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Sample records for mechanics modeling based

  1. Mechanics model for actin-based motility

    NASA Astrophysics Data System (ADS)

    Lin, Yuan

    2009-02-01

    We present here a mechanics model for the force generation by actin polymerization. The possible adhesions between the actin filaments and the load surface, as well as the nucleation and capping of filament tips, are included in this model on top of the well-known elastic Brownian ratchet formulation. A closed form solution is provided from which the force-velocity relationship, summarizing the mechanics of polymerization, can be drawn. Model predictions on the velocity of moving beads driven by actin polymerization are consistent with experiment observations. This model also seems capable of explaining the enhanced actin-based motility of Listeria monocytogenes and beads by the presence of Vasodilator-stimulated phosphoprotein, as observed in recent experiments.

  2. Mechanics model for actin-based motility.

    PubMed

    Lin, Yuan

    2009-02-01

    We present here a mechanics model for the force generation by actin polymerization. The possible adhesions between the actin filaments and the load surface, as well as the nucleation and capping of filament tips, are included in this model on top of the well-known elastic Brownian ratchet formulation. A closed form solution is provided from which the force-velocity relationship, summarizing the mechanics of polymerization, can be drawn. Model predictions on the velocity of moving beads driven by actin polymerization are consistent with experiment observations. This model also seems capable of explaining the enhanced actin-based motility of Listeria monocytogenes and beads by the presence of Vasodilator-stimulated phosphoprotein, as observed in recent experiments.

  3. Requirements for energy based constitutive modeling in tire mechanics

    NASA Technical Reports Server (NTRS)

    Luchini, John R.; Peters, Jim M.; Mars, Will V.

    1995-01-01

    The history, requirements, and theoretical basis of a new energy based constitutive model for (rubber) material elasticity, hysteresis, and failure are presented. Energy based elasticity is handled by many constitutive models, both in one dimension and in three dimensions. Conversion of mechanical energy to heat can be modeled with viscoelasticity or as structural hysteresis. We are seeking unification of elasticity, hysteresis, and failure mechanisms such as fatigue and wear. An energy state characterization for failure criteria of (rubber) materials may provide this unification and also help explain the interaction of temperature effects with failure mechanisms which are described as creation of growth of internal crack surface. Improved structural modeling of tires with FEM should result from such a unified constitutive theory. The theory will also guide experimental work and should enable better interpretation of the results of computational stress analyses.

  4. Phase-field elasticity model based on mechanical jump conditions

    NASA Astrophysics Data System (ADS)

    Schneider, Daniel; Tschukin, Oleg; Choudhury, Abhik; Selzer, Michael; Böhlke, Thomas; Nestler, Britta

    2015-05-01

    Computational models based on the phase-field method typically operate on a mesoscopic length scale and resolve structural changes of the material and furthermore provide valuable information about microstructure and mechanical property relations. An accurate calculation of the stresses and mechanical energy at the transition region is therefore indispensable. We derive a quantitative phase-field elasticity model based on force balance and Hadamard jump conditions at the interface. Comparing the simulated stress profiles calculated with Voigt/Taylor (Annalen der Physik 274(12):573, 1889), Reuss/Sachs (Z Angew Math Mech 9:49, 1929) and the proposed model with the theoretically predicted stress fields in a plate with a round inclusion under hydrostatic tension, we show the quantitative characteristics of the model. In order to validate the elastic contribution to the driving force for phase transition, we demonstrate the absence of excess energy, calculated by Durga et al. (Model Simul Mater Sci Eng 21(5):055018, 2013), in a one-dimensional equilibrium condition of serial and parallel material chains. To validate the driving force for systems with curved transition regions, we relate simulations to the Gibbs-Thompson equilibrium condition (Johnson and Alexander, J Appl Phys 59(8):2735, 1986).

  5. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments.

    PubMed

    van Riel, Natal A W

    2006-12-01

    Systems biology applies quantitative, mechanistic modelling to study genetic networks, signal transduction pathways and metabolic networks. Mathematical models of biochemical networks can look very different. An important reason is that the purpose and application of a model are essential for the selection of the best mathematical framework. Fundamental aspects of selecting an appropriate modelling framework and a strategy for model building are discussed. Concepts and methods from system and control theory provide a sound basis for the further development of improved and dedicated computational tools for systems biology. Identification of the network components and rate constants that are most critical to the output behaviour of the system is one of the major problems raised in systems biology. Current approaches and methods of parameter sensitivity analysis and parameter estimation are reviewed. It is shown how these methods can be applied in the design of model-based experiments which iteratively yield models that are decreasingly wrong and increasingly gain predictive power.

  6. A mechanism-based approach to modeling ductile fracture.

    SciTech Connect

    Bammann, Douglas J.; Hammi, Youssef; Antoun, Bonnie R.; Klein, Patrick A.; Foulk, James W., III; McFadden, Sam X.

    2004-01-01

    Ductile fracture in metals has been observed to result from the nucleation, growth, and coalescence of voids. The evolution of this damage is inherently history dependent, affected by how time-varying stresses drive the formation of defect structures in the material. At some critically damaged state, the softening response of the material leads to strain localization across a surface that, under continued loading, becomes the faces of a crack in the material. Modeling localization of strain requires introduction of a length scale to make the energy dissipated in the localized zone well-defined. In this work, a cohesive zone approach is used to describe the post-bifurcation evolution of material within the localized zone. The relations are developed within a thermodynamically consistent framework that incorporates temperature and rate-dependent evolution relationships motivated by dislocation mechanics. As such, we do not prescribe the evolution of tractions with opening displacements across the localized zone a priori. The evolution of tractions is itself an outcome of the solution of particular, initial boundary value problems. The stress and internal state of the material at the point of bifurcation provides the initial conditions for the subsequent evolution of the cohesive zone. The models we develop are motivated by in-situ scanning electron microscopy of three-point bending experiments using 6061-T6 aluminum and 304L stainless steel, The in situ observations of the initiation and evolution of fracture zones reveal the scale over which the failure mechanisms act. In addition, these observations are essential for motivating the micromechanically-based models of the decohesion process that incorporate the effects of loading mode mixity, temperature, and loading rate. The response of these new cohesive zone relations is demonstrated by modeling the three-point bending configuration used for the experiments. In addition, we survey other methods with the potential

  7. THE FUTURE OF COMPUTER-BASED TOXICITY PREDICTION: MECHANISM-BASED MODELS VS. INFORMATION MINING APPROACHES

    EPA Science Inventory


    The Future of Computer-Based Toxicity Prediction:
    Mechanism-Based Models vs. Information Mining Approaches

    When we speak of computer-based toxicity prediction, we are generally referring to a broad array of approaches which rely primarily upon chemical structure ...

  8. Molecular mechanics modeling of azobenzene-based photoswitches.

    PubMed

    Duchstein, Patrick; Neiss, Christian; Görling, Andreas; Zahn, Dirk

    2012-06-01

    We present an extension of the generalized amber force field to allow the modeling of azobenzenes by means of classical molecular mechanics. TD-DFT calculations were employed to derive different interaction models for 4-hydroxy-4'-methyl-azobenzene, including the ground (S(0)) and S(1) excited state. For both states, partial charges and the -N = N- torsion potentials were characterized. On this basis, we pave the way to large-scale model simulations involving azobenzene molecular switches. Using the example of an isolated molecule, the mechanics of cyclic switching processes are demonstrated by classical molecular dynamics simulations.

  9. A stereo model based upon mechanisms of human binocular vision

    NASA Technical Reports Server (NTRS)

    Griswold, N. C.; Yeh, C. P.

    1986-01-01

    A model for stereo vision, which is based on the human-binocular vision system, is proposed. Data collected from studies of neurophysiology of the human binocular system are discussed. An algorithm for the implementation of this stereo vision model is derived. The algorithm is tested on computer-generated and real scene images. Examples of a computer-generated image and a grey-level image are presented. It is noted that the proposed method is computationally efficient for depth perception, and the results indicate accuracies that are noise tolerant.

  10. A mechanism-based approach for absorption modeling: the Gastro-Intestinal Transit Time (GITT) model.

    PubMed

    Hénin, Emilie; Bergstrand, Martin; Standing, Joseph F; Karlsson, Mats O

    2012-06-01

    Absorption models used in the estimation of pharmacokinetic drug characteristics from plasma concentration data are generally empirical and simple, utilizing no prior information on gastro-intestinal (GI) transit patterns. Our aim was to develop and evaluate an estimation strategy based on a mechanism-based model for drug absorption, which takes into account the tablet movement through the GI transit. This work is an extension of a previous model utilizing tablet movement characteristics derived from magnetic marker monitoring (MMM) and pharmacokinetic data. The new approach, which replaces MMM data with a GI transit model, was evaluated in data sets where MMM data were available (felodipine) or not available (diclofenac). Pharmacokinetic profiles in both datasets were well described by the model according to goodness-of-fit plots. Visual predictive checks showed the model to give superior simulation properties compared with a standard empirical approach (first-order absorption rate + lag-time). This model represents a step towards an integrated mechanism-based NLME model, where the use of physiological knowledge and in vitro–in vivo correlation helps fully characterize PK and generate hypotheses for new formulations or specific populations.

  11. Nonlinear mechanisms determining expiratory flow limitation in mechanical ventilation: a model-based interpretation.

    PubMed

    Barbini, Paolo; Cevenini, Gabriele; Avanzolni, Guido

    2003-09-01

    A nonlinear model of breathing mechanics, in which the tracheobronchial airways are considered in three serial segments, is presented to obtain insights into the mechanisms underlying expiratory flow limitation (EFL) in mechanically ventilated patients. Chronic obstructive pulmonary disease (COPD) and normal conditions were simulated and EFL was detected by application of negative expiratory pressure at the mouth or resistance reduction of the expiratory circuit. Simulation results confirm that both techniques reveal remarkable differences in the flow-volume curves between normal subjects and COPD patients, the former showing absence of EFL and the latter exhibiting EFL over most of the expiration. To interpret the role of different nonlinear mechanisms in producing EFL, different flow-volume curves obtained by changing model parameter values were analyzed. An increase in lower-airway resistance did not give rise to EFL, whereas a change in the pressure-volume characteristic of the intermediate-airway segment, towards increased resistance and easier collapse, significantly modified system behavior. In particular, EFL was observed when this intermediate-segment change was combined with an increase in lower-airway resistance. This evidence suggests that modifications, producing loss of radial traction and consequent narrowing of the airways in the peribronchial region, may play a leading role in EFL in COPD patients.

  12. Finite element based micro-mechanics modeling of textile composites

    NASA Technical Reports Server (NTRS)

    Glaessgen, E. H.; Griffin, O. H., Jr.

    1995-01-01

    Textile composites have the advantage over laminated composites of a significantly greater damage tolerance and resistance to delamination. Currently, a disadvantage of textile composites is the inability to examine the details of the internal response of these materials under load. Traditional approaches to the study fo textile based composite materials neglect many of the geometric details that affect the performance of the material. The present three dimensional analysis, based on the representative volume element (RVE) of a plain weave, allows prediction of the internal details of displacement, strain, stress, and failure quantities. Through this analysis, the effect of geometric and material parameters on the aforementioned quantities are studied.

  13. VISUALIZATION-BASED ANALYSIS FOR A MIXED-INHIBITION BINARY PBPK MODEL: DETERMINATION OF INHIBITION MECHANISM

    EPA Science Inventory

    A physiologically-based pharmacokinetic (PBPK) model incorporating mixed enzyme inhibition was used to determine mechanism of the metabolic interactions occurring during simultaneous inhalation exposures to the organic solvents chloroform and trichloroethylene (TCE).

    V...

  14. Transmission line circuit model of a PPy based trilayer mechanical sensor

    NASA Astrophysics Data System (ADS)

    Khalili, Nazanin; Naguib, Hani E.; Kwon, Roy H.

    2015-04-01

    Many efforts have been devoted to modeling the diffusive impedance of conjugated polymer (CP) based actuators using their equivalent electrical circuits. Employing the same methodology, CP based mechanical sensors can also be treated by an equivalent transmission line circuit and their overall impedance can be modeled, correspondingly. Due to the large number of resources to study the electrical circuits, this technique is a practical tool. Therefore, in this study, an equivalent RC-circuit model including electrochemical parameters is determined to obtain a better perception of the sensing mechanism of these mechanical sensors. Conjugated polymers are capable of generating an output current or voltage upon an induced mechanical deformation or force. This observed behavior in polymer based mechanical sensors is considered as the reverse actuation process. Many outstanding properties of the conjugated polymer actuators including their light weight and biocompatibility are still retained by these sensors. Sensors with a trilayer configuration are capable of operating in air in response to a mechanically induced bending deformation. However, due to their nonlinear behavior and multivariable characteristics, it is required to propose a systematic approach in order to optimize their performance and gain the optimal values of their constituent decision variable. Therefore, the proposed mathematical model is used to define the output voltage of the PPy based mechanical sensor along with the sensitivity of the model to the applied frequency of the induced deformation. Applying a multiobjective optimization algorithm, the optimization problem was solved and the tracking ability of the proposed model was then verified.

  15. Modeling the mechanics of graphene-based polymer composite film measured by the bulge test

    NASA Astrophysics Data System (ADS)

    Zhang, Jian-Jun; Sun, You-yi; Li, Dian-sen; Cao, Yang; Wang, Zuo; Ma, Jing; Zhao, Gui-Zhe

    2015-10-01

    Graphene-based polymer composite films have wide-ranging potential applications, such as in sensors, electromagnetic shielding, absorbing materials, corrosion resistance and so on. In addition, the practical applications of graphene-based polymer composite films are closely related to their mechanical properties. However, the mechanical properties of graphene-based polymer composite films are difficult to characterize with tensile tests. In this paper, the bugle test was used to investigate the mechanical properties of graphene-based polymer composite films. The experimental results show that the Young’s modulus of polymer composite films increases non-linearly with an increase in the doping content of graphene, and viscoelastic deformation is induced under cyclic loading conditions. Moreover, in order to describe their mechanical behavior, an ‘Arruda-Boyce’ finite-strain constitutive model (modified BPA model), based on the strain amplification hypothesis, and a traditional ‘Arruda-Boyce’ model was proposed, which incorporated many of the features of previous theories. The numerical treatment of the modified BPA model associated with finite element analysis is also discussed. This new model is shown to be able to predict the experimentally observed mechanical behavior of graphene based polymer composite films measured by the bugle test effectively.

  16. Transgenerational inheritance: Models and mechanisms of non-DNA sequence-based inheritance.

    PubMed

    Miska, Eric A; Ferguson-Smith, Anne C

    2016-10-07

    Heritability has traditionally been thought to be a characteristic feature of the genetic material of an organism-notably, its DNA. However, it is now clear that inheritance not based on DNA sequence exists in multiple organisms, with examples found in microbes, plants, and invertebrate and vertebrate animals. In mammals, the molecular mechanisms have been challenging to elucidate, in part due to difficulties in designing robust models and approaches. Here we review some of the evidence, concepts, and potential mechanisms of non-DNA sequence-based transgenerational inheritance. We highlight model systems and discuss whether phenotypes are replicated or reconstructed over successive generations, as well as whether mechanisms operate at transcriptional and/or posttranscriptional levels. Finally, we explore the short- and long-term implications of non-DNA sequence-based inheritance. Understanding the effects of non-DNA sequence-based mechanisms is key to a full appreciation of heritability in health and disease.

