinically relevant continuum model.

PubMed

Lehna, Carlee

2011-06-01

This article incorporates the findings from a predominantly qualitative, mixed-method study examining sibling survivors' experiences of a major childhood burn injury into the clinically relevant continuum model as a means of promoting culturally competent and family-centered care. Copyright © 2011 Elsevier Inc. All rights reserved.

Evolution of plastic anisotropy for high-strain-rate computations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schiferl, S.K.; Maudlin, P.J.

1994-12-01

A model for anisotropic material strength, and for changes in the anisotropy due to plastic strain, is described. This model has been developed for use in high-rate, explicit, Lagrangian multidimensional continuum-mechanics codes. The model handles anisotropies in single-phase materials, in particular the anisotropies due to crystallographic texture--preferred orientations of the single-crystal grains. Textural anisotropies, and the changes in these anisotropies, depend overwhelmingly no the crystal structure of the material and on the deformation history. The changes, particularly for a complex deformations, are not amenable to simple analytical forms. To handle this problem, the material model described here includes a texturemore » code, or micromechanical calculation, coupled to a continuum code. The texture code updates grain orientations as a function of tensor plastic strain, and calculates the yield strength in different directions. A yield function is fitted to these yield points. For each computational cell in the continuum simulation, the texture code tracks a particular set of grain orientations. The orientations will change due to the tensor strain history, and the yield function will change accordingly. Hence, the continuum code supplies a tensor strain to the texture code, and the texture code supplies an updated yield function to the continuum code. Since significant texture changes require relatively large strains--typically, a few percent or more--the texture code is not called very often, and the increase in computer time is not excessive. The model was implemented, using a finite-element continuum code and a texture code specialized for hexagonal-close-packed crystal structures. The results for several uniaxial stress problems and an explosive-forming problem are shown.« less

Continuum and three-nucleon force effects on Be 9 energy levels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langhammer, Joachim; Navrátil, Petr; Quaglioni, Sofia

2015-02-05

In this paper, we extend the recently proposed ab initio no-core shell model with continuum to include three-nucleon (3N) interactions beyond the few-body domain. The extended approach allows for the assessment of effects of continuum degrees of freedom as well as of the 3N force in ab initio calculations of structure and reaction observables of p- and lower-sd-shell nuclei. As a first application we concentrate on energy levels of the 9Be system for which all excited states lie above the n- 8Be threshold. For all energy levels, the inclusion of the continuum significantly improves the agreement with experiment, which wasmore » an issue in standard no-core shell model calculations. Furthermore, we find the proper treatment of the continuum indispensable for reliable statements about the quality of the adopted 3N interaction from chiral effective field theory. Finally, in particular, we find the 1/2 + resonance energy, which is of astrophysical interest, in good agreement with experiment.« less

Comparing Multidimensional and Continuum Models of Vocabulary Acquisition: An Empirical Examination of the Vocabulary Knowledge Scale

ERIC Educational Resources Information Center

Stewart, Jeffrey; Batty, Aaron Olaf; Bovee, Nicholas

2012-01-01

Second language vocabulary acquisition has been modeled both as multidimensional in nature and as a continuum wherein the learner's knowledge of a word develops along a cline from recognition through production. In order to empirically examine and compare these models, the authors assess the degree to which the Vocabulary Knowledge Scale (VKS;…

The 'Baldwin Effect' in Wolf-Rayet stars

NASA Technical Reports Server (NTRS)

Morris, Patrick; Conti, Peter S.; Lamers, Henny J. G. L. M.; Koenigsberger, Gloria

1993-01-01

The equivalent widths of a number of emission lines in the spectra of WN-type Wolf-Rayet stars are found to inversely correlate with the luminosity of the underlying continuum. This is the well-known Baldwin Effect that has previously been observed in quasars and some Seyfert I galaxies. The Effect can be inferred from line and continuum predictions in published non-LTE model helium atmospheres and is explainable in terms of differences in wind density among WN stars. Using a simple wind model, we show that the Effect arises from the fact that both the effective radius for the local continuum and the emission measure of the layers above the continuum-forming region depend on the density in the wind. The Effect provides a new method for distance determinations of W-R stars.

Continuum simulation of the discharge of the granular silo: a validation test for the μ(I) visco-plastic flow law.

PubMed

Staron, L; Lagrée, P-Y; Popinet, S

2014-01-01

Using a continuum Navier-Stokes solver with the μ(I) flow law implemented to model the viscous behavior, and the discrete Contact Dynamics algorithm, the discharge of granular silos is simulated in two dimensions from the early stages of the discharge until complete release of the material. In both cases, the Beverloo scaling is recovered. We first do not attempt a quantitative comparison, but focus on the qualitative behavior of velocity and pressure at different locations in the flow. A good agreement for the velocity is obtained in the regions of rapid flows, while areas of slow creep are not entirely captured by the continuum model. The pressure field shows a general good agreement, while bulk deformations are found to be similar in both approaches. The influence of the parameters of the μ(I) flow law is systematically investigated, showing the importance of the dependence on the inertial number I to achieve quantitative agreement between continuum and discrete discharge. However, potential problems involving the systems size, the configuration and "non-local" effects, are suggested. Yet the general ability of the continuum model to reproduce qualitatively the granular behavior is found to be very encouraging.

Cancer stem cell-driven efficacy of trastuzumab (Herceptin): towards a reclassification of clinically HER2-positive breast carcinomas

PubMed Central

Martin-Castillo, Begoña; Lopez-Bonet, Eugeni; Cuyàs, Elisabet; Viñas, Gemma; Pernas, Sonia; Dorca, Joan; Menendez, Javier A.

2015-01-01

Clinically HER2+ (cHER2+) breast cancer (BC) can no longer be considered a single BC disease entity in terms of trastuzumab responsiveness. Here we propose a framework for predicting the response of cHER2+ to trastuzumab that integrates the molecular distinctions of intrinsic BC subtypes with recent knowledge on cancer stem cell (CSC) biology. First, we consider that two interchangeable populations of epithelial-like, aldehyde dehydrogenase (ALDH)-expressing and mesenchymal-like, CD44+CD24−/low CSCs can be found in significantly different proportions across all intrinsic BC subtypes. Second, we overlap all the intrinsic subtypes across cHER2+ BC to obtain a continuum of mixed phenotypes in which one extreme exhibits a high identity with ALDH+ CSCs and the other extreme exhibits a high preponderance of CD44+CD24−/low CSCs. The differential enrichment of trastuzumab-responsive ALDH+ CSCs versus trastuzumab-refractory CD44+CD24−/low CSCs can explain both the clinical behavior and the primary efficacy of trastuzumab in each molecular subtype of cHER2+ (i.e., HER2-enriched/cHER2+, luminal A/cHER2+, luminal B/cHER2+, basal/cHER2+, and claudin-low/cHER2+). The intrinsic plasticity determining the epigenetic ability of cHER2+ tumors to switch between epithelial and mesenchymal CSC states will vary across the continuum of mixed phenotypes, thus dictating their intratumoral heterogeneity and, hence, their evolutionary response to trastuzumab. Because CD44+CD24−/low mesenchymal-like CSCs distinctively possess a highly endocytic activity, the otherwise irrelevant HER2 can open the door to a type of “Trojan horse” approach by employing antibody-drug conjugates such as T-DM1, which will allow a rapid and CSC-targeted delivery of cytotoxic drugs to therapeutically manage trastuzumab-unresponsive basal/cHER2+ BC. Contrary to the current dichotomous model used clinically, our model proposes that a reclassification of cHER2+ tumors based on the spectrum of molecular BC subtypes might inform on their CSC-determined sensitivity to trastuzumab, thus providing a better delineation of the predictive value of cHER2+ in BC by incorporating CSCs-driven intra-tumor heterogeneity into clinical decisions. PMID:26474458

Assessment of current state of the art in modeling techniques and analysis methods for large space structures

NASA Technical Reports Server (NTRS)

Noor, A. K.

1983-01-01

Advances in continuum modeling, progress in reduction methods, and analysis and modeling needs for large space structures are covered with specific attention given to repetitive lattice trusses. As far as continuum modeling is concerned, an effective and verified analysis capability exists for linear thermoelastic stress, birfurcation buckling, and free vibration problems of repetitive lattices. However, application of continuum modeling to nonlinear analysis needs more development. Reduction methods are very effective for bifurcation buckling and static (steady-state) nonlinear analysis. However, more work is needed to realize their full potential for nonlinear dynamic and time-dependent problems. As far as analysis and modeling needs are concerned, three areas are identified: loads determination, modeling and nonclassical behavior characteristics, and computational algorithms. The impact of new advances in computer hardware, software, integrated analysis, CAD/CAM stems, and materials technology is also discussed.

Time dependent reliability model incorporating continuum damage mechanics for high-temperature ceramics

NASA Technical Reports Server (NTRS)

Duffy, Stephen F.; Gyekenyesi, John P.

1989-01-01

Presently there are many opportunities for the application of ceramic materials at elevated temperatures. In the near future ceramic materials are expected to supplant high temperature metal alloys in a number of applications. It thus becomes essential to develop a capability to predict the time-dependent response of these materials. The creep rupture phenomenon is discussed, and a time-dependent reliability model is outlined that integrates continuum damage mechanics principles and Weibull analysis. Several features of the model are presented in a qualitative fashion, including predictions of both reliability and hazard rate. In addition, a comparison of the continuum and the microstructural kinetic equations highlights a strong resemblance in the two approaches.

A nonmonotonic dependence of standard rate constant on reorganization energy for heterogeneous electron transfer processes on electrode surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu Weilin; Li Songtao; Zhou Xiaochun

2006-05-07

In the present work a nonmonotonic dependence of standard rate constant (k{sup 0}) on reorganization energy ({lambda}) was discovered qualitatively from electron transfer (Marcus-Hush-Levich) theory for heterogeneous electron transfer processes on electrode surface. It was found that the nonmonotonic dependence of k{sup 0} on {lambda} is another result, besides the disappearance of the famous Marcus inverted region, coming from the continuum of electronic states in electrode: with the increase of {lambda}, the states for both Process I and Process II ET processes all vary from nonadiabatic to adiabatic state continuously, and the {lambda} dependence of k{sup 0} for Process Imore » is monotonic thoroughly, while for Process II on electrode surface the {lambda} dependence of k{sup 0} could show a nonmonotonicity.« less

Nonlinear waves in solids with slow dynamics: an internal-variable model

PubMed Central

Berjamin, H.; Favrie, N.; Chiavassa, G.

2017-01-01

In heterogeneous solids such as rocks and concrete, the speed of sound diminishes with the strain amplitude of a dynamic loading (softening). This decrease, known as ‘slow dynamics’, occurs at time scales larger than the period of the forcing. Also, hysteresis is observed in the steady-state response. The phenomenological model by Vakhnenko et al. (2004 Phys. Rev. E 70, 015602. (doi:10.1103/PhysRevE.70.015602)) is based on a variable that describes the softening of the material. However, this model is one dimensional and it is not thermodynamically admissible. In the present article, a three-dimensional model is derived in the framework of the finite-strain theory. An internal variable that describes the softening of the material is introduced, as well as an expression of the specific internal energy. A mechanical constitutive law is deduced from the Clausius–Duhem inequality. Moreover, a family of evolution equations for the internal variable is proposed. Here, an evolution equation with one relaxation time is chosen. By construction, this new model of the continuum is thermodynamically admissible and dissipative (inelastic). In the case of small uniaxial deformations, it is shown analytically that the model reproduces qualitatively the main features of real experiments. PMID:28588408

Breakdown and Limit of Continuum Diffusion Velocity for Binary Gas Mixtures from Direct Simulation

NASA Astrophysics Data System (ADS)

Martin, Robert Scott; Najmabadi, Farrokh

2011-05-01

This work investigates the breakdown of the continuum relations for diffusion velocity in inert binary gas mixtures. Values of the relative diffusion velocities for components of a gas mixture may be calculated using of Chapman-Enskog theory and occur not only due to concentration gradients, but also pressure and temperature gradients in the flow as described by Hirschfelder. Because Chapman-Enskog theory employs a linear perturbation around equilibrium, it is expected to break down when the velocity distribution deviates significantly from equilibrium. This breakdown of the overall flow has long been an area of interest in rarefied gas dynamics. By comparing the continuum values to results from Bird's DS2V Monte Carlo code, we propose a new limit on the continuum approach specific to binary gases. To remove the confounding influence of an inconsistent molecular model, we also present the application of the variable hard sphere (VSS) model used in DS2V to the continuum diffusion velocity calculation. Fitting sample asymptotic curves to the breakdown, a limit, Vmax, that is a fraction of an analytically derived limit resulting from the kinetic temperature of the mixture is proposed. With an expected deviation of only 2% between the physical values and continuum calculations within ±Vmax/4, we suggest this as a conservative estimate on the range of applicability for the continuum theory.

Turbulent and Laminar Flow in Karst Conduits Under Unsteady Flow Conditions: Interpretation of Pumping Tests by Discrete Conduit-Continuum Modeling

NASA Astrophysics Data System (ADS)

Giese, M.; Reimann, T.; Bailly-Comte, V.; Maréchal, J.-C.; Sauter, M.; Geyer, T.

2018-03-01

Due to the duality in terms of (1) the groundwater flow field and (2) the discharge conditions, flow patterns of karst aquifer systems are complex. Estimated aquifer parameters may differ by several orders of magnitude from local (borehole) to regional (catchment) scale because of the large contrast in hydraulic parameters between matrix and conduit, their heterogeneity and anisotropy. One approach to deal with the scale effect problem in the estimation of hydraulic parameters of karst aquifers is the application of large-scale experiments such as long-term high-abstraction conduit pumping tests, stimulating measurable groundwater drawdown in both, the karst conduit system as well as the fractured matrix. The numerical discrete conduit-continuum modeling approach MODFLOW-2005 Conduit Flow Process Mode 1 (CFPM1) is employed to simulate laminar and nonlaminar conduit flow, induced by large-scale experiments, in combination with Darcian matrix flow. Effects of large-scale experiments were simulated for idealized settings. Subsequently, diagnostic plots and analyses of different fluxes are applied to interpret differences in the simulated conduit drawdown and general flow patterns. The main focus is set on the question to which extent different conduit flow regimes will affect the drawdown in conduit and matrix depending on the hydraulic properties of the conduit system, i.e., conduit diameter and relative roughness. In this context, CFPM1 is applied to investigate the importance of considering turbulent conditions for the simulation of karst conduit flow. This work quantifies the relative error that results from assuming laminar conduit flow for the interpretation of a synthetic large-scale pumping test in karst.

An Optimization-based Atomistic-to-Continuum Coupling Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olson, Derek; Bochev, Pavel B.; Luskin, Mitchell

2014-08-21

In this paper, we present a new optimization-based method for atomistic-to-continuum (AtC) coupling. The main idea is to cast the latter as a constrained optimization problem with virtual Dirichlet controls on the interfaces between the atomistic and continuum subdomains. The optimization objective is to minimize the error between the atomistic and continuum solutions on the overlap between the two subdomains, while the atomistic and continuum force balance equations provide the constraints. Separation, rather then blending of the atomistic and continuum problems, and their subsequent use as constraints in the optimization problem distinguishes our approach from the existing AtC formulations. Finally,more » we present and analyze the method in the context of a one-dimensional chain of atoms modeled using a linearized two-body potential with next-nearest neighbor interactions.« less

Scoping review of potential quality indicators for hip fracture patient care

PubMed Central

Pitzul, Kristen B; Munce, Sarah E P; Perrier, Laure; Beaupre, Lauren; Morin, Suzanne N; McGlasson, Rhona; Jaglal, Susan B

2017-01-01

Objective The purpose of this study is to identify existing or potential quality of care indicators (ie, current indicators as well as process and outcome measures) in the acute or postacute period, or across the continuum of care for older adults with hip fracture. Design Scoping review. Setting All care settings. Search strategy English peer-reviewed studies published from January 2000 to January 2016 were included. Literature search strategies were developed, and the search was peer-reviewed. Two reviewers independently piloted all forms, and all articles were screened in duplicate. Results The search yielded 2729 unique articles, of which 302 articles were included (11.1%). When indicators (eg, in-hospital mortality, acute care length of stay) and potential indicators (eg, comorbidities developed in hospital, walking ability) were grouped by the outcome or process construct they were trying to measure, the most common constructs were measures of mortality (outcome), length of stay (process) and time-sensitive measures (process). There was heterogeneity in definitions within constructs between studies. There was also a paucity of indicators and potential indicators in the postacute period. Conclusions To improve quality of care for patients with hip fracture and create a more efficient healthcare system, mechanisms for the measurement of quality of care across the entire continuum, not just during the acute period, are required. Future research should focus on decreasing the heterogeneity in definitions of quality indicators and the development and implementation of quality indicators for the postacute period. PMID:28325859

Collocational Processing in Light of the Phraseological Continuum Model: Does Semantic Transparency Matter?

ERIC Educational Resources Information Center

Gyllstad, Henrik; Wolter, Brent

2016-01-01

The present study investigates whether two types of word combinations (free combinations and collocations) differ in terms of processing by testing Howarth's Continuum Model based on word combination typologies from a phraseological tradition. A visual semantic judgment task was administered to advanced Swedish learners of English (n = 27) and…

Comparing and Contrasting American and Japanese Cultural Values Using a Negotiation Continuum Model.

ERIC Educational Resources Information Center

Garrison, Jean A.

A negotiation continuum model can be used to compare and contrast American and Japanese cultural values. Although two basic styles of negotiating--competitive and cooperative--can be identified, there are a number of general principles that govern all negotiations. These include planning and preparing strategies in advance and practicing nonverbal…

A Continuum Model of Social/Sexual Curriculum and Programming Services.

ERIC Educational Resources Information Center

Heler, Ann, Ed.

This packet of materials from the Wayne County (Michigan) Intermediate School District offers a continuum model of social/sexual curriculum and programming services. Materials include: (1) a copy of a district school board policy giving school districts permission to pursue these curriculum areas; (2) staff guidelines for dealing with students…

The May Center for Early Childhood Education: Description of a Continuum of Services Model for Children with Autism.

ERIC Educational Resources Information Center

Campbell, Susan; Cannon, Barbara; Ellis, James T.; Lifter, Karen; Luiselli, James K.; Navalta, Carryl P.; Taras, Marie

1998-01-01

Describes a comprehensive continuum of services model for children with autism developed by a human services agency in Massachusetts, which incorporates these and additional empirically based approaches. Service components, methodologies, and program objectives are described, including representative summary data. Best practice approaches toward…

An experimental comparison between the continuum and single jump descriptions of nonactin-mediated potassium transport through black lipid membranes.

PubMed Central

van Dijk, C; de Levie, R

1985-01-01

The continuum and single jump treatments of ion transport through black lipid membranes predict experimentally distinguishable results, even when the same mechanistic assumptions are made and the same potential-distance profile is used. On the basis of steady-state current-voltage curves for nonactin-mediated transport of potassium ions, we find that the continuum model describes the data accurately, whereas the single jump model fails to do so, for all cases investigated in which capacitance measurements indicate that the membrane thickness varies little with applied potential. PMID:3839420

Multi-Length Scale-Enriched Continuum-Level Material Model for Kevlar-Fiber-Reinforced Polymer-Matrix Composites

DTIC Science & Technology

2012-08-03

is unlimited. Multi-Length Scale-Enriched Continuum-Level Material Model for Kevlar ®-Fiber-Reinforced Polymer-Matrix Composites The views, opinions...12211 Research Triangle Park, NC 27709-2211 ballistics, composites, Kevlar , material models, microstructural defects REPORT DOCUMENTATION PAGE 11... Kevlar ®-Fiber-Reinforced Polymer-Matrix Composites Report Title Fiber-reinforced polymer matrix composite materials display quite complex deformation

Habitat heterogeneity of hadal trenches: Considerations and implications for future studies

NASA Astrophysics Data System (ADS)

Stewart, Heather A.; Jamieson, Alan J.

2018-02-01

The hadal zone largely comprises a series of subduction trenches that do not form part of the continental shelf-slope rise to abyssal plain continuum. Instead they form geographically isolated clusters of deep-sea (6000-11,000 m water depth) environments. There is a growing realization in hadal science that ecological patterns and processes are not driven solely by responses to hydrostatic pressure, with comparable levels of habitat heterogeneity as observed in other marine biozones. Furthermore, this heterogeneity can be expressed at multiple scales from inter-trench levels (degrees of geographical isolation, and biochemical province), to intra-trench levels (variation between trench flanks and axis), topographical features within the trench interior (sedimentary basins, ridges, escarpments, 'deeps', seamounts) to the substrate of the trench floor (seabed-sediment composition, mass movement deposits, bedrock outcrop). Using best available bathymetry data combined with the largest lander-derived imaging dataset that spans the full depth range of three hadal trenches (including adjacent slopes); the Mariana, Kermadec and New Hebrides trenches, the topographic variability, fine-scale habitat heterogeneity and distribution of seabed sediments of these three trenches have been assessed for the first time. As well as serving as the first descriptive study of habitat heterogeneity at hadal depths, this study also provides guidance for future hadal sampling campaigns taking into account geographic isolation, total trench particulate organic matter flux, maximum water depth and area.

Multiscale Modeling of Structurally-Graded Materials Using Discrete Dislocation Plasticity Models and Continuum Crystal Plasticity Models

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.

Numerical investigation of non-perturbative kinetic effects of energetic particles on toroidicity-induced Alfvén eigenmodes in tokamaks and stellarators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slaby, Christoph; Könies, Axel; Kleiber, Ralf

2016-09-15

The resonant interaction of shear Alfvén waves with energetic particles is investigated numerically in tokamak and stellarator geometry using a non-perturbative MHD-kinetic hybrid approach. The focus lies on toroidicity-induced Alfvén eigenmodes (TAEs), which are most easily destabilized by a fast-particle population in fusion plasmas. While the background plasma is treated within the framework of an ideal-MHD theory, the drive of the fast particles, as well as Landau damping of the background plasma, is modelled using the drift-kinetic Vlasov equation without collisions. Building on analytical theory, a fast numerical tool, STAE-K, has been developed to solve the resulting eigenvalue problem usingmore » a Riccati shooting method. The code, which can be used for parameter scans, is applied to tokamaks and the stellarator Wendelstein 7-X. High energetic-ion pressure leads to large growth rates of the TAEs and to their conversion into kinetically modified TAEs and kinetic Alfvén waves via continuum interaction. To better understand the physics of this conversion mechanism, the connections between TAEs and the shear Alfvén wave continuum are examined. It is shown that, when energetic particles are present, the continuum deforms substantially and the TAE frequency can leave the continuum gap. The interaction of the TAE with the continuum leads to singularities in the eigenfunctions. To further advance the physical model and also to eliminate the MHD continuum together with the singularities in the eigenfunctions, a fourth-order term connected to radiative damping has been included. The radiative damping term is connected to non-ideal effects of the bulk plasma and introduces higher-order derivatives to the model. Thus, it has the potential to substantially change the nature of the solution. For the first time, the fast-particle drive, Landau damping, continuum damping, and radiative damping have been modelled together in tokamak- as well as in stellarator geometry.« less

The wetland continuum: a conceptual framework for interpreting biological studies

USGS Publications Warehouse

Euliss, N.H.; LaBaugh, J.W.; Fredrickson, L.H.; Mushet, D.M.; Swanson, G.A.; Winter, T.C.; Rosenberry, D.O.; Nelson, R.D.

2004-01-01

We describe a conceptual model, the wetland continuum, which allows wetland managers, scientists, and ecologists to consider simultaneously the influence of climate and hydrologic setting on wetland biological communities. Although multidimensional, the wetland continuum is most easily represented as a two-dimensional gradient, with ground water and atmospheric water constituting the horizontal and vertical axis, respectively. By locating the position of a wetland on both axes of the continuum, the potential biological expression of the wetland can be predicted at any point in time. The model provides a framework useful in the organization and interpretation of biological data from wetlands by incorporating the dynamic changes these systems undergo as a result of normal climatic variation rather than placing them into static categories common to many wetland classification systems. While we developed this model from the literature available for depressional wetlands in the prairie pothole region of North America, we believe the concept has application to wetlands in many other geographic locations.

Continuum Lowering and Fermi-Surface Rising in Strongly Coupled and Degenerate Plasmas

NASA Astrophysics Data System (ADS)

Hu, S. X.

2017-08-01

Continuum lowering is a well known and important physics concept that describes the ionization potential depression (IPD) in plasmas caused by thermal- or pressure-induced ionization of outer-shell electrons. The existing IPD models are often used to characterize plasma conditions and to gauge opacity calculations. Recent precision measurements have revealed deficits in our understanding of continuum lowering in dense hot plasmas. However, these investigations have so far been limited to IPD in strongly coupled but nondegenerate plasmas. Here, we report a first-principles study of the K -edge shifting in both strongly coupled and fully degenerate carbon plasmas, with quantum molecular dynamics calculations based on the all-electron density-functional theory. The resulting K -edge shifting versus plasma density, as a probe to the continuum lowering and the Fermi-surface rising, is found to be significantly different from predictions of existing IPD models. In contrast, a simple model of "single-atom-in-box," developed in this work, accurately predicts K -edge locations as ab initio calculations provide.

Shape dependence of two-cylinder Rényi entropies for free bosons on a lattice

NASA Astrophysics Data System (ADS)

Chojnacki, Leilee; Cook, Caleb Q.; Dalidovich, Denis; Hayward Sierens, Lauren E.; Lantagne-Hurtubise, Étienne; Melko, Roger G.; Vlaar, Tiffany J.

2016-10-01

Universal scaling terms occurring in Rényi entanglement entropies have the potential to bring new understanding to quantum critical points in free and interacting systems. Quantitative comparisons between analytical continuum theories and numerical calculations on lattice models play a crucial role in advancing such studies. In this paper, we exactly calculate the universal two-cylinder shape dependence of entanglement entropies for free bosons on finite-size square lattices, and compare to approximate functions derived in the continuum using several different Ansätze. Although none of these Ansätze are exact in the thermodynamic limit, we find that numerical fits are in good agreement with continuum functions derived using the anti-de Sitter/conformal field theory correspondence, an extensive mutual information model, and a quantum Lifshitz model. We use fits of our lattice data to these functions to calculate universal scalars defined in the thin-cylinder limit, and compare to values previously obtained for the free boson field theory in the continuum.

Kinetic Monte Carlo simulations of ion-induced ripple formation: Dependence on flux, temperature, and defect concentration in the linear regime

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chason, E.; Chan, W. L.; Bharathi, M. S.

Low-energy ion bombardment produces spontaneous periodic structures (sputter ripples) on many surfaces. Continuum theories describe the pattern formation in terms of ion-surface interactions and surface relaxation kinetics, but many features of these models (such as defect concentration) are unknown or difficult to determine. In this work, we present results of kinetic Monte Carlo simulations that model surface evolution using discrete atomistic versions of the physical processes included in the continuum theories. From simulations over a range of parameters, we obtain the dependence of the ripple growth rate, wavelength, and velocity on the ion flux and temperature. The results are discussedmore » in terms of the thermally dependent concentration and diffusivity of ion-induced surface defects. We find that in the early stages of ripple formation the simulation results are surprisingly well described by the predictions of the continuum theory, in spite of simplifying approximations used in the continuum model.« less

Mesoscopic and continuum modelling of angiogenesis

PubMed Central

Spill, F.; Guerrero, P.; Alarcon, T.; Maini, P. K.; Byrne, H. M.

2016-01-01

Angiogenesis is the formation of new blood vessels from pre-existing ones in response to chemical signals secreted by, for example, a wound or a tumour. In this paper, we propose a mesoscopic lattice-based model of angiogenesis, in which processes that include proliferation and cell movement are considered as stochastic events. By studying the dependence of the model on the lattice spacing and the number of cells involved, we are able to derive the deterministic continuum limit of our equations and compare it to similar existing models of angiogenesis. We further identify conditions under which the use of continuum models is justified, and others for which stochastic or discrete effects dominate. We also compare different stochastic models for the movement of endothelial tip cells which have the same macroscopic, deterministic behaviour, but lead to markedly different behaviour in terms of production of new vessel cells. PMID:24615007

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.

Conformational Modeling of Continuum Structures in Robotics and Structural Biology: A Review

PubMed Central

Chirikjian, G. S.

2016-01-01

Hyper-redundant (or snakelike) manipulators have many more degrees of freedom than are required to position and orient an object in space. They have been employed in a variety of applications ranging from search-and-rescue to minimally invasive surgical procedures, and recently they even have been proposed as solutions to problems in maintaining civil infrastructure and the repair of satellites. The kinematic and dynamic properties of snakelike robots are captured naturally using a continuum backbone curve equipped with a naturally evolving set of reference frames, stiffness properties, and mass density. When the snakelike robot has a continuum architecture, the backbone curve corresponds with the physical device itself. Interestingly, these same modeling ideas can be used to describe conformational shapes of DNA molecules and filamentous protein structures in solution and in cells. This paper reviews several classes of snakelike robots: (1) hyper-redundant manipulators guided by backbone curves; (2) flexible steerable needles; and (3) concentric tube continuum robots. It is then shown how the same mathematical modeling methods used in these robotics contexts can be used to model molecules such as DNA. All of these problems are treated in the context of a common mathematical framework based on the differential geometry of curves, continuum mechanics, and variational calculus. Both coordinate-dependent Euler-Lagrange formulations and coordinate-free Euler-Poincaré approaches are reviewed. PMID:27030786

Conformational Modeling of Continuum Structures in Robotics and Structural Biology: A Review.

PubMed

Chirikjian, G S

Hyper-redundant (or snakelike) manipulators have many more degrees of freedom than are required to position and orient an object in space. They have been employed in a variety of applications ranging from search-and-rescue to minimally invasive surgical procedures, and recently they even have been proposed as solutions to problems in maintaining civil infrastructure and the repair of satellites. The kinematic and dynamic properties of snakelike robots are captured naturally using a continuum backbone curve equipped with a naturally evolving set of reference frames, stiffness properties, and mass density. When the snakelike robot has a continuum architecture, the backbone curve corresponds with the physical device itself. Interestingly, these same modeling ideas can be used to describe conformational shapes of DNA molecules and filamentous protein structures in solution and in cells. This paper reviews several classes of snakelike robots: (1) hyper-redundant manipulators guided by backbone curves; (2) flexible steerable needles; and (3) concentric tube continuum robots. It is then shown how the same mathematical modeling methods used in these robotics contexts can be used to model molecules such as DNA. All of these problems are treated in the context of a common mathematical framework based on the differential geometry of curves, continuum mechanics, and variational calculus. Both coordinate-dependent Euler-Lagrange formulations and coordinate-free Euler-Poincaré approaches are reviewed.