  17. Shape memory behavior of epoxy-based model materials: Tailoring approaches and thermo-mechanical modeling

    NASA Astrophysics Data System (ADS)

    Pandini, Stefano; Avanzini, Andrea; Battini, Davide; Berardi, Mario; Baldi, Francesco; Bignotti, Fabio

    2016-05-01

    A series of structurally related epoxy resins were prepared as model systems for the investigation of the shape memory response, with the aim to assess the possibility of tailoring their thermo-mechanical response and conveniently describing their strain evolution under triggering stimuli with a simple thermoviscoelastic model. The resins formulation was varied in order to obtain systems with controlled glass transition temperature and crosslink density. The shape memory response was investigated by means of properly designed thermo-mechanical cycles, which allowed to measure both the ability to fully recover the applied strain and to exert a stress on a confining medium. The results were also compared with the predictions obtained by finite element simulations of the thermo-mechanical cycle by the employ of a model whose parameters were implemented from classical DMA analysis.

  18. New models of the oculomotor mechanics based on data obtained with chronic muscle force transducers.

    PubMed

    Pfann, K D; Keller, E L; Miller, J M

    1995-01-01

    Several phenomenological models of the oculomotor mechanics that produce saccadic eye movements have been developed. These models have been based on measurements of macroscopic muscle and orbital tissue properties and measurements of eye kinematics during saccades. We recorded the forces generated by the medial and lateral recti during saccades in an alert, behaving monkey using chronically implanted force transducers. With this new data, we tested the ability of the classic saccade models to generate realistic muscle force profiles. Errors in the predictions of the classic saccade models led to a reexamination of the current models of extraocular muscle. Both a phenomenological, Hill-type muscle model and an approximation to Huxley's molecular level muscle model based on the cross-bridge mechanism of contraction (distribution moment model) were derived and studied for monkey extraocular muscle. Simulations of the distribution moment model led to insights suggesting (i) specific modifications in the lumped force/velocity relationship in the Hill-type model that resulted in this type of phenomenological model being able to generate realistic dynamics in extraocular muscle during saccades; (ii) the distribution of activity in the different fiber types in extraocular muscle may be central to the characteristics exhibited by the muscle during saccades; (iii) the transient properties of lengthening muscle such as yielding are not significant during saccades; and (iv) the series elastic component in active muscle may be predominantly generated by the elastic properties of the cross-bridges.

  19. On rate-dependent mechanical model for adaptive magnetorheological elastomer base isolator

    NASA Astrophysics Data System (ADS)

    Li, Yancheng; Li, Jianchun

    2017-04-01

    This paper presents research on the phenomenological model of an adaptive base isolator. The adaptive base isolator is made of field-dependent magnetorheological elastomer (MRE) which can alter its physical property under application of magnetic field. Experimental testing demonstrated that the developed MRE base isolator possesses an amazing ability to vary its stiffness under applied magnetic field. However, several challenges have been encountered when it comes modeling such novel device. For example, under a large deformation, the MRE base isolator exhibits a clear strain stiffening effect and this behavior escalates with the increasing of applied current. In addition, the MRE base isolator has also shown typical rate-dependent behavior. Following a review on mechanical models for viscos-elastic rubber devices, a novel rate-dependent model is proposed in this paper to capture the behavior of the new MRE base isolator. To develop a generalized model, the proposed model was evaluated using its performance under random displacement input and a seismic input. It shows that the proposed rate-dependent model can successfully describe the complex behavior of the device.

  20. Model-Based Fatigue Prognosis of Fiber-Reinforced Laminates Exhibiting Concurrent Damage Mechanisms

    NASA Technical Reports Server (NTRS)

    Corbetta, M.; Sbarufatti, C.; Saxena, A.; Giglio, M.; Goebel, K.

    2016-01-01

    Prognostics of large composite structures is a topic of increasing interest in the field of structural health monitoring for aerospace, civil, and mechanical systems. Along with recent advancements in real-time structural health data acquisition and processing for damage detection and characterization, model-based stochastic methods for life prediction are showing promising results in the literature. Among various model-based approaches, particle-filtering algorithms are particularly capable in coping with uncertainties associated with the process. These include uncertainties about information on the damage extent and the inherent uncertainties of the damage propagation process. Some efforts have shown successful applications of particle filtering-based frameworks for predicting the matrix crack evolution and structural stiffness degradation caused by repetitive fatigue loads. Effects of other damage modes such as delamination, however, are not incorporated in these works. It is well established that delamination and matrix cracks not only co-exist in most laminate structures during the fatigue degradation process but also affect each other's progression. Furthermore, delamination significantly alters the stress-state in the laminates and accelerates the material degradation leading to catastrophic failure. Therefore, the work presented herein proposes a particle filtering-based framework for predicting a structure's remaining useful life with consideration of multiple co-existing damage-mechanisms. The framework uses an energy-based model from the composite modeling literature. The multiple damage-mode model has been shown to suitably estimate the energy release rate of cross-ply laminates as affected by matrix cracks and delamination modes. The model is also able to estimate the reduction in stiffness of the damaged laminate. This information is then used in the algorithms for life prediction capabilities. First, a brief summary of the energy-based damage model

  1. An updated kernel-based Turing model for studying the mechanisms of biological pattern formation.

    PubMed

    Kondo, Shigeru

    2017-02-07

    The reaction-diffusion model presented by Alan Turing has recently been supported by experimental data and accepted by most biologists. However, scientists have recognized shortcomings when the model is used as the working hypothesis in biological experiments, particularly in studies in which the underlying molecular network is not fully understood. To address some such problems, this report proposes a new version of the Turing model. This alternative model is not represented by partial differential equations, but rather by the shape of an activation-inhibition kernel. Therefore, it is named the kernel-based Turing model (KT model). Simulation of the KT model with kernels of various shapes showed that it can generate all standard variations of the stable 2D patterns (spot, stripes and network), as well as some complex patterns that are difficult to generate with conventional mathematical models. The KT model can be used even when the detailed mechanism is poorly known, as the interaction kernel can often be detected by a simple experiment and the KT model simulation can be performed based on that experimental data. These properties of the KT model complement the shortcomings of conventional models and will contribute to the understanding of biological pattern formation.

  2. A dual model of entertainment-based and community-based mechanisms to explore continued participation in online entertainment communities.

    PubMed

    Deng, Yun; Hou, Jinghui; Ma, Xiao; Cai, Shuqin

    2013-05-01

    Online entertainment communities have exploded in popularity and drawn attention from researchers. However, few studies have investigated what leads people to remain active in such communities at the postadoption stage. We proposed and tested a dual model of entertainment-based and community-based mechanisms to examine the factors that affect individuals' continued participation in online entertainment communities. Survival analysis was employed on a longitudinal dataset of 2,302 users collected over 2 years from an online game community. Our results were highly consistent with the theoretical model. Specifically, under the entertainment-based mechanism, our findings showed that the intensities of initial use and frequent use were positive predictors of players' activity lifespan. Under the community-based mechanism, the results demonstrated that the number of guilds a player was affiliated with and the average number of days of being a guild member positively predict players' lifespan in the game. Overall, our study suggests that the entertainment-based mechanism and community-based mechanism are two key drivers that determinate individuals' continued participation in online entertainment communities.

  3. A numerical study of the left ventricle using structure-based bio-mechanical model

    NASA Astrophysics Data System (ADS)

    Zhu, Yunfei; Luo, Xiaoyu; Feng, Yaoqi

    A numerical study of the left ventricle using structure-based bio-mechanical model In space environment, microgravity and radiation can have deleterious effects on the cardiovascular system of the astronauts. The work in this paper is part of an ongoing effort to use mathematical models to provide a better understanding of the impact of long-duration spaceflight on the heart and blood vessels. In this study, we develop a computational left ventricle model before and after myocardium infarction based on cardiovascular mechanical theory. The anatomically realistic model has a rule-based fibre structure and a orthotropic structure-based constitutive model. The differences of deformations in the left ventricle before and after infarction are compared in details. In particular, the effects of fiber direction and fiber dispersion are examined. The disarray of both the fiber and sheet orientation is characterized by a dispersion parameter. The left ventricle volume is calculated from the MRI images and used for the optimization of the parameters of the myocardium. We provide the numerical framework for further study on effects of spaceflight on the cardiovascular system.

  4. A biophysically based mathematical model for the catalytic mechanism of glutathione reductase.

    PubMed

    Pannala, Venkat R; Bazil, Jason N; Camara, Amadou K S; Dash, Ranjan K

    2013-12-01

    Glutathione reductase (GR) catalyzes the reduction of oxidized glutathione (GSSG) to reduced glutathione (GSH) using NADPH as the reducing cofactor, and thereby maintains a constant GSH level in the system. GSH scavenges superoxide (O2(*-)) and hydroxyl radicals (OH) nonenzymatically or by serving as an electron donor to several enzymes involved in reactive oxygen species (ROS) detoxification. In either case, GSH oxidizes to GSSG and is subsequently regenerated by the catalytic action of GR. Although the GR kinetic mechanism has been extensively studied under various experimental conditions with variable substrates and products, the catalytic mechanism has not been studied in terms of a mechanistic model that accounts for the effects of the substrates and products on the reaction kinetics. The aim of this study is therefore to develop a comprehensive mathematical model for the catalytic mechanism of GR. We use available experimental data on GR kinetics from various species/sources to develop the mathematical model and estimate the associated model parameters. The model simulations are consistent with the experimental observation that GR operates via both ping-pong and sequential branching mechanisms based on relevant concentrations of its reaction substrate GSSG. Furthermore, we show the observed pH-dependent substrate inhibition of GR activity by GSSG and bimodal behavior of GR activity with pH. The model presents a unique opportunity to understand the effects of products on the kinetics of GR. The model simulations show that under physiological conditions, where both substrates and products are present, the flux distribution depends on the concentrations of both GSSG and NADP(+), with ping-pong flux operating at low levels and sequential flux dominating at higher levels. The kinetic model of GR may serve as a key module for the development of integrated models for ROS-scavenging systems to understand protection of cells under normal and oxidative stress

  5. Nonlocal continuum-based modeling of mechanical characteristics of nanoscopic structures

    NASA Astrophysics Data System (ADS)

    Rafii-Tabar, Hashem; Ghavanloo, Esmaeal; Fazelzadeh, S. Ahmad

    2016-06-01

    Insight into the mechanical characteristics of nanoscopic structures is of fundamental interest and indeed poses a great challenge to the research communities around the world. These structures are ultra fine in size and consequently performing standard experiments to measure their various properties is an extremely difficult and expensive endeavor. Hence, to predict the mechanical characteristics of the nanoscopic structures, different theoretical models, numerical modeling techniques, and computer-based simulation methods have been developed. Among several proposed approaches, the nonlocal continuum-based modeling is of particular significance because the results obtained from this modeling for different nanoscopic structures are in very good agreement with the data obtained from both experimental and atomistic-based studies. A review of the essentials of this model together with its applications is presented here. Our paper is a self contained presentation of the nonlocal elasticity theory and contains the analysis of the recent works employing this model within the field of nanoscopic structures. In this review, the concepts from both the classical (local) and the nonlocal elasticity theories are presented and their applications to static and dynamic behavior of nanoscopic structures with various morphologies are discussed. We first introduce the various nanoscopic structures, both carbon-based and non carbon-based types, and then after a brief review of the definitions and concepts from classical elasticity theory, and the basic assumptions underlying size-dependent continuum theories, the mathematical details of the nonlocal elasticity theory are presented. A comprehensive discussion on the nonlocal version of the beam, the plate and the shell theories that are employed in modeling of the mechanical properties and behavior of nanoscopic structures is then provided. Next, an overview of the current literature discussing the application of the nonlocal models

  6. Models of dark matter halos based on statistical mechanics: The classical King model

    NASA Astrophysics Data System (ADS)

    Chavanis, Pierre-Henri; Lemou, Mohammed; Méhats, Florian

    2015-03-01

    We consider the possibility that dark matter halos are described by the Fermi-Dirac distribution at finite temperature. This is the case if dark matter is a self-gravitating quantum gas made of massive neutrinos at statistical equilibrium. This is also the case if dark matter can be treated as a self-gravitating collisionless gas experiencing Lynden-Bell's type of violent relaxation. In order to avoid the infinite mass problem and carry out a rigorous stability analysis, we consider the fermionic King model. In this paper, we study the nondegenerate limit leading to the classical King model. This model was initially introduced to describe globular clusters. We propose to apply it also to large dark matter halos where quantum effects are negligible. We determine the caloric curve and study the thermodynamical stability of the different configurations. Equilibrium states exist only above a critical energy Ec in the microcanonical ensemble and only above a critical temperature Tc in the canonical ensemble. For E model to the observations of large dark matter halos. Because of collisions and evaporation, the central density increases while the slope of the halo density profile decreases until an instability takes place. We show that large dark matter halos are relatively well described by the King model at, or close to, the point of marginal microcanonical stability. At that point, the King model generates a density profile that can be approximated by the modified Hubble profile. This profile has a flat core and decreases as r-3 at large distances, like the observational Burkert profile. Less steep halos are unstable. For large halos, the flat core is due to finite temperature effects, not to quantum mechanics. We argue that statistical

  7. Identifying significant covariates for anti-HIV treatment response: mechanism-based differential equation models and empirical semiparametric regression models.

    PubMed

    Huang, Yangxin; Liang, Hua; Wu, Hulin

    2008-10-15

    In this paper, the mechanism-based ordinary differential equation (ODE) model and the flexible semiparametric regression model are employed to identify the significant covariates for antiretroviral response in AIDS clinical trials. We consider the treatment effect as a function of three factors (or covariates) including pharmacokinetics, drug adherence and susceptibility. Both clinical and simulated data examples are given to illustrate these two different kinds of modeling approaches. We found that the ODE model is more powerful to model the mechanism-based nonlinear relationship between treatment effects and virological response biomarkers. The ODE model is also better in identifying the significant factors for virological response, although it is slightly liberal and there is a trend to include more factors (or covariates) in the model. The semiparametric mixed-effects regression model is very flexible to fit the virological response data, but it is too liberal to identify correct factors for the virological response; sometimes it may miss the correct factors. The ODE model is also biologically justifiable and good for predictions and simulations for various biological scenarios. The limitations of the ODE models include the high cost of computation and the requirement of biological assumptions that sometimes may not be easy to validate. The methodologies reviewed in this paper are also generally applicable to studies of other viruses such as hepatitis B virus or hepatitis C virus.

  8. The research Of Multilayer Thermal Insulation With Mechanical Properties Based On Model Analysis Test

    NASA Astrophysics Data System (ADS)

    Lianhua, Yin

    The heat shield of aircraft is made of the major thrusts structure with multilayer thermal insulation part. For protecting against thermo-radiation from larger thrusting force engine,the heat shield is installed around this engine nearby.The multilayer thermal insulation part with multilayer radiation/reflection structure is made of reflection layer and interval layer.At vacuum condition,these materials is higher heat insulation capability than other material,is applied for lots of pats on aircraft extensively.But because of these material is made of metal and nonmetal,it is impossible to receive it's mechanical properties of materials from mechanical tests.These paper describes a new measure of mechanical properties of materials in the heat shield based on model analysis test.At the requirement for the first order lateral frequency,these measure provide for the FEM analysis foundation on the optimization structure of the heat shield.

  9. Mechanical modeling of battery separator based on microstructure image analysis and stochastic characterization

    NASA Astrophysics Data System (ADS)

    Xu, Hongyi; Zhu, Min; Marcicki, James; Yang, Xiao Guang

    2017-03-01

    A microstructure-based modeling method is developed to predict the mechanical behaviors of lithium-ion battery separators. Existing battery separator modeling methods cannot capture the structural features on the microscale. To overcome this issue, we propose an image-based microstructure Representative Volume Element (RVE) modeling method, which facilitates the understanding of the separators' complex macro mechanical behaviors from the perspective of microstructural features. A generic image processing workflow is developed to identify different phases in the microscopic image. The processed RVE image supplies microstructural information to the Finite Element Analysis (FEA). Both mechanical behavior and microstructure evolution are obtained from the simulation. The evolution of microstructure features is quantified using the stochastic microstructure characterization methods. The proposed method successfully captures the anisotropic behavior of the separator under tensile test, and provides insights into the microstructure deformation, such as the growth of voids. We apply the proposed method to a commercially available separator as the demonstration. The analysis results are validated using experimental testing results that are reported in literature.

  10. Models of dark matter halos based on statistical mechanics: The fermionic King model

    NASA Astrophysics Data System (ADS)

    Chavanis, Pierre-Henri; Lemou, Mohammed; Méhats, Florian

    2015-12-01

    We discuss the nature of phase transitions in the fermionic King model which describes tidally truncated quantum self-gravitating systems. This distribution function takes into account the escape of high-energy particles and has a finite mass. On the other hand, the Pauli exclusion principle puts an upper bound on the phase-space density of the system and stabilizes it against gravitational collapse. As a result, there exists a statistical equilibrium state for all accessible values of energy and temperature. We plot the caloric curves and investigate the nature of phase transitions as a function of the degeneracy parameter in both microcanonical and canonical ensembles, extending the work of Chavanis [Int. J. Mod. Phys. B 20, 3113 (2006)] for box-confined configurations. We consider stable and metastable states and emphasize the importance of the latter for systems with long-range interactions. Phase transitions can take place between a "gaseous" phase unaffected by quantum mechanics and a "condensed" phase dominated by quantum mechanics. The phase diagram exhibits two critical points, one in each ensemble, beyond which the phase transitions disappear. There also exists a region of negative specific heats and a situation of ensemble inequivalence for sufficiently large systems. In the microcanonical ensemble, gravitational collapse (gravothermal catastrophe) results in the formation of a small degenerate object containing a small mass. This is accompanied by the expulsion of a hot envelope containing a large mass. In the canonical ensemble, gravitational collapse (isothermal collapse) leads to a small degenerate object containing almost all the mass. It is surrounded by a tenuous envelope. We apply the fermionic King model to the case of dark matter halos made of massive neutrinos following the work of de Vega, Salucci, and Sanchez [Mon. Not. R. Astron. Soc. 442, 2717 (2014)]. The gaseous phase describes large halos and the condensed phase describes dwarf halos

  11. Model-based selection of the robust JAK-STAT activation mechanism.

    PubMed

    Rybiński, Mikołaj; Gambin, Anna

    2012-09-21

    JAK-STAT pathway family is a principal signaling mechanism in eukaryotic cells. Evolutionary conserved roles of this mechanism include control over fundamental processes such as cell growth or apoptosis. Deregulation of the JAK-STAT signaling is frequently associated with cancerogenesis. JAK-STAT pathways become hyper-activated in many human tumors. Therefore, components of these pathways are an attractive target for drugs, which design requires as adequate models as possible. Although, in principle, JAK-STAT signaling is relatively simple, the ambiguities in a receptor activation prevent a clear explanation of the underlying molecular mechanism. Here, we compare four variants of a computational model of the JAK1/2-STAT1 signaling pathway. These variants capture known, basic discrepancies in the mechanism of activation of a cytokine receptor, in the context of all key components of the pathway. We carry out a comparative analysis using mass action kinetics. The investigated differences are so marginal that all models satisfy a goodness of fit criteria to the extent that the state of the art Bayesian model selection (BMS) method fails to significantly promote one model. Therefore, we comparatively investigate changes in a robustness of the JAK1/2-STAT1 pathway variants using the global sensitivity analysis method (GSA), complemented with the identifiability analysis (IA). Both BMS and GSA are used to analyze the models for the varying parameter values. We found out that, both BMS and GSA, narrowed down to the receptor activation component, slightly promote the least complex model. Further, insightful, comprehensive GSA, motivated by the concept of robustness, allowed us to show that the precise order of reactions of a ligand binding and a receptor dimerization is not as important as the on-membrane pre-assembly of the dimers in the absence of ligand. The main value of this work is an evaluation of the usefulness of different model selection methods in a frequently

  12. A hierarchical lattice spring model to simulate the mechanics of 2-D materials-based composites

    NASA Astrophysics Data System (ADS)

    Brely, Lucas; Bosia, Federico; Pugno, Nicola

    2015-07-01

    In the field of engineering materials, strength and toughness are typically two mutually exclusive properties. Structural biological materials such as bone, tendon or dentin have resolved this conflict and show unprecedented damage tolerance, toughness and strength levels. The common feature of these materials is their hierarchical heterogeneous structure, which contributes to increased energy dissipation before failure occurring at different scale levels. These structural properties are the key to exceptional bioinspired material mechanical properties, in particular for nanocomposites. Here, we develop a numerical model in order to simulate the mechanisms involved in damage progression and energy dissipation at different size scales in nano- and macro-composites, which depend both on the heterogeneity of the material and on the type of hierarchical structure. Both these aspects have been incorporated into a 2-dimensional model based on a Lattice Spring Model, accounting for geometrical nonlinearities and including statistically-based fracture phenomena. The model has been validated by comparing numerical results to continuum and fracture mechanics results as well as finite elements simulations, and then employed to study how structural aspects impact on hierarchical composite material properties. Results obtained with the numerical code highlight the dependence of stress distributions on matrix properties and reinforcement dispersion, geometry and properties, and how failure of sacrificial elements is directly involved in the damage tolerance of the material. Thanks to the rapidly developing field of nanocomposite manufacture, it is already possible to artificially create materials with multi-scale hierarchical reinforcements. The developed code could be a valuable support in the design and optimization of these advanced materials, drawing inspiration and going beyond biological materials with exceptional mechanical properties.

  13. Semi-Mechanism-Based Population Pharmacokinetic Modeling of the Hedgehog Pathway Inhibitor Vismodegib.

    PubMed

    Lu, T; Wang, B; Gao, Y; Dresser, M; Graham, R A; Jin, J Y

    2015-11-01

    Vismodegib, approved for the treatment of advanced basal cell carcinoma, has shown unique pharmacokinetic (PK) nonlinearity and binding to α1-acid glycoprotein (AAG) in humans. A semi-mechanism-based population pharmacokinetic (PopPK) model was developed from a meta-dataset of 225 subjects enrolled in five clinical studies to quantitatively describe the clinical PK of vismodegib and identify sources of interindividual variability. Total and unbound vismodegib were analyzed simultaneously, together with time-varying AAG data. The PK of vismodegib was adequately described by a one-compartment model with first-order absorption, first-order elimination of unbound drug, and saturable binding to AAG with fast-equilibrium. The variability of total vismodegib concentration at steady-state was predominantly explained by the range of AAG level. The impact of AAG on unbound concentration was clinically insignificant. Various approaches were evaluated for model validation. The semi-mechanism-based PopPK model described herein provided insightful information on the nonlinear PK and has been utilized for various clinical applications.

  14. Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication

    PubMed Central

    Guarnera, Enrico; Berezovsky, Igor N.

    2016-01-01

    Allostery is one of the pervasive mechanisms through which proteins in living systems carry out enzymatic activity, cell signaling, and metabolism control. Effective modeling of the protein function regulation requires a synthesis of the thermodynamic and structural views of allostery. We present here a structure-based statistical mechanical model of allostery, allowing one to observe causality of communication between regulatory and functional sites, and to estimate per residue free energy changes. Based on the consideration of ligand free and ligand bound systems in the context of a harmonic model, corresponding sets of characteristic normal modes are obtained and used as inputs for an allosteric potential. This potential quantifies the mean work exerted on a residue due to the local motion of its neighbors. Subsequently, in a statistical mechanical framework the entropic contribution to allosteric free energy of a residue is directly calculated from the comparison of conformational ensembles in the ligand free and ligand bound systems. As a result, this method provides a systematic approach for analyzing the energetics of allosteric communication based on a single structure. The feasibility of the approach was tested on a variety of allosteric proteins, heterogeneous in terms of size, topology and degree of oligomerization. The allosteric free energy calculations show the diversity of ways and complexity of scenarios existing in the phenomenology of allosteric causality and communication. The presented model is a step forward in developing the computational techniques aimed at detecting allosteric sites and obtaining the discriminative power between agonistic and antagonistic effectors, which are among the major goals in allosteric drug design. PMID:26939022

  15. Sentence-Based Attentional Mechanisms in Word Learning: Evidence from a Computational Model

    PubMed Central

    Alishahi, Afra; Fazly, Afsaneh; Koehne, Judith; Crocker, Matthew W.

    2012-01-01

    When looking for the referents of novel nouns, adults and young children are sensitive to cross-situational statistics (Yu and Smith, 2007; Smith and Yu, 2008). In addition, the linguistic context that a word appears in has been shown to act as a powerful attention mechanism for guiding sentence processing and word learning (Landau and Gleitman, 1985; Altmann and Kamide, 1999; Kako and Trueswell, 2000). Koehne and Crocker (2010, 2011) investigate the interaction between cross-situational evidence and guidance from the sentential context in an adult language learning scenario. Their studies reveal that these learning mechanisms interact in a complex manner: they can be used in a complementary way when context helps reduce referential uncertainty; they influence word learning about equally strongly when cross-situational and contextual evidence are in conflict; and contextual cues block aspects of cross-situational learning when both mechanisms are independently applicable. To address this complex pattern of findings, we present a probabilistic computational model of word learning which extends a previous cross-situational model (Fazly et al., 2010) with an attention mechanism based on sentential cues. Our model uses a framework that seamlessly combines the two sources of evidence in order to study their emerging pattern of interaction during the process of word learning. Simulations of the experiments of (Koehne and Crocker, 2010, 2011) reveal an overall pattern of results that are in line with their findings. Importantly, we demonstrate that our model does not need to explicitly assign priority to either source of evidence in order to produce these results: learning patterns emerge as a result of a probabilistic interaction between the two clue types. Moreover, using a computational model allows us to examine the developmental trajectory of the differential roles of cross-situational and sentential cues in word learning. PMID:22783211

  16. Mechanism-based model of parasite growth and dihydroartemisinin pharmacodynamics in murine malaria.

    PubMed

    Patel, Kashyap; Batty, Kevin T; Moore, Brioni R; Gibbons, Peter L; Bulitta, Jürgen B; Kirkpatrick, Carl M

    2013-01-01

    Murine models are used to study erythrocytic stages of malaria infection, because parasite morphology and development are comparable to those in human malaria infections. Mechanism-based pharmacokinetic-pharmacodynamic (PK-PD) models for antimalarials are scarce, despite their potential to optimize antimalarial combination therapy. The aim of this study was to develop a mechanism-based growth model (MBGM) for Plasmodium berghei and then characterize the parasiticidal effect of dihydroartemisinin (DHA) in murine malaria (MBGM-PK-PD). Stage-specific (ring, early trophozoite, late trophozoite, and schizont) parasite density data from Swiss mice inoculated with Plasmodium berghei were used for model development in S-ADAPT. A single dose of intraperitoneal DHA (10 to 100 mg/kg) or vehicle was administered 56 h postinoculation. The MBGM explicitly reflected all four erythrocytic stages of the 24-hour P. berghei life cycle. Merozoite invasion of erythrocytes was described by a first-order process that declined with increasing parasitemia. An efflux pathway with subsequent return was additionally required to describe the schizont data, thus representing parasite sequestration or trapping in the microvasculature, with a return to circulation. A 1-compartment model with zero-order absorption described the PK of DHA, with an estimated clearance and distribution volume of 1.95 liters h(-1) and 0.851 liter, respectively. Parasite killing was described by a turnover model, with DHA inhibiting the production of physiological intermediates (IC(50), 1.46 ng/ml). Overall, the MBGM-PK-PD described the rise in parasitemia, the nadir following DHA dosing, and subsequent parasite resurgence. This novel model is a promising tool for studying malaria infections, identifying the stage specificity of antimalarials, and providing insight into antimalarial treatment strategies.

  17. Motion Planning for Concentric Tube Robots Using Mechanics-based Models.

    PubMed

    Torres, Luis G; Alterovitz, Ron

    2011-01-01

    Concentric tube robots have the potential to enable new minimally invasive surgical procedures by curving around anatomical obstacles to reach difficult-to-reach sites in body cavities. Planning motions for these devices is challenging in part due to their complex kinematics; concentric tube robots are composed of thin, pre-curved, telescoping tubes that can achieve a variety of shapes via extension and rotation of each of their constituent tubes. We introduce a new motion planner to maneuver these devices to clinical targets while minimizing the probability of colliding with anatomical obstacles. Unlike prior planners for these devices, we more accurately model device shape using mechanics-based models that consider torsional interaction between the tubes. We also account for the effects of uncertainty in actuation and predicted device shape. We integrate these models with a sampling-based approach based on the Rapidly-Exploring Roadmap to guarantee finding optimal plans as computation time is allowed to increase. We demonstrate our motion planner in simulation using a variety of evaluation scenarios including an anatomy-based neurosurgery case that requires maneuvering to a difficult-to-reach brain tumor at the skull base.

  18. The impacts of information-sharing mechanisms on spatial market formation based on agent-based modeling.

    PubMed

    Li, Qianqian; Yang, Tao; Zhao, Erbo; Xia, Xing'ang; Han, Zhangang

    2013-01-01

    There has been an increasing interest in the geographic aspects of economic development, exemplified by P. Krugman's logical analysis. We show in this paper that the geographic aspects of economic development can be modeled using multi-agent systems that incorporate multiple underlying factors. The extent of information sharing is assumed to be a driving force that leads to economic geographic heterogeneity across locations without geographic advantages or disadvantages. We propose an agent-based market model that considers a spectrum of different information-sharing mechanisms: no information sharing, information sharing among friends and pheromone-like information sharing. Finally, we build a unified model that accommodates all three of these information-sharing mechanisms based on the number of friends who can share information. We find that the no information-sharing model does not yield large economic zones, and more information sharing can give rise to a power-law distribution of market size that corresponds to the stylized fact of city size and firm size distributions. The simulations show that this model is robust. This paper provides an alternative approach to studying economic geographic development, and this model could be used as a test bed to validate the detailed assumptions that regulate real economic agglomeration.

  19. The Impacts of Information-Sharing Mechanisms on Spatial Market Formation Based on Agent-Based Modeling

    PubMed Central

    Li, Qianqian; Yang, Tao; Zhao, Erbo; Xia, Xing’ang; Han, Zhangang

    2013-01-01

    There has been an increasing interest in the geographic aspects of economic development, exemplified by P. Krugman’s logical analysis. We show in this paper that the geographic aspects of economic development can be modeled using multi-agent systems that incorporate multiple underlying factors. The extent of information sharing is assumed to be a driving force that leads to economic geographic heterogeneity across locations without geographic advantages or disadvantages. We propose an agent-based market model that considers a spectrum of different information-sharing mechanisms: no information sharing, information sharing among friends and pheromone-like information sharing. Finally, we build a unified model that accommodates all three of these information-sharing mechanisms based on the number of friends who can share information. We find that the no information-sharing model does not yield large economic zones, and more information sharing can give rise to a power-law distribution of market size that corresponds to the stylized fact of city size and firm size distributions. The simulations show that this model is robust. This paper provides an alternative approach to studying economic geographic development, and this model could be used as a test bed to validate the detailed assumptions that regulate real economic agglomeration. PMID:23484007

  20. Computer-based creativity enhanced conceptual design model for non-routine design of mechanical systems

    NASA Astrophysics Data System (ADS)

    Li, Yutong; Wang, Yuxin; Duffy, Alex H. B.