Comparison of all atom, continuum, and linear fitting empirical models for charge screening effect of aqueous medium surrounding a protein molecule

NASA Astrophysics Data System (ADS)

Takahashi, Takuya; Sugiura, Junnnosuke; Nagayama, Kuniaki

2002-05-01

To investigate the role hydration plays in the electrostatic interactions of proteins, the time-averaged electrostatic potential of the B1 domain of protein G in an aqueous solution was calculated with full atomic molecular dynamics simulations that explicitly considers every atom (i.e., an all atom model). This all atom calculated potential was compared with the potential obtained from an electrostatic continuum model calculation. In both cases, the charge-screening effect was fairly well formulated with an effective relative dielectric constant which increased linearly with increasing charge-charge distance. This simulated linear dependence agrees with the experimentally determined linear relation proposed by Pickersgill. Cut-off approximations for Coulomb interactions failed to reproduce this linear relation. Correlation between the all atom model and the continuum models was found to be better than the respective correlation calculated for linear fitting to the two models. This confirms that the continuum model is better at treating the complicated shapes of protein conformations than the simple linear fitting empirical model. We have tried a sigmoid fitting empirical model in addition to the linear one. When weights of all data were treated equally, the sigmoid model, which requires two fitting parameters, fits results of both the all atom and the continuum models less accurately than the linear model which requires only one fitting parameter. When potential values are chosen as weighting factors, the fitting error of the sigmoid model became smaller, and the slope of both linear fitting curves became smaller. This suggests the screening effect of an aqueous medium within a short range, where potential values are relatively large, is smaller than that expected from the linear fitting curve whose slope is almost 4. To investigate the linear increase of the effective relative dielectric constant, the Poisson equation of a low-dielectric sphere in a high-dielectric medium was solved and charges distributed near the molecular surface were indicated as leading to the apparent linearity.

Multiscale Modeling of Intergranular Fracture in Aluminum: Constitutive Relation For Interface Debonding

NASA Technical Reports Server (NTRS)

Yamakov, V.; Saether, E.; Glaessgen, E. H.

2008-01-01

Intergranular fracture is a dominant mode of failure in ultrafine grained materials. In the present study, the atomistic mechanisms of grain-boundary debonding during intergranular fracture in aluminum are modeled using a coupled molecular dynamics finite element simulation. Using a statistical mechanics approach, a cohesive-zone law in the form of a traction-displacement constitutive relationship, characterizing the load transfer across the plane of a growing edge crack, is extracted from atomistic simulations and then recast in a form suitable for inclusion within a continuum finite element model. The cohesive-zone law derived by the presented technique is free of finite size effects and is statistically representative for describing the interfacial debonding of a grain boundary (GB) interface examined at atomic length scales. By incorporating the cohesive-zone law in cohesive-zone finite elements, the debonding of a GB interface can be simulated in a coupled continuum-atomistic model, in which a crack starts in the continuum environment, smoothly penetrates the continuum-atomistic interface, and continues its propagation in the atomistic environment. This study is a step towards relating atomistically derived decohesion laws to macroscopic predictions of fracture and constructing multiscale models for nanocrystalline and ultrafine grained materials.

A general multiscale framework for the emergent effective elastodynamics of metamaterials

NASA Astrophysics Data System (ADS)

Sridhar, A.; Kouznetsova, V. G.; Geers, M. G. D.

2018-02-01

This paper presents a general multiscale framework towards the computation of the emergent effective elastodynamics of heterogeneous materials, to be applied for the analysis of acoustic metamaterials and phononic crystals. The generality of the framework is exemplified by two key characteristics. First, the underlying formalism relies on the Floquet-Bloch theorem to derive a robust definition of scales and scale separation. Second, unlike most homogenization approaches that rely on a classical volume average, a generalized homogenization operator is defined with respect to a family of particular projection functions. This yields a generalized macro-scale continuum, instead of the classical Cauchy continuum. This enables (in a micromorphic sense) to homogenize the rich dispersive behavior resulting from both Bragg scattering and local resonance. For an arbitrary unit cell, the homogenization projection functions are constructed using the Floquet-Bloch eigenvectors obtained in the desired frequency regime at select high symmetry points, which effectively resolves the emergent phenomena dominating that regime. Furthermore, a generalized Hill-Mandel condition is proposed that ensures power consistency between the homogenized and full-scale model. A high-order spatio-temporal gradient expansion is used to localize the multiscale problem leading to a series of recursive unit cell problems giving the appropriate micro-mechanical corrections. The developed multiscale method is validated against standard numerical Bloch analysis of the dispersion spectra of example unit cells encompassing multiple high-order branches generated by local resonance and/or Bragg scattering.

Theoretical Calculation and Validation of the Water Vapor Continuum Absorption

NASA Technical Reports Server (NTRS)

Ma, Qiancheng; Tipping, Richard H.

1998-01-01

The primary objective of this investigation is the development of an improved parameterization of the water vapor continuum absorption through the refinement and validation of our existing theoretical formalism. The chief advantage of our approach is the self-consistent, first principles, basis of the formalism which allows us to predict the frequency, temperature and pressure dependence of the continuum absorption as well as provide insights into the physical mechanisms responsible for the continuum absorption. Moreover, our approach is such that the calculated continuum absorption can be easily incorporated into satellite retrieval algorithms and climate models. Accurate determination of the water vapor continuum is essential for the next generation of retrieval algorithms which propose to use the combined constraints of multispectral measurements such as those under development for EOS data analysis (e.g., retrieval algorithms based on MODIS and AIRS measurements); current Pathfinder activities which seek to use the combined constraints of infrared and microwave (e.g., HIRS and MSU) measurements to improve temperature and water profile retrievals, and field campaigns which seek to reconcile spectrally-resolved and broad-band measurements such as those obtained as part of FIRE. Current widely used continuum treatments have been shown to produce spectrally dependent errors, with the magnitude of the error dependent on temperature and abundance which produces errors with a seasonal and latitude dependence. Translated into flux, current water vapor continuum parameterizations produce flux errors of order 10 W/sq m, which compared to the 4 W/sq m magnitude of the greenhouse gas forcing and the 1-2 W/sq m estimated aerosol forcing is certainly climatologically significant and unacceptably large. While it is possible to tune the empirical formalisms, the paucity of laboratory measurements, especially at temperatures of interest for atmospheric applications, preclude tuning, the empirical continuum models over the full spectral range of interest for remote sensing and climate applications. Thus, we propose to further develop and refine our existing, far-wing formalism to provide an improved treatment applicable from the near-infrared through the microwave. Based on the results of this investigation, we will provide to the remote sensing/climate modeling community a practical and accurate tabulation of the continuum absorption covering the near-infrared through the microwave region of the spectrum for the range of temperatures and pressures of interest for atmospheric applications.

Theoretical Calculation and Validation of the Water Vapor Continuum Absorption

NASA Technical Reports Server (NTRS)

Ma, Qiancheng; Tipping, Richard H.

1998-01-01

The primary objective of this investigation is the development of an improved parameterization of the water vapor continuum absorption through the refinement and validation of our existing theoretical formalism. The chief advantage of our approach is the self-consistent, first principles, basis of the formalism which allows us to predict the frequency, temperature and pressure dependence of the continuum absorption as well as provide insights into the physical mechanisms responsible for the continuum absorption. Moreover, our approach is such that the calculated continuum absorption can be easily incorporated into satellite retrieval algorithms and climate models. Accurate determination of the water vapor continuum is essential for the next generation of retrieval algorithms which propose to use the combined constraints of multi-spectral measurements such as those under development for EOS data analysis (e.g., retrieval algorithms based on MODIS and AIRS measurements); current Pathfinder activities which seek to use the combined constraints of infrared and microwave (e.g., HIRS and MSU) measurements to improve temperature and water profile retrievals, and field campaigns which seek to reconcile spectrally-resolved and broad-band measurements such as those obtained as part of FIRE. Current widely used continuum treatments have been shown to produce spectrally dependent errors, with the magnitude of the error dependent on temperature and abundance which produces errors with a seasonal and latitude dependence. Translated into flux, current water vapor continuum parameterizations produce flux errors of order 10 W/ml, which compared to the 4 W/m' magnitude of the greenhouse gas forcing and the 1-2 W/m' estimated aerosol forcing is certainly climatologically significant and unacceptably large. While it is possible to tune the empirical formalisms, the paucity of laboratory measurements, especially at temperatures of interest for atmospheric applications, preclude tuning the empirical continuum models over the full spectral range of interest for remote sensing and climate applications. Thus, we propose to further develop and refine our existing far-wing formalism to provide an improved treatment applicable from the near-infrared through the microwave. Based on the results of this investigation, we will provide to the remote sensing/climate modeling community a practical and accurate tabulation of the continuum absorption covering the near-infrared through the microwave region of the spectrum for the range of temperatures and pressures of interest for atmospheric applications.

Predicting electromyographic signals under realistic conditions using a multiscale chemo-electro-mechanical finite element model.

PubMed

Mordhorst, Mylena; Heidlauf, Thomas; Röhrle, Oliver

2015-04-06

This paper presents a novel multiscale finite element-based framework for modelling electromyographic (EMG) signals. The framework combines (i) a biophysical description of the excitation-contraction coupling at the half-sarcomere level, (ii) a model of the action potential (AP) propagation along muscle fibres, (iii) a continuum-mechanical formulation of force generation and deformation of the muscle, and (iv) a model for predicting the intramuscular and surface EMG. Owing to the biophysical description of the half-sarcomere, the model inherently accounts for physiological properties of skeletal muscle. To demonstrate this, the influence of membrane fatigue on the EMG signal during sustained contractions is investigated. During a stimulation period of 500 ms at 100 Hz, the predicted EMG amplitude decreases by 40% and the AP propagation velocity decreases by 15%. Further, the model can take into account contraction-induced deformations of the muscle. This is demonstrated by simulating fixed-length contractions of an idealized geometry and a model of the human tibialis anterior muscle (TA). The model of the TA furthermore demonstrates that the proposed finite element model is capable of simulating realistic geometries, complex fibre architectures, and can include different types of heterogeneities. In addition, the TA model accounts for a distributed innervation zone, different fibre types and appeals to motor unit discharge times that are based on a biophysical description of the α motor neurons.

Predicting electromyographic signals under realistic conditions using a multiscale chemo–electro–mechanical finite element model

PubMed Central

Mordhorst, Mylena; Heidlauf, Thomas; Röhrle, Oliver

2015-01-01

This paper presents a novel multiscale finite element-based framework for modelling electromyographic (EMG) signals. The framework combines (i) a biophysical description of the excitation–contraction coupling at the half-sarcomere level, (ii) a model of the action potential (AP) propagation along muscle fibres, (iii) a continuum-mechanical formulation of force generation and deformation of the muscle, and (iv) a model for predicting the intramuscular and surface EMG. Owing to the biophysical description of the half-sarcomere, the model inherently accounts for physiological properties of skeletal muscle. To demonstrate this, the influence of membrane fatigue on the EMG signal during sustained contractions is investigated. During a stimulation period of 500 ms at 100 Hz, the predicted EMG amplitude decreases by 40% and the AP propagation velocity decreases by 15%. Further, the model can take into account contraction-induced deformations of the muscle. This is demonstrated by simulating fixed-length contractions of an idealized geometry and a model of the human tibialis anterior muscle (TA). The model of the TA furthermore demonstrates that the proposed finite element model is capable of simulating realistic geometries, complex fibre architectures, and can include different types of heterogeneities. In addition, the TA model accounts for a distributed innervation zone, different fibre types and appeals to motor unit discharge times that are based on a biophysical description of the α motor neurons. PMID:25844148

ANFO Response to Low-Stress Planar Impacts

NASA Astrophysics Data System (ADS)

Cooper, Marcia; Trott, Wayne; Schmitt, Robert; Short, Mark; Jackson, Scott

2011-06-01

Ammonium Nitrate plus Fuel Oil (ANFO) is a non-ideal explosive where the mixing behavior of the mm-diameter prills with the absorbed fuel oil is of critical importance for chemical energy release. The large-scale heterogeneity of ANFO establishes conditions uniquely suitable for observation using the spatially- and temporally-resolved line-imaging ORVIS (optically recording velocity interferometer system) diagnostic. The first demonstration of transmitted wave profiles in ANFO from low-stress planar impacts using a single-stage gas gun is reported. The experimental stresses simulate the compressive wave conditions preceding detonation providing insight into dominant mesoscale processes. Distributions of particle velocity as related to mean prill diameters and observations of between-prill jetting are reported. Use of the measured distributions of particle velocity for collaboration with mesoscale model development and the statistically-averaged values for contribution to continuum model development is discussed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Laser pulse control of ultrafast heterogeneous electron transfer: a computational study.

PubMed

Wang, Luxia; May, Volkhard

2004-10-22

Laser pulse control of the photoinduced 90 fs charge injection from perylene into the conduction band of TiO2 is studied theoretically. The approach accounts for the electronic-ground state of the dye, the first excited state, the ionized state formed after charge injection, and the continuum of the electronic states in the conduction band, all defined vs a single reaction coordinate. To address different control tasks optimal control theory is combined with a full quantum dynamical description of the electron-vibrational motion accompanying the charge injection process. First it is proved in which way the charge injection time can be changed by tailored laser pulses. In a second step a pump-dump scheme from the perylene ground state to the first excited electronic state and back to the ground state is discussed. Because of the strong coupling of the excited perylene state to the band continuum of TiO2 this control task is more suited to an experimental test than the direct control of the charge injection.

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells.

PubMed

Macaulay, Iain C; Svensson, Valentine; Labalette, Charlotte; Ferreira, Lauren; Hamey, Fiona; Voet, Thierry; Teichmann, Sarah A; Cvejic, Ana

2016-02-02

The transcriptional programs that govern hematopoiesis have been investigated primarily by population-level analysis of hematopoietic stem and progenitor cells, which cannot reveal the continuous nature of the differentiation process. Here we applied single-cell RNA-sequencing to a population of hematopoietic cells in zebrafish as they undergo thrombocyte lineage commitment. By reconstructing their developmental chronology computationally, we were able to place each cell along a continuum from stem cell to mature cell, refining the traditional lineage tree. The progression of cells along this continuum is characterized by a highly coordinated transcriptional program, displaying simultaneous suppression of genes involved in cell proliferation and ribosomal biogenesis as the expression of lineage specific genes increases. Within this program, there is substantial heterogeneity in the expression of the key lineage regulators. Overall, the total number of genes expressed, as well as the total mRNA content of the cell, decreases as the cells undergo lineage commitment. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Stochastic simulation tools and continuum models for describing two-dimensional collective cell spreading with universal growth functions

NASA Astrophysics Data System (ADS)

Jin, Wang; Penington, Catherine J.; McCue, Scott W.; Simpson, Matthew J.

2016-10-01

Two-dimensional collective cell migration assays are used to study cancer and tissue repair. These assays involve combined cell migration and cell proliferation processes, both of which are modulated by cell-to-cell crowding. Previous discrete models of collective cell migration assays involve a nearest-neighbour proliferation mechanism where crowding effects are incorporated by aborting potential proliferation events if the randomly chosen target site is occupied. There are two limitations of this traditional approach: (i) it seems unreasonable to abort a potential proliferation event based on the occupancy of a single, randomly chosen target site; and, (ii) the continuum limit description of this mechanism leads to the standard logistic growth function, but some experimental evidence suggests that cells do not always proliferate logistically. Motivated by these observations, we introduce a generalised proliferation mechanism which allows non-nearest neighbour proliferation events to take place over a template of r≥slant 1 concentric rings of lattice sites. Further, the decision to abort potential proliferation events is made using a crowding function, f(C), which accounts for the density of agents within a group of sites rather than dealing with the occupancy of a single randomly chosen site. Analysing the continuum limit description of the stochastic model shows that the standard logistic source term, λ C(1-C), where λ is the proliferation rate, is generalised to a universal growth function, λ C f(C). Comparing the solution of the continuum description with averaged simulation data indicates that the continuum model performs well for many choices of f(C) and r. For nonlinear f(C), the quality of the continuum-discrete match increases with r.

Stochastic simulation tools and continuum models for describing two-dimensional collective cell spreading with universal growth functions.

PubMed

Jin, Wang; Penington, Catherine J; McCue, Scott W; Simpson, Matthew J

2016-10-07

Two-dimensional collective cell migration assays are used to study cancer and tissue repair. These assays involve combined cell migration and cell proliferation processes, both of which are modulated by cell-to-cell crowding. Previous discrete models of collective cell migration assays involve a nearest-neighbour proliferation mechanism where crowding effects are incorporated by aborting potential proliferation events if the randomly chosen target site is occupied. There are two limitations of this traditional approach: (i) it seems unreasonable to abort a potential proliferation event based on the occupancy of a single, randomly chosen target site; and, (ii) the continuum limit description of this mechanism leads to the standard logistic growth function, but some experimental evidence suggests that cells do not always proliferate logistically. Motivated by these observations, we introduce a generalised proliferation mechanism which allows non-nearest neighbour proliferation events to take place over a template of [Formula: see text] concentric rings of lattice sites. Further, the decision to abort potential proliferation events is made using a crowding function, f(C), which accounts for the density of agents within a group of sites rather than dealing with the occupancy of a single randomly chosen site. Analysing the continuum limit description of the stochastic model shows that the standard logistic source term, [Formula: see text], where λ is the proliferation rate, is generalised to a universal growth function, [Formula: see text]. Comparing the solution of the continuum description with averaged simulation data indicates that the continuum model performs well for many choices of f(C) and r. For nonlinear f(C), the quality of the continuum-discrete match increases with r.

Cross-continuum Care Continuity: Achieving Seamless Care and Managing Comorbidities.

PubMed

Boston-Fleischhauer, Carol; Rose, Robert; Hartwig, Laurie

As healthcare systems continue to design care models responsive to payment changes and the assumption of clinical and financial risk, the need exists for a comprehensive approach to address cross-continuum care transitions. This article will highlight key learnings from the Nurse Executive Center's research on achieving care continuity. The business case for developing a cross-continuum care transition strategy will be discussed, as well as systemic enablers for the achievement of seamless care. A case study example of 1 system's solution for supporting the multiple comorbid patient population as part of its cross-continuum care transition strategy will be examined.

SEACAS Theory Manuals: Part II. Nonlinear Continuum Mechanics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Attaway, S.W.; Laursen, T.A.; Zadoks, R.I.

1998-09-01

This report summarizes the key continuum mechanics concepts required for the systematic prescription and numerical solution of finite deformation solid mechanics problems. Topics surveyed include measures of deformation appropriate for media undergoing large deformations, stress measures appropriate for such problems, balance laws and their role in nonlinear continuum mechanics, the role of frame indifference in description of large deformation response, and the extension of these theories to encompass two dimensional idealizations, structural idealizations, and rigid body behavior. There are three companion reports that describe the problem formulation, constitutive modeling, and finite element technology for nonlinear continuum mechanics systems.

Microstructural comparison of the kinematics of discrete and continuum dislocations models

NASA Astrophysics Data System (ADS)

Sandfeld, Stefan; Po, Giacomo

2015-12-01

The Continuum Dislocation Dynamics (CDD) theory and the Discrete Dislocation Dynamics (DDD) method are compared based on concise mathematical formulations of the coarse graining of discrete data. A numerical tool for converting from a discrete to a continuum representation of a given dislocation configuration is developed, which allows to directly compare both simulation approaches based on continuum quantities (e.g. scalar density, geometrically necessary densities, mean curvature). Investigating the evolution of selected dislocation configurations within analytically given velocity fields for both DDD and CDD reveals that CDD contains a surprising number of important microstructural details.

A series RCL circuit theory for analyzing non-steady-state water uptake of maize plants.

PubMed

Zhuang, Jie; Yu, Gui-Rui; Nakayama, Keiichi

2014-10-22

Understanding water uptake and transport through the soil-plant continuum is vital for ecosystem management and agricultural water use. Plant water uptake under natural conditions is a non-steady transient flow controlled by root distribution, plant configuration, soil hydraulics, and climatic conditions. Despite significant progress in model development, a mechanistic description of transient water uptake has not been developed or remains incomplete. Here, based on advanced electrical network theory (RLC circuit theory), we developed a non-steady state biophysical model to mechanistically analyze the fluctuations of uptake rates in response to water stress. We found that the non-steady-state model captures the nature of instantaneity and hysteresis of plant water uptake due to the considerations of water storage in plant xylem and coarse roots (capacitance effect), hydraulic architecture of leaf system (inductance effect), and soil-root contact (fuse effect). The model provides insights into the important role of plant configuration and hydraulic heterogeneity in helping plants survive an adverse environment. Our tests against field data suggest that the non-steady-state model has great potential for being used to interpret the smart water strategy of plants, which is intrinsically determined by stem size, leaf size/thickness and distribution, root system architecture, and the ratio of fine-to-coarse root lengths.

Thermal-mechanical-chemical responses of polymer-bonded explosives using a mesoscopic reactive model under impact loading.

PubMed

Wang, XinJie; Wu, YanQing; Huang, FengLei

2017-01-05

A mesoscopic framework is developed to quantify the thermal-mechanical-chemical responses of polymer-bonded explosive (PBX) samples under impact loading. A mesoscopic reactive model is developed for the cyclotetramethylenetetranitramine (HMX) crystal, which incorporates nonlinear elasticity, crystal plasticity, and temperature-dependent chemical reaction. The proposed model was implemented in the finite element code ABAQUS by the user subroutine VUMAT. A series of three-dimensional mesoscale models were constructed and calculated under low-strength impact loading scenarios from 100m/s to 600m/s where only the first wave transit is studied. Crystal anisotropy and microstructural heterogeneity are responsible for the nonuniform stress field and fluctuations of the stress wave front. At a critical impact velocity (≥300m/s), a chemical reaction is triggered because the temperature contributed by the volumetric and plastic works is sufficiently high. Physical quantities, including stress, temperature, and extent of reaction, are homogenized from those across the microstructure at the mesoscale to compare with macroscale measurements, which will advance the continuum-level models. The framework presented in this study has important implications in understanding hot spot ignition processes and improving predictive capabilities in energetic materials. Copyright © 2016 Elsevier B.V. All rights reserved.

A 2.5D Reactive Transport Model for Fracture Alteration Simulation

DOE PAGES

Deng, Hang; Molins, Sergi; Steefel, Carl; ...

2016-06-30

Understanding fracture alteration resulting from geochemical reactions is critical in predicting fluid migration in the subsurface and is relevant to multiple environmental challenges. Here in this paper, we present a novel 2.5D continuum reactive transport model that captures and predicts the spatial pattern of fracture aperture change and the development of an altered layer in the near-fracture region. The model considers permeability heterogeneity in the fracture plane and updates fracture apertures and flow fields based on local reactions. It tracks the reaction front of each mineral phase and calculates the thickness of the altered layer. Given this treatment, the modelmore » is able to account for the diffusion limitation on reaction rates associated with the altered layer. The model results are in good agreement with an experimental study in which a CO 2-acidified brine was injected into a fracture in the Duperow Dolomite, causing dissolution of calcite and dolomite that result in the formation of a preferential flow channel and an altered layer. Finally, with an effective diffusion coefficient consistent with the experimentally observed porosity of the altered layer, the model captures the progressive decrease in the dissolution rate of the fast-reacting mineral in the altered layer.« less

Hydraulic tomography of discrete networks of conduits and fractures in a karstic aquifer by using a deterministic inversion algorithm

NASA Astrophysics Data System (ADS)

Fischer, P.; Jardani, A.; Lecoq, N.

2018-02-01

In this paper, we present a novel inverse modeling method called Discrete Network Deterministic Inversion (DNDI) for mapping the geometry and property of the discrete network of conduits and fractures in the karstified aquifers. The DNDI algorithm is based on a coupled discrete-continuum concept to simulate numerically water flows in a model and a deterministic optimization algorithm to invert a set of observed piezometric data recorded during multiple pumping tests. In this method, the model is partioned in subspaces piloted by a set of parameters (matrix transmissivity, and geometry and equivalent transmissivity of the conduits) that are considered as unknown. In this way, the deterministic optimization process can iteratively correct the geometry of the network and the values of the properties, until it converges to a global network geometry in a solution model able to reproduce the set of data. An uncertainty analysis of this result can be performed from the maps of posterior uncertainties on the network geometry or on the property values. This method has been successfully tested for three different theoretical and simplified study cases with hydraulic responses data generated from hypothetical karstic models with an increasing complexity of the network geometry, and of the matrix heterogeneity.

Spiraling down the river continuum: stream ecology and the U-shaped curve

Treesearch

Jackson R. Webster

2007-01-01

The spiraling concept provides an explicit approach to modeling the longitudinal linkages within a river continuum. I developed a spiraling-based model for particulate organic C dynamics in the Little Tennessee River to synthesize existing data and to illustrate our current understanding of ecosystem processes in river ecosystems. The Little Tennessee River is a medium...

Breakdown parameter for kinetic modeling of multiscale gas flows.

PubMed

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 Fiber Kinking: Computational Micromechanics and a Mesoscale Continuum Damage Mechanics Models

NASA Technical Reports Server (NTRS)

Herraez, Miguel; Bergan, Andrew C.; Gonzalez, Carlos; Lopes, Claudio S.

2017-01-01

In this work, the fiber kinking phenomenon, which is known as the failure mechanism that takes place when a fiber reinforced polymer is loaded under longitudinal compression, is studied. A computational micromechanics model is employed to interrogate the assumptions of a recently developed mesoscale continuum damage mechanics (CDM) model for fiber kinking based on the deformation gradient decomposition (DGD) and the LaRC04 failure criteria.

Ionized absorbers, ionized emitters, and the X-ray spectrum of active galactic nuclei

NASA Technical Reports Server (NTRS)

Netzer, Hagai

1993-01-01

Broad absorption features are common in the X-ray spectrum of low-luminosity AGNs. The features have been modeled by leaky neutral absorbers or by highly ionized gas that completely occult the continuum source. Such models are incomplete since they do not take into account all the physical processes in the gas. In particular, no previous model included the X-ray emission by the ionized absorbing gas and the reflection of the continuum source radiation. The present work discusses the emission, absorption, and reflection properties of photoionized gases with emphasis on conditions thought to prevail in AGNs. It shows that such gas is likely to produce intense X-ray line and continuum radiation and to reflect a sizable fraction of the nonstellar continuum at all energies. If such gas is indeed responsible for the observed X-ray absorption, then absorption edges are much weaker than commonly assumed, and some residual X-ray continuum is likely to be observed even if the line of sight is completely blocked. Moreover, X-ray emission features may show up in sources not showing X-ray absorption. This has immense consequences for medium-resolution X-ray missions, such as BBXRT and Astro-D, and for the planned high-resolution experiments on board XMM and AXAF.

Simulation of Turbulent Combustion Fields of Shock-Dispersed Aluminum Using the AMR Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuhl, A L; Bell, J B; Beckner, V E

2006-11-02

We present a Model for simulating experiments of combustion in Shock-Dispersed-Fuel (SDF) explosions. The SDF charge consisted of a 0.5-g spherical PETN booster, surrounded by 1-g of fuel powder (flake Aluminum). Detonation of the booster charge creates a high-temperature, high-pressure source (PETN detonation products gases) that both disperses the fuel and heats it. Combustion ensues when the fuel mixes with air. The gas phase is governed by the gas-dynamic conservation laws, while the particle phase obeys the continuum mechanics laws for heterogeneous media. The two phases exchange mass, momentum and energy according to inter-phase interaction terms. The kinetics model usedmore » an empirical particle burn relation. The thermodynamic model considers the air, fuel and booster products to be of frozen composition, while the Al combustion products are assumed to be in equilibrium. The thermodynamic states were calculated by the Cheetah code; resulting state points were fit with analytic functions suitable for numerical simulations. Numerical simulations of combustion of an Aluminum SDF charge in a 6.4-liter chamber were performed. Computed pressure histories agree with measurements.« less

A Geometrically Nonlinear Phase Field Theory of Brittle Fracture

DTIC Science & Technology

2014-10-01

of crack propagation. Philos Mag 91:75–95 Sun X, Khaleel M (2004) Modeling of glass fracture damage using continuum damage mechanics -static spherical...elastic fracture mechanics ). Engineering finite element (FE) simula- tions often invoke continuum damage mechanics the- ories, wherein the tangent...stiffness of a material ele- ment degrades as “damage” accumulates.Conventional continuum damage mechanics theories (Clayton and McDowell 2003, 2004; Sun and

Series Pneumatic Artificial Muscles (sPAMs) and Application to a Soft Continuum Robot.

PubMed

Greer, Joseph D; Morimoto, Tania K; Okamura, Allison M; Hawkes, Elliot W

2017-01-01

We describe a new series pneumatic artificial muscle (sPAM) and its application as an actuator for a soft continuum robot. The robot consists of three sPAMs arranged radially round a tubular pneumatic backbone. Analogous to tendons, the sPAMs exert a tension force on the robot's pneumatic backbone, causing bending that is approximately constant curvature. Unlike a traditional tendon driven continuum robot, the robot is entirely soft and contains no hard components, making it safer for human interaction. Models of both the sPAM and soft continuum robot kinematics are presented and experimentally verified. We found a mean position accuracy of 5.5 cm for predicting the end-effector position of a 42 cm long robot with the kinematic model. Finally, closed-loop control is demonstrated using an eye-in-hand visual servo control law which provides a simple interface for operation by a human. The soft continuum robot with closed-loop control was found to have a step-response rise time and settling time of less than two seconds.

Series Pneumatic Artificial Muscles (sPAMs) and Application to a Soft Continuum Robot

PubMed Central

Greer, Joseph D.; Morimoto, Tania K.; Okamura, Allison M.; Hawkes, Elliot W.

2017-01-01

We describe a new series pneumatic artificial muscle (sPAM) and its application as an actuator for a soft continuum robot. The robot consists of three sPAMs arranged radially round a tubular pneumatic backbone. Analogous to tendons, the sPAMs exert a tension force on the robot’s pneumatic backbone, causing bending that is approximately constant curvature. Unlike a traditional tendon driven continuum robot, the robot is entirely soft and contains no hard components, making it safer for human interaction. Models of both the sPAM and soft continuum robot kinematics are presented and experimentally verified. We found a mean position accuracy of 5.5 cm for predicting the end-effector position of a 42 cm long robot with the kinematic model. Finally, closed-loop control is demonstrated using an eye-in-hand visual servo control law which provides a simple interface for operation by a human. The soft continuum robot with closed-loop control was found to have a step-response rise time and settling time of less than two seconds. PMID:29379672

Hybrid continuum-coarse-grained modeling of erythrocytes

NASA Astrophysics Data System (ADS)

Lyu, Jinming; Chen, Paul G.; Boedec, Gwenn; Leonetti, Marc; Jaeger, Marc

2018-06-01

The red blood cell (RBC) membrane is a composite structure, consisting of a phospholipid bilayer and an underlying membrane-associated cytoskeleton. Both continuum and particle-based coarse-grained RBC models make use of a set of vertices connected by edges to represent the RBC membrane, which can be seen as a triangular surface mesh for the former and a spring network for the latter. Here, we present a modeling approach combining an existing continuum vesicle model with a coarse-grained model for the cytoskeleton. Compared to other two-component approaches, our method relies on only one mesh, representing the cytoskeleton, whose velocity in the tangential direction of the membrane may be different from that of the lipid bilayer. The finitely extensible nonlinear elastic (FENE) spring force law in combination with a repulsive force defined as a power function (POW), called FENE-POW, is used to describe the elastic properties of the RBC membrane. The mechanical interaction between the lipid bilayer and the cytoskeleton is explicitly computed and incorporated into the vesicle model. Our model includes the fundamental mechanical properties of the RBC membrane, namely fluidity and bending rigidity of the lipid bilayer, and shear elasticity of the cytoskeleton while maintaining surface-area and volume conservation constraint. We present three simulation examples to demonstrate the effectiveness of this hybrid continuum-coarse-grained model for the study of RBCs in fluid flows.

Constitutive Modeling of Nanotube/Polymer Composites with Various Nanotube Orientations

NASA Technical Reports Server (NTRS)

Odegard, Gregory M.; Gates, Thomas S.