    2014-11-01

    Computer-based conceptual design for routine design has made great strides, yet non-routine design has not been given due attention, and it is still poorly automated. Considering that the function-behavior-structure(FBS) model is widely used for modeling the conceptual design process, a computer-based creativity enhanced conceptual design model(CECD) for non-routine design of mechanical systems is presented. In the model, the leaf functions in the FBS model are decomposed into and represented with fine-grain basic operation actions(BOA), and the corresponding BOA set in the function domain is then constructed. Choosing building blocks from the database, and expressing their multiple functions with BOAs, the BOA set in the structure domain is formed. Through rule-based dynamic partition of the BOA set in the function domain, many variants of regenerated functional schemes are generated. For enhancing the capability to introduce new design variables into the conceptual design process, and dig out more innovative physical structure schemes, the indirect function-structure matching strategy based on reconstructing the combined structure schemes is adopted. By adjusting the tightness of the partition rules and the granularity of the divided BOA subsets, and making full use of the main function and secondary functions of each basic structure in the process of reconstructing of the physical structures, new design variables and variants are introduced into the physical structure scheme reconstructing process, and a great number of simpler physical structure schemes to accomplish the overall function organically are figured out. The creativity enhanced conceptual design model presented has a dominant capability in introducing new deign variables in function domain and digging out simpler physical structures to accomplish the overall function, therefore it can be utilized to solve non-routine conceptual design problem.

  1. A Mechanism-based Model for Deformation Twinning in Polycrystalline FCC Steel

    SciTech Connect

    Wang, Yuan; Sun, Xin; Wang, Y. D.; Hu, Xiaohua; Zbib, Hussein M.

    2014-06-01

    Deformation twinning, a common and important plastic deformation mechanism, is the key contributor to the excellent combination of strength and ductility in twinning-induced plasticity (TWIP) steel. In the open literature, a significant amount of research has been reported on the microstructural characteristics of deformation twinning and its influence on the overall deformation behavior of TWIP steel. In this study, we examine the feasibility of a mechanism-based crystal plasticity model in simulating the microstructural level deformation characteristics of TWIP steel. To this end, a model considering both double-slip and double-twin is developed to investigate the stress-strain behavior and local microstructural features related to the formation and growth of micro-twins in low stacking fault energy (SFE) TWIP steel. The twin systems are described as pseudo-slips that can be activated when their resolved shear stress reaches the corresponding critical value. A hardening law that accounts for the interaction among the slip and twin systems is also developed. Numerical simulations for dDifferent mesh sizes and single crystal patch tests under different loading modes are carried out to verify the modeling procedure. Our simulation results reveal that, despite its simple nature, the double-slip/double-twin model can capture the key deformation features of TWIP steel, including twin volume fraction evolution, continuous strain hardening, and the final fracture in the form of strain localization.

  2. Treatment-based Markov chain models clarify mechanisms of invasion in an invaded grassland community

    PubMed Central

    Nelis, Lisa Castillo; Wootton, J. Timothy

    2010-01-01

    What are the relative roles of mechanisms underlying plant responses in grassland communities invaded by both plants and mammals? What type of community can we expect in the future given current or novel conditions? We address these questions by comparing Markov chain community models among treatments from a field experiment on invasive species on Robinson Crusoe Island, Chile. Because of seed dispersal, grazing and disturbance, we predicted that the exotic European rabbit (Oryctolagus cuniculus) facilitates epizoochorous exotic plants (plants with seeds that stick to the skin an animal) at the expense of native plants. To test our hypothesis, we crossed rabbit exclosure treatments with disturbance treatments, and sampled the plant community in permanent plots over 3 years. We then estimated Markov chain model transition probabilities and found significant differences among treatments. As hypothesized, this modelling revealed that exotic plants survive better in disturbed areas, while natives prefer no rabbits or disturbance. Surprisingly, rabbits negatively affect epizoochorous plants. Markov chain dynamics indicate that an overall replacement of native plants by exotic plants is underway. Using a treatment-based approach to multi-species Markov chain models allowed us to examine the changes in the importance of mechanisms in response to experimental impacts on communities. PMID:19864293

  3. Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

    PubMed

    Sankar, Punnaivanam; Aghila, Gnanasekaran

    2007-01-01

    The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

  4. Elastoplastic contact mechanics model of rough surface based on fractal theory

    NASA Astrophysics Data System (ADS)

    Yuan, Yuan; Gan, Li; Liu, Kai; Yang, Xiaohui

    2017-01-01

    Because the result of the MB fractal model contradicts with the classical contact mechanics, a revised elastoplastic contact model of a single asperity is developed based on fractal theory. The critical areas of a single asperity are scale dependent, with an increase in the contact load and contact area, a transition from elastic, elastoplastic to full plastic deformation takes place in this order. In considering the size distribution function, analytic expression between the total contact load and the real contact area on the contact surface is obtained. The elastic, elastoplastic and full plastic contact load are obtained by the critical elastic contact area of the biggest asperity and maximun contact area of a single asperity. The results show that a rough surface is firstly in elastic deformation. As the load increases, elastoplastic or full plastic deformation takes place. For constant characteristic length scale G, the slope of load-area relation is proportional to fractal dimension D. For constant fractal dimension D, the slope of load-area relation is inversely proportional to G. For constant D and G, the slope of load-area relation is inversely proportional to property of the material ϕ, namely with the same load, the material of rough surface is softer, and the total contact area is larger. The contact mechanics model provides a foundation for study of the friction, wear and seal performance of rough surfaces.

  5. A model-based decision support system for critiquing mechanical ventilation treatments.

    PubMed

    Tehrani, Fleur T; Abbasi, Soraya

    2012-06-01

    A computerized system for critiquing mechanical ventilation treatments is presented that can be used as an aide to the intensivist. The presented system is based on the physiological model of the subject's respiratory system. It uses modified versions of previously developed models of adult and neonatal respiratory systems to simulate the effects of different ventilator treatments on the patient's blood gases. The physiological models that have been used for research and teaching purposes by many researchers in the field include lungs, body tissue, and the brain tissue. The lung volume is continuously time-varying and the effects of shunt in the lung, changes in cardiac output and cerebral blood flow, and the arterial transport delays are included in the system. Evaluation tests were done on adult and neonate patients with different diagnoses. In both groups combined, the differences between the arterial partial pressures of CO(2) predicted by the system and the experimental values were 1.86 ± 1.6 mmHg (mean ± SD), and the differences between the predicted arterial hemoglobin oxygen saturation values, S(aO2), and the experimental values measured by using pulse oximetry, S(pO2), were 0.032 ± 0.02 (mean ± SD). The proposed system has the potential to be used alone or in combination with other decision support systems to set ventilation parameters and optimize treatment for patients on mechanical ventilation.

  6. Mechanical Behavior of Cells within a Cell-Based Model of Wheat Leaf Growth

    PubMed Central

    Zubairova, Ulyana; Nikolaev, Sergey; Penenko, Aleksey; Podkolodnyy, Nikolay; Golushko, Sergey; Afonnikov, Dmitry; Kolchanov, Nikolay

    2016-01-01

    Understanding the principles and mechanisms of cell growth coordination in plant tissue remains an outstanding challenge for modern developmental biology. Cell-based modeling is a widely used technique for studying the geometric and topological features of plant tissue morphology during growth. We developed a quasi-one-dimensional model of unidirectional growth of a tissue layer in a linear leaf blade that takes cell autonomous growth mode into account. The model allows for fitting of the visible cell length using the experimental cell length distribution along the longitudinal axis of a wheat leaf epidermis. Additionally, it describes changes in turgor and osmotic pressures for each cell in the growing tissue. Our numerical experiments show that the pressures in the cell change over the cell cycle, and in symplastically growing tissue, they vary from cell to cell and strongly depend on the leaf growing zone to which the cells belong. Therefore, we believe that the mechanical signals generated by pressures are important to consider in simulations of tissue growth as possible targets for molecular genetic regulators of individual cell growth. PMID:28018409

  7. Mindfulness-based treatment to prevent addictive behavior relapse: theoretical models and hypothesized mechanisms of change.

    PubMed

    Witkiewitz, Katie; Bowen, Sarah; Harrop, Erin N; Douglas, Haley; Enkema, Matthew; Sedgwick, Carly

    2014-04-01

    Mindfulness-based treatments are growing in popularity among addiction treatment providers, and several studies suggest the efficacy of incorporating mindfulness practices into the treatment of addiction, including the treatment of substance use disorders and behavioral addictions (i.e., gambling). The current paper provides a review of theoretical models of mindfulness in the treatment of addiction and several hypothesized mechanisms of change. We provide an overview of mindfulness-based relapse prevention (MBRP), including session content, treatment targets, and client feedback from participants who have received MBRP in the context of empirical studies. Future research directions regarding operationalization and measurement, identifying factors that moderate treatment effects, and protocol adaptations for specific populations are discussed.

  8. Particle-Based Geometric and Mechanical Modelling of Woven Technical Textiles and Reinforcements for Composites

    NASA Astrophysics Data System (ADS)

    Samadi, Reza

    affecting the textile geometry and constitutive behaviour under evolving loading; 5) validating simulation results with experimental trials; and 6) demonstrating the applicability of the simulation procedure to textile reinforcements featuring large numbers of small fibres as used in PMCs. As a starting point, the effects of reinforcement configuration on the in-plane permeability of textile reinforcements, through-thickness thermal conductivity of PMCs and in-plane stiffness of unidirectional and bidirectional PMCs were quantified systematically and correlated with specific geometric parameters. Variability was quantified for each property at a constant fibre volume fraction. It was observed that variability differed strongly between properties; as such, the simulated behaviour can be related to variability levels seen in experimental measurements. The effects of the geometry of textile reinforcements on the aforementioned processing and performance properties of the textiles and PMCs made from these textiles was demonstrated and validated, but only for simple cases as thorough and credible geometric models were not available at the onset of this work. Outcomes of this work were published in a peer-reviewed journal [101]. Through this thesis it was demonstrated that predicting changes in textile geometry prior and during loading is feasible using the proposed particle-based modelling method. The particle-based modelling method relies on discrete mechanics and offers an alternative to more traditional methods based on continuum mechanics. Specifically it alleviates issues caused by large strains and management of intricate, evolving contact present in finite element simulations. The particle-based modelling method enables credible, intricate modelling of the geometry of textiles at the mesoscopic scale as well as faithful mechanical modelling under load. Changes to textile geometry and configuration due to the normal compaction pressure, stress relaxation, in-plane shear

  9. AUTOPILOT-BT: a system for knowledge and model based mechanical ventilation.

    PubMed

    Lozano, S; Möller, K; Brendle, A; Gottlieb, D; Schumann, S; Stahl, C A; Guttmann, J

    2008-01-01

    A closed-loop system (AUTOPILOT-BT) for the control of mechanical ventilation was designed to: 1) autonomously achieve goals specified by the clinician, 2) optimize the ventilator settings with respect to the underlying disease and 3) automatically adapt to the individual properties and specific disease status of the patient. The current realization focuses on arterial oxygen saturation (SpO(2)), end-tidal CO(2) pressure (P(et)CO(2)), and positive end-expiratory pressure (PEEP) maximizing respiratory system compliance (C(rs)). The "AUTOPILOT-BT" incorporates two different knowledge sources: a fuzzy logic control reflecting expert knowledge and a mathematical model based system that provides individualized patient specific information. A first evaluation test with respect to desired end-tidal-CO(2)-level was accomplished using an experimental setup to simulate three different metabolic CO(2) production rates by means of a physical lung simulator. The outcome of ventilator settings made by the "AUTOPILOT-BT" system was compared to those produced by clinicians. The model based control system proved to be superior to the clinicians as well as to a pure fuzzy logic based control with respect to precision and required settling time into the optimal ventilation state.

  10. Topology evolution model for wireless multi-hop network based on socially inspired mechanism

    NASA Astrophysics Data System (ADS)

    Luo, Xiaojuan; Hu, Yuhen; Zhu, Yu

    2014-12-01

    In this paper, topology evolution problem is addressed for improving the network performance in wireless multi-hop networks. A novel topology model based on social inspired mechanism with energy-aware and local-world features is proposed to handle the time-varying nature of wireless multi-hop network. A series of theoretical analysis and numerical simulation to the social inspired evolution network are conducted. Firstly, the degree distribution of this social inspired model represents a transition between exponential to power-law scaling with increasing the local world scale. Secondly, the clustering coefficient and the average path length decrease sharply as generally local-world scale increases a little. Finally, we found that the robustness and fragility of the proposed network model against random failures and attacks also display a transition between the random and the scale-free ones when the scale of local-world increasing. This local-world social inspired network model can maintain the robustness of scale-free networks and can improve the network reliance against intentional attacks.

  11. An explicit surface-potential-based MOSFET model incorporating the quantum mechanical effects

    NASA Astrophysics Data System (ADS)

    Basu, Dipanjan; Dutta, Aloke K.

    2006-07-01

    An explicit surface-potential-based MOSFET model has been proposed in this work here, which takes into account the quantum mechanical effects that arise in deep-submicron MOSFETs. The coupled Schrödinger's and Poisson's equations have been solved by using a variational wave function approach, as proposed by Fang and Howard. The resulting surface potential model is analytical, technology mapped, and completely continuous over the entire range of operation. The surface potential and the inversion charge density calculated using the proposed model show good match with the results of the numerical simulations obtained from a self-consistent Schrödinger-Poisson solver for a wide range of substrate doping and oxide thickness. The simulated values of the drain current match closely with the experimental results published elsewhere. The device small-signal parameters, e.g., transconductance, output conductance, etc., pass the standard benchmark tests suggested by Suyama and Tsividis qualitatively, thereby validating the approach of the model presented.

  12. Modeling of magneto-mechanical response of magnetorheological elastomers (MRE) and MRE-based systems: a review

    NASA Astrophysics Data System (ADS)

    Asun Cantera, M.; Behrooz, Majid; Gibson, Ronald F.; Gordaninejad, Faramarz

    2017-02-01

    This article is a review of models that capture the magneto-mechanical response of magnetorheological elastomers (MREs) and MRE-based systems. Where available, experimental validations of models are also discussed. The models are categorized as either particle interaction-based, magnetoelastic response-based, magnetoviscoelastic response-based, or models including the effects of environmental conditions and fatigue. Analytical, numerical, finite element, and phenomenological investigations that explore changes in stiffness and damping of anisotropic MREs are reviewed. Phenomenological models of MRE systems used in different applications are also examined.

  13. Thermodynamics-based models for the magneto-mechanical response of magnetic shape memory alloys

    NASA Astrophysics Data System (ADS)

    LaMaster, Douglas H.

    toward this i-direction. The energy required to rotate these magnetization vectors is called the anisotropy energy. Because MSMAs have unusually high anisotropy energy requirements [4, 5], it can become more energetically favorable to reorient variants into ξi and align the magnetic easy axis with the applied magnetic field, rather than to rotate the magnetization vector in the i-direction, toward the hard axis. In this manner, an MSMA can experience the same response to magnetic field as it does to a compressive stress: variant reorientation. As variants reorient, the MSMA will compress in one direction and elongate in another direction, enabling their use as actuators. Additionally, magnetization vectors change direction as they align with the short length of the reorienting variant. As the internal magnetization changes, the MSMA can produce changes in the external magnetic field, which can induce a current within a surrounding coil. Utilizing this can lead to the design of either power harvesters or sensors. This work builds upon that of others, notably that of Kiefer and Lagoudas [6-9], to present several thermodynamic-based continuum models to predict the response of an MSMA to magneto-mechanical loading. The first model is 2D, and allows for any magneto-mechanical loading in two directions. The 2D model includes evolution rules for domain fractions, magnetization vector rotation, and variant reorientation. The next two models are 3D, and include evolution rules for domain wall motion and variant re- orientation. The first 3D model neglects magnetization vector rotation to present a simpler model that is less computationally intensive, while the second 3D model in- cludes all known mechanisms present in the microstructure to give a more generalized and complete model. These models are all more general than any other continuum, thermodynamics-based model in the literature. No other 2D continuum, thermodynamics-based model allows for general 2D magneto-mechanical

  14. A model of stereocilia adaptation based on single molecule mechanical studies of myosin I.

    PubMed Central

    Batters, Christopher; Wallace, Mark I; Coluccio, Lynne M; Molloy, Justin E

    2004-01-01

    We have used an optical tweezers-based apparatus to perform single molecule mechanical experiments using the unconventional myosins, Myo1b and Myo1c. The single-headed nature and slow ATPase kinetics of these myosins make them ideal for detailed studies of the molecular mechanism of force generation by acto-myosin. Myo1c exhibits several features that have not been seen using fast skeletal muscle myosin II. (i) The working stroke occurs in two, distinct phases, producing an initial 3 nm and then a further 1.5 nm of movement. (ii) Two types of binding interaction were observed: short-lived ATP-independent binding events that produced no movement and longer-lived, ATP-dependent events that produced a full working stroke. The stiffness of both types of interaction was similar. (iii) In a new type of experiment, using feedback to apply controlled displacements to a single acto-myosin cross-bridge, we found abrupt changes in force during attachment of the acto-Myo1b cross-bridge, a result that is consistent with the classical 'T2' behaviour of single muscle fibres. Given that these myosins might exhibit the classical T2 behaviour, we propose a new model to explain the slow phase of sensory adaptation of the hair cells of the inner ear. PMID:15647165

  15. A model of task-deletion mechanism based on the priority queueing system of Barabási

    NASA Astrophysics Data System (ADS)

    Zhou, Bin; Xie, Jia-Rong; Yan, Xiao-Yong; Wang, Nianxin; Wang, Bing-Hong

    2017-01-01

    In this paper, we propose a model of task-deletion mechanism based on the priority queueing system of Barabási (2005) to deep research the pattern diversity of human behaviors. The analytical solution for our model with two tasks is presented. In different cases of the parameter of task-deletion, our model can produce rich statistical behavior patterns, which are consistent with lots of empirical studies. Therefore, the model can theoretically explain more human behavior phenomena than the model of Barabási. These results have important significance for understanding the mechanism of pattern diversity of human behaviors.

  16. Volcanic plume height measured by seismic waves based on a mechanical model

    USGS Publications Warehouse

    Prejean, Stephanie G.; Brodsky, Emily E.

    2011-01-01

    In August 2008 an unmonitored, largely unstudied Aleutian volcano, Kasatochi, erupted catastrophically. Here we use seismic data to infer the height of large eruptive columns such as those of Kasatochi based on a combination of existing fluid and solid mechanical models. In so doing, we propose a connection between a common, observable, short-period seismic wave amplitude to the physics of an eruptive column. To construct a combined model, we estimate the mass ejection rate of material from the vent on the basis of the plume height, assuming that the height is controlled by thermal buoyancy for a continuous plume. Using the estimated mass ejection rate, we then derive the equivalent vertical force on the Earth through a momentum balance. Finally, we calculate the far-field surface waves resulting from the vertical force. The model performs well for recent eruptions of Kasatochi and Augustine volcanoes if v, the velocity of material exiting the vent, is 120-230 m s-1. The consistency between the seismically inferred and measured plume heights indicates that in these cases the far-field ~1 s seismic energy radiated by fluctuating flow in the volcanic jet during the eruption is a useful indicator of overall mass ejection rates. Thus, use of the model holds promise for characterizing eruptions and evaluating ash hazards to aircraft in real time on the basis of far-field short-period seismic data. This study emphasizes the need for better measurements of eruptive plume heights and a more detailed understanding of the full spectrum of seismic energy radiated coeruptively.

  17. Volcanic plume height measured by seismic waves based on a mechanical model

    NASA Astrophysics Data System (ADS)

    Prejean, Stephanie G.; Brodsky, Emily E.

    2011-01-01

    In August 2008 an unmonitored, largely unstudied Aleutian volcano, Kasatochi, erupted catastrophically. Here we use seismic data to infer the height of large eruptive columns such as those of Kasatochi based on a combination of existing fluid and solid mechanical models. In so doing, we propose a connection between a common, observable, short-period seismic wave amplitude to the physics of an eruptive column. To construct a combined model, we estimate the mass ejection rate of material from the vent on the basis of the plume height, assuming that the height is controlled by thermal buoyancy for a continuous plume. Using the estimated mass ejection rate, we then derive the equivalent vertical force on the Earth through a momentum balance. Finally, we calculate the far-field surface waves resulting from the vertical force. The model performs well for recent eruptions of Kasatochi and Augustine volcanoes if v, the velocity of material exiting the vent, is 120-230 m s-1. The consistency between the seismically inferred and measured plume heights indicates that in these cases the far-field ˜1 s seismic energy radiated by fluctuating flow in the volcanic jet during the eruption is a useful indicator of overall mass ejection rates. Thus, use of the model holds promise for characterizing eruptions and evaluating ash hazards to aircraft in real time on the basis of far-field short-period seismic data. This study emphasizes the need for better measurements of eruptive plume heights and a more detailed understanding of the full spectrum of seismic energy radiated coeruptively.

  18. Mechanical characterization and modelling of Lorentz force based MEMS magnetic field sensors

    NASA Astrophysics Data System (ADS)

    Gkotsis, P.; Lara-Castro, M.; López-Huerta, F.; Herrera-May, A. L.; Raskin, J.-P.

    2015-10-01

    In this work we present experimental results from dynamic and static tests on miniature magnetic field sensors which are based on Micro Electro Mechanical Systems (MEMS) technologies. These MEMS magnetometers were fabricated on SOI wafers using Si bulk micromachining techniques and they operate at the first resonant frequency under the action of the Lorentz force which arises when a current flows through them in the presence of an external magnetic field. Sensing is based on piezoresistive principles and high sensitivity is expected from devices that show high total quality factors Qtot. We investigate here the energy loss mechanisms and the temperature rise due to Joule heating effects in the resonators of the magnetometers by performing tests both in air and under vacuum conditions. Testing was performed using laser Doppler Vibrometry and white light interferometry. At each pressure different driving currents have been applied and Qtot was extracted. It is found that Qtot varies with pressure between two limiting values: a low one in air which was between 17 and 500 for the tested devices and a high one in vacuum which in the case of one of our devices was equal to 2800. The amplitude of the applied current is also affecting the Q value at a certain pressure due to the rise of thermal stress in the resonating structures. The sensitivity of the sensors in air was experimentally measured using a Helmholtz coil and an oscilloscope and values between 72 mV T-1 and 513 mV T-1 were obtained from the tested devices. We further attempt to estimate the temperature rise in the devices due to Joule heating effects by combining the topography scans which were experimentally obtained with results from thermomechanical analysis of the sensors using Finite Element Modelling.

  19. [Research on monitoring mechanical wear state based on oil spectrum multi-dimensional time series model].

    PubMed

    Xu, Chao; Zhang, Pei-lin; Ren, Guo-quan; Li, Bing; Yang, Ning

    2010-11-01

    A new method using oil atomic spectrometric analysis technology to monitor the mechanical wear state was proposed. Multi-dimensional time series model of oil atomic spectrometric data of running-in period was treated as the standard model. Residues remained after new data were processed by the standard model. The residues variance matrix was selected as the features of the corresponding wear state. Then, high dimensional feature vectors were reduced through the principal component analysis and the first three principal components were extracted to represent the wear state. Euclidean distance was computed for feature vectors to classify the testing samples. Thus, the mechanical wear state was identified correctly. The wear state of a specified track vehicle engine was effectively identified, which verified the validity of the proposed method. Experimental results showed that introducing the multi-dimensional time series model to oil spectrometric analysis can fuse the spectrum data and improve the accuracy of monitoring mechanical wear state.

  20. Experimental and modeling study on charge storage/transfer mechanism of graphene-based supercapacitors

    NASA Astrophysics Data System (ADS)

    Ban, Shuai; Jing, Xie; Zhou, Hongjun; Zhang, Lei; Zhang, Jiujun

    2014-12-01

    A symmetrical graphene-based supercapacitor is constructed for studying the charge-transfer mechanism within the graphene-based electrodes using both experiment measurements and molecular simulation. The in-house synthesized graphene is characterized by XRD, SEM and BET measurements for morphology and surface area. It is observed that the electric capacity of graphene electrode can be reduced by both high internal resistance and limited mass transfer. Computer modeling is conducted at the molecular level to characterize the diffusion behavior of electrolyte ions to the interior of electrode with emphasis on the unique 2D confinement imposed by graphene layers. Although graphene powder poses a moderate internal surface of 400 m2 g-1, the capacitance performance of graphene electrode can be as good as that of commercial activated carbon which has an overwhelming surface area of 1700 m2 g-1. An explanation to this abnormal correlation is that graphene material has an intrinsic capability of adaptively reorganizing its microporous structure in response to intercalation of ions and immergence of electrolyte solvent. The accessible surface of graphene is believed to be dramatically enlarged for ion adsorption during the charging process of capacitor.

  1. Towards a physics-based multiscale modelling of the electro-mechanical coupling in electro-active polymers

    PubMed Central

    Menzel, Andreas; deBotton, Gal

    2016-01-01

    Owing to the increasing number of industrial applications of electro-active polymers (EAPs), there is a growing need for electromechanical models which accurately capture their behaviour. To this end, we compare the predicted behaviour of EAPs undergoing homogeneous deformations according to three electromechanical models. The first model is a phenomenological continuum-based model composed of the mechanical Gent model and a linear relationship between the electric field and the polarization. The electrical and the mechanical responses according to the second model are based on the physical structure of the polymer chain network. The third model incorporates a neo-Hookean mechanical response and a physically motivated microstructurally based long-chains model for the electrical behaviour. In the microstructural-motivated models, the integration from the microscopic to the macroscopic levels is accomplished by the micro-sphere technique. Four types of homogeneous boundary conditions are considered and the behaviours determined according to the three models are compared. For the microstructurally motivated models, these analyses are performed and compared with the widely used phenomenological model for the first time. Some of the aspects revealed in this investigation, such as the dependence of the intensity of the polarization field on the deformation, highlight the need for an in-depth investigation of the relationships between the structure and the behaviours of the EAPs at the microscopic level and their overall macroscopic response. PMID:27118885

  2. 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.

  3. Toward modular biological models: defining analog modules based on referent physiological mechanisms

    PubMed Central

    2014-01-01

    Background Currently, most biomedical models exist in isolation. It is often difficult to reuse or integrate models or their components, in part because they are not modular. Modular components allow the modeler to think more deeply about the role of the model and to more completely address a modeling project’s requirements. In particular, modularity facilitates component reuse and model integration for models with different use cases, including the ability to exchange modules during or between simulations. The heterogeneous nature of biology and vast range of wet-lab experimental platforms call for modular models designed to satisfy a variety of use cases. We argue that software analogs of biological mechanisms are reasonable candidates for modularization. Biomimetic software mechanisms comprised of physiomimetic mechanism modules offer benefits that are unique or especially important to multi-scale, biomedical modeling and simulation. Results We present a general, scientific method of modularizing mechanisms into reusable software components that we call physiomimetic mechanism modules (PMMs). PMMs utilize parametric containers that partition and expose state information into physiologically meaningful groupings. To demonstrate, we modularize four pharmacodynamic response mechanisms adapted from an in silico liver (ISL). We verified the modularization process by showing that drug clearance results from in silico experiments are identical before and after modularization. The modularized ISL achieves validation targets drawn from propranolol outflow profile data. In addition, an in silico hepatocyte culture (ISHC) is created. The ISHC uses the same PMMs and required no refactoring. The ISHC achieves validation targets drawn from propranolol intrinsic clearance data exhibiting considerable between-lab variability. The data used as validation targets for PMMs originate from both in vitro to in vivo experiments exhibiting large fold differences in time scale

  4. A multi-scale continuum model of skeletal muscle mechanics predicting force enhancement based on actin-titin interaction.

    PubMed

    Heidlauf, Thomas; Klotz, Thomas; Rode, Christian; Altan, Ekin; Bleiler, Christian; Siebert, Tobias; Röhrle, Oliver

    2016-12-01

    Although recent research emphasises the possible role of titin in skeletal muscle force enhancement, this property is commonly ignored in current computational models. This work presents the first biophysically based continuum-mechanical model of skeletal muscle that considers, in addition to actin-myosin interactions, force enhancement based on actin-titin interactions. During activation, titin attaches to actin filaments, which results in a significant reduction in titin's free molecular spring length and therefore results in increased titin forces during a subsequent stretch. The mechanical behaviour of titin is included on the microscopic half-sarcomere level of a multi-scale chemo-electro-mechanical muscle model, which is based on the classic sliding-filament and cross-bridge theories. In addition to titin stress contributions in the muscle fibre direction, the continuum-mechanical constitutive relation accounts for geometrically motivated, titin-induced stresses acting in the muscle's cross-fibre directions. Representative simulations of active stretches under maximal and submaximal activation levels predict realistic magnitudes of force enhancement in fibre direction. For example, stretching the model by 20 % from optimal length increased the isometric force at the target length by about 30 %. Predicted titin-induced stresses in the muscle's cross-fibre directions are rather insignificant. Including the presented development in future continuum-mechanical models of muscle function in dynamic situations will lead to more accurate model predictions during and after lengthening contractions.

  5. Multi-scale modeling of soft fibrous tissues based on proteoglycan mechanics.

    PubMed

    Linka, Kevin; Khiêm, Vu Ngoc; Itskov, Mikhail

    2016-08-16

    Collagen in the form of fibers or fibrils is an essential source of strength and structural integrity in most organs of the human body. Recently, with the help of complex experimental setups, a paradigm change concerning the mechanical contribution of proteoglycans (PGs) took place. Accordingly, PG connections protect the surrounding collagen fibrils from over-stretching rather than transmitting load between them. In this paper, we describe the reported PG mechanics and incorporate it into a multi-scale model of soft fibrous tissues. To this end, a nano-to-micro model of a single collagen fiber is developed by taking the entropic-energetic transition on the collagen molecule level into account. The microscopic damage occurring inside the collagen fiber is elucidated by sliding of PGs as well as by over-stretched collagen molecules. Predictions of this two-constituent-damage model are compared to experimental data available in the literature.