2002-01-01

In this study, a technique has been proposed for developing constitutive models for polymer composite systems reinforced with single-walled carbon nanotubes (SWNT) with various orientations with respect to the bulk material coordinates. A nanotube, the local polymer adjacent to the nanotube, and the nanotube/polymer interface have been modeled as an equivalent-continuum fiber by using an equivalent-continuum modeling method. The equivalent-continuum fiber accounts for the local molecular structure and bonding information and serves as a means for incorporating micromechanical analyses for the prediction of bulk mechanical properties of SWNT/polymer composite. As an example, the proposed approach is used for the constitutive modeling of a SWNT/LaRC-SI (with a PmPV interface) composite system, with aligned nanotubes, three-dimensionally randomly oriented nanotubes, and nanotubes oriented with varying degrees of axisymmetry. It is shown that the Young s modulus is highly dependent on the SWNT orientation distribution.

Role of Hydrodynamic and Mineralogical Heterogeneities on Reactive Transport Processes.

NASA Astrophysics Data System (ADS)

Luquot, L.; Garcia-Rios, M.; soler Sagarra, J.; Gouze, P.; Martinez-Perez, L.; Carrera, J.

2017-12-01

Predicting reactive transport at large scale, i.e., Darcy- and field- scale, is still challenging considering the number of heterogeneities that may be present from nm- to pore-scale. It is well documented that conventional continuum-scale approaches oversimplify and/or ignore many important aspects of rock structure, chemical reactions, fluid displacement and transport, which, as a consequence, results in uncertainties when applied to field-scale operations. The changes in flow and reactive transport across the different spatial and temporal scales are of central concern in many geological applications such as groundwater systems, geo-energy, rock building heritage and geological storage... In this presentation, we will discuss some laboratory and numerical results on how local heterogeneities (structural, hydrodynamic and mineralogical) can affect the localization and the rate of the reaction processes. Different flow through laboratory experiments using various rock samples will be presented, from simple monomineral rocks such as limestone samples, and more complex rocks composed of different minerals with a large range of kinetic reactions. A new numerical approach based on multirate water mixing approach will be presented and applied to one of the laboratory experiment in order to analyze and distinguish the effect of the mineralogy distribution and the hydrodynamic heterogeneity on the total reaction rate.

Mechanics of low-dimensional carbon nanostructures: Atomistic, continuum, and multi-scale approaches

NASA Astrophysics Data System (ADS)

Mahdavi, Arash

A new multiscale modeling technique called the Consistent Atomic-scale Finite Element (CAFE) method is introduced. Unlike traditional approaches for linking the atomic structure to its equivalent continuum, this method directly connects the atomic degrees of freedom to a reduced set of finite element degrees of freedom without passing through an intermediate homogenized continuum. As a result, there is no need to introduce stress and strain measures at the atomic level. The Tersoff-Brenner interatomic potential is used to calculate the consistent tangent stiffness matrix of the structure. In this finite element formulation, all local and non-local interactions between carbon atoms are taken into account using overlapping finite elements. In addition, a consistent hierarchical finite element modeling technique is developed for adaptively coarsening and refining the mesh over different parts of the model. This process is consistent with the underlying atomic structure and, by refining the mesh to the scale of atomic spacing, molecular dynamic results can be recovered. This method is valid across the scales and can be used to concurrently model atomistic and continuum phenomena so, in contrast with most other multi-scale methods, there is no need to introduce artificial boundaries for coupling atomistic and continuum regions. Effect of the length scale of the nanostructure is also included in the model by building the hierarchy of elements from bottom up using a finite size atom cluster as the building block. To be consistent with the bravais multi-lattice structure of sp2-bonded carbon, two independent displacement fields are used for reducing the order of the model. Sparse structure of the stiffness matrix of these nanostructures is exploited to reduce the memory requirement and to speed up the formation of the system matrices and solution of the equilibrium equations. Applicability of the method is shown with several examples of the nonlinear mechanics of carbon nanotubes and carbon nanocones subject to different loadings and boundary conditions. This finite element technique is also used to study the natural frequencies of low-dimensional carbon nanostructures and comparing the results with those of a homogenized isotropic continuum shell. Conclusion is that, replacing the atomic lattice with an isotropic continuum shell for a graphene sheet does not significantly affect the vibration frequencies while in the case of carbon nanotubes and carbon nanocones there is a significant difference between the natural frequencies of the atomistic model and its continuum counterpart. In the case of the carbon nanotube, continuum model successfully captures the beam bending vibration modes while overestimating frequencies of the modes in which the cross-section undergoes significant deformation. Furthermore, in the case of carbon nanotubes, the continuum shell exhibits a torsional mode which appears to be an artifact resulting from the small nominal thickness typically used in the continuum shell approximation of these nanostructures. Results of this study indicate that isotropic continuum shell models, while simple and useful in static analysis, cannot accurately predict the vibration frequencies of these nanostructures. We have studied the bistable nature of single-walled carbon nanotubes by investigating the change in the tube's energy as it is compressed between flat rigid indenters of various widths. Assuming the nanotube deformed uniformly along its length and modeling the cross-section as an inextensible, non-linear beam we found that tubes with a radius greater than 12 A are bistable and that tubes with a radius greater than 25 A have a lower energy in the collapsed state than in the inflated state. The difference in energy between the collapsed and inflated states decreases nearly linearly with increasing tube radius. While the inflated state remains stable for tubes of all diameters, the energy barrier keeping the tube from collapsing approaches zero as the tube radius increases. We also demonstrate why collapse with a wide indenter may be difficult to observe in narrow tubes. A reduced-order model is developed for the dynamics of the carbon nanotube atomic force microscope probes. Bending behavior of the nanotube probe is modeled using Euler's elastica. A nonlinear moment-curvature relationship is implemeneted to account for the ovalization of the cross section of the nanotube during bending. Van der Waal forces acting between tube and the substrate is integrated over the surface of the tube and used as distributed follower forces acting on the equivalent elastica. Approximating the behavior of the nanotube with an elastica proved to be a very effiecient technique for modeling these nanostructures.

Ranges of applicability for the continuum beam model in the mechanics of carbon nanotubes and nanorods

NASA Technical Reports Server (NTRS)

Harik, V. M.

2001-01-01

Limitations in the validity of the continuum beam model for carbon nanotubes (NTs) and nanorods are examined. Applicability of all assumptions used in the model is restricted by the two criteria for geometric parameters that characterize the structure of NTs. The key non-dimensional parameters that control the NT buckling behavior are derived via dimensional analysis of the nanomechanical problem. A mechanical law of geometric similitude for NT buckling is extended from continuum mechanics for different molecular structures. A model applicability map, where two classes of beam-like NTs are identified, is constructed for distinct ranges of non-dimensional parameters. Expressions for the critical buckling loads and strains are tailored for two classes of NTs and compared with the data provided by the molecular dynamics simulations. copyright 2001 Elsevier Science Ltd. All rights reserved.

Quantum mechanical/molecular mechanical/continuum style solvation model: time-dependent density functional theory.

PubMed

Thellamurege, Nandun M; Cui, Fengchao; Li, Hui

2013-08-28

A combined quantum mechanical/molecular mechanical/continuum (QM/MMpol/C) style method is developed for time-dependent density functional theory (TDDFT, including long-range corrected TDDFT) method, induced dipole polarizable force field, and induced surface charge continuum model. Induced dipoles and induced charges are included in the TDDFT equations to solve for the transition energies, relaxed density, and transition density. Analytic gradient is derived and implemented for geometry optimization and molecular dynamics simulation. QM/MMpol/C style DFT and TDDFT methods are used to study the hydrogen bonding of the photoactive yellow protein chromopore in ground state and excited state.

High-order continuum kinetic method for modeling plasma dynamics in phase space

DOE PAGES

Vogman, G. V.; Colella, P.; Shumlak, U.

2014-12-15

Continuum methods offer a high-fidelity means of simulating plasma kinetics. While computationally intensive, these methods are advantageous because they can be cast in conservation-law form, are not susceptible to noise, and can be implemented using high-order numerical methods. Advances in continuum method capabilities for modeling kinetic phenomena in plasmas require the development of validation tools in higher dimensional phase space and an ability to handle non-cartesian geometries. To that end, a new benchmark for validating Vlasov-Poisson simulations in 3D (x,v x,v y) is presented. The benchmark is based on the Dory-Guest-Harris instability and is successfully used to validate a continuummore » finite volume algorithm. To address challenges associated with non-cartesian geometries, unique features of cylindrical phase space coordinates are described. Preliminary results of continuum kinetic simulations in 4D (r,z,v r,v z) phase space are presented.« less

Numerical simulation of asphalt mixtures fracture using continuum models

NASA Astrophysics Data System (ADS)

Szydłowski, Cezary; Górski, Jarosław; Stienss, Marcin; Smakosz, Łukasz

2018-01-01

The paper considers numerical models of fracture processes of semi-circular asphalt mixture specimens subjected to three-point bending. Parameter calibration of the asphalt mixture constitutive models requires advanced, complex experimental test procedures. The highly non-homogeneous material is numerically modelled by a quasi-continuum model. The computational parameters are averaged data of the components, i.e. asphalt, aggregate and the air voids composing the material. The model directly captures random nature of material parameters and aggregate distribution in specimens. Initial results of the analysis are presented here.

A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure.

PubMed

Kojic, M; Milosevic, M; Kojic, N; Kim, K; Ferrari, M; Ziemys, A

2014-02-01

Mass transport by diffusion within composite materials may depend not only on internal microstructural geometry, but also on the chemical interactions between the transported substance and the material of the microstructure. Retrospectively, there is a gap in methods and theory to connect material microstructure properties with macroscale continuum diffusion characteristics. Here we present a new hierarchical multiscale model for diffusion within composite materials that couples material microstructural geometry and interactions between diffusing particles and the material matrix. This model, which bridges molecular dynamics (MD) and the finite element (FE) method, is employed to construct a continuum diffusion model based on a novel numerical homogenization procedure. The procedure is general and robust for evaluating constitutive material parameters of the continuum model. These parameters include the traditional bulk diffusion coefficients and, additionally, the distances from the solid surface accounting for surface interaction effects. We implemented our models to glucose diffusion through the following two geometrical/material configurations: tightly packed silica nanospheres, and a complex fibrous structure surrounding nanospheres. Then, rhodamine 6G diffusion analysis through an aga-rose gel network was performed, followed by a model validation using our experimental results. The microstructural model, numerical homogenization and continuum model offer a new platform for modeling and predicting mass diffusion through complex biological environment and within composite materials that are used in a wide range of applications, like drug delivery and nanoporous catalysts.

A multiscale MD–FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure

PubMed Central

Kojic, M.; Milosevic, M.; Kojic, N.; Kim, K.; Ferrari, M.; Ziemys, A.

2014-01-01

Mass transport by diffusion within composite materials may depend not only on internal microstructural geometry, but also on the chemical interactions between the transported substance and the material of the microstructure. Retrospectively, there is a gap in methods and theory to connect material microstructure properties with macroscale continuum diffusion characteristics. Here we present a new hierarchical multiscale model for diffusion within composite materials that couples material microstructural geometry and interactions between diffusing particles and the material matrix. This model, which bridges molecular dynamics (MD) and the finite element (FE) method, is employed to construct a continuum diffusion model based on a novel numerical homogenization procedure. The procedure is general and robust for evaluating constitutive material parameters of the continuum model. These parameters include the traditional bulk diffusion coefficients and, additionally, the distances from the solid surface accounting for surface interaction effects. We implemented our models to glucose diffusion through the following two geometrical/material configurations: tightly packed silica nanospheres, and a complex fibrous structure surrounding nanospheres. Then, rhodamine 6G diffusion analysis through an aga-rose gel network was performed, followed by a model validation using our experimental results. The microstructural model, numerical homogenization and continuum model offer a new platform for modeling and predicting mass diffusion through complex biological environment and within composite materials that are used in a wide range of applications, like drug delivery and nanoporous catalysts. PMID:24578582

Atomistic to continuum modeling of solidification microstructures

DOE PAGES

Karma, Alain; Tourret, Damien

2015-09-26

We summarize recent advances in modeling of solidification microstructures using computational methods that bridge atomistic to continuum scales. We first discuss progress in atomistic modeling of equilibrium and non-equilibrium solid–liquid interface properties influencing microstructure formation, as well as interface coalescence phenomena influencing the late stages of solidification. The latter is relevant in the context of hot tearing reviewed in the article by M. Rappaz in this issue. We then discuss progress to model microstructures on a continuum scale using phase-field methods. We focus on selected examples in which modeling of 3D cellular and dendritic microstructures has been directly linked tomore » experimental observations. Finally, we discuss a recently introduced coarse-grained dendritic needle network approach to simulate the formation of well-developed dendritic microstructures. The approach reliably bridges the well-separated scales traditionally simulated by phase-field and grain structure models, hence opening new avenues for quantitative modeling of complex intra- and inter-grain dynamical interactions on a grain scale.« less

Electrical Matching at Metal/Molecule Contacts for Efficient Heterogeneous Charge Transfer.

PubMed

Sato, Shino; Iwase, Shigeru; Namba, Kotaro; Ono, Tomoya; Hara, Kenji; Fukuoka, Atsushi; Uosaki, Kohei; Ikeda, Katsuyoshi

2018-02-27

In a metal/molecule hybrid system, unavoidable electrical mismatch exists between metal continuum states and frontier molecular orbitals. This causes energy loss in the electron conduction across the metal/molecule interface. For efficient use of energy in a metal/molecule hybrid system, it is necessary to control interfacial electronic structures. Here we demonstrate that electrical matching between a gold substrate and π-conjugated molecular wires can be obtained by using monatomic foreign metal interlayers, which can change the degree of d-π* back-donation at metal/anchor contacts. This interfacial control leads to energy level alignment between the Fermi level of the metal electrode and conduction molecular orbitals, resulting in resonant electron conduction in the metal/molecule hybrid system. When this method is applied to molecule-modified electrocatalysts, the heterogeneous electrochemical reaction rate is considerably improved with significant suppression of energy loss at the internal electron conduction.

The responsibility continuum: never primary, coresident and caregiver--heterogeneity in the African-American grandmother experience.

PubMed

Lee, Rosalyn D; Ensminger, Margaret E; LaVeist, Thomas A

2005-01-01

This article examines diversity among 542 African-American grandmothers from the Woodlawn Longitudinal Study. Women were categorized on the basis of their household composition, degree of care provided to grandchildren, and status of primary caregiver to grandchildren during lifetime. Overall, 67.7% of the sample engaged in parenting and exchange behaviors at high or moderate levels. Twenty-seven percent of the sample coresided with and provided care to grandchildren, 28% did not coreside but had been primary caregivers in the past, and 45% did not coreside and had never been primarily responsible for a grandchild. Heterogeneity was found among seven grandmother types on economic measures, life events, and grandchild characteristics. Grandmothers with earlier primary responsibility and those currently in homes of three or more generations were associated with poor outcomes. Policy and practice can be informed by additional research on status, context, and timing of assumption of responsibilities for grandchildren.

Continuum electromechanical modeling of protein-membrane interactions

NASA Astrophysics Data System (ADS)

Zhou, Y. C.; Lu, Benzhuo; Gorfe, Alemayehu A.

2010-10-01

A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the electrostatic solvation energy of the system, and equilibrium membrane deformation is obtained by minimizing the electroelastic energy functional with respect to the dielectric interface. The model is illustrated with the systems with increasing geometry complexity and captures the sensitivity of membrane curvature to the permanent and mobile charge distributions.

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.

PubMed

Brackley, C A; Morozov, A N; Marenduzzo, D

2014-04-07

An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions relating to both bending and twisting of the rod are derived for both continuous and discrete cases, and results are compared with numerical simulations. Finally, two possible implementations of the discretised model in the multi-purpose molecular dynamics software package LAMMPS are described.

RXTE Observation of the Tycho Supernova Remnant

NASA Technical Reports Server (NTRS)

The, Lih-Sin

1998-01-01

SN1006 [4] and Cas A [1, 9] supernova remnants have been shown convincingly to have a hard X-ray power-law continuum. This continuum is thought to be the synchrotron radiation from accelerated electrons of approx. 100 TeV at the shock fronts. Our goal of AO2 RXTE observation is to detect the hard X-ray continuum and to determine the nature of the continuum from Tycho SNR. A detection of a power-law continuum from Tycho SNR can strongly argue for SNRs are the source of cosmic rays with the first order Fermi acceleration as the energizing process. We report the results of our AO2 RXTE 1 x 10(exp 5) sec observation of Tycho SNR. We detect two components of the X-ray spectrum from Tycho SNR both at better than 3 omega confidence. The best two component models are: bremsstrahlung (kT=2.67 +/- 0.13 keV) + bremsstrahlung (kT=7.07 +/- 2.21/1.72 keV) or bremsstrahlung (kT=2.36 +/- 0.21/0.57 keV) + power-law (gamma=2.58 +/- 0.12/0.09 ). This result is an improvement compaxed with the previous most sensitive X-ray measurements by Ginga which shows Tycho's observed X-ray continuum requires a two-component model to yield acceptable fits with the hard component parameters being highly uncertain. Our RXTE measurements constrain all parameter within 3o, ranges. However, we cannot yet distinguish between thermal and nonthermal models for the hard component. In the followings, we describe what we accomplished in the period covered by the grant proposal.

Stellar Absorption Line Analysis of Local Star-forming Galaxies: The Relation between Stellar Mass, Metallicity, Dust Attenuation, and Star Formation Rate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jabran Zahid, H.; Kudritzki, Rolf-Peter; Ho, I-Ting

We analyze the optical continuum of star-forming galaxies in the Sloan Digital Sky Survey by fitting stacked spectra with stellar population synthesis models to investigate the relation between stellar mass, stellar metallicity, dust attenuation, and star formation rate. We fit models calculated with star formation and chemical evolution histories that are derived empirically from multi-epoch observations of the stellar mass–star formation rate and the stellar mass–gas-phase metallicity relations, respectively. We also fit linear combinations of single-burst models with a range of metallicities and ages. Star formation and chemical evolution histories are unconstrained for these models. The stellar mass–stellar metallicity relationsmore » obtained from the two methods agree with the relation measured from individual supergiant stars in nearby galaxies. These relations are also consistent with the relation obtained from emission-line analysis of gas-phase metallicity after accounting for systematic offsets in the gas-phase metallicity. We measure dust attenuation of the stellar continuum and show that its dependence on stellar mass and star formation rate is consistent with previously reported results derived from nebular emission lines. However, stellar continuum attenuation is smaller than nebular emission line attenuation. The continuum-to-nebular attenuation ratio depends on stellar mass and is smaller in more massive galaxies. Our consistent analysis of stellar continuum and nebular emission lines paves the way for a comprehensive investigation of stellar metallicities of star-forming and quiescent galaxies.« less

Statistical Model of Dynamic Markers of the Alzheimer's Pathological Cascade.

PubMed

Balsis, Steve; Geraci, Lisa; Benge, Jared; Lowe, Deborah A; Choudhury, Tabina K; Tirso, Robert; Doody, Rachelle S

2018-05-05

Alzheimer's disease (AD) is a progressive disease reflected in markers across assessment modalities, including neuroimaging, cognitive testing, and evaluation of adaptive function. Identifying a single continuum of decline across assessment modalities in a single sample is statistically challenging because of the multivariate nature of the data. To address this challenge, we implemented advanced statistical analyses designed specifically to model complex data across a single continuum. We analyzed data from the Alzheimer's Disease Neuroimaging Initiative (ADNI; N = 1,056), focusing on indicators from the assessments of magnetic resonance imaging (MRI) volume, fluorodeoxyglucose positron emission tomography (FDG-PET) metabolic activity, cognitive performance, and adaptive function. Item response theory was used to identify the continuum of decline. Then, through a process of statistical scaling, indicators across all modalities were linked to that continuum and analyzed. Findings revealed that measures of MRI volume, FDG-PET metabolic activity, and adaptive function added measurement precision beyond that provided by cognitive measures, particularly in the relatively mild range of disease severity. More specifically, MRI volume, and FDG-PET metabolic activity become compromised in the very mild range of severity, followed by cognitive performance and finally adaptive function. Our statistically derived models of the AD pathological cascade are consistent with existing theoretical models.

Mapping local deformation behavior in single cell metal lattice structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlton, Holly D.; Lind, Jonathan; Messner, Mark C.

The deformation behavior of metal lattice structures is extremely complex and challenging to predict, especially since strain is not uniformly distributed throughout the structure. Understanding and predicting the failure behavior for these types of light-weighting structures is of great interest due to the excellent scaling of stiffness- and strength-to weight ratios they display. Therefore, there is a need to perform simplified experiments that probe unit cell mechanisms. This study reports on high resolution mapping of the heterogeneous structural response of single unit cells to the macro-scale loading condition. Two types of structures, known to show different stress-strain responses, were evaluatedmore » using synchrotron radiation micro-tomography while performing in-situ uniaxial compression tests to capture the local micro-strain deformation. These structures included the octet-truss, a stretch-dominated lattice, and the rhombic-dodecahedron, a bend-dominated lattice. The tomographic analysis showed that the stretch- and bend-dominated lattices exhibit different failure mechanisms and that the defects built into the structure cause a heterogeneous localized deformation response. Also shown here is a change in failure mode for stretch-dominated lattices, where there appears to be a transition from buckling to plastic yielding for samples with a relative density between 10 and 20%. In conclusion, the experimental results were also used to inform computational studies designed to predict the mesoscale deformation behavior of lattice structures. Here an equivalent continuum model and a finite element model were used to predict both local strain fields and mechanical behavior of lattices with different topologies.« less

Mapping local deformation behavior in single cell metal lattice structures

DOE PAGES

Carlton, Holly D.; Lind, Jonathan; Messner, Mark C.; ...

2017-02-08

The deformation behavior of metal lattice structures is extremely complex and challenging to predict, especially since strain is not uniformly distributed throughout the structure. Understanding and predicting the failure behavior for these types of light-weighting structures is of great interest due to the excellent scaling of stiffness- and strength-to weight ratios they display. Therefore, there is a need to perform simplified experiments that probe unit cell mechanisms. This study reports on high resolution mapping of the heterogeneous structural response of single unit cells to the macro-scale loading condition. Two types of structures, known to show different stress-strain responses, were evaluatedmore » using synchrotron radiation micro-tomography while performing in-situ uniaxial compression tests to capture the local micro-strain deformation. These structures included the octet-truss, a stretch-dominated lattice, and the rhombic-dodecahedron, a bend-dominated lattice. The tomographic analysis showed that the stretch- and bend-dominated lattices exhibit different failure mechanisms and that the defects built into the structure cause a heterogeneous localized deformation response. Also shown here is a change in failure mode for stretch-dominated lattices, where there appears to be a transition from buckling to plastic yielding for samples with a relative density between 10 and 20%. In conclusion, the experimental results were also used to inform computational studies designed to predict the mesoscale deformation behavior of lattice structures. Here an equivalent continuum model and a finite element model were used to predict both local strain fields and mechanical behavior of lattices with different topologies.« less

Water Vapor Self-Continuum by Cavity Ring Down Spectroscopy in the 1.6 Micron Transparency Window

NASA Astrophysics Data System (ADS)

Campargue, Alain; Kassi, Samir; Mondelain, Didier

2014-06-01

Since its discovery one century ago, a deep and unresolved controversy remains on the nature of the water vapor continuum. Several interpretations are proposed: accumulated effect of the distant wings of many individual spectral lines, metastable or true bound water dimers, collision-induced absorption. The atmospheric science community has largely sidestepped this controversy, and has adopted a pragmatic approach: most radiative transfer codes used in climate modelling, numerical weather prediction and remote sensing use the MT_CKD model which is a semi-empirical formulation of the continuum The MT_CKD cross-sections were tuned to available observations in the mid-infrared but in the absence of experimental constraints, the extrapolated near infrared (NIR) values are much more hazardous. Due to the weakness of the broadband absorption signal to be measured, very few measurements of the water vapor continuum are available in the NIR windows especially for temperature conditions relevant for our atmosphere. This is in particular the case for the 1.6 μm window where the very few available measurements show a large disagreement. Here we present the first measurements of the water vapor self-continuum cross-sections in the 1.6 μm window by cavity ring down spectroscopy (CRDS). The pressure dependence of the absorption continuum was investigated during pressure cycles up to 12 Torr for selected wavenumber values. The continuum level is observed to deviate from the expected quadratic dependence with pressure. This deviation is interpreted as due to a significant contribution of water adsorbed on the super mirrors to the cavity loss rate. The pressure dependence is well reproduced by a second order polynomial. We interpret the linear and quadratic terms as the adsorbed water and vapour water contribution, respectively. The derived self-continuum cross sections, measured between 5875 and 6450 wn, shows a minimum value around 6300 wn. These cross sections will be compared to the existing experimental data and models, especially to recent FTS measurements and to the last version of the MT_CKD 2.5 model. Mlawer, E.J., V.H. Payne, J.L. Moncet, et al. (2012), Phil. Trans. R. Soc. A, 370, 2520-2556. Mondelain, D., A. Aradj, S. Kassi, et al. (2013), JQSRT, 130, 381-391.

HYDROGEN BALMER CONTINUUM IN SOLAR FLARES DETECTED BY THE INTERFACE REGION IMAGING SPECTROGRAPH (IRIS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heinzel, P.; Kleint, L., E-mail: pheinzel@asu.cas.cz

We present a novel observation of the white light flare (WLF) continuum, which was significantly enhanced during the X1 flare on 2014 March 29 (SOL2014-03-29T17:48). Data from the Interface Region Imaging Spectrograph (IRIS) in its near-UV channel show that at the peak of the continuum enhancement, the contrast at the quasi-continuum window above 2813 Å reached 100%-200% and can be even larger closer to Mg II lines. This is fully consistent with the hydrogen recombination Balmer-continuum emission, which follows an impulsive thermal and non-thermal ionization caused by the precipitation of electron beams through the chromosphere. However, a less probable photosphericmore » continuum enhancement cannot be excluded. The light curves of the Balmer continuum have an impulsive character with a gradual fading, similar to those detected recently in the optical region on the Solar Optical Telescope on board Hinode. This observation represents a first Balmer-continuum detection from space far beyond the Balmer limit (3646 Å), eliminating seeing effects known to complicate the WLF detection. Moreover, we use a spectral window so far unexplored for flare studies, which provides the potential to study the Balmer continuum, as well as many metallic lines appearing in emission during flares. Combined with future ground-based observations of the continuum near the Balmer limit, we will be able to disentangle various scenarios of the WLF origin. IRIS observations also provide a critical quantitative measure of the energy radiated in the Balmer continuum, which constrains various models of the energy transport and deposit during flares.« less

Quantum mechanical/molecular mechanical/continuum style solvation model: second order Møller-Plesset perturbation theory.

PubMed

Thellamurege, Nandun M; Si, Dejun; Cui, Fengchao; Li, Hui

2014-05-07

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.

Waste IPSC : Thermal-Hydrologic-Chemical-Mechanical (THCM) modeling and simulation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freeze, Geoffrey A.; Wang, Yifeng; Arguello, Jose Guadalupe, Jr.

2010-10-01

Waste IPSC Objective is to develop an integrated suite of high performance computing capabilities to simulate radionuclide movement through the engineered components and geosphere of a radioactive waste storage or disposal system: (1) with robust thermal-hydrologic-chemical-mechanical (THCM) coupling; (2) for a range of disposal system alternatives (concepts, waste form types, engineered designs, geologic settings); (3) for long time scales and associated large uncertainties; (4) at multiple model fidelities (sub-continuum, high-fidelity continuum, PA); and (5) in accordance with V&V and software quality requirements. THCM Modeling collaborates with: (1) Other Waste IPSC activities: Sub-Continuum Processes (and FMM), Frameworks and Infrastructure (and VU,more » ECT, and CT); (2) Waste Form Campaign; (3) Used Fuel Disposition (UFD) Campaign; and (4) ASCEM.« less

Continuum Lowering and Fermi-Surface Rising in Strongly Coupled and Degenerate Plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, S. X.

Here, continuum lowering is a well-known and important physics concept that describes the ionization potential depression (IPD) in plasmas caused by thermal-/pressure-induced ionization of outer-shell electrons. The existing IPD models are often used to characterize plasma conditions and to gauge opacity calculations. Recent precision measurements have revealed deficits in our understanding of continuum lowering in dense hot plasmas. However, these investigations have so far been limited to IPD in strongly coupled but nondegenerate plasmas. Here, we report a first-principles study of the K-edge shifting in both strongly coupled and fully degenerate carbon plasmas, with quantum molecular dynamics (QMD) calculations basedmore » on the all-electron density-functional theory (DFT). The resulted K-edge shifting versus plasma density, as a probe to the continuum lowering and the Fermi-surface rising, is found to be significantly different from predictions of existing IPD models. In contrast, a simple model of “single atom in box” (SAIB), developed in this work, accurately predicts K-edge locations as what ab-initio calculations provide.« less

Continuum vs. spring network models of airway-parenchymal interdependence

PubMed Central

Ma, Baoshun

2012-01-01

The outward tethering forces exerted by the lung parenchyma on the airways embedded within it are potent modulators of the ability of the airway smooth muscle to shorten. Much of our understanding of these tethering forces is based on treating the parenchyma as an elastic continuum; yet, on a small enough scale, the lung parenchyma in two dimensions would seem to be more appropriately described as a discrete spring network. We therefore compared how the forces and displacements in the parenchyma surrounding a contracting airway are predicted to differ depending on whether the parenchyma is modeled as an elastic continuum or as a spring network. When the springs were arranged hexagonally to represent alveolar walls, the predicted parenchymal stresses and displacements propagated substantially farther away from the airway than when the springs were arranged in a triangular pattern or when the parenchyma was modeled as a continuum. Thus, to the extent that the parenchyma in vivo behaves as a hexagonal spring network, our results suggest that the range of interdependence forces due to airway contraction may have a greater influence than was previously thought. PMID:22500006

Continuum Lowering and Fermi-Surface Rising in Strongly Coupled and Degenerate Plasmas

DOE PAGES

Hu, S. X.

2017-08-10

Here, continuum lowering is a well-known and important physics concept that describes the ionization potential depression (IPD) in plasmas caused by thermal-/pressure-induced ionization of outer-shell electrons. The existing IPD models are often used to characterize plasma conditions and to gauge opacity calculations. Recent precision measurements have revealed deficits in our understanding of continuum lowering in dense hot plasmas. However, these investigations have so far been limited to IPD in strongly coupled but nondegenerate plasmas. Here, we report a first-principles study of the K-edge shifting in both strongly coupled and fully degenerate carbon plasmas, with quantum molecular dynamics (QMD) calculations basedmore » on the all-electron density-functional theory (DFT). The resulted K-edge shifting versus plasma density, as a probe to the continuum lowering and the Fermi-surface rising, is found to be significantly different from predictions of existing IPD models. In contrast, a simple model of “single atom in box” (SAIB), developed in this work, accurately predicts K-edge locations as what ab-initio calculations provide.« less

LTE modeling of inhomogeneous chromospheric structure using high-resolution limb observations

NASA Technical Reports Server (NTRS)

Lindsey, C.

1987-01-01

The paper discusses considerations relevant to LTE modeling of rough atmospheres. Particular attention is given to the application of recent high-resolution observations of the solar limb in the far-infrared and radio continuum to the modeling of chromospheric spicules. It is explained how the continuum limb observations can be combined with morphological knowledge of spicule structure to model the physical conditions in chromospheric spicules. This discussion forms the basis for a chromospheric model presented in a parallel publication based on observations ranging from 100 microns to 2.6 mm.

Co- and post-seismic shallow fault physics from near-field geodesy, seismic tomography, and mechanical modeling

NASA Astrophysics Data System (ADS)

Nevitt, J.; Brooks, B. A.; Catchings, R.; Goldman, M.; Criley, C.; Chan, J. H.; Glennie, C. L.; Ericksen, T. L.; Madugo, C. M.

2017-12-01

The physics governing near-surface fault slip and deformation are largely unknown, introducing significant uncertainty into seismic hazard models. Here we combine near-field measurements of surface deformation from the 2014 M6.0 South Napa earthquake with high-resolution seismic imaging and finite element models to investigate the effects of rupture speed, elastic heterogeneities, and plasticity on shallow faulting. We focus on two sites that experienced either predominantly co-seismic or post-seismic slip. We measured surface deformation with mobile laser scanning of deformed vine rows within 300 m of the fault at 1 week and 1 month after the event. Shear strain profiles for the co- and post-seismic sites are similar, with maxima of 0.012 and 0.013 and values exceeding 0.002 occurring within 26 m- and 18 m-wide zones, respectively. That the rupture remained buried at the two sites and produced similar deformation fields suggests that permanent deformation due to dynamic stresses did not differ significantly from the quasi-static case, which might be expected if the rupture decelerated as it approached the surface. Active-source seismic surveys, 120 m in length with 1 m geophone/shot spacing, reveal shallow compliant zones of reduced shear modulus. For the co- and post-seismic sites, the tomographic anomaly (Vp/Vs > 5) at 20 m depth has a width of 80 m and 50 m, respectively, much wider than the observed surface displacement fields. We investigate this discrepancy with a suite of finite element models in which a planar fault is buried 5 m below the surface. The model continuum is defined by either homogeneous or heterogeneous elastic properties, with or without Drucker-Prager plastic yielding, with properties derived from lab testing of similar near-surface materials. We find that plastic yielding can greatly narrow the surface displacement zone, but that the width of this zone is largely insensitive to changes in the elastic structure (i.e., the presence of a compliant zone).

An Off-Lattice Hybrid Discrete-Continuum Model of Tumor Growth and Invasion

PubMed Central

Jeon, Junhwan; Quaranta, Vito; Cummings, Peter T.

2010-01-01

Abstract We have developed an off-lattice hybrid discrete-continuum (OLHDC) model of tumor growth and invasion. The continuum part of the OLHDC model describes microenvironmental components such as matrix-degrading enzymes, nutrients or oxygen, and extracellular matrix (ECM) concentrations, whereas the discrete portion represents individual cell behavior such as cell cycle, cell-cell, and cell-ECM interactions and cell motility by the often-used persistent random walk, which can be depicted by the Langevin equation. Using this framework of the OLHDC model, we develop a phenomenologically realistic and bio/physically relevant model that encompasses the experimentally observed superdiffusive behavior (at short times) of mammalian cells. When systemic simulations based on the OLHDC model are performed, tumor growth and its morphology are found to be strongly affected by cell-cell adhesion and haptotaxis. There is a combination of the strength of cell-cell adhesion and haptotaxis in which fingerlike shapes, characteristic of invasive tumor, are observed. PMID:20074513

Modeling two-phase flow in PEM fuel cell channels

NASA Astrophysics Data System (ADS)

Wang, Yun; Basu, Suman; Wang, Chao-Yang

2008-05-01

This paper is concerned with the simultaneous flow of liquid water and gaseous reactants in mini-channels of a proton exchange membrane (PEM) fuel cell. Envisaging the mini-channels as structured and ordered porous media, we develop a continuum model of two-phase channel flow based on two-phase Darcy's law and the M2 formalism, which allow estimate of the parameters key to fuel cell operation such as overall pressure drop and liquid saturation profiles along the axial flow direction. Analytical solutions of liquid water saturation and species concentrations along the channel are derived to explore the dependences of these physical variables vital to cell performance on operating parameters such as flow stoichiometric ratio and relative humility. The two-phase channel model is further implemented for three-dimensional numerical simulations of two-phase, multi-component transport in a single fuel-cell channel. Three issues critical to optimizing channel design and mitigating channel flooding in PEM fuel cells are fully discussed: liquid water buildup towards the fuel cell outlet, saturation spike in the vicinity of flow cross-sectional heterogeneity, and two-phase pressure drop. Both the two-phase model and analytical solutions presented in this paper may be applicable to more general two-phase flow phenomena through mini- and micro-channels.

Non-uniform Continuum Model for Solvated Species Based on Frozen-Density Embedding Theory: The Study Case of Solvatochromism of Coumarin 153.

PubMed

Shedge, Sapana V; Zhou, Xiuwen; Wesolowski, Tomasz A

2014-09-01

Recent application of the Frozen-Density Embedding Theory based continuum model of the solvent, which is used for calculating solvatochromic shifts in the UV/Vis range, are reviewed. In this model, the solvent is represented as a non-uniform continuum taking into account both the statistical nature of the solvent and specific solute-solvent interactions. It offers, therefore, a computationally attractive alternative to methods in which the solvent is described at atomistic level. The evaluation of the solvatochromic shift involves only two calculations of excitation energy instead of at least hundreds needed to account for inhomogeneous broadening. The present review provides a detailed graphical analysis of the key quantities of this model: the average charge density of the solvent (<ρB>) and the corresponding Frozen-Density Embedding Theory derived embedding potential for coumarin 153.

A continuum model of transcriptional bursting

PubMed Central

Corrigan, Adam M; Tunnacliffe, Edward; Cannon, Danielle; Chubb, Jonathan R

2016-01-01

Transcription occurs in stochastic bursts. Early models based upon RNA hybridisation studies suggest bursting dynamics arise from alternating inactive and permissive states. Here we investigate bursting mechanism in live cells by quantitative imaging of actin gene transcription, combined with molecular genetics, stochastic simulation and probabilistic modelling. In contrast to early models, our data indicate a continuum of transcriptional states, with a slowly fluctuating initiation rate converting the gene between different levels of activity, interspersed with extended periods of inactivity. We place an upper limit of 40 s on the lifetime of fluctuations in elongation rate, with initiation rate variations persisting an order of magnitude longer. TATA mutations reduce the accessibility of high activity states, leaving the lifetime of on- and off-states unchanged. A continuum or spectrum of gene states potentially enables a wide dynamic range for cell responses to stimuli. DOI: http://dx.doi.org/10.7554/eLife.13051.001 PMID:26896676

Combined binary collision and continuum mechanics model applied to focused ion beam milling of a silicon membrane

NASA Astrophysics Data System (ADS)

Hobler, Gerhard

2015-06-01

Many experiments indicate the importance of stress and stress relaxation upon ion implantation. In this paper, a model is proposed that is capable of describing ballistic effects as well as stress relaxation by viscous flow. It combines atomistic binary collision simulation with continuum mechanics. The only parameters that enter the continuum model are the bulk modulus and the radiation-induced viscosity. The shear modulus can also be considered but shows only minor effects. A boundary-fitted grid is proposed that is usable both during the binary collision simulation and for the spatial discretization of the force balance equations. As an application, the milling of a slit into an amorphous silicon membrane with a 30 keV focused Ga beam is studied, which demonstrates the relevance of the new model compared to a more heuristic approach used in previous work.

Evaporation in Capillary Porous Media at the Perfect Piston-Like Invasion Limit: Evidence of Nonlocal Equilibrium Effects

NASA Astrophysics Data System (ADS)

Attari Moghaddam, Alireza; Prat, Marc; Tsotsas, Evangelos; Kharaghani, Abdolreza

2017-12-01

The classical continuum modeling of evaporation in capillary porous media is revisited from pore network simulations of the evaporation process. The computed moisture diffusivity is characterized by a minimum corresponding to the transition between liquid and vapor transport mechanisms confirming previous interpretations. Also the study suggests an explanation for the scattering generally observed in the moisture diffusivity obtained from experimental data. The pore network simulations indicate a noticeable nonlocal equilibrium effect leading to a new interpretation of the vapor pressure-saturation relationship classically introduced to obtain the one-equation continuum model of evaporation. The latter should not be understood as a desorption isotherm as classically considered but rather as a signature of a nonlocal equilibrium effect. The main outcome of this study is therefore that nonlocal equilibrium two-equation model must be considered for improving the continuum modeling of evaporation.

Toward lattice fractional vector calculus

NASA Astrophysics Data System (ADS)

Tarasov, Vasily E.

2014-09-01

An analog of fractional vector calculus for physical lattice models is suggested. We use an approach based on the models of three-dimensional lattices with long-range inter-particle interactions. The lattice analogs of fractional partial derivatives are represented by kernels of lattice long-range interactions, where the Fourier series transformations of these kernels have a power-law form with respect to wave vector components. In the continuum limit, these lattice partial derivatives give derivatives of non-integer order with respect to coordinates. In the three-dimensional description of the non-local continuum, the fractional differential operators have the form of fractional partial derivatives of the Riesz type. As examples of the applications of the suggested lattice fractional vector calculus, we give lattice models with long-range interactions for the fractional Maxwell equations of non-local continuous media and for the fractional generalization of the Mindlin and Aifantis continuum models of gradient elasticity.

Development and application of computational aerothermodynamics flowfield computer codes

NASA Technical Reports Server (NTRS)

Venkatapathy, Ethiraj

1993-01-01

Computations are presented for one-dimensional, strong shock waves that are typical of those that form in front of a reentering spacecraft. The fluid mechanics and thermochemistry are modeled using two different approaches. The first employs traditional continuum techniques in solving the Navier-Stokes equations. The second-approach employs a particle simulation technique (the direct simulation Monte Carlo method, DSMC). The thermochemical models employed in these two techniques are quite different. The present investigation presents an evaluation of thermochemical models for nitrogen under hypersonic flow conditions. Four separate cases are considered. The cases are governed, respectively, by the following: vibrational relaxation; weak dissociation; strong dissociation; and weak ionization. In near-continuum, hypersonic flow, the nonequilibrium thermochemical models employed in continuum and particle simulations produce nearly identical solutions. Further, the two approaches are evaluated successfully against available experimental data for weakly and strongly dissociating flows.

Physical Habitat and Energy Inputs Determine Freshwater Invertebrate Communities in Reference and Cranberry Farm Impacted Northeastern Coastal Zone Streams

NASA Astrophysics Data System (ADS)

Lander, D. M. P.; McCanty, S. T.; Dimino, T. F.; Christian, A. D.

2016-02-01

The River Continuum Concept (RCC) predicts stream biological communities based on dominant physical structures and energy inputs into streams and predicts how these features and corresponding communities change along the stream continuum. Verifying RCC expectations is important for creating valid points of comparison during stream ecosystem evaluation. These reference expectations are critical for restoration projects, such as the restoration of decommissioned cranberry bogs. Our research compares the physical habitat and freshwater invertebrate functional feeding groups (FWIFFG) of reference, active cranberry farming, and cranberry farm passive restoration sites in Northeastern Coastal Zone streams of Massachusetts to the specific RCC FWIFFG predictions. We characterized stream physical habitat using a semi-quantitative habitat characterization protocol and sampled freshwater invertebrates using the U.S. EPA standard 20-jab multi-habitat protocol. We expected that stream habitat would be most homogeneous at active farming stations, intermediate at restoration stations, and most heterogeneous at reference stations. Furthermore, we expected reference stream FWIFFG would be accurately predicted by the RCC and distributions at restoration and active sites would vary significantly. Habitat data was analyzed using a principle component analysis and results confirmed our predictions showing more homogeneous habitat for the active and reference stations, while showing a more heterogeneous habitat at the reference stations. The FWIFFG chi-squared analysis showed significant deviation from our specific RCC FWIFFG predictions. Because published FWIFFG distributions did not match our empirical values for a least disturbed Northeastern Coastal Zone headwater stream, using our data as a community structure template for current and future restoration projects is not recommend without further considerations.

Continuous Shape Estimation of Continuum Robots Using X-ray Images

PubMed Central

Lobaton, Edgar J.; Fu, Jinghua; Torres, Luis G.; Alterovitz, Ron

2015-01-01

We present a new method for continuously and accurately estimating the shape of a continuum robot during a medical procedure using a small number of X-ray projection images (e.g., radiographs or fluoroscopy images). Continuum robots have curvilinear structure, enabling them to maneuver through constrained spaces by bending around obstacles. Accurately estimating the robot’s shape continuously over time is crucial for the success of procedures that require avoidance of anatomical obstacles and sensitive tissues. Online shape estimation of a continuum robot is complicated by uncertainty in its kinematic model, movement of the robot during the procedure, noise in X-ray images, and the clinical need to minimize the number of X-ray images acquired. Our new method integrates kinematics models of the robot with data extracted from an optimally selected set of X-ray projection images. Our method represents the shape of the continuum robot over time as a deformable surface which can be described as a linear combination of time and space basis functions. We take advantage of probabilistic priors and numeric optimization to select optimal camera configurations, thus minimizing the expected shape estimation error. We evaluate our method using simulated concentric tube robot procedures and demonstrate that obtaining between 3 and 10 images from viewpoints selected by our method enables online shape estimation with errors significantly lower than using the kinematic model alone or using randomly spaced viewpoints. PMID:26279960

Continuous Shape Estimation of Continuum Robots Using X-ray Images.

PubMed

Lobaton, Edgar J; Fu, Jinghua; Torres, Luis G; Alterovitz, Ron

2013-05-06

We present a new method for continuously and accurately estimating the shape of a continuum robot during a medical procedure using a small number of X-ray projection images (e.g., radiographs or fluoroscopy images). Continuum robots have curvilinear structure, enabling them to maneuver through constrained spaces by bending around obstacles. Accurately estimating the robot's shape continuously over time is crucial for the success of procedures that require avoidance of anatomical obstacles and sensitive tissues. Online shape estimation of a continuum robot is complicated by uncertainty in its kinematic model, movement of the robot during the procedure, noise in X-ray images, and the clinical need to minimize the number of X-ray images acquired. Our new method integrates kinematics models of the robot with data extracted from an optimally selected set of X-ray projection images. Our method represents the shape of the continuum robot over time as a deformable surface which can be described as a linear combination of time and space basis functions. We take advantage of probabilistic priors and numeric optimization to select optimal camera configurations, thus minimizing the expected shape estimation error. We evaluate our method using simulated concentric tube robot procedures and demonstrate that obtaining between 3 and 10 images from viewpoints selected by our method enables online shape estimation with errors significantly lower than using the kinematic model alone or using randomly spaced viewpoints.

Dissipation consistent fabric tensor definition from DEM to continuum for granular media

NASA Astrophysics Data System (ADS)

Li, X. S.; Dafalias, Y. F.

2015-05-01

In elastoplastic soil models aimed at capturing the impact of fabric anisotropy, a necessary ingredient is a measure of anisotropic fabric in the form of an evolving tensor. While it is possible to formulate such a fabric tensor based on indirect phenomenological observations at the continuum level, it is more effective and insightful to have the tensor defined first based on direct particle level microstructural observations and subsequently deduce a corresponding continuum definition. A practical means able to provide such observations, at least in the context of fabric evolution mechanisms, is the discrete element method (DEM). Some DEM defined fabric tensors such as the one based on the statistics of interparticle contact normals have already gained widespread acceptance as a quantitative measure of fabric anisotropy among researchers of granular material behavior. On the other hand, a fabric tensor in continuum elastoplastic modeling has been treated as a tensor-valued internal variable whose evolution must be properly linked to physical dissipation. Accordingly, the adaptation of a DEM fabric tensor definition to a continuum constitutive modeling theory must be thermodynamically consistent in regards to dissipation mechanisms. The present paper addresses this issue in detail, brings up possible pitfalls if such consistency is violated and proposes remedies and guidelines for such adaptation within a recently developed Anisotropic Critical State Theory (ACST) for granular materials.

Numerical simulations of continuum-driven winds of super-Eddington stars

NASA Astrophysics Data System (ADS)

van Marle, A. J.; Owocki, S. P.; Shaviv, N. J.

2008-09-01

We present the results of numerical simulations of continuum-driven winds of stars that exceed the Eddington limit and compare these against predictions from earlier analytical solutions. Our models are based on the assumption that the stellar atmosphere consists of clumped matter, where the individual clumps have a much larger optical thickness than the matter between the clumps. This `porosity' of the stellar atmosphere reduces the coupling between radiation and matter, since photons tend to escape through the more tenuous gas between the clumps. This allows a star that formally exceeds the Eddington limit to remain stable, yet produce a steady outflow from the region where the clumps become optically thin. We have made a parameter study of wind models for a variety of input conditions in order to explore the properties of continuum-driven winds. The results show that the numerical simulations reproduce quite closely the analytical scalings. The mass-loss rates produced in our models are much larger than can be achieved by line driving. This makes continuum driving a good mechanism to explain the large mass-loss and flow speeds of giant outbursts, as observed in η Carinae and other luminous blue variable stars. Continuum driving may also be important in population III stars, since line driving becomes ineffective at low metallicities. We also explore the effect of photon tiring and the limits it places on the wind parameters.

Reverberation Mapping of the Continuum Source in Active Galactic Nuclei

NASA Astrophysics Data System (ADS)

Fausnaugh, Michael Martin

I present results from a monitoring campaign of 11 active galactic nuclei (AGN) conducted in Spring of 2014. I use the reverberation mapping method to probe the interior structures of the AGN, specifically the broad line regions (BLRs) and accretion disks. One of these AGN, NGC 5548, was also subject to multi-wavelength (X-ray, UV, optical, and near-IR) monitoring using 25 ground-based telescopes and four space-based facilities. For NGC 5548, I detect lags between the continuum emission at different wavelengths that follow a trend consistent with the prediction for continuum reprocessing by an accretion disk with temperature profile T ∝ R -3/4. However, the lags imply a disk radius that is 3 times larger than the prediction from standard thin-disk models. The lags at wavelengths longer than the Vband are also equal to or greater than the lags of high-ionization-state emission lines (such as HeII lambda1640 and lambda4686), suggesting that the continuum-emitting source is of a physical size comparable to the inner broad-line region. Using optical spectra from the Large Binocular Telescope, I estimate the bias of the interband continuum lags due to BLR emission observed in the filters, and I find that the bias for filters with high levels of BLR contamination (˜20%) can be important for the shortest continuum lags. This likely has a significant impact on the u and U bands owing to Balmer continuum emission. I then develop a new procedure for the internal (night-to-night) calibration of time series spectra that can reach precisions of ˜1 millimagnitude and improves traditional techniques by up to a factor of 5. At this level, other systematic issues (e.g., the nightly sensitivity functions and Fe II contamination) limit the final precision of the observed light curves. Using the new calibration method, I next present the data and first results from the optical spectroscopic monitoring component of the reverberation mapping campaign. Five AGN were sufficiently variable to measure continuum-Hbeta lags and super-massive black hole masses: MCG+08-11-011, NGC 2617, NGC 4051, 3C 382, and Mrk 374. I also obtain Hgamma and HeII lags for all objects except 3C 382. The HeII lags indicate radial stratification of the BLR, and the masses derived from different emission lines are in general agreement. The relative responsivities of these lines to continuum variations are also in qualitative agreement with photoionization models. Finally, I measure optical continuum lags for the two most variable targets, MCG+08-11-011 and NGC 2617. I again find lags consistent with geometrically thin accretion-disk models that have temperature profiles T ∝ R-3/4. The observed lags are larger than predictions based on standard thin-disk theory by factors of 3.3 for MCG+08-11-011 and 2.3 for NGC 2617. Using a physical model, these differences can be explained if the mass accretion rates are larger than inferred from the optical continuum luminosity by a factor of 4.3 in MCG+08-11-011 and a factor of 1.3 in NGC 2617. While the X-ray variability in NGC 2617 precedes the UV/optical variability, the long 2.6 day lag is problematic for coronal reprocessing models.

A Continuum Method for Determining Membrane Protein Insertion Energies and the Problem of Charged Residues

PubMed Central

Choe, Seungho; Hecht, Karen A.; Grabe, Michael

2008-01-01

Continuum electrostatic approaches have been extremely successful at describing the charged nature of soluble proteins and how they interact with binding partners. However, it is unclear whether continuum methods can be used to quantitatively understand the energetics of membrane protein insertion and stability. Recent translation experiments suggest that the energy required to insert charged peptides into membranes is much smaller than predicted by present continuum theories. Atomistic simulations have pointed to bilayer inhomogeneity and membrane deformation around buried charged groups as two critical features that are neglected in simpler models. Here, we develop a fully continuum method that circumvents both of these shortcomings by using elasticity theory to determine the shape of the deformed membrane and then subsequently uses this shape to carry out continuum electrostatics calculations. Our method does an excellent job of quantitatively matching results from detailed molecular dynamics simulations at a tiny fraction of the computational cost. We expect that this method will be ideal for studying large membrane protein complexes. PMID:18474636

Characterization of double continuum formulations of transport through pore-scale information

NASA Astrophysics Data System (ADS)

Porta, G.; Ceriotti, G.; Bijeljic, B.

2016-12-01

Information on pore-scale characteristics is becoming increasingly available at unprecedented levels of detail from modern visualization/data-acquisition techniques. These advancements are not completely matched by corresponding developments of operational procedures according to which we can engineer theoretical findings aiming at improving our ability to reduce the uncertainty associated with the outputs of continuum-scale models to be employed at large scales. We present here a modeling approach which rests on pore-scale information to achieve a complete characterization of a double continuum model of transport and fluid-fluid reactive processes. Our model makes full use of pore-scale velocity distributions to identify mobile and immobile regions. We do so on the basis of a pointwise (in the pore space) evaluation of the relative strength of advection and diffusion time scales, as rendered by spatially variable values of local Péclet numbers. After mobile and immobile regions are demarcated, we build a simplified unit cell which is employed as a representative proxy of the real porous domain. This model geometry is then employed to simplify the computation of the effective parameters embedded in the double continuum transport model, while retaining relevant information from the pore-scale characterization of the geometry and velocity field. We document results which illustrate the applicability of the methodology to predict transport of a passive tracer within two- and three-dimensional media upon comparison with direct pore-scale numerical simulation of transport in the same geometrical settings. We also show preliminary results about the extension of this model to fluid-fluid reactive transport processes. In this context, we focus on results obtained in two-dimensional porous systems. We discuss the impact of critical quantities required as input to our modeling approach to obtain continuum-scale outputs. We identify the key limitations of the proposed methodology and discuss its capability also in comparison with alternative approaches grounded, e.g., on nonlocal and particle-based approximations.

Toward generalized continuum models of granular soil and granular soil-tire interaction: A combined discrete element and thermomicromechanical continuum analysis of densely packed assemblies

DTIC Science & Technology

2007-04-30

flow and deformation of soils in contact with metallic and/or rubber -like bodies” Proceedings, 13th International Conference of the ISTVS 1, pp 201-208...soil- tyre interaction problem”, Proceedings, First North American Workshop on Modeling the Mechanics of Off-Road Mobility. Paper GL-94-30 U.S

Non-Equilbrium Fermi Gases

DTIC Science & Technology

2016-02-02

understanding is the experimental verification of a new model of light-induced loss spectra, employing continuum-dressed basis states, which agrees in...and additional qualifiers separated by commas, e.g. Smith, Richard, J, Jr. 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES). Self -explanatory... verification of a new model of light-induced loss spectra, employing continuum-dressed basis states, which agrees in shape and magnitude with all of our

Atmospheric absorption of terahertz radiation and water vapor continuum effects

NASA Astrophysics Data System (ADS)

Slocum, David M.; Slingerland, Elizabeth J.; Giles, Robert H.; Goyette, Thomas M.

2013-09-01

The water vapor continuum absorption spectrum was investigated using Fourier Transform Spectroscopy. The transmission of broadband terahertz radiation from 0.300 to 1.500 THz was recorded for multiple path lengths and relative humidity levels. The absorption coefficient as a function of frequency was determined and compared with theoretical predictions and available water vapor absorption data. The prediction code is able to separately model the different parts of atmospheric absorption for a range of experimental conditions. A variety of conditions were accurately modeled using this code including both self and foreign gas broadening for low and high water vapor pressures for many different measurement techniques. The intensity and location of the observed absorption lines were also in good agreement with spectral databases. However, there was a discrepancy between the resonant line spectrum simulation and the observed absorption spectrum in the atmospheric transmission windows caused by the continuum absorption. A small discrepancy remained even after using the best available data from the literature to account for the continuum absorption. From the experimental and resonant line simulation spectra the air-broadening continuum parameter was calculated and compared with values available in the literature.

An oculomotor continuum from exploration to fixation

PubMed Central

Otero-Millan, Jorge; Macknik, Stephen L.; Langston, Rachel E.; Martinez-Conde, Susana

2013-01-01

During visual exploration, saccadic eye movements scan the scene for objects of interest. During attempted fixation, the eyes are relatively still but often produce microsaccades. Saccadic rates during exploration are higher than those of microsaccades during fixation, reinforcing the classic view that exploration and fixation are two distinct oculomotor behaviors. An alternative model is that fixation and exploration are not dichotomous, but are instead two extremes of a functional continuum. Here, we measured the eye movements of human observers as they either fixed their gaze on a small spot or scanned natural scenes of varying sizes. As scene size diminished, so did saccade rates, until they were continuous with microsaccadic rates during fixation. Other saccadic properties varied as function of image size as well, forming a continuum with microsaccadic parameters during fixation. This saccadic continuum extended to nonrestrictive, ecological viewing conditions that allowed all types of saccades and fixation positions. Eye movement simulations moreover showed that a single model of oculomotor behavior can explain the saccadic continuum from exploration to fixation, for images of all sizes. These findings challenge the view that exploration and fixation are dichotomous, suggesting instead that visual fixation is functionally equivalent to visual exploration on a spatially focused scale. PMID:23533278

Altered effective connectivity of default model brain network underlying amnestic MCI

NASA Astrophysics Data System (ADS)

Yan, Hao; Wang, Yonghui; Tian, Jie

2012-02-01

Mild cognitive impairment (MCI) is the transitional, heterogeneous continuum from healthy elderly to Alzheimer's disease (AD). Previous studies have shown that brain functional activity in the default mode network (DMN) is impaired in MCI patients. However, the altered effective connectivity of the DMN in MCI patients remains largely unknown. The present study combined an independent component analysis (ICA) approach with Granger causality analysis (mGCA) to investigate the effective connectivity within the DMN in 12 amnestic MCI patients and 12 age-matched healthy elderly. Compared to the healthy control, the MCI exhibited decreased functional activity in the posterior DMN regions, as well as a trend towards activity increases in anterior DMN regions. Results from mGCA further supported this conclusion that the causal influence projecting to the precuneus/PCC became much weaker in MCI, while stronger interregional interactions emerged within the frontal-parietal cortices. These findings suggested that abnormal effective connectivity within the DMN may elucidate the dysfunctional and compensatory processes in MCI brain networks.

Molecular Modeling of Lipid Membrane Curvature Induction by a Peptide: More than Simply Shape

PubMed Central

Sodt, Alexander J.; Pastor, Richard W.

2014-01-01

Molecular dynamics simulations of an amphipathic helix embedded in a lipid bilayer indicate that it will induce substantial positive curvature (e.g., a tube of diameter 20 nm at 16% surface coverage). The induction is twice that of a continuum model prediction that only considers the shape of the inclusion. The discrepancy is explained in terms of the additional presence of specific interactions described only by the molecular model. The conclusion that molecular shape alone is insufficient to quantitatively model curvature is supported by contrasting molecular and continuum models of lipids with large and small headgroups (choline and ethanolamine, respectively), and of the removal of a lipid tail (modeling a lyso-lipid). For the molecular model, curvature propensity is analyzed by computing the derivative of the free energy with respect to bending. The continuum model predicts that the inclusion will soften the bilayer near the headgroup region, an effect that may weaken curvature induction. The all-atom predictions are consistent with experimental observations of the degree of tubulation by amphipathic helices and variation of the free energy of binding to liposomes. PMID:24806928

A numerical study of different projection-based model reduction techniques applied to computational homogenisation

NASA Astrophysics Data System (ADS)

Soldner, Dominic; Brands, Benjamin; Zabihyan, Reza; Steinmann, Paul; Mergheim, Julia

2017-10-01

Computing the macroscopic material response of a continuum body commonly involves the formulation of a phenomenological constitutive model. However, the response is mainly influenced by the heterogeneous microstructure. Computational homogenisation can be used to determine the constitutive behaviour on the macro-scale by solving a boundary value problem at the micro-scale for every so-called macroscopic material point within a nested solution scheme. Hence, this procedure requires the repeated solution of similar microscopic boundary value problems. To reduce the computational cost, model order reduction techniques can be applied. An important aspect thereby is the robustness of the obtained reduced model. Within this study reduced-order modelling (ROM) for the geometrically nonlinear case using hyperelastic materials is applied for the boundary value problem on the micro-scale. This involves the Proper Orthogonal Decomposition (POD) for the primary unknown and hyper-reduction methods for the arising nonlinearity. Therein three methods for hyper-reduction, differing in how the nonlinearity is approximated and the subsequent projection, are compared in terms of accuracy and robustness. Introducing interpolation or Gappy-POD based approximations may not preserve the symmetry of the system tangent, rendering the widely used Galerkin projection sub-optimal. Hence, a different projection related to a Gauss-Newton scheme (Gauss-Newton with Approximated Tensors- GNAT) is favoured to obtain an optimal projection and a robust reduced model.

A software platform for continuum modeling of ion channels based on unstructured mesh

NASA Astrophysics Data System (ADS)

Tu, B.; Bai, S. Y.; Chen, M. X.; Xie, Y.; Zhang, L. B.; Lu, B. Z.

2014-01-01

Most traditional continuum molecular modeling adopted finite difference or finite volume methods which were based on a structured mesh (grid). Unstructured meshes were only occasionally used, but an increased number of applications emerge in molecular simulations. To facilitate the continuum modeling of biomolecular systems based on unstructured meshes, we are developing a software platform with tools which are particularly beneficial to those approaches. This work describes the software system specifically for the simulation of a typical, complex molecular procedure: ion transport through a three-dimensional channel system that consists of a protein and a membrane. The platform contains three parts: a meshing tool chain for ion channel systems, a parallel finite element solver for the Poisson-Nernst-Planck equations describing the electrodiffusion process of ion transport, and a visualization program for continuum molecular modeling. The meshing tool chain in the platform, which consists of a set of mesh generation tools, is able to generate high-quality surface and volume meshes for ion channel systems. The parallel finite element solver in our platform is based on the parallel adaptive finite element package PHG which wass developed by one of the authors [1]. As a featured component of the platform, a new visualization program, VCMM, has specifically been developed for continuum molecular modeling with an emphasis on providing useful facilities for unstructured mesh-based methods and for their output analysis and visualization. VCMM provides a graphic user interface and consists of three modules: a molecular module, a meshing module and a numerical module. A demonstration of the platform is provided with a study of two real proteins, the connexin 26 and hemolysin ion channels.