  6. Analysis of the twin spacing and grain size effects on mechanical properties in hierarchically nanotwinned face-centered cubic metals based on a mechanism-based plasticity model

    NASA Astrophysics Data System (ADS)

    Zhu, Linli; Qu, Shaoxing; Guo, Xiang; Lu, Jian

    2015-03-01

    Hierarchical twin lamellae in polycrystalline face-centered cubic (fcc) metals possess a possibility to achieve higher strength with keeping an acceptable elongation. The present work is concerned with the analysis of twin spacing and grain size-dependent plastic performance in hierarchically nanotwinned fcc metals using a generalized strain-gradient plasticity model. The dislocation density-based physical model for constitutive description of nanotwinned fcc metals is expanded for the hierarchical structures of nanotwins. The strengthening mechanism and the failure behavior in these hierarchical nanostructures are studied to evaluate the strength and ductility. Moreover, the transition twin spacing between the strengthening and softening is obtained in different order of twin lamellae. A dislocation-based model on nucleating deformation twins is presented to predict the critical twin spacing in the lowest twin lamellae for generating the subordinate twin lamellae. Our simulation results demonstrate that the existence of the hierarchical nanotwins gives rise to a significant enhancement in the strength, and the resulting global flow stresses are sensitive to the twin spacings of the hierarchical twin lamellae and the grain size. Two softening stages are observed with variation of twin spacing, and the relevant transition twin spacing depends on the microstructural size in hierarchically nanotwinned metals. We further find that the predicted failure strain decreases with decreasing the twin spacing, which is quite different from the case of the individually nanotwinned fcc metals. The critical twin spacing for generating subordinate twins also depends on the twin spacing of superordinate twin lamellae and the grain size. These findings suggest that the high yield strength and good ductility can be achieved by optimizing the grain size and the twin spacings in the hierarchical twins.

  7. A Modified Wilson Cycle Scenario Based on Thermo-Mechanical Model

    NASA Astrophysics Data System (ADS)

    Baes, M.; Sobolev, S. V.

    2014-12-01

    The major problem of classical Wilson Cycle concept is the suggested conversion of the passive continental margin to the active subduction zone. Previous modeling studies assumed either unusually thick felsic continental crust at the margin (over 40 km) or unusually low lithospheric thickness (less than 70 km) to simulate this process. Here we propose a new triggering factor in subduction initiation process that is mantle suction force. Based on this proposal we suggest a modification of Wilson Cycle concept. Sometime after opening and extension of oceanic basin, continental passive margin moves over the slab remnants of the former active subduction zones in deep mantle. Such slab remnants or deep slabs of neighboring active subduction zones produce a suction mantle flow introducing additional compression at the passive margin. It results in the initiation of a new subduction zone, hence starting the closing phase of Wilson Cycle. In this scenario the weakness of continental crust near the passive margin which is inherited from the rifting phase and horizontal push force induced from far-field topographic gradient within the continent facilitate and speed up subduction initiation process. Our thermo-mechanical modeling shows that after a few tens of million years a shear zone may indeed develop along the passive margin that has typical two-layered 35 km thick continental crust and thermal lithosphere thicker than 100 km if there is a broad mantle down-welling flow below the margin. Soon after formation of this shear zone oceanic plate descends into mantle and subduction initiates. Subduction initiation occurs following over-thrusting of continental crust and retreating of future trench. In models without far-field topographic gradient within the continent subduction initiation requires weaker passive margin. Our results also indicate that subduction initiation depends on several parameters such as magnitude, domain size and location of suction mantle flow

  8. A meshfree method based on the peridynamic model of solid mechanics.

    SciTech Connect

    Silling, Stewart Andrew; Askari, Ebrahim

    2005-01-01

    An alternative theory of solid mechanics, known as the peridynamic theory, formulates problems in terms of integral equations rather than partial differential equations. This theory assumes that particles in a continuum interact with each other across a finite distance, as in molecular dynamics. Damage is incorporated in the theory at the level of these two-particle interactions, so localization and fracture occur as a natural outgrowth of the equation of motion and constitutive models. A numerical method for solving dynamic problems within the peridynamic theory is described. Accuracy and numerical stability are discussed. Examples illustrate the properties of the method for modeling brittle dynamic crack growth.

  9. Use of agent-based modeling to explore the mechanisms of intracellular phosphorus heterogeneity in cultured phytoplankton.

    PubMed

    Fredrick, Neil D; Berges, John A; Twining, Benjamin S; Nuñez-Milland, Daliangelis; Hellweger, Ferdi L

    2013-07-01

    There can be significant intraspecific individual-level heterogeneity in the intracellular P of phytoplankton, which can affect the population-level growth rate. Several mechanisms can create this heterogeneity, including phenotypic variability in various physiological functions (e.g., nutrient uptake rate). Here, we use modeling to explore the contribution of various mechanisms to the heterogeneity in phytoplankton grown in a laboratory culture. An agent-based model simulates individual cells and their intracellular P. Heterogeneity is introduced by randomizing parameters (e.g., maximum uptake rate) of daughter cells at division. The model was calibrated to observations of the P quota of individual cells of the centric diatom Thalassiosira pseudonana, which were obtained using synchrotron X-ray fluorescence (SXRF). A number of simulations, with individual mechanisms of heterogeneity turned off, then were performed. Comparison of the coefficient of variation (CV) of these and the baseline simulation (i.e., all mechanisms turned on) provides an estimate of the relative contribution of these mechanisms. The results show that the mechanism with the largest contribution to variability is the parameter characterizing the maximum intracellular P, which, when removed, results in a CV of 0.21 compared to a CV of 0.37 with all mechanisms turned on. This suggests that nutrient/element storage capabilities/mechanisms are important determinants of intrapopulation heterogeneity.

  10. Ubiquity: a framework for physiological/mechanism-based pharmacokinetic/pharmacodynamic model development and deployment.

    PubMed

    Harrold, John M; Abraham, Anson K

    2014-04-01

    Practitioners of pharmacokinetic/pharmacodynamic modeling routinely employ various software packages that enable them to fit differential equation based mechanistic or empirical models to biological/pharmacological data. The availability and choice of different analytical tools, while enabling, can also pose a significant challenge in terms of both, implementation and transferability. A package has been developed that addresses these issues by creating a simple text-based format, which provides methods to reduce coding complexity and enables the modeler to describe the components of the model based on the underlying physiochemical processes. A Perl script builds the system for multiple formats (ADAPT, MATLAB, Berkeley Madonna, etc.), enabling analysis across several software packages and reducing the chance for transcription error. Workflows can then be built around this package, which can increase efficiency and model availability. As a proof of concept, tools are included that allow models constructed in this format to be run with MATLAB both at the scripting level and through a generic graphical application that can be compiled and run as a stand-alone application.

  11. A mathematical description of a growing cell colony based on the mechanical bidomain model

    NASA Astrophysics Data System (ADS)

    Auddya, Debabrata; Roth, Bradley J.

    2017-03-01

    The mechanical bidomain model is used to describe a colony of cells growing on a substrate. Analytical expressions are derived for the intracellular and extracellular displacements. Mechanotransduction events are driven by the difference between the displacements in the two spaces, corresponding to the force acting on integrins. The equation for the displacement consists of two terms: one proportional to the radius that is the same in the intracellular and extracellular spaces (the monodomain term) and one that is proportional to a modified Bessel function that is responsible for mechanotransduction (the bidomain term). The model predicts that mechanotransduction occurs within a few length constants of the colony’s edge, and an expression for the length constant contains the intracellular and extracellular shear moduli and the spring constant of the integrins coupling the two spaces. The model predictions are qualitatively consistent with experiments on human embryonic stem cell colonies, in which differentiation is localized near the edge.

  12. Regulation of amniotic fluid volume: mathematical model based on intramembranous transport mechanisms.

    PubMed

    Brace, Robert A; Anderson, Debra F; Cheung, Cecilia Y

    2014-11-15

    Experimentation in late-gestation fetal sheep has suggested that regulation of amniotic fluid (AF) volume occurs primarily by modulating the rate of intramembranous transport of water and solutes across the amnion into underlying fetal blood vessels. In order to gain insight into intramembranous transport mechanisms, we developed a computer model that allows simulation of experimentally measured changes in AF volume and composition over time. The model included fetal urine excretion and lung liquid secretion as inflows into the amniotic compartment plus fetal swallowing and intramembranous absorption as outflows. By using experimental flows and solute concentrations for urine, lung liquid, and swallowed fluid in combination with the passive and active transport mechanisms of the intramembranous pathway, we simulated AF responses to basal conditions, intra-amniotic fluid infusions, fetal intravascular infusions, urine replacement, and tracheoesophageal occlusion. The experimental data are consistent with four intramembranous transport mechanisms acting in concert: 1) an active unidirectional bulk transport of AF with all dissolved solutes out of AF into fetal blood presumably by vesicles; 2) passive bidirectional diffusion of solutes, such as sodium and chloride, between fetal blood and AF; 3) passive bidirectional water movement between AF and fetal blood; and 4) unidirectional transport of lactate into the AF. Further, only unidirectional bulk transport is dynamically regulated. The simulations also identified areas for future study: 1) identifying intramembranous stimulators and inhibitors, 2) determining the semipermeability characteristics of the intramembranous pathway, and 3) characterizing the vesicles that are the primary mediators of intramembranous transport.

  13. Development of Antipsychotic Medications with Novel Mechanisms of Action Based on Computational Modeling of Hippocampal Neuropathology

    PubMed Central

    Siekmeier, Peter J.; vanMaanen, David P.

    2013-01-01

    A large number of cellular level abnormalities have been identified in the hippocampus of schizophrenic subjects. Nonetheless, it remains uncertain how these pathologies interact at a system level to create clinical symptoms, and this has hindered the development of more effective antipsychotic medications. Using a 72-processor supercomputer, we created a tissue level hippocampal simulation, featuring multicompartmental neuron models with multiple ion channel subtypes and synaptic channels with realistic temporal dynamics. As an index of the schizophrenic phenotype, we used the specific inability of the model to attune to 40 Hz (gamma band) stimulation, a well-characterized abnormality in schizophrenia. We examined several possible combinations of putatively schizophrenogenic cellular lesions by systematically varying model parameters representing NMDA channel function, dendritic spine density, and GABA system integrity, conducting 910 trials in total. Two discrete “clusters” of neuropathological changes were identified. The most robust was characterized by co-occurring modest reductions in NMDA system function (-30%) and dendritic spine density (-30%). Another set of lesions had greater NMDA hypofunction along with low level GABA system dysregulation. To the schizophrenic model, we applied the effects of 1,500 virtual medications, which were implemented by varying five model parameters, independently, in a graded manner; the effects of known drugs were also applied. The simulation accurately distinguished agents that are known to lack clinical efficacy, and identified novel mechanisms (e.g., decrease in AMPA conductance decay time constant, increase in projection strength of calretinin-positive interneurons) and combinations of mechanisms that could re-equilibrate model behavior. These findings shed light on the mechanistic links between schizophrenic neuropathology and the gamma band oscillatory abnormalities observed in the illness. As such, they generate

  14. Coarsening of the Sn-Pb Solder Microstructure in Constitutive Model-Based Predictions of Solder Joint Thermal Mechanical Fatigue

    SciTech Connect

    Vianco, P.T.; Burchett, S.N.; Neilsen, M.K.; Rejent, J.A.; Frear, D.R.

    1999-04-12

    Thermal mechanical fatigue (TMF) is an important damage mechanism for solder joints exposed to cyclic temperature environments. Predicting the service reliability of solder joints exposed to such conditions requires two knowledge bases: first, the extent of fatigue damage incurred by the solder microstructure leading up to fatigue crack initiation, must be quantified in both time and space domains. Secondly, fatigue crack initiation and growth must be predicted since this metric determines, explicitly, the loss of solder joint functionality as it pertains to its mechanical fastening as well as electrical continuity roles. This paper will describe recent progress in a research effort to establish a microstructurally-based, constitutive model that predicts TMF deformation to 63Sn-37Pb solder in electronic solder joints up to the crack initiation step. The model is implemented using a finite element setting; therefore, the effects of both global and local thermal expansion mismatch conditions in the joint that would arise from temperature cycling.

  15. Atomistic modeling of thermodynamic properties of Pu-Ga alloys based on the Invar mechanism

    NASA Astrophysics Data System (ADS)

    Lee, Tongsik; Taylor, Christopher D.; Lawson, A. C.; Conradson, Steven D.; Chen, Shao Ping; Caro, A.; Valone, Steven M.; Baskes, Michael I.

    2014-05-01

    We present an atomistic model that accounts for a range of anomalous thermodynamic properties of the fcc δ phase of Pu-Ga alloys in terms of the Invar mechanism. Two modified embedded atom method potentials are employed to represent competing electronic states in δ-Pu, each of which has an individual configuration dependence as well as distinct interactions with gallium. Using classical Monte Carlo simulations, we compute the temperature dependence of various thermodynamic properties for different dilute gallium concentrations. The model reproduces the observed effects of excessive volume reduction along with a rapid shift in thermal expansion from negative to positive values with increasing gallium concentration. It also predicts progressive stiffening upon dilute-gallium alloying, while the calculated thermal softening is nearly independent of the gallium concentration in agreement with resonant ultrasound spectroscopy measurements in the literature. Analysis of the local structure predicted by the model indicates that the distribution of the gallium atoms is not completely random in the δ phase due to the presence of short-range order associated with the Invar mechanism. This effect is consistent with the nanoscale heterogeneity in local gallium concentration which is observed in recent extended x-ray absorption fine structure spectroscopy experiments. Implications of the Invar effect for phase stability and physical interpretations of the two states are also discussed.

  16. A mechanical model for predicting the probability of osteoporotic hip fractures based in DXA measurements and finite element simulation

    PubMed Central

    2012-01-01

    Background Osteoporotic hip fractures represent major cause of disability, loss of quality of life and even mortality among the elderly population. Decisions on drug therapy are based on the assessment of risk factors for fracture, from BMD measurements. The combination of biomechanical models with clinical studies could better estimate bone strength and supporting the specialists in their decision. Methods A model to assess the probability of fracture, based on the Damage and Fracture Mechanics has been developed, evaluating the mechanical magnitudes involved in the fracture process from clinical BMD measurements. The model is intended for simulating the degenerative process in the skeleton, with the consequent lost of bone mass and hence the decrease of its mechanical resistance which enables the fracture due to different traumatisms. Clinical studies were chosen, both in non-treatment conditions and receiving drug therapy, and fitted to specific patients according their actual BMD measures. The predictive model is applied in a FE simulation of the proximal femur. The fracture zone would be determined according loading scenario (sideway fall, impact, accidental loads, etc.), using the mechanical properties of bone obtained from the evolutionary model corresponding to the considered time. Results BMD evolution in untreated patients and in those under different treatments was analyzed. Evolutionary curves of fracture probability were obtained from the evolution of mechanical damage. The evolutionary curve of the untreated group of patients presented a marked increase of the fracture probability, while the curves of patients under drug treatment showed variable decreased risks, depending on the therapy type. Conclusion The FE model allowed to obtain detailed maps of damage and fracture probability, identifying high-risk local zones at femoral neck and intertrochanteric and subtrochanteric areas, which are the typical locations of osteoporotic hip fractures. The

  17. Mechanics of materials model

    NASA Technical Reports Server (NTRS)

    Meister, Jeffrey P.