Constitutive Modeling of Nanotube-Reinforced Polymer Composites

NASA Technical Reports Server (NTRS)

Odegard, G. M.; Gates, T. S.; Wise, K. E.; Park, C.; Siochi, E. J.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

In this study, a technique is presented for developing constitutive models for polymer composite systems reinforced with single-walled carbon nanotubes (SWNT). Because the polymer molecules are on the same size scale as the nanotubes, the interaction at the polymer/nanotube interface is highly dependent on the local molecular structure and bonding. At these small length scales, the lattice structures of the nanotube and polymer chains cannot be considered continuous, and the bulk mechanical properties can no longer be determined through traditional micromechanical approaches that are formulated by using continuum mechanics. It is proposed herein that the nanotube, the local polymer near the nanotube, and the nanotube/polymer interface can be modeled as an effective continuum fiber using an equivalent-continuum modeling method. The effective fiber serves as a means for incorporating micromechanical analyses for the prediction of bulk mechanical properties of SWNT/polymer composites with various nanotube lengths, concentrations, and orientations. As an example, the proposed approach is used for the constitutive modeling of two SWNT/polyimide composite systems.

An incompressible two-dimensional multiphase particle-in-cell model for dense particle flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snider, D.M.; O`Rourke, P.J.; Andrews, M.J.

1997-06-01

A two-dimensional, incompressible, multiphase particle-in-cell (MP-PIC) method is presented for dense particle flows. The numerical technique solves the governing equations of the fluid phase using a continuum model and those of the particle phase using a Lagrangian model. Difficulties associated with calculating interparticle interactions for dense particle flows with volume fractions above 5% have been eliminated by mapping particle properties to a Eulerian grid and then mapping back computed stress tensors to particle positions. This approach utilizes the best of Eulerian/Eulerian continuum models and Eulerian/Lagrangian discrete models. The solution scheme allows for distributions of types, sizes, and density of particles,more » with no numerical diffusion from the Lagrangian particle calculations. The computational method is implicit with respect to pressure, velocity, and volume fraction in the continuum solution thus avoiding courant limits on computational time advancement. MP-PIC simulations are compared with one-dimensional problems that have analytical solutions and with two-dimensional problems for which there are experimental data.« less

Quantum mechanical/molecular mechanical/continuum style solvation model: Second order Møller-Plesset perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thellamurege, Nandun M.; Si, Dejun; Cui, Fengchao

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths ofmore » the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.« less

Numerical modelling of bifurcation and localisation in cohesive-frictional materials

NASA Astrophysics Data System (ADS)

de Borst, René

1991-12-01

Methods are reviewed for analysing highly localised failure and bifurcation modes in discretised mechanical systems as typically arise in numerical simulations of failure in soils, rocks, metals and concrete. By the example of a plane-strain biaxial test it is shown that strain softening and lack of normality in elasto-plastic constitutive equations and the ensuing loss of ellipticity of the governing field equations cause a pathological mesh dependence of numerical solutions for such problems, thus rendering the results effectively meaningless. The need for introduction of higher-order continuum models is emphasised to remedy this shortcoming of the conventional approach. For one such a continuum model, namely the unconstrained Cosserat continuum, it is demonstrated that meaningful and convergent solutions (in the sense that a finite width of the localisation zone is computed upon mesh refinement) can be obtained.

A continuum state variable theory to model the size-dependent surface energy of nanostructures.

PubMed

Jamshidian, Mostafa; Thamburaja, Prakash; Rabczuk, Timon

2015-10-14

We propose a continuum-based state variable theory to quantify the excess surface free energy density throughout a nanostructure. The size-dependent effect exhibited by nanoplates and spherical nanoparticles i.e. the reduction of surface energy with reducing nanostructure size is well-captured by our continuum state variable theory. Our constitutive theory is also able to predict the reducing energetic difference between the surface and interior (bulk) portions of a nanostructure with decreasing nanostructure size.

Computation of forces arising from the polarizable continuum model within the domain-decomposition paradigm

NASA Astrophysics Data System (ADS)

Gatto, Paolo; Lipparini, Filippo; Stamm, Benjamin

2017-12-01

The domain-decomposition (dd) paradigm, originally introduced for the conductor-like screening model, has been recently extended to the dielectric Polarizable Continuum Model (PCM), resulting in the ddPCM method. We present here a complete derivation of the analytical derivatives of the ddPCM energy with respect to the positions of the solute's atoms and discuss their efficient implementation. As it is the case for the energy, we observe a quadratic scaling, which is discussed and demonstrated with numerical tests.

Constitutive Relationships and Models in Continuum Theories of Multiphase Flows. [conferences

NASA Technical Reports Server (NTRS)

Decker, Rand (Editor)

1989-01-01

In April, 1989, a workshop on constitutive relationships and models in continuum theories of multiphase flows was held at NASA's Marshall Space Flight Center. Topics of constitutive relationships for the partial or per phase stresses, including the concept of solid phase pressure are discussed. Models used for the exchange of mass, momentum, and energy between the phases in a multiphase flow are also discussed. The program, abstracts, and texts of the presentations from the workshop are included.

Modeling of Pedestrian Flows Using Hybrid Models of Euler Equations and Dynamical Systems

NASA Astrophysics Data System (ADS)

Bärwolff, Günter; Slawig, Thomas; Schwandt, Hartmut

2007-09-01

In the last years various systems have been developed for controlling, planning and predicting the traffic of persons and vehicles, in particular under security aspects. Going beyond pure counting and statistical models, approaches were found to be very adequate and accurate which are based on well-known concepts originally developed in very different research areas, namely continuum mechanics and computer science. In the present paper, we outline a continuum mechanical approach for the description of pedestrain flow.

Dynamic Modelling for Planar Extensible Continuum Robot Manipulators

DTIC Science & Technology

2006-01-01

5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7... octopus arm [18]. The OCTARM, shown in Figure 1, is a three-section robot with nine degrees of freedom. Aside from two axis bending with constant... octopus arm. However, while allowing extensibility, the model is based on an approximation (by a Þnite number of linear models) to the true continuum

On the value of surface saturated area dynamics mapped with thermal infrared imagery for modeling the hillslope-riparian-stream continuum

NASA Astrophysics Data System (ADS)

Glaser, Barbara; Klaus, Julian; Frei, Sven; Frentress, Jay; Pfister, Laurent; Hopp, Luisa

2016-10-01

The highly dynamic processes within a hillslope-riparian-stream (HRS) continuum are known to affect streamflow generation, but are yet not fully understood. Within this study, we simulated a headwater HRS continuum in western Luxembourg with an integrated hydrologic surface subsurface model (HydroGeoSphere). The model was setup with thorough consideration of catchment-specific attributes and we performed a multicriteria model evaluation (4 years) with special focus on the temporally varying spatial patterns of surface saturation. We used a portable thermal infrared (TIR) camera to map surface saturation with a high spatial resolution and collected 20 panoramic snapshots of the riparian zone (approx. 10 m × 20 m) under different hydrologic conditions. Qualitative and quantitative comparison of the processed TIR panoramas and the corresponding model output panoramas revealed a good agreement between spatiotemporal dynamic model and field surface saturation patterns. A double logarithmic linear relationship between surface saturation extent and discharge was similar for modeled and observed data. This provided confidence in the capability of an integrated hydrologic surface subsurface model to represent temporal and spatial water flux dynamics at small (HRS continuum) scales. However, model scenarios with different parameterizations of the riparian zone showed that discharge and surface saturation were controlled by different parameters and hardly influenced each other. Surface saturation only affected very fast runoff responses with a small volumetric contribution to stream discharge, indicating that the dynamic surface saturation in the riparian zone does not necessarily imply a major control on runoff generation.

Dynamic analysis of Space Shuttle/RMS configuration using continuum approach

NASA Technical Reports Server (NTRS)

Ramakrishnan, Jayant; Taylor, Lawrence W., Jr.

1994-01-01

The initial assembly of Space Station Freedom involves the Space Shuttle, its Remote Manipulation System (RMS) and the evolving Space Station Freedom. The dynamics of this coupled system involves both the structural and the control system dynamics of each of these components. The modeling and analysis of such an assembly is made even more formidable by kinematic and joint nonlinearities. The current practice of modeling such flexible structures is to use finite element modeling in which the mass and interior dynamics is ignored between thousands of nodes, for each major component. The model characteristics of only tens of modes are kept out of thousands which are calculated. The components are then connected by approximating the boundary conditions and inserting the control system dynamics. In this paper continuum models are used instead of finite element models because of the improved accuracy, reduced number of model parameters, the avoidance of model order reduction, and the ability to represent the structural and control system dynamics in the same system of equations. Dynamic analysis of linear versions of the model is performed and compared with finite element model results. Additionally, the transfer matrix to continuum modeling is presented.

Does Severity of Depression Predict Magnitude of Productivity Loss?

PubMed Central

Beck, Arne; Crain, A. Lauren; Solberg, Leif I.; Unützer, Jürgen; Glasgow, Russell E.; Maciosek, Michael V.; Whitebird, Robin

2014-01-01

PURPOSE Depression is associated with lowered work functioning, including absence, productivity impairment, and decreased job retention. However, few studies have examined depression symptoms across a continuum of severity in relationship to the magnitude of work impairment in a large and heterogeneous patient population. This study assessed the relationship between depression symptom severity and productivity loss among patients initiated on antidepressants. METHODS Data were obtained from patients participating in the DIAMOND Initiative (Depression Improvement Across Minnesota: Offering a New Direction), a statewide quality improvement collaborative to provide enhanced depression care. Patients newly started on antidepressants were surveyed with the Patient Health Questionnaire (PHQ-9), a measure of depression symptom severity, the Work Productivity and Activity Impairment questionnaire (WPAI) a measure of productivity loss, and items on health status and demographics. RESULTS We analyzed data from the 771 patients who reported current employment. General linear models adjusting for demographics and health status showed a significant linear, monotonic relationship between depression symptom severity and productivity loss (p<.0001). Even minor levels of depression symptoms were associated with decrements in work function. Greater productivity loss also was associated with full-time vs. part-time employment status (p<.001), fair or poor health (p=.05), and “not coupled” marital status (p=.07). CONCLUSIONS This study illustrated the relationship between the severity of depression symptoms and work function, suggesting that even minor levels of depression are associated with productivity loss. Employers may find it beneficial to invest in effective treatments for employees across the continuum of depression severity. PMID:25295792

Isostaticity in Cosserat Continuum

DTIC Science & Technology

2012-01-01

Geotech . Eng. Div. 106(4), 419–433 (1980) 13. Walker, D.M., Tordesillas, A., Thornton, C., Behringer, R.P., Zhang, J., Peters, J.F.: Percolating contact...thermomicromechanical approach to multiscale continuum modeling of dense granular materials. Acta Geotech . 3, 225–240 (2008) 17. Oda, M., Takemura, T

Grain transport mechanics in shallow flow

USDA-ARS?s Scientific Manuscript database

A physical model based on continuum multiphase flow is described to represent saltating transport of grains in shallow overland flows. The two-phase continuum flow of water and sediment considers coupled St.Venant type equations. The interactive cumulative effect of grains is incorporated by a dispe...

Grain transport mechanics in shallow overland flow

USDA-ARS?s Scientific Manuscript database

A physical model based on continuum multiphase flow is described to represent saltating transport of grains in shallow overland flow. The two phase continuum flow of water and sediment considers coupled St.Venant type equations. The interactive cumulative effect of grains is incorporated by a disper...

Multi-Length Scale-Enriched Continuum-Level Material Model for Kevlar (registered trademark)-Fiber-Reinforced Polymer-Matrix Composites

DTIC Science & Technology

2013-03-01

of coarser-scale materials and structures containing Kevlar fibers (e.g., yarns, fabrics, plies, lamina, and laminates ). Journal of Materials...Multi-Length Scale-Enriched Continuum-Level Material Model for Kevlar -Fiber-Reinforced Polymer-Matrix Composites M. Grujicic, B. Pandurangan, J.S...extensive set of molecular-level computational analyses regarding the role of various microstructural/morphological defects on the Kevlar fiber

Continuum-kinetic-microscopic model of lung clearance due to core-annular fluid entrainment

PubMed Central

Mitran, Sorin

2013-01-01

The human lung is protected against aspirated infectious and toxic agents by a thin liquid layer lining the interior of the airways. This airway surface liquid is a bilayer composed of a viscoelastic mucus layer supported by a fluid film known as the periciliary liquid. The viscoelastic behavior of the mucus layer is principally due to long-chain polymers known as mucins. The airway surface liquid is cleared from the lung by ciliary transport, surface tension gradients, and airflow shear forces. This work presents a multiscale model of the effect of airflow shear forces, as exerted by tidal breathing and cough, upon clearance. The composition of the mucus layer is complex and variable in time. To avoid the restrictions imposed by adopting a viscoelastic flow model of limited validity, a multiscale computational model is introduced in which the continuum-level properties of the airway surface liquid are determined by microscopic simulation of long-chain polymers. A bridge between microscopic and continuum levels is constructed through a kinetic-level probability density function describing polymer chain configurations. The overall multiscale framework is especially suited to biological problems due to the flexibility afforded in specifying microscopic constituents, and examining the effects of various constituents upon overall mucus transport at the continuum scale. PMID:23729842

Continuum-kinetic-microscopic model of lung clearance due to core-annular fluid entrainment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitran, Sorin, E-mail: mitran@unc.edu

2013-07-01

The human lung is protected against aspirated infectious and toxic agents by a thin liquid layer lining the interior of the airways. This airway surface liquid is a bilayer composed of a viscoelastic mucus layer supported by a fluid film known as the periciliary liquid. The viscoelastic behavior of the mucus layer is principally due to long-chain polymers known as mucins. The airway surface liquid is cleared from the lung by ciliary transport, surface tension gradients, and airflow shear forces. This work presents a multiscale model of the effect of airflow shear forces, as exerted by tidal breathing and cough,more » upon clearance. The composition of the mucus layer is complex and variable in time. To avoid the restrictions imposed by adopting a viscoelastic flow model of limited validity, a multiscale computational model is introduced in which the continuum-level properties of the airway surface liquid are determined by microscopic simulation of long-chain polymers. A bridge between microscopic and continuum levels is constructed through a kinetic-level probability density function describing polymer chain configurations. The overall multiscale framework is especially suited to biological problems due to the flexibility afforded in specifying microscopic constituents, and examining the effects of various constituents upon overall mucus transport at the continuum scale.« less

Continuum-kinetic-microscopic model of lung clearance due to core-annular fluid entrainment

NASA Astrophysics Data System (ADS)

Mitran, Sorin

2013-07-01

The human lung is protected against aspirated infectious and toxic agents by a thin liquid layer lining the interior of the airways. This airway surface liquid is a bilayer composed of a viscoelastic mucus layer supported by a fluid film known as the periciliary liquid. The viscoelastic behavior of the mucus layer is principally due to long-chain polymers known as mucins. The airway surface liquid is cleared from the lung by ciliary transport, surface tension gradients, and airflow shear forces. This work presents a multiscale model of the effect of airflow shear forces, as exerted by tidal breathing and cough, upon clearance. The composition of the mucus layer is complex and variable in time. To avoid the restrictions imposed by adopting a viscoelastic flow model of limited validity, a multiscale computational model is introduced in which the continuum-level properties of the airway surface liquid are determined by microscopic simulation of long-chain polymers. A bridge between microscopic and continuum levels is constructed through a kinetic-level probability density function describing polymer chain configurations. The overall multiscale framework is especially suited to biological problems due to the flexibility afforded in specifying microscopic constituents, and examining the effects of various constituents upon overall mucus transport at the continuum scale.

Effect of drug particle size in ultrasound compacted tablets. Continuum percolation model approach.

PubMed

Millán, Mónica; Caraballo, Isidoro

2006-03-09

The main objective of this work is to study the influence of the drug particle size on the pharmaceutical availability of ultrasound compacted tablets. Inert matrix systems containing different drug particle sizes were prepared using both, an ultrasound-assisted press and a traditional eccentric machine. Potassium chloride was used as drug model and Eudragit RS-PM as matrix forming excipient. The excipient particle size was kept constant. The cross-sectional microphotographs of ultrasound tablets show the existence of a quasi-continuum medium. Keeping constant the drug load, US-tablets showed very similar release rates, whereas for traditional tablets, an increase in the particle size resulted in a clear decrease in the release rate. In these tablets, the excipient forms an almost continuum medium. In an infinite theoretical system of these characteristics, the size of the drug particles will not modify the percolation threshold. The percolation of the excipient in this system can be assimilated to a continuum percolation model. In accordance with the proposed model, a lower influence of the drug particle size on the drug release rate was obtained for the US-tablets in comparison with traditional tablets. This fact can be indicative of the similarity of the drug percolation thresholds in these systems.

Model Reduction in Biomechanics

NASA Astrophysics Data System (ADS)

Feng, Yan

The mechanical characteristic of the cell is primarily performed by the cytoskeleton. Microtubules, actin, and intermediate filaments are the three main cytoskeletal polymers. Of these, microtubules are the stiffest and have multiple functions within a cell that include: providing tracks for intracellular transport, transmitting the mechanical force necessary for cell division during mitosis, and providing sufficient stiffness for propulsion in flagella and cilia. Microtubule mechanics has been studied by a variety of methods: detailed molecular dynamics (MD), coarse-grained models, engineering type models, and elastic continuum models. In principle, atomistic MD simulations should be able to predict all desired mechanical properties of a single molecule, however, in practice the large computational resources are required to carry out a simulation of larger biomolecular system. Due to the limited accessibility using even the most ambitious all-atom models and the demand for the multiscale molecular modeling and simulation, the emergence of the reduced models is critically important to provide the capability for investigating the biomolecular dynamics that are critical to many biological processes. Then the coarse-grained models, such as elastic network models and anisotropic network models, have been shown to bequite accurate in predicting microtubule mechanical response, but still requires significant computational resources. On the other hand, the microtubule is treated as comprising materials with certain continuum material properties. Such continuum models, especially Euler-Bernoulli beam models, are often used to extract mechanical parameters from experimental results. The microtubule is treated as comprising materials with certain continuum material properties. Such continuum models, especially Euler-Bernoulli beam models in which the biomolecular system is assumed as homogeneous isotropic materials with solid cross-sections, are often used to extract mechanical parameters from experimental results. However, in real biological world, these homogeneous and isotropic assumptions are usually invalidate. Thus, instead of using hypothesized model, a specific continuum model at mesoscopic scale can be introduced based upon data reduction of the results from molecular simulations at atomistic level. Once a continuum model is established, it can provide details on the distribution of stresses and strains induced within the biomolecular system which is useful in determining the distribution and transmission of these forces to the cytoskeletal and sub-cellular components, and help us gain a better understanding in cell mechanics. A data-driven model reduction approach to the problem of microtubule mechanics as an application is present, a beam element is constructed for microtubules based upon data reduction of the results from molecular simulation of the carbon backbone chain of alphabeta-tubulin dimers. The data base of mechanical responses to various types of loads from molecular simulation is reduced to dominant modes. The dominant modes are subsequently used to construct the stiffness matrix of a beam element that captures the anisotropic behavior and deformation mode coupling that arises from a microtubule's spiral structure. In contrast to standard Euler-Bernoulli or Timoshenko beam elements, the link between forces and node displacements results not from hypothesized deformation behavior, but directly from the data obtained by molecular scale simulation. Differences between the resulting microtubule data-driven beam model (MTDDBM) and standard beam elements are presented, with a focus on coupling of bending, stretch, shear deformations. The MTDDBM is just as economical to use as a standard beam element, and allows accurate reconstruction of the mechanical behavior of structures within a cell as exemplified in a simple model of a component element of the mitotic spindle.

Alteration of interleaflet coupling due to compounds displaying rapid translocation in lipid membranes

PubMed Central

Reigada, Ramon

2016-01-01

The spatial coincidence of lipid domains at both layers of the cell membrane is expected to play an important role in many cellular functions. Competition between the surface interleaflet tension and a line hydrophobic mismatch penalty are conjectured to determine the transversal behavior of laterally heterogeneous lipid membranes. Here, by a combination of molecular dynamics simulations, a continuum field theory and kinetic equations, I demonstrate that the presence of small, rapidly translocating molecules residing in the lipid bilayer may alter its transversal behavior by favoring the spatial coincidence of similar lipid phases. PMID:27596355

Evidence of weak land-atmosphere coupling under varying bare soil conditions: Are fully coupled Darcy/Navier-Stokes models necessary for simulating soil moisture dynamics?

NASA Astrophysics Data System (ADS)

Illangasekare, T. H.; Trautz, A. C.; Howington, S. E.; Cihan, A.

2017-12-01

It is a well-established fact that the land and atmosphere form a continuum in which the individual domains are coupled by heat and mass transfer processes such as bare-soil evaporation. Soil moisture dynamics can be simulated at the representative elementary volume (REV) scale using decoupled and fully coupled Darcy/Navier-Stokes models. Decoupled modeling is an asynchronous approach in which flow and transport in the soil and atmosphere is simulated independently; the two domains are coupled out of time-step via prescribed flux parameterizations. Fully coupled modeling in contrast, solves the governing equations for flow and transport in both domains simultaneously with the use of coupling interface boundary conditions. This latter approach, while being able to provide real-time two-dimensional feedbacks, is considerably more complex and computationally intensive. In this study, we investigate whether fully coupled models are necessary, or if the simpler decoupled models can sufficiently capture soil moisture dynamics under varying land preparations. A series of intermediate-scale physical and numerical experiments were conducted in which soil moisture distributions and evaporation estimates were monitored at high spatiotemporal resolutions for different heterogeneous packing and soil roughness scenarios. All experimentation was conducted at the newly developed Center for Experimental Study of Subsurface Environmental Processes (CESEP) wind tunnel-porous media user test-facility at the Colorado School of. Near-surface atmospheric measurements made during the experiments demonstrate that the land-atmosphere coupling was relatively weak and insensitive to the applied edaphic and surface conditions. Simulations with a decoupled multiphase heat and mass transfer model similarly show little sensitivity to local variations in atmospheric forcing; a single, simple flux parameterization can sufficiently capture the soil moisture dynamics (evaporation and redistribution) as long as the subsurface conditions (i.e., heterogeneity) are properly described. These findings suggest that significant improvements to simulations results should not be expected if fully coupled modeling were adopted in scenarios of weak land-atmosphere coupling in the context of bare soil evaporation.

Water vapor self-continuum absorption measurements in the 4.0 and 2.1 μm transparency windows

NASA Astrophysics Data System (ADS)

Richard, L.; Vasilchenko, S.; Mondelain, D.; Ventrillard, I.; Romanini, D.; Campargue, A.

2017-11-01

In a recent contribution [A. Campargue, S. Kassi, D. Mondelain, S. Vasilchenko, D. Romanini, Accurate laboratory determination of the near infrared water vapor self-continuum: A test of the MT_CKD model. J. Geophys. Res. Atmos., 121,13,180-13,203, doi:10.1002/2016JD025531], we reported accurate water vapor absorption continuum measurements by Cavity Ring-down Spectroscopy (CRDS) and Optical-Feedback-Cavity Enhanced Absorption Spectroscopy (OF-CEAS) at selected spectral points of 4 near infrared transparency windows. In the present work, the self-continuum cross-sections, CS, are determined for two new spectral points. The 2491 cm-1 spectral point in the region of maximum transparency of the 4.0 μm window was measured by OF-CEAS in the 23-52 °C temperature range. The 4435 cm-1 spectral point of the 2.1 μm window was measured by CRDS at room temperature. The self-continuum cross-sections were determined from the pressure squared dependence of the continuum absorption. Comparison to the literature shows a reasonable agreement with 1970 s and 1980 s measurements using a grating spectrograph in the 4.0 μm window and a very good consistency with our previous laser measurements in the 2.1 μm window. For both studied spectral points, our values are much smaller than previous room temperature measurements by Fourier Transform Spectroscopy. Significant deviations (up to about a factor 4) are noted compared to the widely used semi empirical MT_CKD model of the absorption continuum. The measured temperature dependence at 2491 cm-1 is consistent with previous high temperature measurements in the 4.0 μm window and follows an exp(D0/kT) law, D0 being the dissociation energy of the water dimer.

A mesoscopic bridging scale method for fluids and coupling dissipative particle dynamics with continuum finite element method

PubMed Central

Kojic, Milos; Filipovic, Nenad; Tsuda, Akira

2012-01-01

A multiscale procedure to couple a mesoscale discrete particle model and a macroscale continuum model of incompressible fluid flow is proposed in this study. We call this procedure the mesoscopic bridging scale (MBS) method since it is developed on the basis of the bridging scale method for coupling molecular dynamics and finite element models [G.J. Wagner, W.K. Liu, Coupling of atomistic and continuum simulations using a bridging scale decomposition, J. Comput. Phys. 190 (2003) 249–274]. We derive the governing equations of the MBS method and show that the differential equations of motion of the mesoscale discrete particle model and finite element (FE) model are only coupled through the force terms. Based on this coupling, we express the finite element equations which rely on the Navier–Stokes and continuity equations, in a way that the internal nodal FE forces are evaluated using viscous stresses from the mesoscale model. The dissipative particle dynamics (DPD) method for the discrete particle mesoscale model is employed. The entire fluid domain is divided into a local domain and a global domain. Fluid flow in the local domain is modeled with both DPD and FE method, while fluid flow in the global domain is modeled by the FE method only. The MBS method is suitable for modeling complex (colloidal) fluid flows, where continuum methods are sufficiently accurate only in the large fluid domain, while small, local regions of particular interest require detailed modeling by mesoscopic discrete particles. Solved examples – simple Poiseuille and driven cavity flows illustrate the applicability of the proposed MBS method. PMID:23814322

Hydraulic fracture propagation modeling and data-based fracture identification

NASA Astrophysics Data System (ADS)

Zhou, Jing

Successful shale gas and tight oil production is enabled by the engineering innovation of horizontal drilling and hydraulic fracturing. Hydraulically induced fractures will most likely deviate from the bi-wing planar pattern and generate complex fracture networks due to mechanical interactions and reservoir heterogeneity, both of which render the conventional fracture simulators insufficient to characterize the fractured reservoir. Moreover, in reservoirs with ultra-low permeability, the natural fractures are widely distributed, which will result in hydraulic fractures branching and merging at the interface and consequently lead to the creation of more complex fracture networks. Thus, developing a reliable hydraulic fracturing simulator, including both mechanical interaction and fluid flow, is critical in maximizing hydrocarbon recovery and optimizing fracture/well design and completion strategy in multistage horizontal wells. A novel fully coupled reservoir flow and geomechanics model based on the dual-lattice system is developed to simulate multiple nonplanar fractures' propagation in both homogeneous and heterogeneous reservoirs with or without pre-existing natural fractures. Initiation, growth, and coalescence of the microcracks will lead to the generation of macroscopic fractures, which is explicitly mimicked by failure and removal of bonds between particles from the discrete element network. This physics-based modeling approach leads to realistic fracture patterns without using the empirical rock failure and fracture propagation criteria required in conventional continuum methods. Based on this model, a sensitivity study is performed to investigate the effects of perforation spacing, in-situ stress anisotropy, rock properties (Young's modulus, Poisson's ratio, and compressive strength), fluid properties, and natural fracture properties on hydraulic fracture propagation. In addition, since reservoirs are buried thousands of feet below the surface, the parameters used in the reservoir flow simulator have large uncertainty. Those biased and uncertain parameters will result in misleading oil and gas recovery predictions. The Ensemble Kalman Filter is used to estimate and update both the state variables (pressure and saturations) and uncertain reservoir parameters (permeability). In order to directly incorporate spatial information such as fracture location and formation heterogeneity into the algorithm, a new covariance matrix method is proposed. This new method has been applied to a simplified single-phase reservoir and a complex black oil reservoir with complex structures to prove its capability in calibrating the reservoir parameters.

Boron nitride nanotube-based biosensing of various bacterium/viruses: continuum modelling-based simulation approach.

PubMed

Panchal, Mitesh B; Upadhyay, Sanjay H

2014-09-01

In this study, the feasibility of single walled boron nitride nanotube (SWBNNT)-based biosensors has been ensured considering the continuum modelling-based simulation approach, for mass-based detection of various bacterium/viruses. Various types of bacterium or viruses have been taken into consideration at the free-end of the cantilevered configuration of the SWBNNT, as a biosensor. Resonant frequency shift-based analysis has been performed with the adsorption of various bacterium/viruses considered as additional mass to the SWBNNT-based sensor system. The continuum mechanics-based analytical approach, considering effective wall thickness has been considered to validate the finite element method (FEM)-based simulation results, based on continuum volume-based modelling of the SWBNNT. As a systematic analysis approach, the FEM-based simulation results are found in excellent agreement with the analytical results, to analyse the SWBNNTs for their wide range of applications such as nanoresonators, biosensors, gas-sensors, transducers and so on. The obtained results suggest that by using the SWBNNT of smaller size the sensitivity of the sensor system can be enhanced and detection of the bacterium/virus having mass of 4.28 × 10⁻²⁴ kg can be effectively performed.

Determination of lead in flour samples directly by solid sampling high resolution continuum source graphite furnace atomic absorption spectrometry

NASA Astrophysics Data System (ADS)

Tinas, Hande; Ozbek, Nil; Akman, Suleyman

2018-02-01

In this study, lead concentrations in various flour samples were determined by high-resolution continuum source graphite furnace atomic absorption spectrometry with solid sampling. Since samples were analyzed directly, the risks and disadvantages of sample digestion were eliminated. Solid flour samples were dried, weighed on the platforms, Pd was added as a modifier and introduced directly into a graphite tube using a manual solid sampler. Platforms and tubes were coated with Zr. The optimized pyrolysis and atomization temperatures were 800 °C and 2200 °C, respectively. The sensitivities of lead in various flour certified reference materials (CRMs) and aqueous standards were not significantly different. Therefore, aqueous standards were safely used for calibration. The absolute limit of detection and characteristic mass were 7.2 pg and 9.0 pg of lead, respectively. The lead concentrations in different types of flour samples were found in the range of 25-52 μg kg- 1. Finally, homogeneity factors representing the heterogeneity of analyte distribution for lead in flour samples were determined.

NIH support of Centers for AIDS Research and Department of Health Collaborative Public Health Research: advancing CDC's Enhanced Comprehensive HIV Prevention Planning project.

PubMed

Greenberg, Alan E; Purcell, David W; Gordon, Christopher M; Flores, Stephen; Grossman, Cynthia; Fisher, Holly H; Barasky, Rebecca J

2013-11-01

The contributions reported in this supplemental issue highlight the relevance of NIH-funded CEWG research to health department–supported HIV prevention and care activities in the 9 US cities with the highest numbers of AIDS cases. The project findings have the potential to enhance ongoing HIV treatment and care services and to advance the wider scientific agenda. The HIV testing to care continuum, while providing a framework to help track progress on national goals, also can reflect the heterogeneities of local epidemics. The collaborative research that is highlighted in this issue not only reflects a locally driven research agenda but also demonstrates research methods, data collection tools, and collaborative processes that could be encouraged across jurisdictions. Projects such as these, capitalizing on the integrated efforts of NIH, CDC, DOH, and academic institutions, have the potential to contribute to improvements in the HIV care continuum in these communities, bringing us closer to realizing the HIV prevention and treatment goals of the NHAS.

Evidence for Periodicity in 43 year-long Monitoring of NGC 5548

NASA Astrophysics Data System (ADS)

Bon, E.; Zucker, S.; Netzer, H.; Marziani, P.; Bon, N.; Jovanović, P.; Shapovalova, A. I.; Komossa, S.; Gaskell, C. M.; Popović, L. Č.; Britzen, S.; Chavushyan, V. H.; Burenkov, A. N.; Sergeev, S.; La Mura, G.; Valdés, J. R.; Stalevski, M.

2016-08-01

We present an analysis of 43 years (1972 to 2015) of spectroscopic observations of the Seyfert 1 galaxy NGC 5548. This includes 12 years of new unpublished observations (2003 to 2015). We compiled about 1600 Hβ spectra and analyzed the long-term spectral variations of the 5100 Å continuum and the Hβ line. Our analysis is based on standard procedures, including the Lomb-Scargle method, which is known to be rather limited to such heterogeneous data sets, and a new method developed specifically for this project that is more robust and reveals a ˜5700 day periodicity in the continuum light curve, the Hβ light curve, and the radial velocity curve of the red wing of the Hβ line. The data are consistent with orbital motion inside the broad emission line region of the source. We discuss several possible mechanisms that can explain this periodicity, including orbiting dusty and dust-free clouds, a binary black hole system, tidal disruption events, and the effect of an orbiting star periodically passing through an accretion disk.

Homogeneous spectral spanning of terahertz semiconductor lasers with radio frequency modulation.

PubMed

Wan, W J; Li, H; Zhou, T; Cao, J C

2017-03-08

Homogeneous broadband and electrically pumped semiconductor radiation sources emitting in the terahertz regime are highly desirable for various applications, including spectroscopy, chemical sensing, and gas identification. In the frequency range between 1 and 5 THz, unipolar quantum cascade lasers employing electron inter-subband transitions in multiple-quantum-well structures are the most powerful semiconductor light sources. However, these devices are normally characterized by either a narrow emission spectrum due to the narrow gain bandwidth of the inter-subband optical transitions or an inhomogeneous broad terahertz spectrum from lasers with heterogeneous stacks of active regions. Here, we report the demonstration of homogeneous spectral spanning of long-cavity terahertz semiconductor quantum cascade lasers based on a bound-to-continuum and resonant phonon design under radio frequency modulation. At a single drive current, the terahertz spectrum under radio frequency modulation continuously spans 330 GHz (~8% of the central frequency), which is the record for single plasmon waveguide terahertz lasers with a bound-to-continuum design. The homogeneous broadband terahertz sources can be used for spectroscopic applications, i.e., GaAs etalon transmission measurement and ammonia gas identification.

Homogeneous spectral spanning of terahertz semiconductor lasers with radio frequency modulation

PubMed Central

Wan, W. J.; Li, H.; Zhou, T.; Cao, J. C.

2017-01-01

Homogeneous broadband and electrically pumped semiconductor radiation sources emitting in the terahertz regime are highly desirable for various applications, including spectroscopy, chemical sensing, and gas identification. In the frequency range between 1 and 5 THz, unipolar quantum cascade lasers employing electron inter-subband transitions in multiple-quantum-well structures are the most powerful semiconductor light sources. However, these devices are normally characterized by either a narrow emission spectrum due to the narrow gain bandwidth of the inter-subband optical transitions or an inhomogeneous broad terahertz spectrum from lasers with heterogeneous stacks of active regions. Here, we report the demonstration of homogeneous spectral spanning of long-cavity terahertz semiconductor quantum cascade lasers based on a bound-to-continuum and resonant phonon design under radio frequency modulation. At a single drive current, the terahertz spectrum under radio frequency modulation continuously spans 330 GHz (~8% of the central frequency), which is the record for single plasmon waveguide terahertz lasers with a bound-to-continuum design. The homogeneous broadband terahertz sources can be used for spectroscopic applications, i.e., GaAs etalon transmission measurement and ammonia gas identification. PMID:28272492

Workplace disaster preparedness and response: the employee assistance program continuum of services.

PubMed

Paul, Jan; Blum, Dorothy

2005-01-01

Response programs for workplace critical and traumatic events are becoming an acknowledged and sought after standard of care. The current trauma literature recognizes what goes on in the workplace between the Employee Assistance Program (EAP) and management. The authors have taken this intra-organizational relationship, assimilated the information, and developed a model that recognizes and supports management throughout the continuum of response to workplace traumatic events. The model recognizes the EAP as an important workplace resource and tool in management's ability to strike the balance of managing the workforce while assisting in recovery following workplace trauma. The introduced concept defines the continuum and highlights the before, during, and after phases, showing how EAP supports management in most effectively doing their job.

A Size-Luminosity Relationship for Protoplanetary Disks in Lupus

NASA Astrophysics Data System (ADS)

Terrell, Marie; Andrews, Sean

2018-01-01

The sizes of the 340 GHz continuum emission from 56 protoplanetary disks in the Lupus star-forming region were measured by modeling their ALMA visibility profiles. We describe the mechanism for these measurements and some preliminary results regarding the correlation between the continuum luminosities and sizes.

A Framework for Health Communication Across the HIV Treatment Continuum

PubMed Central

Van Lith, Lynn M.; Mallalieu, Elizabeth C.; Packman, Zoe R.; Myers, Emily; Ahanda, Kim Seifert; Harris, Emily; Gurman, Tilly; Figueroa, Maria-Elena

2017-01-01

Background: As test and treat rolls out, effective interventions are needed to address the determinants of outcomes across the HIV treatment continuum and ensure that people infected with HIV are promptly tested, initiate treatment early, adhere to treatment, and are virally suppressed. Communication approaches offer viable options for promoting relevant behaviors across the continuum. Conceptual Framework: This article introduces a conceptual framework, which can guide the development of effective health communication interventions and activities that aim to impact behaviors across the HIV treatment continuum in low- and medium-income countries. The framework includes HIV testing and counseling, linkage to care, retention in pre-antiretroviral therapy and antiretroviral therapy initiation in one single-stage linkage to care and treatment, and adherence for viral suppression. The determinants of behaviors vary across the continuum and include both facilitators and barriers with communication interventions designed to focus on specific determinants presented in the model. At each stage, relevant determinants occur at the various levels of the social–ecological model: intrapersonal, interpersonal, health services, community, and policy. Effective health communication interventions have mainly relied on mHealth, interpersonal communication through service providers and peers, community support groups, and treatment supporters. Discussion: The conceptual framework and evidence presented highlight areas across the continuum where health communication can significantly impact treatment outcomes to reach the 90-90-90 goals by strategically addressing key behavioral determinants. As test and treat rolls out, multifaceted health communication approaches will be critical. PMID:27930606

Differential porosimetry and permeametry for random porous media.

PubMed

Hilfer, R; Lemmer, A

2015-07-01

Accurate determination of geometrical and physical properties of natural porous materials is notoriously difficult. Continuum multiscale modeling has provided carefully calibrated realistic microstructure models of reservoir rocks with floating point accuracy. Previous measurements using synthetic microcomputed tomography (μ-CT) were based on extrapolation of resolution-dependent properties for discrete digitized approximations of the continuum microstructure. This paper reports continuum measurements of volume and specific surface with full floating point precision. It also corrects an incomplete description of rotations in earlier publications. More importantly, the methods of differential permeametry and differential porosimetry are introduced as precision tools. The continuum microstructure chosen to exemplify the methods is a homogeneous, carefully calibrated and characterized model for Fontainebleau sandstone. The sample has been publicly available since 2010 on the worldwide web as a benchmark for methodical studies of correlated random media. High-precision porosimetry gives the volume and internal surface area of the sample with floating point accuracy. Continuum results with floating point precision are compared to discrete approximations. Differential porosities and differential surface area densities allow geometrical fluctuations to be discriminated from discretization effects and numerical noise. Differential porosimetry and Fourier analysis reveal subtle periodic correlations. The findings uncover small oscillatory correlations with a period of roughly 850μm, thus implying that the sample is not strictly stationary. The correlations are attributed to the deposition algorithm that was used to ensure the grain overlap constraint. Differential permeabilities are introduced and studied. Differential porosities and permeabilities provide scale-dependent information on geometry fluctuations, thereby allowing quantitative error estimates.

Gating Mechanisms of Mechanosensitive Channels of Large Conductance, I: A Continuum Mechanics-Based Hierarchical Framework

PubMed Central

Chen, Xi; Cui, Qiang; Tang, Yuye; Yoo, Jejoong; Yethiraj, Arun

2008-01-01

A hierarchical simulation framework that integrates information from molecular dynamics (MD) simulations into a continuum model is established to study the mechanical response of mechanosensitive channel of large-conductance (MscL) using the finite element method (FEM). The proposed MD-decorated FEM (MDeFEM) approach is used to explore the detailed gating mechanisms of the MscL in Escherichia coli embedded in a palmitoyloleoylphosphatidylethanolamine lipid bilayer. In Part I of this study, the framework of MDeFEM is established. The transmembrane and cytoplasmic helices are taken to be elastic rods, the loops are modeled as springs, and the lipid bilayer is approximated by a three-layer sheet. The mechanical properties of the continuum components, as well as their interactions, are derived from molecular simulations based on atomic force fields. In addition, analytical closed-form continuum model and elastic network model are established to complement the MDeFEM approach and to capture the most essential features of gating. In Part II of this study, the detailed gating mechanisms of E. coli-MscL under various types of loading are presented and compared with experiments, structural model, and all-atom simulations, as well as the analytical models established in Part I. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction. PMID:18390626

A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins

PubMed Central

Xiao, Li; Diao, Jianxiong; Greene, D'Artagnan; Wang, Junmei; Luo, Ray

2017-01-01

Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. Computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows:1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. 2) The highly different accessibility in the membrane and water regions are addressed with a two-step, two-probe grid labeling procedure, and 3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 Å for globular proteins is a very reasonable default value for membrane protein simulations. It gives the best compromise in reproducing the explicit water distributions in membrane channel proteins, at least in the water accessible pore/channel regions that we focus on. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe a good agreement with experiment results. PMID:28564540

A framework for understanding cancer comparative effectiveness research data needs.

PubMed

Carpenter, William R; Meyer, Anne-Marie; Abernethy, Amy P; Stürmer, Til; Kosorok, Michael R

2012-11-01

Randomized controlled trials remain the gold standard for evaluating cancer intervention efficacy. Randomized trials are not always feasible, practical, or timely and often don't adequately reflect patient heterogeneity and real-world clinical practice. Comparative effectiveness research can leverage secondary data to help fill knowledge gaps randomized trials leave unaddressed; however, comparative effectiveness research also faces shortcomings. The goal of this project was to develop a new model and inform an evolving framework articulating cancer comparative effectiveness research data needs. We examined prevalent models and conducted semi-structured discussions with 76 clinicians and comparative effectiveness research researchers affiliated with the Agency for Healthcare Research and Quality's cancer comparative effectiveness research programs. A new model was iteratively developed and presents cancer comparative effectiveness research and important measures in a patient-centered, longitudinal chronic care model better reflecting contemporary cancer care in the context of the cancer care continuum, rather than a single-episode, acute-care perspective. Immediately relevant for federally funded comparative effectiveness research programs, the model informs an evolving framework articulating cancer comparative effectiveness research data needs, including evolutionary enhancements to registries and epidemiologic research data systems. We discuss elements of contemporary clinical practice, methodology improvements, and related needs affecting comparative effectiveness research's ability to yield findings clinicians, policy makers, and stakeholders can confidently act on. Copyright © 2012 Elsevier Inc. All rights reserved.

A framework for understanding cancer comparative effectiveness research data needs

PubMed Central

Carpenter, William R; Meyer, Anne-Marie; Abernethy, Amy P.; Stürmer, Til; Kosorok, Michael R.

2012-01-01

Objective Randomized controlled trials remain the gold standard for evaluating cancer intervention efficacy. Randomized trials are not always feasible, practical, or timely, and often don’t adequately reflect patient heterogeneity and real-world clinical practice. Comparative effectiveness research can leverage secondary data to help fill knowledge gaps randomized trials leave unaddressed; however, comparative effectiveness research also faces shortcomings. The goal of this project was to develop a new model and inform an evolving framework articulating cancer comparative effectiveness research data needs. Study Design and Setting We examined prevalent models and conducted semi-structured discussions with 76 clinicians and comparative effectiveness research researchers affiliated with the Agency for Healthcare Research and Quality’s cancer comparative effectiveness research programs. Results A new model was iteratively developed, and presents cancer comparative effectiveness research and important measures in a patient-centered, longitudinal chronic care model better-reflecting contemporary cancer care in the context of the cancer care continuum, rather than a single-episode, acute-care perspective. Conclusion Immediately relevant for federally-funded comparative effectiveness research programs, the model informs an evolving framework articulating cancer comparative effectiveness research data needs, including evolutionary enhancements to registries and epidemiologic research data systems. We discuss elements of contemporary clinical practice, methodology improvements, and related needs affecting comparative effectiveness research’s ability to yield findings clinicians, policymakers, and stakeholders can confidently act on. PMID:23017633

Crash energy management on the base of Movable cellular automata method

NASA Astrophysics Data System (ADS)

Psakhie, Serguei; Dmitriev, Andrei; Shilko, Evgueni; Tatarintsev, Evgueni; Korostelev, Serguei

2001-06-01

One of the main problems of materials science is increasing of structure's viability under dynamic loading. In general, a solution is the management of transformation of the energy of loading to the energy of destroying of the least important parts and details of the structure. It has to be noted that similar problem also exists in materials science, since a majority of modern materials are heterogeneous and have a complex internal structure. To optimize this structure for working under dynamic loading it is necessary to take into account the redistribution of elastic energy including phase transformation, generation and accumulation of micro-damages, etc. As far as real experiments on destroying the complex objects are sufficiently expensive and getting of detailed information is often associates with essential difficulties, the methods of computer modeling are used in solving the similar problems. As a rule, these are the methods of continuum mechanics. Although essential achievements have been obtained on the basis of these methods the continuum approach has several limitations, connected first of all with the possibility of description of generation of damages, formation and development of cracks and mass mixing effects. These problems may be solved on the basis of the Movable Cellular Automata (MCA) method, which has been successfully used for modeling fracture of the different material and structures In the paper behavior and peculiarities of failure of complex structures and materials under dynamic loading are studied on the basis of computer modeling. The results shown that sometimes even small changes of the internal structure leads to the significant increasing of the viability of the complex structures and materials. It is due to the elastic energy flux change over during the dynamical loading. This effect may be explained by the fact that elastic energy fluxes define the current stress concentration. Namely, because the area of inclusions are subjected by the largest displacement and due to less Young modulus of inclusions the loading pulses are transferred towards the other parts of the sample. This leads to "blurring" of the stress concentrators and conservation of wholeness of the structure. In its turn, this leads to essential raising up of threshold value of "injected" energy, i.e. the energy absorbed by the structure before loss of its carrying capacity. Practically, elastic energy "circulates" in the structure until a stress concentrator appears, which power will be sufficient for forming a macro-cracks. The results demonstrate a possibility of managing the fracture process under dynamic loading and raising viability of structures and heterogeneous materials by changing their internal structure, geometry, so by entering the specific inclusions.

The application of single particle hydrodynamics in continuum models of multiphase flow

NASA Technical Reports Server (NTRS)

Decker, Rand

1988-01-01

A review of the application of single particle hydrodynamics in models for the exchange of interphase momentum in continuum models of multiphase flow is presented. Considered are the equations of motion for a laminar, mechanical two phase flow. Inherent to this theory is a model for the interphase exchange of momentum due to drag between the dispersed particulate and continuous fluid phases. In addition, applications of two phase flow theory to de-mixing flows require the modeling of interphase momentum exchange due to lift forces. The applications of single particle analysis in deriving models for drag and lift are examined.

Validation of the Continuum of Care Conceptual Model for Athletic Therapy

PubMed Central

Lafave, Mark R.; Butterwick, Dale; Eubank, Breda

2015-01-01

Utilization of conceptual models in field-based emergency care currently borrows from existing standards of medical and paramedical professions. The purpose of this study was to develop and validate a comprehensive conceptual model that could account for injuries ranging from nonurgent to catastrophic events including events that do not follow traditional medical or prehospital care protocols. The conceptual model should represent the continuum of care from the time of initial injury spanning to an athlete's return to participation in their sport. Finally, the conceptual model should accommodate both novices and experts in the AT profession. This paper chronicles the content validation steps of the Continuum of Care Conceptual Model for Athletic Therapy (CCCM-AT). The stages of model development were domain and item generation, content expert validation using a three-stage modified Ebel procedure, and pilot testing. Only the final stage of the modified Ebel procedure reached a priori 80% consensus on three domains of interest: (1) heading descriptors; (2) the order of the model; (3) the conceptual model as a whole. Future research is required to test the use of the CCCM-AT in order to understand its efficacy in teaching and practice within the AT discipline. PMID:26464897

HIV service delivery models towards 'Zero AIDS-related Deaths': a collaborative case study of 6 Asia and Pacific countries.

PubMed

Fujita, Masami; Poudel, Krishna C; Green, Kimberly; Wi, Teodora; Abeyewickreme, Iyanthi; Ghidinelli, Massimo; Kato, Masaya; Vun, Mean Chhi; Sopheap, Seng; San, Khin Ohnmar; Bollen, Phavady; Rai, Krishna Kumar; Dahal, Atul; Bhandari, Durga; Boas, Peniel; Yaipupu, Jessica; Sirinirund, Petchsri; Saonuam, Pairoj; Duong, Bui Duc; Nhan, Do Thi; Thu, Nguyen Thi Minh; Jimba, Masamine

2015-04-24

In the Asia-Pacific region, limited systematic assessment has been conducted on HIV service delivery models. Applying an analytical framework of the continuum of prevention and care, this study aimed to assess HIV service deliveries in six Asia and Pacific countries from the perspective of service availability, linking approaches and performance monitoring for maximizing HIV case detection and retention. Each country formed a review team that provided published and unpublished information from the national HIV program. Four types of continuum were examined: (i) service linkages between key population outreach and HIV diagnosis (vertical-community continuum); (ii) chronic care provision across HIV diagnosis and treatment (chronological continuum); (iii) linkages between HIV and other health services (horizontal continuum); and (iv) comprehensive care sites coordinating care provision (hub and heart of continuum). Regarding the vertical-community continuum, all districts had voluntary counselling and testing (VCT) in all countries except for Myanmar and Vietnam. In these two countries, limited VCT availability was a constraint for referring key populations reached. All countries monitored HIV testing coverage among key populations. Concerning the chronological continuum, the proportion of districts/townships having antiretroviral treatment (ART) was less than 70% except in Thailand, posing a barrier for accessing pre-ART/ART care. Mechanisms for providing chronic care and monitoring retention were less developed for VCT/pre-ART process compared to ART process in all countries. On the horizontal continuum, the availability of HIV testing for tuberculosis patients and pregnant women was limited and there were sub-optimal linkages between tuberculosis, antenatal care and HIV services except for Cambodia and Thailand. These two countries indicated higher HIV testing coverage than other countries. Regarding hub and heart of continuum, all countries had comprehensive care sites with different degrees of community involvement. The analytical framework was useful to identify similarities and considerable variations in service availability and linking approaches across the countries. The study findings would help each country critically adapt and adopt global recommendations on HIV service decentralization, linkages and integration. Especially, the findings would inform cross-fertilization among the countries and national HIV program reviews to determine county-specific measures for maximizing HIV case detection and retention.

Wave propagation in equivalent continuums representing truss lattice materials

DOE PAGES

Messner, Mark C.; Barham, Matthew I.; Kumar, Mukul; ...

2015-07-29

Stiffness scales linearly with density in stretch-dominated lattice meta-materials offering the possibility of very light yet very stiff structures. Current additive manufacturing techniques can assemble structures from lattice materials, but the design of such structures will require accurate, efficient simulation methods. Equivalent continuum models have several advantages over discrete truss models of stretch dominated lattices, including computational efficiency and ease of model construction. However, the development an equivalent model suitable for representing the dynamic response of a periodic truss in the small deformation regime is complicated by microinertial effects. This study derives a dynamic equivalent continuum model for periodic trussmore » structures suitable for representing long-wavelength wave propagation and verifies it against the full Bloch wave theory and detailed finite element simulations. The model must incorporate microinertial effects to accurately reproduce long wavelength characteristics of the response such as anisotropic elastic soundspeeds. Finally, the formulation presented here also improves upon previous work by preserving equilibrium at truss joints for simple lattices and by improving numerical stability by eliminating vertices in the effective yield surface.« less

Ash Dispersal in Planetary Atmospheres: Continuum vs. Non-continuum Effects

NASA Astrophysics Data System (ADS)

Fagents, S. A.; Baloga, S. M.; Glaze, L. S.

2013-12-01

The dispersal of ash from a volcanic vent on any given planet is dictated by particle properties (density, shape, and size distribution), the intensity of the eruptive source, and the characteristics of the planetary environment (atmospheric structure, wind field, and gravity) into which the ash is erupted. Relating observations of potential pyroclastic deposits to source locations and eruption conditions requires a detailed quantitative understanding of the settling rates of individual particles under changing ambient conditions. For atmospheres that are well described by continuum mechanics, the conventional Newtonian description of particle motion allows particle settling velocities to be related to particle characteristics via a drag coefficient. However, under rarefied atmospheric conditions (i.e., on Mars and at high altitude on Earth), non-continuum effects become important for ash-sized particles, and an equation of motion based on statistical mechanics is required for calculating particle motion. We have developed a rigorous new treatment of particle settling under variable atmospheric conditions and applied it to Earth and Mars. When non-continuum effects are important (as dictated by the mean free path of atmospheric gas relative to the particle size), fall velocities are greater than those calculated by continuum mechanics. When continuum conditions (i.e., higher atmospheric densities) are reached during descent, our model switches to a conventional formulation that determines the appropriate drag coefficient as the particle transits varying atmospheric properties. The variation of settling velocity with altitude allows computation of particle trajectories, fall durations and downwind dispersal. Our theoretical and numerical analyses show that several key, competing factors strongly influence the downwind trajectories of ash particles and the extents of the resulting deposits. These factors include: the shape of the particles (non-spherical particles fall more slowly than spherical particle shapes commonly adopted in settling models); the formation of particle aggregates, which enhances settling rates; and the lagging of particle motion behind the ambient wind field, which results in less widely dispersed deposits. Above all, any particles experiencing non-continuum effects settle faster and are less widely dispersed than particles falling in an entirely continuum regime. Our model results demonstrate the complex interplay of these factors in the Martian environment, and our approach provides a basis for relating deposits observed in planetary datasets to candidate volcanic sources and eruption conditions. This allows for a critical reassessment of the potential for explosive volcanism to contribute to extremely widespread, fine-grained, layered deposits such as the Medusae Fossae Formation.

Steps Toward Determination of the Size and Structure of the Broad-Line Region in Active Galactic Nuclei XVI: A 13 Year Study of Spectral Variability in NGC 5548

NASA Technical Reports Server (NTRS)

Peterson, B. M.; Berlind, P.; Bertram, R.; Bischoff, K.; Bochkarev, N. G.; Burenkov, A. N.; Calkins, M.; Carrasco, L.; Chavushyan, V. H.

2002-01-01

We present the final installment of an intensive 13 year study of variations of the optical continuum and broad H beta emission line in the Seyfert 1 galaxy NGC 5548. The database consists of 1530 optical continuum measurements and 1248 H beta measurements. The H beta variations follow the continuum variations closely, with a typical time delay of about 20 days. However, a year-by-year analysis shows that the magnitude of emission-line time delay is correlated with the mean continuum flux. We argue that the data are consistent with the simple model prediction between the size of the broad-line region and the ionizing luminosity, r is proportional to L(sup 1/2)(sub ion). Moreover, the apparently linear nature of the correlation between the H beta response time and the nonstellar optical continuum F(sub opt) arises as a consequence of the changing shape of the continuum as it varies, specifically F(sub opt) is proportional to F(sup 0.56)(sub UV).

Incorporation of the TIP4P water model into a continuum solvent for computing solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2014-10-01

The continuum solvent model is one of the commonly used strategies to compute solvation free energy especially for large-scale conformational transitions such as protein folding or to calculate the binding affinity of protein-protein/ligand interactions. However, the dielectric polarization for computing solvation free energy from the continuum solvent is different than that obtained from molecular dynamic simulations. To mimic the dielectric polarization surrounding a solute in molecular dynamic simulations, the first-shell water molecules was modeled using a charge distribution of TIP4P in a hard sphere; the time-averaged charge distribution from the first-shell water molecules were estimated based on the coordination number of the solute, and the orientation distribution of the first-shell waters and the intermediate water molecules were treated as that of a bulk solvent. Based on this strategy, an equation describing the solvation free energy of ions was derived.

Hybrid discrete/continuum algorithms for stochastic reaction networks

DOE PAGES

Safta, Cosmin; Sargsyan, Khachik; Debusschere, Bert; ...

2014-10-22

Direct solutions of the Chemical Master Equation (CME) governing Stochastic Reaction Networks (SRNs) are generally prohibitively expensive due to excessive numbers of possible discrete states in such systems. To enhance computational efficiency we develop a hybrid approach where the evolution of states with low molecule counts is treated with the discrete CME model while that of states with large molecule counts is modeled by the continuum Fokker-Planck equation. The Fokker-Planck equation is discretized using a 2nd order finite volume approach with appropriate treatment of flux components to avoid negative probability values. The numerical construction at the interface between the discretemore » and continuum regions implements the transfer of probability reaction by reaction according to the stoichiometry of the system. As a result, the performance of this novel hybrid approach is explored for a two-species circadian model with computational efficiency gains of about one order of magnitude.« less

PowderSim: Lagrangian Discrete and Mesh-Free Continuum Simulation Code for Cohesive Soils

NASA Technical Reports Server (NTRS)

Johnson, Scott; Walton, Otis; Settgast, Randolph

2013-01-01

PowderSim is a calculation tool that combines a discrete-element method (DEM) module, including calibrated interparticle-interaction relationships, with a mesh-free, continuum, SPH (smoothed-particle hydrodynamics) based module that utilizes enhanced, calibrated, constitutive models capable of mimicking both large deformations and the flow behavior of regolith simulants and lunar regolith under conditions anticipated during in situ resource utilization (ISRU) operations. The major innovation introduced in PowderSim is to use a mesh-free method (SPH-based) with a calibrated and slightly modified critical-state soil mechanics constitutive model to extend the ability of the simulation tool to also address full-scale engineering systems in the continuum sense. The PowderSim software maintains the ability to address particle-scale problems, like size segregation, in selected regions with a traditional DEM module, which has improved contact physics and electrostatic interaction models.

Numerical study of multiscale compaction-initiated detonation

NASA Astrophysics Data System (ADS)

Gambino, J. R.; Schwendeman, D. W.; Kapila, A. K.

2018-02-01

A multiscale model of heterogeneous condensed-phase explosives is examined computationally to determine the course of transient events following the application of a piston-driven stimulus. The model is a modified version of that introduced by Gonthier (Combust Sci Technol 175(9):1679-1709, 2003. https://doi.org/10.1080/00102200302373) in which the explosive is treated as a porous, compacting medium at the macro-scale and a collection of closely packed spherical grains capable of undergoing reaction and diffusive heat transfer at the meso-scale. A separate continuum description is ascribed to each scale, and the two scales are coupled together in an energetically consistent manner. Following piston-induced compaction, localized energy deposition at the sites of intergranular contact creates hot spots where reaction begins preferentially. Reaction progress at the macro-scale is determined by the spatial average of that at the grain scale. A parametric study shows that combustion at the macro-scale produces an unsteady detonation with a cyclical character, in which the lead shock loses strength and is overtaken by a stronger secondary shock generated in the partially reacted material behind it. The secondary shock in turn becomes the new lead shock and the process repeats itself.

Heterogeneous growth-induced prestrain in the heart

PubMed Central

Genet, M.; Rausch, M.; Lee, L.C.; Choy, S.; Zhao, X.; Kassab, G.S.; Kozerke, S.; Guccione, J.M.; Kuhl, E.

2015-01-01

Even when entirely unloaded, biological structures are not stress-free, as shown by Y.C. Fung’s seminal opening angle experiment on arteries and the left ventricle. As a result of this prestrain, subject-specific geometries extracted from medical imaging do not represent an unloaded reference configuration necessary for mechanical analysis, even if the structure is externally unloaded. Here we propose a new computational method to create physiological residual stress fields in subject-specific left ventricular geometries using the continuum theory of fictitious configurations combined with a fixed-point iteration. We also reproduced the opening angle experiment on four swine models, to characterize the range of normal opening angle values. The proposed method generates residual stress fields which can reliably reproduce the range of opening angles between 8.7±1.8 and 16.6 ± 13.7 as measured experimentally. We demonstrate that including the effects of prestrain reduces the left ventricular stiffness by up to 40%, thus facilitating the ventricular filling, which has a significant impact on cardiac function. This method can improve the fidelity of subject-specific models to improve our understanding of cardiac diseases and to optimize treatment options. PMID:25913241

A Malthusian curb on spatial structure in microorganism populations.

PubMed

Martin, A P

2004-10-07

That all organisms are born in the company of a parent but die alone is a fundamental biological asymmetry. It has been suggested that this provides a deep-rooted source of spatial pattern formation for microorganisms even at the scale of the population. Such a theory, however, neglects the strong influence in nature of the limited and spatially variable availability of food. The tendency, first recognized by Thomas Malthus in the 18th century, of a population to out-strip its food resources will eventually lead, through local starvation, to the suppression of a heterogeneity growing within a population. Using a generic model it is demonstrated that including local food limitation of breeding strongly dampens spatial structure otherwise resulting from birth and death. The extent of this damping is shown to be a function of the strength of the coupling between organisms and their food and of the total abundance of organic material. Moreover, this work provides an example of a density-dependent process acting to diminish spatial structure rather than to create it and highlights the rich variety of behaviour that is missed by continuum models which fail to represent such local dynamics.

Effective Boundary Conditions for Continuum Method of Investigation of Rarefied Gas Flow over Blunt Body

NASA Astrophysics Data System (ADS)

Brykina, I. G.; Rogov, B. V.; Semenov, I. L.; Tirskiy, G. A.

2011-05-01

Super- and hypersonic rarefied gas flow over blunt bodies is investigated by using asymptotically correct viscous shock layer (VSL) model with effective boundary conditions and thin viscous shock layer model. Correct shock and wall conditions for VSL are proposed with taking into account terms due to the curvature which are significant at low Reynolds number. These conditions improve original Davis's VSL model [1]. Numerical calculation of Krook equation [2] is carried out to verify continuum results. Continuum numerical and asymptotic solutions are compared with kinetic solution, free-molecule flow solution and with DSMC solutions [3, 4, 5] over a wide range of free-stream Knudsen number Kn∞. It is shown that taking into account terms with shock and surface curvatures have a pronounced effect on skin friction and heat-transfer in transitional flow regime. Using the asymptotically correct VSL model with effective boundary conditions significantly extends the range of its applicability to higher Kn∞ numbers.

An extended continuum model considering optimal velocity change with memory and numerical tests

NASA Astrophysics Data System (ADS)

Qingtao, Zhai; Hongxia, Ge; Rongjun, Cheng

2018-01-01

In this paper, an extended continuum model of traffic flow is proposed with the consideration of optimal velocity changes with memory. The new model's stability condition and KdV-Burgers equation considering the optimal velocities change with memory are deduced through linear stability theory and nonlinear analysis, respectively. Numerical simulation is carried out to study the extended continuum model, which explores how optimal velocity changes with memory affected velocity, density and energy consumption. Numerical results show that when considering the effects of optimal velocity changes with memory, the traffic jams can be suppressed efficiently. Both the memory step and sensitivity parameters of optimal velocity changes with memory will enhance the stability of traffic flow efficiently. Furthermore, numerical results demonstrates that the effect of optimal velocity changes with memory can avoid the disadvantage of historical information, which increases the stability of traffic flow on road, and so it improve the traffic flow stability and minimize cars' energy consumptions.