    1987-01-01

    The Mechanics of Materials Model (MOMM) is a three-dimensional inelastic structural analysis code for use as an early design stage tool for hot section components. MOMM is a stiffness method finite element code that uses a network of beams to characterize component behavior. The MOMM contains three material models to account for inelastic material behavior. These include the simplified material model, which assumes a bilinear stress-strain response; the state-of-the-art model, which utilizes the classical elastic-plastic-creep strain decomposition; and Walker's viscoplastic model, which accounts for the interaction between creep and plasticity that occurs under cyclic loading conditions.

  18. Statistical mechanics of competitive resource allocation using agent-based models

    NASA Astrophysics Data System (ADS)

    Chakraborti, Anirban; Challet, Damien; Chatterjee, Arnab; Marsili, Matteo; Zhang, Yi-Cheng; Chakrabarti, Bikas K.

    2015-01-01

    Demand outstrips available resources in most situations, which gives rise to competition, interaction and learning. In this article, we review a broad spectrum of multi-agent models of competition (El Farol Bar problem, Minority Game, Kolkata Paise Restaurant problem, Stable marriage problem, Parking space problem and others) and the methods used to understand them analytically. We emphasize the power of concepts and tools from statistical mechanics to understand and explain fully collective phenomena such as phase transitions and long memory, and the mapping between agent heterogeneity and physical disorder. As these methods can be applied to any large-scale model of competitive resource allocation made up of heterogeneous adaptive agent with non-linear interaction, they provide a prospective unifying paradigm for many scientific disciplines.

  19. Mechanism-based model of a mass rapid transit system: A perspective

    NASA Astrophysics Data System (ADS)

    Legara, Erika Fille; Khoon, Lee Kee; Guang, Hung Gih; Monterola, Christopher

    2015-01-01

    In this paper, we discuss our findings on the spatiotemporal dynamics within the mass rapid transit (MRT) system of Singapore. We show that the trip distribution of Origin-Destination (OD) station pairs follows a power-law, implying the existence of critical OD pairs. We then present and discuss the empirically validated agent-based model (ABM) we have developed. The model allows recreation of the observed statistics and the setting up of various scenarios and their effects on the system, such as increasing the commuter population and the propagation of travel delays within the transportation network. The proposed model further enables identification of bottlenecks that can cause the MRT to break down, and consequently provide foresight on how such disruptions can possibly be managed. This can potentially provide a versatile approach for transport planners and government regulators to make quantifiable policies that optimally balance cost and convenience as a function of the number of the commuting public.

  20. Non-ablative hyperthermic mesenchymal regeneration: a proposed mechanism of action based on the Vivev model

    NASA Astrophysics Data System (ADS)

    Vos, Jeffrey A.; Livengood, Ryan H.; Jessop, Morris; Coad, James E.

    2011-03-01

    Novel non-ablative hyperthermic medical devices are currently being developed, in association with cryogen surface cooling, to rejuvenate tissues without collagen scarring. These devices have been designed to remodel skin, manage urinary stress incontinence, and more recently, treat vaginal laxity. In contrast to the thermal injury and reparative healing associated with higher energy ablation systems, these lower energy non-ablative systems are designed to subtly modify the collagen, stimulate the fibroblasts, and maintain a functional tissue architecture that subsequently promotes tissue rejuvenation and restoration. While these devices have primarily relied on clinical outcome questionnaires and satisfaction surveys to establish efficacy, a physiologic explanation for the induced tissue changes and tightening has not been well documented. Recent histology studies, using the Viveve ovine vaginal treatment model, have identified changes that propose both a mechanism of action and a tissue remodeling timeline for such non-ablative hyperthermic devices. The Viveve model results are consistent with subtle connective tissue changes leading to fibroblast stimulation and subsequent collagen replacement and augmentation. Unlike tissue ablation devices that cause thermal necrosis, these non-ablative devices renew the targeted tissue without dense collagenous scarring over a period of 3 or more months. The spectrum of histologic findings, as illustrated in the Viveve ovine vaginal model, further support the previously documented safety and efficacy profiles for low-dose non-ablative hyperthermic devices that rejuvenate and tighten submucosal tissues.

  1. Wear-mechanism modelling

    SciTech Connect

    Ashby, M.F. . Dept. of Engineering)

    1993-03-01

    Goals of the program are to calculate the surface temperatures in dry sliding, develop a soft wear tester for ceramics, survey the wear mechanisms in brittle solids, and couple the temperature calculations with models to give wear maps for brittle solids. (DLC)

  2. A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation

    NASA Astrophysics Data System (ADS)

    Delile, Julien; Herrmann, Matthieu; Peyriéras, Nadine; Doursat, René

    2017-01-01

    The study of multicellular development is grounded in two complementary domains: cell biomechanics, which examines how physical forces shape the embryo, and genetic regulation and molecular signalling, which concern how cells determine their states and behaviours. Integrating both sides into a unified framework is crucial to fully understand the self-organized dynamics of morphogenesis. Here we introduce MecaGen, an integrative modelling platform enabling the hypothesis-driven simulation of these dual processes via the coupling between mechanical and chemical variables. Our approach relies upon a minimal `cell behaviour ontology' comprising mesenchymal and epithelial cells and their associated behaviours. MecaGen enables the specification and control of complex collective movements in 3D space through a biologically relevant gene regulatory network and parameter space exploration. Three case studies investigating pattern formation, epithelial differentiation and tissue tectonics in zebrafish early embryogenesis, the latter with quantitative comparison to live imaging data, demonstrate the validity and usefulness of our framework.

  3. Mechanical Model Analysis for Quantitative Evaluation of Liver Fibrosis Based on Ultrasound Tissue Elasticity Imaging

    NASA Astrophysics Data System (ADS)

    Shiina, Tsuyoshi; Maki, Tomonori; Yamakawa, Makoto; Mitake, Tsuyoshi; Kudo, Masatoshi; Fujimoto, Kenji

    2012-07-01

    Precise evaluation of the stage of chronic hepatitis C with respect to fibrosis has become an important issue to prevent the occurrence of cirrhosis and to initiate appropriate therapeutic intervention such as viral eradication using interferon. Ultrasound tissue elasticity imaging, i.e., elastography can visualize tissue hardness/softness, and its clinical usefulness has been studied to detect and evaluate tumors. We have recently reported that the texture of elasticity image changes as fibrosis progresses. To evaluate fibrosis progression quantitatively on the basis of ultrasound tissue elasticity imaging, we introduced a mechanical model of fibrosis progression and simulated the process by which hepatic fibrosis affects elasticity images and compared the results with those clinical data analysis. As a result, it was confirmed that even in diffuse diseases like chronic hepatitis, the patterns of elasticity images are related to fibrous structural changes caused by hepatic disease and can be used to derive features for quantitative evaluation of fibrosis stage.

  4. Study of detecting mechanism of carbon nanotubes gas sensor based on multi-stable stochastic resonance model.

    PubMed

    Jingyi, Zhu

    2015-01-01

    The detecting mechanism of carbon nanotubes gas sensor based on multi-stable stochastic resonance (MSR) model was studied in this paper. A numerically stimulating model based on MSR was established. And gas-ionizing experiment by adding electronic white noise to induce 1.65 MHz periodic component in the carbon nanotubes gas sensor was performed. It was found that the signal-to-noise ratio (SNR) spectrum displayed 2 maximal values, which accorded to the change of the broken-line potential function. The experimental results of gas-ionizing experiment demonstrated that periodic component of 1.65 MHz had multiple MSR phenomena, which was in accordance with the numerical stimulation results. In this way, the numerical stimulation method provides an innovative method for the detecting mechanism research of carbon nanotubes gas sensor.

  5. Mechanical analysis of congestive heart failure caused by bundle branch block based on an electromechanical canine heart model

    NASA Astrophysics Data System (ADS)

    Dou, Jianhong; Xia, Ling; Zhang, Yu; Shou, Guofa; Wei, Qing; Liu, Feng; Crozier, Stuart

    2009-01-01

    Asynchronous electrical activation, induced by bundle branch block (BBB), can cause reduced ventricular function. However, the effects of BBB on the mechanical function of heart are difficult to assess experimentally. Many heart models have been developed to investigate cardiac properties during BBB but have mainly focused on the electrophysiological properties. To date, the mechanical function of BBB has not been well investigated. Based on a three-dimensional electromechanical canine heart model, the mechanical properties of complete left and right bundle branch block (LBBB and RBBB) were simulated. The anatomical model as well as the fiber orientations of a dog heart was reconstructed from magnetic resonance imaging (MRI) and diffusion tensor MRI (DT-MRI). Using the solutions of reaction-diffusion equations and with a strategy of parallel computation, the asynchronous excitation propagation and intraventricular conduction in BBB was simulated. The mechanics of myocardial tissues were computed with time-, sarcomere length-dependent uniaxial active stress initiated at the time of depolarization. The quantification of mechanical intra- and interventricular asynchrony of BBB was then investigated using the finite-element method with an eight-node isoparametric element. The simulation results show that (1) there exists inter- and intraventricular systolic dyssynchrony during BBB; (2) RBBB may have more mechanical synchrony and better systolic function of the left ventricle (LV) than LBBB; (3) the ventricles always move toward the early-activated ventricle; and (4) the septum experiences higher stress than left and right ventricular free walls in BBB. The simulation results validate clinical and experimental recordings of heart deformation and provide regional quantitative estimates of ventricular wall strain and stress. The present work suggests that an electromechanical heart model, incorporating real geometry and fiber orientations, may be helpful for better

  6. Mechanical analysis of congestive heart failure caused by bundle branch block based on an electromechanical canine heart model.

    PubMed

    Dou, Jianhong; Xia, Ling; Zhang, Yu; Shou, Guofa; Wei, Qing; Liu, Feng; Crozier, Stuart

    2009-01-21

    Asynchronous electrical activation, induced by bundle branch block (BBB), can cause reduced ventricular function. However, the effects of BBB on the mechanical function of heart are difficult to assess experimentally. Many heart models have been developed to investigate cardiac properties during BBB but have mainly focused on the electrophysiological properties. To date, the mechanical function of BBB has not been well investigated. Based on a three-dimensional electromechanical canine heart model, the mechanical properties of complete left and right bundle branch block (LBBB and RBBB) were simulated. The anatomical model as well as the fiber orientations of a dog heart was reconstructed from magnetic resonance imaging (MRI) and diffusion tensor MRI (DT-MRI). Using the solutions of reaction-diffusion equations and with a strategy of parallel computation, the asynchronous excitation propagation and intraventricular conduction in BBB was simulated. The mechanics of myocardial tissues were computed with time-, sarcomere length-dependent uniaxial active stress initiated at the time of depolarization. The quantification of mechanical intra- and interventricular asynchrony of BBB was then investigated using the finite-element method with an eight-node isoparametric element. The simulation results show that (1) there exists inter- and intraventricular systolic dyssynchrony during BBB; (2) RBBB may have more mechanical synchrony and better systolic function of the left ventricle (LV) than LBBB; (3) the ventricles always move toward the early-activated ventricle; and (4) the septum experiences higher stress than left and right ventricular free walls in BBB. The simulation results validate clinical and experimental recordings of heart deformation and provide regional quantitative estimates of ventricular wall strain and stress. The present work suggests that an electromechanical heart model, incorporating real geometry and fiber orientations, may be helpful for better

  7. Computational model for the cell-mechanical response of the osteocyte cytoskeleton based on self-stabilizing tensegrity structures.

    PubMed

    Kardas, Dieter; Nackenhorst, Udo; Balzani, Daniel

    2013-01-01

    The mechanism by which mechanical stimulation on osteocytes results in biochemical signals that initiate the remodeling process inside living bone tissue is largely unknown. Even the type of stimulation acting on these cells is not yet clearly identified. However, the cytoskeleton of osteocytes is suggested to play a major role in the mechanosensory process due to the direct connection to the nucleus. In this paper, a computational approach to model and simulate the cell structure of osteocytes based on self-stabilizing tensegrity structures is suggested. The computational model of the cell consists of the major components with respect to mechanical aspects: the integrins that connect the cell with the extracellular bone matrix, and different types of protein fibers (microtubules and intermediate filaments) that form the cytoskeleton, the membrane-cytoskeleton (microfilaments), the nucleus and the centrosome. The proposed geometrical cell models represent the cell in its physiological environment which is necessary in order to give a statement on the cell behavior in vivo. Studies on the mechanical response of osteocytes after physiological loading and in particular the mechanical response of the nucleus show that the load acting on the nucleus is rising with increasing deformation applied to the integrins.

  8. Mechanical analysis of three dimensional woven carbon fiber-reinforced composites using fiber-based continuum model

    NASA Astrophysics Data System (ADS)

    Ahn, Hyunchul; An, Yongsan; Yu, Woong-Ryeol

    2016-10-01

    A new numerical method for analyzing the mechanical behavior of three-dimensional (3D) woven carbon fiber-reinforced composites was developed by considering changes in the fiber orientation and calculating the stress increments due to incremental deformations. The model consisted of four steps, starting update of the yarn orientation based on incremental deformation gradient. The stiffness matrix was then computed using the updated yarn orientation. Next, partial damage and propagation were incorporated into the stress calculation using modified ply discount method. The failure conditions were obtained by testing the unidirectional composites and formulated using Puck's criterion. This numerical model was finally implemented into commercial finite element software, ABAQUS, as a user material subroutine. As for experiment, 3D woven composite samples was manufactured using laboratory built-in system and characterized, the results of which were compared with simulated results, demonstrating that the current numerical model can properly predict the mechanical behavior of 3D fiber-reinforced composites.

  9. The design and modelling of a comb-drive-based microengine for mechanism drive applications

    NASA Astrophysics Data System (ADS)

    Garcia, E. J.; Sniegowski, J. J.

    The design and modelling of a comb-drive-based microengine is presented. The motivation for developing such a device came from our own need to drive specific micromechanisms. Difficulty in connecting an external load to an existing micromotor and insufficient torque led us to a design which uses the comb drive concept of Tang, Nguyen, and Howe, to convert linear oscillatory motion into rotational motion. The microengine provides output in the form of a continuously rotating output gear that is capable of delivering torque to a micromechanism. The microengine can be operated at varying speeds and its motion can be reversed. Modelling of the system indicates that dynamic effects are important and that the device behaves in ways similar to that of 'high speed' machinery. Processing considerations address the elimination of natural interferences that arise when conformally deposited polysilicon films form the links, joints, and gears. The resultant device is completely batch fabricated without the need for manual assembly steps.

  10. A macroscopic multi-mechanism based constitutive model for the thermo-mechanical cyclic degeneration of shape memory effect of NiTi shape memory alloy

    NASA Astrophysics Data System (ADS)

    Yu, Chao; Kang, Guozheng; Kan, Qianhua

    2017-01-01

    A macroscopic based multi-mechanism constitutive model is constructed in the framework of irreversible thermodynamics to describe the degeneration of shape memory effect occurring in the thermo-mechanical cyclic deformation of NiTi shape memory alloys (SMAs). Three phases, austenite A, twinned martensite Mt and detwinned martensite Md , as well as the phase transitions occurring between each pair of phases (A→ M t , Mt→ A , A→ M d , Md→ A , and Mt→ M d) are considered in the proposed model. Meanwhile, two kinds of inelastic deformation mechanisms, martensite transformation-induced plasticity and reorientation-induced plasticity, are used to explain the degeneration of shape memory effects of NiTi SMAs. The evolution equations of internal variables are proposed by attributing the degeneration of shape memory effect to the interaction between the three phases (A, Mt , and Md) and plastic deformation. Finally, the capability of the proposed model is verified by comparing the predictions with the experimental results of NiTi SMAs. It is shown that the degeneration of shape memory effect and its dependence on the loading level can be reasonably described by the proposed model.