Influence of spatial variation of phenomenological parameters on the modeling of boundary conditions for flows with dynamic wetting

NASA Astrophysics Data System (ADS)

Hizumi, Yuka; Omori, Takeshi; Yamaguchi, Yasutaka; Kajisima, Takeo

2014-11-01

For reliable prediction of multiphase flows in micro- and nano-scales, continuum models are expected to account for small scale physics near the contact line (CL) region. Some existing works (for example the series of papers by the group of Qian and Ren) have been successful in deriving continuum models and corresponding boundary conditions which reproduce well the molecular dynamics (MD) simulation results. Their studies, however, did not fully address the issue of adsorption layer especially in the CL region, and it is still not clear if general conclusion can be deduced from their results. In the present study we investigate in detail the local viscosity and the corresponding stress tensor formulation in the solid-liquid interface and in the CL region of immiscible two-phase Couette flows by means of MD simulation. The application limit of the generalized Navier boundary condition and the continuum model with uniform viscosity is addressed by systematic coarse-graining of sampling bins.

Understanding the shock and detonation response of high explosives at the continuum and meso scales

NASA Astrophysics Data System (ADS)

Handley, C. A.; Lambourn, B. D.; Whitworth, N. J.; James, H. R.; Belfield, W. J.

2018-03-01

The shock and detonation response of high explosives has been an active research topic for more than a century. In recent years, high quality data from experiments using embedded gauges and other diagnostic techniques have inspired the development of a range of new high-fidelity computer models for explosives. The experiments and models have led to new insights, both at the continuum scale applicable to most shock and detonation experiments, and at the mesoscale relevant to hotspots and burning within explosive microstructures. This article reviews the continuum and mesoscale models, and their application to explosive phenomena, gaining insights to aid future model development and improved understanding of the physics of shock initiation and detonation propagation. In particular, it is argued that "desensitization" and the effect of porosity on high explosives can both be explained by the combined effect of thermodynamics and hydrodynamics, rather than the traditional hotspot-based explanations linked to pressure-dependent reaction rates.

Model of fracture of metal melts and the strength of melts under dynamic conditions

NASA Astrophysics Data System (ADS)

Mayer, P. N.; Mayer, A. E.

2015-07-01

The development of a continuum model of deformation and fracture of melts is needed for the description of the behavior of metals in extreme states, in particular, under high-current electron and ultrashort laser irradiation. The model proposed includes the equations of mechanics of a two-phase continuum and the equations of the kinetics of phase transitions. The change (exchange) of the volumes of dispersed and carrier phases and of the number of dispersed particles is described, and the energy and mass exchange between the phases due to phase transitions is taken into account. Molecular dynamic (MD) calculations are carried out with the use of the LAMMPS program. The continuum model is verified by MD, computational, and experimental data. The strength of aluminum, copper, and nickel is determined at various temperatures and strain rates. It is shown that an increase in the strain rate leads to an increase in the strength of a liquid metal, while an increase in temperature leads to a decrease in its strength.

Derivation of a continuum model and the energy law for moving contact lines with insoluble surfactants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Zhen, E-mail: matzz@nus.edu.sg; Xu, Shixin, E-mail: matxs@nus.edu.sg; Ren, Weiqing, E-mail: matrw@nus.edu.sg

2014-06-15

A continuous model is derived for the dynamics of two immiscible fluids with moving contact lines and insoluble surfactants based on thermodynamic principles. The continuum model consists of the Navier-Stokes equations for the dynamics of the two fluids and a convection-diffusion equation for the evolution of the surfactant on the fluid interface. The interface condition, the boundary condition for the slip velocity, and the condition for the dynamic contact angle are derived from the consideration of energy dissipations. Different types of energy dissipations, including the viscous dissipation, the dissipations on the solid wall and at the contact line, as wellmore » as the dissipation due to the diffusion of surfactant, are identified from the analysis. A finite element method is developed for the continuum model. Numerical experiments are performed to demonstrate the influence of surfactant on the contact line dynamics. The different types of energy dissipations are compared numerically.« less

Equilibrium and kinetic models for colloid release under transient solution chemistry conditions.

PubMed

Bradford, Scott A; Torkzaban, Saeed; Leij, Feike; Simunek, Jiri

2015-10-01

We present continuum models to describe colloid release in the subsurface during transient physicochemical conditions. Our modeling approach relates the amount of colloid release to changes in the fraction of the solid surface area that contributes to retention. Equilibrium, kinetic, equilibrium and kinetic, and two-site kinetic models were developed to describe various rates of colloid release. These models were subsequently applied to experimental colloid release datasets to investigate the influence of variations in ionic strength (IS), pH, cation exchange, colloid size, and water velocity on release. Various combinations of equilibrium and/or kinetic release models were needed to describe the experimental data depending on the transient conditions and colloid type. Release of Escherichia coli D21g was promoted by a decrease in solution IS and an increase in pH, similar to expected trends for a reduction in the secondary minimum and nanoscale chemical heterogeneity. The retention and release of 20nm carboxyl modified latex nanoparticles (NPs) were demonstrated to be more sensitive to the presence of Ca(2+) than D21g. Specifically, retention of NPs was greater than D21g in the presence of 2mM CaCl2 solution, and release of NPs only occurred after exchange of Ca(2+) by Na(+) and then a reduction in the solution IS. These findings highlight the limitations of conventional interaction energy calculations to describe colloid retention and release, and point to the need to consider other interactions (e.g., Born, steric, and/or hydration forces) and/or nanoscale heterogeneity. Temporal changes in the water velocity did not have a large influence on the release of D21g for the examined conditions. This insensitivity was likely due to factors that reduce the applied hydrodynamic torque and/or increase the resisting adhesive torque; e.g., macroscopic roughness and grain-grain contacts. Our analysis and models improve our understanding and ability to describe the amounts and rates of colloid release and indicate that episodic colloid transport is expected under transient physicochemical conditions. Published by Elsevier B.V.

Parameterizations of Chromospheric Condensations in dG and dMe Model Flare Atmospheres

NASA Astrophysics Data System (ADS)

Kowalski, Adam F.; Allred, Joel C.

2018-01-01

The origin of the near-ultraviolet and optical continuum radiation in flares is critical for understanding particle acceleration and impulsive heating in stellar atmospheres. Radiative-hydrodynamic (RHD) simulations in 1D have shown that high energy deposition rates from electron beams produce two flaring layers at T ∼ 104 K that develop in the chromosphere: a cooling condensation (downflowing compression) and heated non-moving (stationary) flare layers just below the condensation. These atmospheres reproduce several observed phenomena in flare spectra, such as the red-wing asymmetry of the emission lines in solar flares and a small Balmer jump ratio in M dwarf flares. The high beam flux simulations are computationally expensive in 1D, and the (human) timescales for completing NLTE models with adaptive grids in 3D will likely be unwieldy for some time to come. We have developed a prescription for predicting the approximate evolved states, continuum optical depth, and emergent continuum flux spectra of RHD model flare atmospheres. These approximate prescriptions are based on an important atmospheric parameter: the column mass ({m}{ref}) at which hydrogen becomes nearly completely ionized at the depths that are approximately in steady state with the electron beam heating. Using this new modeling approach, we find that high energy flux density (>F11) electron beams are needed to reproduce the brightest observed continuum intensity in IRIS data of the 2014 March 29 X1 solar flare, and that variation in {m}{ref} from 0.001 to 0.02 g cm‑2 reproduces most of the observed range of the optical continuum flux ratios at the peak of M dwarf flares.

A continuum membrane model for small deformations of a spider orb-web

NASA Astrophysics Data System (ADS)

Morassi, Antonino; Soler, Alejandro; Zaera, Ramón

2017-09-01

In this paper we propose a continuum membrane model for the infinitesimal deformation of a spider web. The model is derived in the simple context of axially-symmetric webs formed by radial threads connected with circumferential threads belonging to concentric circles. Under suitable assumption on the tensile pre-stress acting in the referential configuration, the out-of-plane static equilibrium and the free transverse and in-plane vibration of a supported circular orb-web are studied in detail. The accuracy of the model in describing a discrete spider web is numerically investigated.

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

PubMed Central

Ryall, Ben; Eydallin, Gustavo

2012-01-01

Summary: Diversity in adaptive responses is common within species and populations, especially when the heterogeneity of the frequently large populations found in environments is considered. By focusing on events in a single clonal population undergoing a single transition, we discuss how environmental cues and changes in growth rate initiate a multiplicity of adaptive pathways. Adaptation is a comprehensive process, and stochastic, regulatory, epigenetic, and mutational changes can contribute to fitness and overlap in timing and frequency. We identify culture history as a major determinant of both regulatory adaptations and microevolutionary change. Population history before a transition determines heterogeneities due to errors in translation, stochastic differences in regulation, the presence of aged, damaged, cheating, or dormant cells, and variations in intracellular metabolite or regulator concentrations. It matters whether bacteria come from dense, slow-growing, stressed, or structured states. Genotypic adaptations are history dependent due to variations in mutation supply, contingency gene changes, phase variation, lateral gene transfer, and genome amplifications. Phenotypic adaptations underpin genotypic changes in situations such as stress-induced mutagenesis or prophage induction or in biofilms to give a continuum of adaptive possibilities. Evolutionary selection additionally provides diverse adaptive outcomes in a single transition and generally does not result in single fitter types. The totality of heterogeneities in an adapting population increases the chance that at least some individuals meet immediate or future challenges. However, heterogeneity complicates the adaptomics of single transitions, and we propose that subpopulations will need to be integrated into future population biology and systems biology predictions of bacterial behavior. PMID:22933562

Water vapor absorption in the atmospheric window at 239 GHz

NASA Technical Reports Server (NTRS)

Bauer, A.; Godon, M.; Carlier, J.; Ma, Q.

1995-01-01

Absolute absorption rates of pure water vapor and mixtures of water vapor and nitrogen have been measured in the atmospheric window at 239 GHz. The dependence on pressure as well as temperature has been obtained. The experimental data are compared with several theoretical or empirical models, and satisfactory agreement is obtained with the models involving a continuum; in the case of pure water vapor, the continuum contribution based upon recent theoretical developments gives good results. The temperature dependence is stronger than that proposed in a commonly used atmospheric transmission model.

Continuum model for hydrogen pickup in zirconium alloys of LWR fuel cladding

NASA Astrophysics Data System (ADS)

Wang, Xing; Zheng, Ming-Jie; Szlufarska, Izabela; Morgan, Dane

2017-04-01

A continuum model for calculating the time-dependent hydrogen pickup fractions in various Zirconium alloys under steam and pressured water oxidation has been developed in this study. Using only one fitting parameter, the effective hydrogen gas partial pressure at the oxide surface, a qualitative agreement is obtained between the predicted and previously measured hydrogen pickup fractions. The calculation results therefore demonstrate that H diffusion through the dense oxide layer plays an important role in the hydrogen pickup process. The limitations and possible improvement of the model are also discussed.

On deformation of complex continuum immersed in a plane space

NASA Astrophysics Data System (ADS)

Kovalev, V. A.; Murashkin, E. V.; Radayev, Y. N.

2018-05-01

The present paper is devoted to mathematical modelling of complex continua deformations considered as immersed in an external plane space. The complex continuum is defined as a differential manifold supplied with metrics induced by the external space. A systematic derivation of strain tensors by notion of isometric immersion of the complex continuum into a plane space of a higher dimension is proposed. Problem of establishing complete systems of irreducible objective strain and extrastrain tensors for complex continuum immersed in an external plane space is resolved. The solution to the problem is obtained by methods of the field theory and the theory of rational algebraic invariants. Strain tensors of the complex continuum are derived as irreducible algebraic invariants of contravariant vectors of the external space emerging as functional arguments in the complex continuum action density. Present analysis is restricted to rational algebraic invariants. Completeness of the considered systems of rational algebraic invariants is established for micropolar elastic continua. Rational syzygies for non-quadratic invariants are discussed. Objective strain tensors (indifferent to frame rotations in the external plane space) for micropolar continuum are alternatively obtained by properly combining multipliers of polar decompositions of deformation and extra-deformation gradients. The latter is realized only for continua immersed in a plane space of the equal mathematical dimension.

Transport Phenomena of Water in Molecular Fluidic Channels

PubMed Central

Vo, Truong Quoc; Kim, BoHung

2016-01-01

In molecular-level fluidic transport, where the discrete characteristics of a molecular system are not negligible (in contrast to a continuum description), the response of the molecular water system might still be similar to the continuum description if the time and ensemble averages satisfy the ergodic hypothesis and the scale of the average is enough to recover the classical thermodynamic properties. However, even in such cases, the continuum description breaks down on the material interfaces. In short, molecular-level liquid flows exhibit substantially different physics from classical fluid transport theories because of (i) the interface/surface force field, (ii) thermal/velocity slip, (iii) the discreteness of fluid molecules at the interface and (iv) local viscosity. Therefore, in this study, we present the result of our investigations using molecular dynamics (MD) simulations with continuum-based energy equations and check the validity and limitations of the continuum hypothesis. Our study shows that when the continuum description is subjected to the proper treatment of the interface effects via modified boundary conditions, the so-called continuum-based modified-analytical solutions, they can adequately predict nanoscale fluid transport phenomena. The findings in this work have broad effects in overcoming current limitations in modeling/predicting the fluid behaviors of molecular fluidic devices. PMID:27650138

Bulbous head formation in bidisperse shallow granular flows over inclined planes

NASA Astrophysics Data System (ADS)

Denissen, I.; Thornton, A.; Weinhart, T.; Luding, S.

2017-12-01

Predicting the behaviour of hazardous natural granular flows (e.g. debris-flows and pyroclastic flows) is vital for an accurate assessment of the risks posed by such events. In these situations, an inversely graded vertical particle-size distribution develops, with larger particles on top of smaller particles. As the surface velocity of such flows is larger than the mean velocity, the larger material is then transported to the flow front. This creates a downstream size-segregation structure, resulting in a flow front composed purely of large particles, that are generally more frictional in geophysical flows. Thus, this segregation process reduces the mobility of the flow front, resulting in the formation of, a so-called, bulbous head. One of the main challenges of simulating these hazardous natural granular flows is the enormous number of particles they contain, which makes discrete particle simulations too computationally expensive to be practically useful. Continuum methods are able to simulate the bulk flow- and segregation behaviour of such flows, but have to make averaging approximations that reduce the huge number of degrees of freedom to a few continuum fields. Small-scale periodic discrete particle simulations can be used to determine the material parameters needed for the continuum model. In this presentation, we use a depth-averaged model to predict the flow profile for particulate chute flows, based on flow height, depth-averaged velocity and particle-size distribution [1], and show that the bulbous head structure naturally emerges from this model. The long-time behaviour of this solution of the depth-averaged continuum model converges to a novel travelling wave solution [2]. Furthermore, we validate this framework against computationally expensive 3D particle simulations, where we see surprisingly good agreement between both approaches, considering the approximations made in the continuum model. We conclude by showing that the travelling distance and height of a bidisperse granular avalanche can be well predicted by our continuum model. REFERENCES [1] M. J. Woodhouse, A. R. Thornton, C. G. Johnson, B. P. Kokelaar, J. M. N. T. Gray, J. Fluid Mech., 709, 543-580 (2012) [2] I.F.C. Denissen, T. Weinhart, A. Te Voortwis, S. Luding, J. M. N. T. Gray, A. R. Thornton, under review with J. Fluid Mech. (2017)

VLTI-GRAVITY measurements of cool evolved stars

NASA Astrophysics Data System (ADS)

Wittkowski, M.; Rau, G.; Chiavassa, A.; Höfner, S.; Scholz, M.; Wood, P. R.; de Wit, W. J.; Eisenhauer, F.; Haubois, X.; Paumard, T.

2018-06-01

Context. Dynamic model atmospheres of Mira stars predict variabilities in the photospheric radius and in atmospheric molecular layers which are not yet strongly constrained by observations. Aims: Here we measure the variability of the oxygen-rich Mira star R Peg in near-continuum and molecular bands. Methods: We used near-infrared K-band spectro-interferometry with a spectral resolution of about 4000 obtained at four epochs between post-maximum and minimum visual phases employing the newly available GRAVITY beam combiner at the Very Large Telescope Interferometer (VLTI). Results: Our observations show a continuum radius that is anti-correlated with the visual lightcurve. Uniform disc (UD) angular diameters at a near-continuum wavelength of 2.25 μm are steadily increasing with values of 8.7 ± 0.1 mas, 9.4 ± 0.1 mas, 9.8 ± 0.1 mas, and 9.9 ± 0.1 mas at visual phases of 0.15, 0.36, 0,45, 0.53, respectively. UD diameters at a bandpass around 2.05 μm, dominated by water vapour, follow the near-continuum variability at larger UD diameters between 10.7 mas and 11.7 mas. UD diameters at the CO 2-0 bandhead, instead, are correlated with the visual lightcurve and anti-correlated with the near-continuum UD diameters, with values between 12.3 mas and 11.7 mas. Conclusions: The observed anti-correlation between continuum radius and visual lightcurve is consistent with an earlier study of the oxygen-rich Mira S Lac, and with recent 1D CODEX dynamic model atmosphere predictions. The amplitude of the variation is comparable to the earlier observations of S Lac, and smaller than predicted by CODEX models. The wavelength-dependent visibility variations at our epochs can be reproduced by a set of CODEX models at model phases between 0.3 and 0.6. The anti-correlation of water vapour and CO contributions at our epochs suggests that these molecules undergo different processes in the extended atmosphere along the stellar cycle. The newly available GRAVITY instrument is suited to conducting longer time series observations, which are needed to provide strong constraints on the model-predicted intra- and inter-cycle variability. Based on observations made with the VLT Interferometer at Paranal Observatory under programme IDs 60.A-9176 and 098.D-0647.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Hong, E-mail: h-yu@seu.edu.cn; Chen, Hong-Bo

In this article, a new semi-continuum model is built to describe the fundamental vibration frequency of the silicon nanowires in <111> orientation. The Keating potential model and the discrete nature in the width and the thickness direction of the silicon nanowires in <111> orientation are applied in the new semi-continuum model. Based on the Keating model and the principle of conservation of energy, the vibration frequency of the silicon nanowires with the triangle, the rhombus, and the hexagon cross sections are derived. It is indicated that the calculation results based on this new model are accordant with the simulation resultsmore » of the software based on molecular dynamics (MD).« less

Multiscale Simulations of Reactive Transport

NASA Astrophysics Data System (ADS)

Tartakovsky, D. M.; Bakarji, J.

2014-12-01

Discrete, particle-based simulations offer distinct advantages when modeling solute transport and chemical reactions. For example, Brownian motion is often used to model diffusion in complex pore networks, and Gillespie-type algorithms allow one to handle multicomponent chemical reactions with uncertain reaction pathways. Yet such models can be computationally more intensive than their continuum-scale counterparts, e.g., advection-dispersion-reaction equations. Combining the discrete and continuum models has a potential to resolve the quantity of interest with a required degree of physicochemical granularity at acceptable computational cost. We present computational examples of such "hybrid models" and discuss the challenges associated with coupling these two levels of description.

M Dwarf Flare Continuum Variations on One-second Timescales: Calibrating and Modeling of ULTRACAM Flare Color Indices

NASA Astrophysics Data System (ADS)

Kowalski, Adam F.; Mathioudakis, Mihalis; Hawley, Suzanne L.; Wisniewski, John P.; Dhillon, Vik S.; Marsh, Tom R.; Hilton, Eric J.; Brown, Benjamin P.

2016-04-01

We present a large data set of high-cadence dMe flare light curves obtained with custom continuum filters on the triple-beam, high-speed camera system ULTRACAM. The measurements provide constraints for models of the near-ultraviolet (NUV) and optical continuum spectral evolution on timescales of ≈1 s. We provide a robust interpretation of the flare emission in the ULTRACAM filters using simultaneously obtained low-resolution spectra during two moderate-sized flares in the dM4.5e star YZ CMi. By avoiding the spectral complexity within the broadband Johnson filters, the ULTRACAM filters are shown to characterize bona fide continuum emission in the NUV, blue, and red wavelength regimes. The NUV/blue flux ratio in flares is equivalent to a Balmer jump ratio, and the blue/red flux ratio provides an estimate for the color temperature of the optical continuum emission. We present a new “color-color” relationship for these continuum flux ratios at the peaks of the flares. Using the RADYN and RH codes, we interpret the ULTRACAM filter emission using the dominant emission processes from a radiative-hydrodynamic flare model with a high nonthermal electron beam flux, which explains a hot, T ≈ 104 K, color temperature at blue-to-red optical wavelengths and a small Balmer jump ratio as observed in moderate-sized and large flares alike. We also discuss the high time resolution, high signal-to-noise continuum color variations observed in YZ CMi during a giant flare, which increased the NUV flux from this star by over a factor of 100. Based on observations obtained with the Apache Point Observatory 3.5 m telescope, which is owned and operated by the Astrophysical Research Consortium, based on observations made with the William Herschel Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofsica de Canarias, and observations, and based on observations made with the ESO Telescopes at the La Silla Paranal Observatory under programme ID 085.D-0501(A).

Multiscale modeling and simulation for nano/micro materials

NASA Astrophysics Data System (ADS)

Wang, Xianqiao

Continuum description and atomic description used to be two distinct methods in the community of modeling and simulations. Science and technology have become so advanced that our understanding of many physical phenomena involves the concepts of both. So our goal now is to build a bridge to make atoms and continua communicate with each other. Micromorphic theory (MMT) envisions a material body as a continuous collection of deformable particles; each possesses finite size and inner structure. It is considered as the most successful top-down formulation of a two-level continuum model to bridge the gap between the micro level and macro level. Therefore MMT can be expected to unveil many new classes of physical phenomena that fall beyond classical field theories. In this work, the constitutive equations for generalized Micromorphic thermoviscoelastic solid and generalized Micromorphic fluid have been formulated. To enlarge the domain of applicability of MMT, from nano, micro to macro, we take a bottom-up approach to re-derive the generalized atomistic field theory (AFT) comprehensively and completely and establish the relationship between AFT and MMT. Finite element (FE) method is then implemented to pursue the numerical solutions of the governing equations derived in AFT. When the finest mesh is used, i.e., the size of FE mesh is equal to the lattice constant of the material, the computational model becomes identical to molecular dynamics simulation. When a coarse mesh is used, the resulting model is a coarse-grained model, the majority of the degrees of freedom are eliminated and the computational cost is largely reduced. When the coarse mesh and finest mesh exist concurrently, i.e., the finest mesh is used in the critical regions and the coarser mesh is used in the far field, it leads naturally to a concurrent atomistic/continuum model. Atomic scale, coarse-grained scale and concurrent atomistic/continuum simulations have demonstrated the potential capability of AFT to simulate most grand challenging problems in nano/micro physics, and shown that AFT has the advantages of both atomic model and MMT. Therefore, AFT has accomplished the mission to bridge the gap between continuum mechanics and atomic physics.

Translating caring theory across the continuum from inpatient to ambulatory care.

PubMed

Tonges, Mary; McCann, Meghan; Strickler, Jeff

2014-06-01

While theory-based practice is a Magnet® characteristic, translating theories to practice remains challenging. As a result, theory-guided practice remains an ideal rather than a realized goal in many organizations. This article provides an overview of a research-derived caring theory, a translational model for theory-driven practice, implementation of a delivery model designed to translate theory across the acute and ambulatory care continuum, and resulting outcomes in oncology clinics and the emergency department.

Gamma rays from active galactic nuclei

NASA Technical Reports Server (NTRS)

Kazanas, Demosthenes

1990-01-01

The general properties of Active Galactic Nuclei (AGN) and quasars are reviewed with emphasis on their continuum spectral emission. Two general classes of models for the continuum are outlined and critically reviewed in view of the impending GRO (Gamma Ray Observatory) launch and observations. The importance of GRO in distinguishing between these models and in general in furthering the understanding of AGN is discussed. The very broad terms the status of the current understanding of AGN are discussed.

Microstructure-Based Fatigue Life Prediction Methods for Naval Steel Structures

DTIC Science & Technology

1993-01-30

approach is to work with the lognormal random variable model proposed by Yang et al . [2], which avoids these difficulties. The simplest form of the...I Al - I I 11. and Ti-alloys [ 10- 111 correlate with the elastic modulus only in the continuum growth regime. On the other hand. compilation of...growth. In fact, Eq. (5) implies that microstructure plays no role in the continuum growth regime. Theoretical models of Frost, et al . [35], and

Complexity and multifractal behaviors of multiscale-continuum percolation financial system for Chinese stock markets

NASA Astrophysics Data System (ADS)

Zeng, Yayun; Wang, Jun; Xu, Kaixuan

2017-04-01

A new financial agent-based time series model is developed and investigated by multiscale-continuum percolation system, which can be viewed as an extended version of continuum percolation system. In this financial model, for different parameters of proportion and density, two Poisson point processes (where the radii of points represent the ability of receiving or transmitting information among investors) are applied to model a random stock price process, in an attempt to investigate the fluctuation dynamics of the financial market. To validate its effectiveness and rationality, we compare the statistical behaviors and the multifractal behaviors of the simulated data derived from the proposed model with those of the real stock markets. Further, the multiscale sample entropy analysis is employed to study the complexity of the returns, and the cross-sample entropy analysis is applied to measure the degree of asynchrony of return autocorrelation time series. The empirical results indicate that the proposed financial model can simulate and reproduce some significant characteristics of the real stock markets to a certain extent.

Rotator cuff tendinopathy: a model for the continuum of pathology and related management.

PubMed

Lewis, Jeremy S

2010-10-01

Pathology of the soft tissues of the shoulder including the musculotendinous rotator cuff and subacromial bursa are extremely common and are a principal cause of pain and suffering. Competing theories have been proposed to explain the pathoaetiology of rotator cuff pathology at specific stages and presentations of the condition. This review proposes a model to describe the continuum of the rotator cuff pathology from asymptomatic tendon through full thickness rotator cuff tears. The pathoaetiology of rotator cuff failure is multifactorial and results from a combination of intrinsic, extrinsic and environmental factors. Recently a new and generic model detailing the continuum of tendon pathology has been proposed. This model is relevant for the rotator cuff and provides a framework to stage the continuity of rotator cuff pathology. Furthermore, it provides a structure to identify the substantial deficiencies in our knowledge base and areas where research would improve our understanding of the pathological and repair process, together with assessment and management. The strength of this model adapted for the rotator cuff tendons and subacromial bursa will be tested in its ability to incorporate and adapt to emerging research.

Polymer Fluid Dynamics: Continuum and Molecular Approaches.

PubMed

Bird, R B; Giacomin, A J

2016-06-07

To solve problems in polymer fluid dynamics, one needs the equations of continuity, motion, and energy. The last two equations contain the stress tensor and the heat-flux vector for the material. There are two ways to formulate the stress tensor: (a) One can write a continuum expression for the stress tensor in terms of kinematic tensors, or (b) one can select a molecular model that represents the polymer molecule and then develop an expression for the stress tensor from kinetic theory. The advantage of the kinetic theory approach is that one gets information about the relation between the molecular structure of the polymers and the rheological properties. We restrict the discussion primarily to the simplest stress tensor expressions or constitutive equations containing from two to four adjustable parameters, although we do indicate how these formulations may be extended to give more complicated expressions. We also explore how these simplest expressions are recovered as special cases of a more general framework, the Oldroyd 8-constant model. Studying the simplest models allows us to discover which types of empiricisms or molecular models seem to be worth investigating further. We also explore equivalences between continuum and molecular approaches. We restrict the discussion to several types of simple flows, such as shearing flows and extensional flows, which are of greatest importance in industrial operations. Furthermore, if these simple flows cannot be well described by continuum or molecular models, then it is not necessary to lavish time and energy to apply them to more complex flow problems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kowalski, Adam F.; Mathioudakis, Mihalis; Hawley, Suzanne L.

We present a large data set of high-cadence dMe flare light curves obtained with custom continuum filters on the triple-beam, high-speed camera system ULTRACAM. The measurements provide constraints for models of the near-ultraviolet (NUV) and optical continuum spectral evolution on timescales of ≈1 s. We provide a robust interpretation of the flare emission in the ULTRACAM filters using simultaneously obtained low-resolution spectra during two moderate-sized flares in the dM4.5e star YZ CMi. By avoiding the spectral complexity within the broadband Johnson filters, the ULTRACAM filters are shown to characterize bona fide continuum emission in the NUV, blue, and red wavelength regimes. Themore » NUV/blue flux ratio in flares is equivalent to a Balmer jump ratio, and the blue/red flux ratio provides an estimate for the color temperature of the optical continuum emission. We present a new “color–color” relationship for these continuum flux ratios at the peaks of the flares. Using the RADYN and RH codes, we interpret the ULTRACAM filter emission using the dominant emission processes from a radiative-hydrodynamic flare model with a high nonthermal electron beam flux, which explains a hot, T ≈ 10{sup 4} K, color temperature at blue-to-red optical wavelengths and a small Balmer jump ratio as observed in moderate-sized and large flares alike. We also discuss the high time resolution, high signal-to-noise continuum color variations observed in YZ CMi during a giant flare, which increased the NUV flux from this star by over a factor of 100.« less

Low-Density Nozzle Flow by the Direct Simulation Monte Carlo and Continuum Methods

NASA Technical Reports Server (NTRS)

Chung, Chang-Hong; Kim, Sku C.; Stubbs, Robert M.; Dewitt, Kenneth J.

1994-01-01

Two different approaches, the direct simulation Monte Carlo (DSMC) method based on molecular gasdynamics, and a finite-volume approximation of the Navier-Stokes equations, which are based on continuum gasdynamics, are employed in the analysis of a low-density gas flow in a small converging-diverging nozzle. The fluid experiences various kinds of flow regimes including continuum, slip, transition, and free-molecular. Results from the two numerical methods are compared with Rothe's experimental data, in which density and rotational temperature variations along the centerline and at various locations inside a low-density nozzle were measured by the electron-beam fluorescence technique. The continuum approach showed good agreement with the experimental data as far as density is concerned. The results from the DSMC method showed good agreement with the experimental data, both in the density and the rotational temperature. It is also shown that the simulation parameters, such as the gas/surface interaction model, the energy exchange model between rotational and translational modes, and the viscosity-temperature exponent, have substantial effects on the results of the DSMC method.

Fracture-Based Mesh Size Requirements for Matrix Cracks in Continuum Damage Mechanics Models

NASA Technical Reports Server (NTRS)

Leone, Frank A.; Davila, Carlos G.; Mabson, Gerald E.; Ramnath, Madhavadas; Hyder, Imran

2017-01-01

This paper evaluates the ability of progressive damage analysis (PDA) finite element (FE) models to predict transverse matrix cracks in unidirectional composites. The results of the analyses are compared to closed-form linear elastic fracture mechanics (LEFM) solutions. Matrix cracks in fiber-reinforced composite materials subjected to mode I and mode II loading are studied using continuum damage mechanics and zero-thickness cohesive zone modeling approaches. The FE models used in this study are built parametrically so as to investigate several model input variables and the limits associated with matching the upper-bound LEFM solutions. Specifically, the sensitivity of the PDA FE model results to changes in strength and element size are investigated.

Comparison of Nernst-Planck and reaction rate models for multiply occupied channels.

PubMed Central

Levitt, D G

1982-01-01

The Nernst-Planck continuum equation for a channel that can be occupied by at most two ions is solved for two different physical cases. The first case is for the assumption that the water and ion cannot get around each other anywhere in the channel, so that if there are two ions in the channel the distance between them is fixed by the number of water molecules between them. The second case is for the assumption that there are regions at he ends of the channel where the ions and water can get around each other. For these two cases, the validity of the simple two-site reaction-rate approximation when there is a continuously varying central energy barrier was evaluated by comparing it with the exact Nernst-Planck solution. For the first continuum case, the kinetics for the continuum and reaction-rate models are nearly identical. For the second case, the agreement depends on the strength of the ion-ion interaction energy. For a low interaction energy (large channel diameter) a high ion concentrations, there is a large difference in the flux as a function of voltage for the two models-with the continuum flux becoming more than four times larger at 250 mV. Simple analytical expressions are derived for the two-ion continuum channel for the case where the ends are in equilibrium with the bulk solution and for the case where ion mobility becomes zero when there are two ions in the channel. The implications of these results for biological channels are discussed. PMID:6280783

PT-symmetry breaking with divergent potentials: Lattice and continuum cases

NASA Astrophysics Data System (ADS)

Joglekar, Yogesh N.; Scott, Derek D.; Saxena, Avadh

2014-09-01

We investigate the parity- and time-reversal (PT-) symmetry breaking in lattice models in the presence of long-ranged, non-Hermitian, PT-symmetric potentials that remain finite or become divergent in the continuum limit. By scaling analysis of the fragile PT threshold for an open finite lattice, we show that continuum loss-gain potentials Vα(x)∝i|x|αsgn(x) have a positive PT-breaking threshold for α >-2, and a zero threshold for α ≤-2. When α <0 localized states with complex (conjugate) energies in the continuum energy band occur at higher loss-gain strengths. We investigate the signatures of PT-symmetry breaking in coupled waveguides, and show that the emergence of localized states dramatically shortens the relevant time scale in the PT-symmetry broken region.

An Elastic Model of Blebbing in Nuclear Lamin Meshworks

NASA Astrophysics Data System (ADS)

Funkhouser, Chloe; Sknepnek, Rastko; Shimi, Takeshi; Goldman, Anne; Goldman, Robert; Olvera de La Cruz, Monica

2013-03-01

A two-component continuum elastic model is introduced to analyze a nuclear lamin meshwork, a structural element of the lamina of the nuclear envelope. The main component of the lamina is a meshwork of lamin protein filaments providing mechanical support to the nucleus and also playing a role in gene expression. Abnormalities in nuclear shape are associated with a variety of pathologies, including some forms of cancer and Hutchinson-Gilford progeria syndrome, and are often characterized by protruding structures termed nuclear blebs. Nuclear blebs are rich in A-type lamins and may be related to pathological gene expression. We apply the two-dimensional elastic shell model to determine which characteristics of the meshwork could be responsible for blebbing, including heterogeneities in the meshwork thickness and mesh size. We find that if one component of the lamin meshwork, rich in A-type lamins, has a tendency to form a larger mesh size than that rich in B-type lamins, this is sufficient to cause segregation of the lamin components and also to form blebs rich in A-type lamins. The model produces structures with comparable morphologies and mesh size distributions as the lamin meshworks of real, pathological nuclei. Funded by US DoE Award DEFG02-08ER46539 and by the DDR&E and AFOSR under Award FA9550-10-1-0167; simulations performed on NU Quest cluster

Micromechanics Based Failure Analysis of Heterogeneous Materials

NASA Astrophysics Data System (ADS)

Sertse, Hamsasew M.

In recent decades, heterogeneous materials are extensively used in various industries such as aerospace, defense, automotive and others due to their desirable specific properties and excellent capability of accumulating damage. Despite their wide use, there are numerous challenges associated with the application of these materials. One of the main challenges is lack of accurate tools to predict the initiation, progression and final failure of these materials under various thermomechanical loading conditions. Although failure is usually treated at the macro and meso-scale level, the initiation and growth of failure is a complex phenomena across multiple scales. The objective of this work is to enable the mechanics of structure genome (MSG) and its companion code SwiftComp to analyze the initial failure (also called static failure), progressive failure, and fatigue failure of heterogeneous materials using micromechanics approach. The initial failure is evaluated at each numerical integration point using pointwise and nonlocal approach for each constituent of the heterogeneous materials. The effects of imperfect interfaces among constituents of heterogeneous materials are also investigated using a linear traction-displacement model. Moreover, the progressive and fatigue damage analyses are conducted using continuum damage mechanics (CDM) approach. The various failure criteria are also applied at a material point to analyze progressive damage in each constituent. The constitutive equation of a damaged material is formulated based on a consistent irreversible thermodynamics approach. The overall tangent modulus of uncoupled elastoplastic damage for negligible back stress effect is derived. The initiation of plasticity and damage in each constituent is evaluated at each numerical integration point using a nonlocal approach. The accumulated plastic strain and anisotropic damage evolution variables are iteratively solved using an incremental algorithm. The damage analyses are performed for both brittle failure/high cycle fatigue (HCF) for negligible plastic strain and ductile failure/low cycle fatigue (LCF) for large plastic strain. The proposed approach is incorporated in SwiftComp and used to predict the initial failure envelope, stress-strain curve for various loading conditions, and fatigue life of heterogeneous materials. The combined effects of strain hardening and progressive fatigue damage on the effective properties of heterogeneous materials are also studied. The capability of the current approach is validated using several representative examples of heterogeneous materials including binary composites, continuous fiber-reinforced composites, particle-reinforced composites, discontinuous fiber-reinforced composites, and woven composites. The predictions of MSG are also compared with the predictions obtained using various micromechanics approaches such as Generalized Methods of Cells (GMC), Mori-Tanaka (MT), and Double Inclusions (DI) and Representative Volume Element (RVE) Analysis (called as 3-dimensional finite element analysis (3D FEA) in this document). This study demonstrates that a micromechanics based failure analysis has a great potential to rigorously and more accurately analyze initiation and progression of damage in heterogeneous materials. However, this approach requires material properties specific to damage analysis, which are needed to be independently calibrated for each constituent.

Mortality along the continuum of HIV care in Rwanda: a model-based analysis.

PubMed

Bendavid, Eran; Stauffer, David; Remera, Eric; Nsanzimana, Sabin; Kanters, Steve; Mills, Edward J

2016-12-01

HIV is the leading cause of death among adults in sub-Saharan Africa. However, mortality along the HIV care continuum is poorly described. We combine demographic, epidemiologic, and health services data to estimate where are people with HIV dying along Rwanda's care continuum. We calibrated an age-structured HIV disease and transmission stochastic simulation model to the epidemic in Rwanda. We estimate mortality among HIV-infected individuals in the following states: untested, tested without establishing care in an antiretroviral therapy (ART) program (unlinked), in care before initiating ART (pre-ART), lost to follow-up (LTFU) following ART initiation, and retained in active ART care. We estimated mortality among people living with HIV in Rwanda through 2025 under current conditions, and with improvements to the HIV care continuum. In 2014, the greatest portion of deaths occurred among those untested (35.4%), followed by those on ART (34.1%), reflecting the large increase in the population on ART. Deaths among those LTFU made up 11.8% of all deaths among HIV-infected individuals in 2014, and in the base case this portion increased to 18.8% in 2025, while the contribution to mortality declined among those untested, unlinked, and in pre-ART. In our model only combined improvements to multiple aspects of the HIV care continuum were projected to reduce the total number of deaths among those with HIV, estimated at 8177 in 2014, rising to 10,659 in the base case, and declining to 5,691 with combined improvements in 2025. Mortality among those untested for HIV contributes a declining portion of deaths among HIV-infected individuals in Rwanda, but the portion of deaths among those LTFU is expected to increase the most over the next decade. Combined improvements to the HIV care continuum might be needed to reduce the number of deaths among those with HIV.

A high-resolution extraterrestrial solar spectrum and water vapour continuum at near infrared wavelengths from ground-based spectrometer measurements

NASA Astrophysics Data System (ADS)

Menang, K. P.

A high resolution extraterrestrial solar spectrum (CAVIAR solar spectrum) and water vapour continuum have been derived in near infrared windows from 2000-10000 cm-1 (105μm), by applying the Langley technique to calibrated ground-based high-resolution Fourier transform spectrometer measurements, made under clear-sky conditions. The effect of the choice of an extraterrestrial solar spectrum for radiative transfer calculations of clear-sky absorption and heating rates in the near infrared was also studied. There is a good agreement between the solar lines strengths and positions of the CAVIAR solar spectrum and those from both high-resolution satellite and ground-based measurements in their regions of spectral overlap. However, there are significant differences between the structure of the CAVIAR solar spectrum and spectra from models. Many of the detected lines are missing from widely-used modelled extraterrestrial solar spectrum. The absolute level and hence wavenumber-integrated solar irradiance of the CAVIAR solar spectrum was also found to be 8% lower than the satellite-based Thuillier et al spectra from 5200-10000 cm-1. Using different extraterrestrial solar spectra for radiative transfer calculations in the near infrared led to differences of up to about 11 W m-2 (8.2%) in the absorbed solar irradiance while the tropospheric and stratospheric heating rates could respectively differ by up to about 0.13K day-1 (8.1%) and 0.19 K day-1 (7.6%) for an overhead Sun and mid-latitude summer atmosphere. This work has shown that the widely-used empirically modelled continuum may be underestimating the strength of the water vapour continuum from 2000-10000 cm-1, with the derived continuum up to more than 2 orders of magnitude stronger at some wavenumbers in the windows. The derived continuum is also stronger than that implied by laboratory measurements, by a factor of up to 40 in some spectral regions.

A Nonlocal Peridynamic Plasticity Model for the Dynamic Flow and Fracture of Concrete.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogler, Tracy; Lammi, Christopher James

A nonlocal, ordinary peridynamic constitutive model is formulated to numerically simulate the pressure-dependent flow and fracture of heterogeneous, quasi-brittle ma- terials, such as concrete. Classical mechanics and traditional computational modeling methods do not accurately model the distributed fracture observed within this family of materials. The peridynamic horizon, or range of influence, provides a characteristic length to the continuum and limits localization of fracture. Scaling laws are derived to relate the parameters of peridynamic constitutive model to the parameters of the classical Drucker-Prager plasticity model. Thermodynamic analysis of associated and non-associated plastic flow is performed. An implicit integration algorithm is formu-more » lated to calculate the accumulated plastic bond extension and force state. The gov- erning equations are linearized and the simulation of the quasi-static compression of a cylinder is compared to the classical theory. A dissipation-based peridynamic bond failure criteria is implemented to model fracture and the splitting of a concrete cylinder is numerically simulated. Finally, calculation of the impact and spallation of a con- crete structure is performed to assess the suitability of the material and failure models for simulating concrete during dynamic loadings. The peridynamic model is found to accurately simulate the inelastic deformation and fracture behavior of concrete during compression, splitting, and dynamically induced spall. The work expands the types of materials that can be modeled using peridynamics. A multi-scale methodology for simulating concrete to be used in conjunction with the plasticity model is presented. The work was funded by LDRD 158806.« less

Exploring mechanisms of transport and persistence of environmental DNA (eDNA)

NASA Astrophysics Data System (ADS)

Shogren, A.; Tank, J. L.; Riis, T.; Rosi, E. J.; Bolster, D.

2017-12-01

Sampling for eDNA is a non-intrusive method to detect species presence without direct observation, which allows for earlier detection and more rapid response than conventional sampling methods. However, our current understanding of how eDNA is transported and persists in flowing waters (e.g., streams and rivers) remains imprecise; in flowing waters, the target organism may be some distance away from where the eDNA in water is collected. It is uncertain how the unique transport properties of suspended eDNA or the inherent heterogeneity of natural flowing systems may impact the probability of downstream eDNA detection. To improve understanding of eDNA fate, we first conducted experimental releases and modeled the impact of benthic substrate heterogeneity and size on eDNA transport and retention in streams. We also used recirculating artificial streams to constrain estimates of eDNA degradation in systems with varying flow and microbial biofilm coverage. We found that eDNA retention in streams is substrate-specific, and that streambed hydraulics have significant influence on how far eDNA is transported downstream. Through the degradation experiments, we found that eDNA degradation is strongly context dependent, but even in systems with low velocity, eDNA can remain detectable in the water column >24hrs after introduction. This differential persistence of eDNA particles confirms that eDNA dynamics in flowing waters are not constant along a spatial continuum, which complicates interpretation of a positive detection in flowing waters, which presents a scaling problem for future modeling efforts to support transport predictions. To test our experimental results in a natural system, we compared our previous estimates for eDNA transport, retention, and degradation to field data collected during a longitudinal field survey for zebra mussel eDNA on the Gudena River in Silkeborg, Denmark. We found that though heterogeneity indeed complicates scaling efforts to extrapolate results from small experimental streams to larger natural systems, we can use the small-scale experiments to improve how we interpret spatial variation in eDNA signal in larger scale flowing systems.

HESS Opinions: The complementary merits of competing modelling philosophies in hydrology

NASA Astrophysics Data System (ADS)

Hrachowitz, Markus; Clark, Martyn P.

2017-08-01

In hydrology, two somewhat competing philosophies form the basis of most process-based models. At one endpoint of this continuum are detailed, high-resolution descriptions of small-scale processes that are numerically integrated to larger scales (e.g. catchments). At the other endpoint of the continuum are spatially lumped representations of the system that express the hydrological response via, in the extreme case, a single linear transfer function. Many other models, developed starting from these two contrasting endpoints, plot along this continuum with different degrees of spatial resolutions and process complexities. A better understanding of the respective basis as well as the respective shortcomings of different modelling philosophies has the potential to improve our models. In this paper we analyse several frequently communicated beliefs and assumptions to identify, discuss and emphasize the functional similarity of the seemingly competing modelling philosophies. We argue that deficiencies in model applications largely do not depend on the modelling philosophy, although some models may be more suitable for specific applications than others and vice versa, but rather on the way a model is implemented. Based on the premises that any model can be implemented at any desired degree of detail and that any type of model remains to some degree conceptual, we argue that a convergence of modelling strategies may hold some value for advancing the development of hydrological models.

Consistent Continuum Particle Modeling of Hypersonic Flows and Development of HybridSimulation Capability

DTIC Science & Technology

2017-07-01

Directorate 3550 Aberdeen Avenue SE Kirtland AFB, NM 87117-5776 AFRL /RVBYE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) AFRL -RV-PS-TR-2017-0152 12. DISTRIBUTION...Belvoir, VA 22060-6218 AFRL /RVIL Kirtland AFB, NM 87117-5776 Official Record Copy AFRL /RVBYE/Dr. Raymond Bemish 1 cy Approved for public release... AFRL -RV-PS- TR-2017-0152 AFRL -RV-PS- TR-2017-0152 CONSISTENT CONTINUUM-PARTICLE MODELING OF HYPERSONIC FLOWS AND DEVELOPMENT OF HYBRID

The Role of Molecular Motors in the Mechanics of Active Gels and the Effects of Inertia, Hydrodynamic Interaction and Compressibility in Passive Microrheology

DTIC Science & Technology

2014-07-01

to use the two-point microrheology technique 88 to measure the complex compressibility of biopolymers and cell components such as F-actin and...loads [23, 115]. Several works have used a continuum-mechanics level of description to model self- organization [64, 2] and rheology [79, 12, 33] of...morphogenesis [94]. Several works have used a continuum-mechanics level of description to model self- organization [64, 2] and rheology [79, 12, 33] of

Spreading of nonmotile bacteria on a hard agar plate: Comparison between agent-based and stochastic simulations

NASA Astrophysics Data System (ADS)

Rana, Navdeep; Ghosh, Pushpita; Perlekar, Prasad

2017-11-01

We study spreading of a nonmotile bacteria colony on a hard agar plate by using agent-based and continuum models. We show that the spreading dynamics depends on the initial nutrient concentration, the motility, and the inherent demographic noise. Population fluctuations are inherent in an agent-based model, whereas for the continuum model we model them by using a stochastic Langevin equation. We show that the intrinsic population fluctuations coupled with nonlinear diffusivity lead to a transition from a diffusion limited aggregation type of morphology to an Eden-like morphology on decreasing the initial nutrient concentration.

Small-amplitude acoustics in bulk granular media

NASA Astrophysics Data System (ADS)

Henann, David L.; Valenza, John J., II; Johnson, David L.; Kamrin, Ken

2013-10-01

We propose and validate a three-dimensional continuum modeling approach that predicts small-amplitude acoustic behavior of dense-packed granular media. The model is obtained through a joint experimental and finite-element study focused on the benchmark example of a vibrated container of grains. Using a three-parameter linear viscoelastic constitutive relation, our continuum model is shown to quantitatively predict the effective mass spectra in this geometry, even as geometric parameters for the environment are varied. Further, the model's predictions for the surface displacement field are validated mode-by-mode against experiment. A primary observation is the importance of the boundary condition between grains and the quasirigid walls.

Radiation of partially ionized atomic hydrogen

NASA Technical Reports Server (NTRS)

Soon, W. H.; Kunc, J. A.

1990-01-01

A nonlinear collisional-radiative model for determination of production of electrons, positive and negative ions, excited atoms, and spectral and continuum line intensities in stationary partially ionized atomic hydrogen is presented. Transport of radiation is included by coupling the rate equations for production of the electrons, ions, and excited atoms with the radiation escape factors, which are not constant but depend on plasma conditions. It is found that the contribution of the negative ion emission to the total continuum emission can be important. Comparison of the calculated total continuum emission coefficient, including the negative ion emission, is in good agreement with experimental results.

Continuum analyzing power for 4He(p-->,p') at 100 MeV

NASA Astrophysics Data System (ADS)

Lawrie, J. J.; Whittal, D. M.; Cowley, A. A.

1990-08-01

Distorted-wave impulse approximation calculations of the continuum analyzing power for the inclusive reaction 4He(p-->,p') at an incident energy of 100 MeV are presented. In addition to the quasifree knockout of nucleons, contributions from the knockout of deuteron, triton, and helion clusters are taken into account, together with a breakup component. Whereas nucleon knockout by itself does not account for the experimentally observed analyzing power, the inclusion of clusters has a large effect. Thus a simple knockout model is able to provide a reasonable description of the experimental continuum analyzing power.

The polarization of continuum radiation in sunspots. I - Rayleigh and Thomson scattering

NASA Technical Reports Server (NTRS)

Finn, G. D.; Jefferies, J. T.

1974-01-01

Expressions are derived for the Stokes parameters of light scattered by a layer of free electrons and hydrogen atoms in a sunspot. A physically reasonable sunspot model was found so that the direction of the calculated linear polarization agrees reasonably with observations. The magnitude of the calculated values of the linear polarization agrees generally with values observed in the continuum at 5830 A. Circular polarization in the continuum also accompanies electron scattering in spot regions; however for commonly accepted values of the longitudinal magnetic field, the predicted circular polarization is much smaller than observed.

Mechanism of asymmetric lineshape broadening in GaAs1-xNx Raman spectra

NASA Astrophysics Data System (ADS)

Mialitsin, Aleksej; Fluegel, Brian; Ptak, Aaron; Mascarenhas, Angelo

2012-07-01

Resonance Raman spectroscopy is used to probe the asymmetric broadening of the LO phonon linewidth in a dilute GaAs1-xNx alloy (x=0.41%). Electronic Raman scattering from a broad continuum is observed that gets enhanced concurrently with the LO phonon linewidth under resonance. The Fano interaction between the LO phonon and the electronic continuum is used to develop a model that satisfactorily explains the origin of the asymmetric LO phonon linewidth broadening in this abnormal alloy as arising due to coupling between the discrete and the continuum configurations.

Dynamics of basaltic glass dissolution - Capturing microscopic effects in continuum scale models

NASA Astrophysics Data System (ADS)

Aradóttir, E. S. P.; Sigfússon, B.; Sonnenthal, E. L.; Björnsson, G.; Jónsson, H.

2013-11-01

The method of 'multiple interacting continua' (MINC) was applied to include microscopic rate-limiting processes in continuum scale reactive transport models of basaltic glass dissolution. The MINC method involves dividing the system up to ambient fluid and grains, using a specific surface area to describe the interface between the two. The various grains and regions within grains can then be described by dividing them into continua separated by dividing surfaces. Millions of grains can thus be considered within the method without the need to explicity discretizing them. Four continua were used for describing a dissolving basaltic glass grain; the first one describes the ambient fluid around the grain, while the second, third and fourth continuum refer to a diffusive leached layer, the dissolving part of the grain and the inert part of the grain, respectively. The model was validated using the TOUGHREACT simulator and data from column flow through experiments of basaltic glass dissolution at low, neutral and high pH values. Successful reactive transport simulations of the experiments and overall adequate agreement between measured and simulated values provides validation that the MINC approach can be applied for incorporating microscopic effects in continuum scale basaltic glass dissolution models. Equivalent models can be used when simulating dissolution and alteration of other minerals. The study provides an example of how numerical modeling and experimental work can be combined to enhance understanding of mechanisms associated with basaltic glass dissolution. Column outlet concentrations indicated basaltic glass to dissolve stoichiometrically at pH 3. Predictive simulations with the developed MINC model indicated significant precipitation of secondary minerals within the column at neutral and high pH, explaining observed non-stoichiometric outlet concentrations at these pH levels. Clay, zeolite and hydroxide precipitation was predicted to be most abundant within the column.

Active learning of constitutive relation from mesoscopic dynamics for macroscopic modeling of non-Newtonian flows

NASA Astrophysics Data System (ADS)

Zhao, Lifei; Li, Zhen; Caswell, Bruce; Ouyang, Jie; Karniadakis, George Em

2018-06-01

We simulate complex fluids by means of an on-the-fly coupling of the bulk rheology to the underlying microstructure dynamics. In particular, a continuum model of polymeric fluids is constructed without a pre-specified constitutive relation, but instead it is actively learned from mesoscopic simulations where the dynamics of polymer chains is explicitly computed. To couple the bulk rheology of polymeric fluids and the microscale dynamics of polymer chains, the continuum approach (based on the finite volume method) provides the transient flow field as inputs for the (mesoscopic) dissipative particle dynamics (DPD), and in turn DPD returns an effective constitutive relation to close the continuum equations. In this multiscale modeling procedure, we employ an active learning strategy based on Gaussian process regression (GPR) to minimize the number of expensive DPD simulations, where adaptively selected DPD simulations are performed only as necessary. Numerical experiments are carried out for flow past a circular cylinder of a non-Newtonian fluid, modeled at the mesoscopic level by bead-spring chains. The results show that only five DPD simulations are required to achieve an effective closure of the continuum equations at Reynolds number Re = 10. Furthermore, when Re is increased to 100, only one additional DPD simulation is required for constructing an extended GPR-informed model closure. Compared to traditional message-passing multiscale approaches, applying an active learning scheme to multiscale modeling of non-Newtonian fluids can significantly increase the computational efficiency. Although the method demonstrated here obtains only a local viscosity from the polymer dynamics, it can be extended to other multiscale models of complex fluids whose macro-rheology is unknown.

Theory of molecular rate processes in the presence of intense laser radiation

NASA Technical Reports Server (NTRS)

George, T. F.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.; Lam, K.-S.; Bellum, J. C.; Lee, H.-W.; Slutsky, M. S.; Lin, J.-T.

1979-01-01

The present paper deals with the influence of intense laser radiation on gas-phase molecular rate processes. Representations of the radiation field, the particle system, and the interaction involving these two entities are discussed from a general rather than abstract point of view. The theoretical methods applied are outlined, and the formalism employed is illustrated by application to a variety of specific processes. Quantum mechanical and semiclassical treatments of representative atom-atom and atom-diatom collision processes in the presence of a field are examined, and examples of bound-continuum processes and heterogeneous catalysis are discussed within the framework of both quantum-mechanical and semiclassical theories.

On Thermodynamic Constraints upon Turbulence Modeling

NASA Astrophysics Data System (ADS)

Huang, Yu-Ning; Durst, Franz

2000-11-01

Turbulence is a continuum phenomenon which can be described within the framework of continuum mechanics. Such foundation has the potential for improving turbulence modeling, making it less heuristic and more rational. In the present research, we consider the compatibility of turbulence modeling with the second law of thermodynamics. We show that the Clausius-Planck inequality, as an expression of the principle of entropy growth, places a thermodynamic restriction upon the turbulence modeling of an incompressible Navier-Stokes fluid in an isothermal temperature field. This thermodynamic restriction is given in the form of an inequality, which ensures non-negativeness of the mean internal dissipation. As an illustration, we show the thermodynamic constraints on the modeling of a few typical homogeneous turbulent flows.

Molecular continua for polymeric liquids in large-amplitude oscillatory shear flow

NASA Astrophysics Data System (ADS)

Giacomin, A. Jeffrey; Saengow, Chaimongkol

2018-05-01

In this paper, we connect a molecular description of the rheology of a polymeric liquid to a continuum description, and then test this connection for large-amplitude oscillatory shear (LAOS) flow. Specifically, for the continuum description, we use the 6-constant Oldroyd framework, and for the molecular, we use the simplest relevant molecular model, the suspension of rigid dumbbells. By relevant, we mean predicting at least higher harmonics in the shear stress response in LAOS. We call this connection a molecular continuum, and we examine two ways of arriving at this connection. The first goes through the retarded motion expansion, and the second expands each of a set of specific material functions (complex, steady shear, and steady uniaxial extensional viscosities). Both ways involve in comparing the coefficients of expansions and then solve for the six constants of the continuum framework in terms of the two constants of the rigid dumbbell suspension. The purpose of a molecular continuum is that many well-known results for rigid dumbbell suspensions in other flow fields can also be easily obtained, without having to firstly find the orientation distribution function. In this paper, we focus on the recent result for the rigid dumbbell suspension in LAOS. We compare the accuracies of the retarded motion molecular continuum (RMMC) with the material function molecular continuum (MFMC). We find the RMMC to be the most accurate for LAOS.

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model.

PubMed

Liang, Wenkel; Chapman, Craig T; Ding, Feizhi; Li, Xiaosong

2012-03-01

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. © 2012 American Chemical Society

On the choice of boundary conditions in continuum models of continental deformation

NASA Technical Reports Server (NTRS)

Wdowinski, Shimon; O'Connell, Richard J.

1990-01-01

Recent studies of continental deformation have treated the lithosphere as a viscous medium and investigated the time evolution of the deformation caused by tectonic and buoyancy forces. This paper examines the differences between (1) continuum models that keep velocity boundary conditions constant with time and (2) models that keep stress boundary conditions constant with time. These differences are demonstrated by using a simple example of a continental lithosphere that is subjected to horizontal compression. The results show that in (2) the indentation velocity decreases with time, while in (1) the indentation velocity remains constant with time.

Do some x-ray stars have white dwarf companions

NASA Technical Reports Server (NTRS)

Mccollum, Bruce

1995-01-01

Some Be stars which are intermittent X-ray sources may have white dwarf companions rather than neutron stars. It is not possible to prove or rule out the existence of Be + WD systems using X-ray or optical data. However, the presence of a white dwarf could be established by the detection of its EUV continuum shortward of the Be star's continuum turnover at 100 A. Either the detection or the nondetection of Be + WD systems would have implications for models of Be star variability, models of Be binary system formation and evolution, and models of wind-fed accretion.

Do Some X-ray Stars Have White Dwarf Companions?

NASA Technical Reports Server (NTRS)

McCollum, Bruce

1995-01-01

Some Be stars which are intermittent C-ray sources may have white dwarf companions rather than neutron stars. It is not possible to prove or rule out the existence of Be+WD systems using X-ray or optical data. However, the presence of a white dwarf could be established by the detection of its EUV continuum shortward of the Be star's continuum turnover at 1OOOA. Either the detection or the nondetection of Be+WD systems would have implications for models of Be star variability, models of Be binary system formation and evolution, and models of wind-fed accretion.

Second law of thermodynamics in volume diffusion hydrodynamics in multicomponent gas mixtures

NASA Astrophysics Data System (ADS)

Dadzie, S. Kokou

2012-10-01

We presented the thermodynamic structure of a new continuum flow model for multicomponent gas mixtures. The continuum model is based on a volume diffusion concept involving specific species. It is independent of the observer's reference frame and enables a straightforward tracking of a selected species within a mixture composed of a large number of constituents. A method to derive the second law and constitutive equations accompanying the model is presented. Using the configuration of a rotating fluid we illustrated an example of non-classical flow physics predicted by new contributions in the entropy and constitutive equations.

Severity of depression and magnitude of productivity loss.

PubMed

Beck, Arne; Crain, A Lauren; Solberg, Leif I; Unützer, Jürgen; Glasgow, Russell E; Maciosek, Michael V; Whitebird, Robin

2011-01-01

Depression is associated with lowered work functioning, including absences, impaired productivity, and decreased job retention. Few studies have examined depression symptoms across a continuum of severity in relationship to the magnitude of work impairment in a large and heterogeneous patient population, however. We assessed the relationship between depression symptom severity and productivity loss among patients initiating treatment for depression. Data were obtained from patients participating in the DIAMOND (Depression Improvement Across Minnesota: Offering a New Direction) initiative, a statewide quality improvement collaborative to provide enhanced depression care. Patients newly started on antidepressants were surveyed with the Patient Health Questionnaire 9-item screen (PHQ-9), a measure of depression symptom severity; the Work Productivity and Activity Impairment (WPAI) questionnaire, a measure of loss in productivity; and items on health status and demographics. We analyzed data from the 771 patients who reported being currently employed. General linear models adjusting for demographics and health status showed a significant linear, monotonic relationship between depression symptom severity and productivity loss: with every 1-point increase in PHQ-9 score, patients experienced an additional mean productivity loss of 1.65% (P <.001). Even minor levels of depression symptoms were associated with decrements in work function. Full-time vs part-time employment status and self-reported fair or poor health vs excellent, very good, or good health were also associated with a loss of productivity (P <.001 and P=.045, respectively). This study shows a relationship between the severity of depression symptoms and work function, and suggests that even minor levels of depression are associated with a loss of productivity. Employers may find it beneficial to invest in effective treatments for depressed employees across the continuum of depression severity.

Computational modeling of the effective Young's modulus values of fullerene molecules: a combined molecular dynamics simulation and continuum shell model.

PubMed

Ghavanloo, Esmaeal; Izadi, Razie; Nayebi, Ali

2018-02-28

Estimating the Young's modulus of a structure in the nanometer size range is a difficult task. The reliable determination of this parameter is, however, important in both basic and applied research. In this study, by combining molecular dynamics (MD) simulations and continuum shell theory, we designed a new approach to determining the Young's modulus values of different spherical fullerenes. The results indicate that the Young's modulus values of fullerene molecules decrease nonlinearly with increasing molecule size and understandably tend to the Young's modulus of an ideal flat graphene sheet at large molecular radii. To the best of our knowledge, this is first time that a combined atomistic-continuum method which can predict the Young's modulus values of fullerene molecules with high precision has been reported.

The influence of continuum radiation fields on hydrogen radio recombination lines

NASA Astrophysics Data System (ADS)

Prozesky, Andri; Smits, Derck P.

2018-05-01

Calculations of hydrogen departure coefficients using a model with the angular momentum quantum levels resolved that includes the effects of external radiation fields are presented. The stimulating processes are important at radio frequencies and can influence level populations. New numerical techniques with a solid mathematical basis have been incorporated into the model to ensure convergence of the solution. Our results differ from previous results by up to 20 per cent. A direct solver with a similar accuracy but more efficient than the iterative method is used to evaluate the influence of continuum radiation on the hydrogen population structure. The effects on departure coefficients of continuum radiation from dust, the cosmic microwave background, the stellar ionising radiation, and free-free radiation are quantified. Tables of emission and absorption coefficients for interpreting observed radio recombination lines are provided.