  11. A simplified quantum mechanical model for nanowire transistors based on non-linear variational calculus

    NASA Astrophysics Data System (ADS)

    Carrillo-Nuñez, H.; Magnus, Wim; Peeters, F. M.

    2010-09-01

    A simplified quantum mechanical model is developed to investigate quantum transport features such as the electron concentration and the current flowing through a silicon nanowire metal-oxide-semiconductor field-effect transistor (MOSFET). In particular, the electron concentration is extracted from a self-consistent solution of the Schrödinger and Poisson equations as well as the ballistic Boltzmann equation which have been solved by exploiting a nonlinear variational principle within the framework of the generalized local density approximation. A suitable action functional has been minimized and details of the implementation and its numerical minimization are given. The current density and its related current-voltage characteristics are calculated from the one-dimensional ballistic steady-state Boltzmann transport equation which is solved analytically by using the method of characteristic curves. The straightforward implementation, the computational speed and the good qualitative behavior of the transport characteristics observed in our approach make it a promising simulation method for modeling quantum transport in nanowire MOSFETs.

  12. Incorporating Micro-Mechanics Based Damage Models into Earthquake Rupture Simulations

    NASA Astrophysics Data System (ADS)

    Bhat, H.; Rosakis, A.; Sammis, C. G.

    2012-12-01

    The micromechanical damage mechanics formulated by Ashby and Sammis, 1990 and generalized by Deshpande and Evans 2008 has been extended to allow for a more generalized stress state and to incorporate an experimentally motivated new crack growth (damage evolution) law that is valid over a wide range of loading rates. This law is sensitive to both the crack tip stress field and its time derivative. Incorporating this feature produces additional strain-rate sensitivity in the constitutive response. The model is also experimentally verified by predicting the failure strength of Dionysus-Pentelicon marble over a wide range of strain rates. Model parameters determined from quasi-static experiments were used to predict the failure strength at higher loading rates. Agreement with experimental results was excellent. After this verification step the constitutive law was incorporated into a Finite Element Code focused on simulating dynamic earthquake ruptures with specific focus on the ends of the fault (fault tip process zone) and the resulting strong ground motion radiation was studied.

  13. On the applicability of STDP-based learning mechanisms to spiking neuron network models

    NASA Astrophysics Data System (ADS)

    Sboev, A.; Vlasov, D.; Serenko, A.; Rybka, R.; Moloshnikov, I.

    2016-11-01

    The ways to creating practically effective method for spiking neuron networks learning, that would be appropriate for implementing in neuromorphic hardware and at the same time based on the biologically plausible plasticity rules, namely, on STDP, are discussed. The influence of the amount of correlation between input and output spike trains on the learnability by different STDP rules is evaluated. A usability of alternative combined learning schemes, involving artificial and spiking neuron models is demonstrated on the iris benchmark task and on the practical task of gender recognition.

  14. Detailed numerical investigation of the dissipative stochastic mechanics based neuron model.

    PubMed

    Güler, Marifi

    2008-10-01

    Recently, a physical approach for the description of neuronal dynamics under the influence of ion channel noise was proposed in the realm of dissipative stochastic mechanics (Güler, Phys Rev E 76:041918, 2007). Led by the presence of a multiple number of gates in an ion channel, the approach establishes a viewpoint that ion channels are exposed to two kinds of noise: the intrinsic noise, associated with the stochasticity in the movement of gating particles between the inner and the outer faces of the membrane, and the topological noise, associated with the uncertainty in accessing the permissible topological states of open gates. Renormalizations of the membrane capacitance and of a membrane voltage dependent potential function were found to arise from the mutual interaction of the two noisy systems. The formalism therein was scrutinized using a special membrane with some tailored properties giving the Rose-Hindmarsh dynamics in the deterministic limit. In this paper, the resultant computational neuron model of the above approach is investigated in detail numerically for its dynamics using time-independent input currents. The following are the major findings obtained. The intrinsic noise gives rise to two significant coexisting effects: it initiates spiking activity even in some range of input currents for which the corresponding deterministic model is quiet and causes bursting in some other range of input currents for which the deterministic model fires tonically. The renormalization corrections are found to augment the above behavioral transitions from quiescence to spiking and from tonic firing to bursting, and, therefore, the bursting activity is found to take place in a wider range of input currents for larger values of the correction coefficients. Some findings concerning the diffusive behavior in the voltage space are also reported.

  15. Mechanics of non-critical fold-thrust belts based on finite element models

    NASA Astrophysics Data System (ADS)

    Simpson, Guy

    2011-03-01

    The mechanics of fold-thrust belts and accretionary wedges is investigated using a two dimensional, plane strain, elastic-plastic (cohesive Mohr-Coulomb) mechanical model solved with the Finite Element Method. Results show that when a layer with an initially non-critical geometry is compressed from the rear, it does not form a wedge that is at failure throughout, as assumed in critical wedge theory. Rather, the wedge consists of narrow plastic shear zones that propagate sequentially outward with time, loading rocks ahead while unloading rocks behind. Not only are stress states within the wedge not everywhere at failure but principal stress orientations vary strongly in time and space, particularly across shear zones, near the basal detachment and in the hanging wall of active structures, where local surface extension may be observed. The reason the investigated wedges are not stressed to compressive failure throughout is related to strength reduction associated with strain localisation that enables material outside shear zones to unload and return to an elastic stress state. This mechanism is intrinsic to elastic-plastic materials and occurs regardless of any material degradation such as loss of cohesion. Even though the stress state of the investigated wedges is generally non-critical, the overall geometry may still be consistent with cohesionless critical wedge theory, since the local surface slope is created when a particular part of the wedge is at a limit state. Prowedge tapers display non self-similar growth through time but eventually evolve to the minimum critical taper. Retrowedges on the other hand, may get caught within this initial transient state and thus may have tapers anywhere between the minimum and maximum critical taper. However, if the basal detachment is such that lateral propagation is not kinematically inhibited, retrowedges are shown to also eventually evolve towards minimum critical tapers, resulting in a symmetrical doubly-vergent orogen

  16. Modelling Cochlear Mechanics

    PubMed Central

    Elliott, Stephen J.; Teal, Paul D.

    2014-01-01

    The cochlea plays a crucial role in mammal hearing. The basic function of the cochlea is to map sounds of different frequencies onto corresponding characteristic positions on the basilar membrane (BM). Sounds enter the fluid-filled cochlea and cause deflection of the BM due to pressure differences between the cochlear fluid chambers. These deflections travel along the cochlea, increasing in amplitude, until a frequency-dependent characteristic position and then decay away rapidly. The hair cells can detect these deflections and encode them as neural signals. Modelling the mechanics of the cochlea is of help in interpreting experimental observations and also can provide predictions of the results of experiments that cannot currently be performed due to technical limitations. This paper focuses on reviewing the numerical modelling of the mechanical and electrical processes in the cochlea, which include fluid coupling, micromechanics, the cochlear amplifier, nonlinearity, and electrical coupling. PMID:25136555

  17. A cell-based computational model of early embryogenesis coupling mechanical behaviour and gene regulation

    PubMed Central

    Delile, Julien; Herrmann, Matthieu; Peyriéras, Nadine; Doursat, René

    2017-01-01

    The study of multicellular development is grounded in two complementary domains: cell biomechanics, which examines how physical forces shape the embryo, and genetic regulation and molecular signalling, which concern how cells determine their states and behaviours. Integrating both sides into a unified framework is crucial to fully understand the self-organized dynamics of morphogenesis. Here we introduce MecaGen, an integrative modelling platform enabling the hypothesis-driven simulation of these dual processes via the coupling between mechanical and chemical variables. Our approach relies upon a minimal ‘cell behaviour ontology' comprising mesenchymal and epithelial cells and their associated behaviours. MecaGen enables the specification and control of complex collective movements in 3D space through a biologically relevant gene regulatory network and parameter space exploration. Three case studies investigating pattern formation, epithelial differentiation and tissue tectonics in zebrafish early embryogenesis, the latter with quantitative comparison to live imaging data, demonstrate the validity and usefulness of our framework. PMID:28112150

  18. Mechanical modeling of cholesterol crystallization in atherosclerotic plaques base on Micro-OCT images (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Luo, Yuemei; Liu, Xinyu; Chen, Si; Cui, Dongyao; Wang, Xianghong; Liu, Linbo

    2016-02-01

    Plaque rupture is the critical cause of cardiovascular thrombosis but this process is still under discussion. Recent studies show that, during crystallization, cholesterol crystals in atheromatous plaques accumulate rapidly in a limited space and may result in plaque rupture. However, the actual role of cholesterol crystals on plaque rupture remains unclear due to the lack of detailed morphological information of cholesterol crystals. In this study, we used a Micro-optical coherence tomography (µOCT) setup with 1-2 µm spatial resolution to extract the geometry of cholesterol crystals from human atherosclerotic artery ex vivo firstly. With measured dimensions of cholesterol crystals by this µOCT system (the average length and thickness of 269.1±80.16 µm and 3.0±0.33 µm), we developed a two-dimensional mechanical model in which rectangular shaped cholesterol crystals distribute at different locations spatially. We predicted the stress on the thin cap induced by the expansion of cholesterol crystals by use of finite-element method. Since a large portion of plaques (58%) rupture at points of peak circumferential stress (PCS), we used PCS as the primary indicator of plaque stability with blood pressure of 14.6 kPa on the lumen. The results demonstrate that loading of the concentrated crystals especially at the cap shoulder destabilize the plaque by proportionally increasing the PCS, while evenly distributed crystals loading along the cap might impose less PCS to the plaque than the concentrated case.

  19. Actin-based gravity-sensing mechanisms in unicellular plant model systems

    NASA Astrophysics Data System (ADS)

    Braun, Markus; Limbach, Christoph

    2005-08-01

    Considerable progress has been made in the understanding of the molecular and cellular mechanisms underlying gravity sensing and gravity-oriented polarized growth in single-celled rhizoids and protonemata of the characean algae. It is well known that the actin cytoskeleton plays a key role in these processes. Numerous actin-binding proteins control apical actin polymerization and the dynamic remodeling of the actin arrangement. An actomyosin-based system mediates the delivery and incorporation of secretory vesicles at the growing tip and coordinates the tip-high gradient of cytoplasmic free calcium which is required for local exocytosis. Additionally, the actomyosin system precisely controls the position of statoliths and, upon a change in orientation relative to the gravity vector, directs sedimenting statoliths to the confined graviperception sites of the plasma membrane where gravitropic signalling is initiated. The upward growth response of protonemata is preceded by an actin-dependent relocalization of the Ca2+-gradient to the upper flank. The downward growth response of rhizoids, however, is caused by differential growth of the opposite flankes due to a local reduction of cytoplasmic free calcium limited to the plasma membrane area where statoliths are sedimented. Thus, constant actin polymerization in the growing tip and the spatiotemporal control of actin remodeling are essential for gravity sensing and gravity-oriented polarized growth of characean rhizoids and protonemata.

  20. Microseismic forward modeling based on different focal mechanisms used by the seismic moment tensor and elastic wave equation

    NASA Astrophysics Data System (ADS)

    Li, Huijian; Wang, Runqiu; Cao, Siyuan

    2015-04-01

    The source mechanisms of microseismics in hydraulic fracturing present guiding significance to the research on source types, crustal stress analysis and crack prediction. Numerical simulations based on various source mechanisms can be used to investigate the stress characteristics and response characteristics of different source types. In this paper, a method based on the seismic moment tensor (SMT) and elastic wave equation (EWE) was presented for forward modeling. Additionally, we have given the expressions of nine couples of force which can be combined into different kinds of source types. The calculations of wave fields and records with three basic types of sources showed the features in homogeneous isotropic and anisotropic media by the finite-difference (FD) method. Lastly, analysis of the relationship between the polarizing angle and incident angle provided us with some evidence to distinguish the type of media in single media. The work offers methods of instruction for identification and interpretation in microseismic monitoring.

  1. Mechanisms and Modelling of Environment-Dependent Fatigue Crack Growth in a Nickel Based Superalloy

    DTIC Science & Technology

    1991-12-12

    controlling mechanisms of this environment-dependent crack growth stage in Alloy 718 in order to develop the ability to predict the crack growth performance...stage crack-tip oxidation mechanism. According to this mechanism, the oxygen partial pressure controls the preferential formation of the oxide layers at...network. The reduction in grain boundary ductility due to oxidation is balanced by considering the effective strain at the crack tip resulting from

  2. Identification and design of novel polymer-based mechanical transducers: A nano-structural model for thin film indentation

    NASA Astrophysics Data System (ADS)

    Villanueva, Joshua; Huang, Qian; Sirbuly, Donald J.

    2014-09-01

    Mechanical characterization is important for understanding small-scale systems and developing devices, particularly at the interface of biology, medicine, and nanotechnology. Yet, monitoring sub-surface forces is challenging with current technologies like atomic force microscopes (AFMs) or optical tweezers due to their probe sizes and sophisticated feedback mechanisms. An alternative transducer design relying on the indentation mechanics of a compressible thin polymer would be an ideal system for more compact and versatile probes, facilitating measurements in situ or in vivo. However, application-specific tuning of a polymer's mechanical properties can be burdensome via experimental optimization. Therefore, efficient transducer design requires a fundamental understanding of how synthetic parameters such as the molecular weight and grafting density influence the bulk material properties that determine the force response. In this work, we apply molecular-level polymer scaling laws to a first order elastic foundation model, relating the conformational state of individual polymer chains to the macroscopic compression of thin film systems. A parameter sweep analysis was conducted to observe predicted model trends under various system conditions and to understand how nano-structural elements influence the material stiffness. We validate the model by comparing predicted force profiles to experimental AFM curves for a real polymer system and show that it has reasonable predictive power for initial estimates of the force response, displaying excellent agreement with experimental force curves. We also present an analysis of the force sensitivity of an example transducer system to demonstrate identification of synthetic protocols based on desired mechanical properties. These results highlight the usefulness of this simple model as an aid for the design of a new class of compact and tunable nanomechanical force transducers.

  3. Identification and design of novel polymer-based mechanical transducers: A nano-structural model for thin film indentation

    SciTech Connect

    Villanueva, Joshua; Huang, Qian; Sirbuly, Donald J.

    2014-09-14

    Mechanical characterization is important for understanding small-scale systems and developing devices, particularly at the interface of biology, medicine, and nanotechnology. Yet, monitoring sub-surface forces is challenging with current technologies like atomic force microscopes (AFMs) or optical tweezers due to their probe sizes and sophisticated feedback mechanisms. An alternative transducer design relying on the indentation mechanics of a compressible thin polymer would be an ideal system for more compact and versatile probes, facilitating measurements in situ or in vivo. However, application-specific tuning of a polymer's mechanical properties can be burdensome via experimental optimization. Therefore, efficient transducer design requires a fundamental understanding of how synthetic parameters such as the molecular weight and grafting density influence the bulk material properties that determine the force response. In this work, we apply molecular-level polymer scaling laws to a first order elastic foundation model, relating the conformational state of individual polymer chains to the macroscopic compression of thin film systems. A parameter sweep analysis was conducted to observe predicted model trends under various system conditions and to understand how nano-structural elements influence the material stiffness. We validate the model by comparing predicted force profiles to experimental AFM curves for a real polymer system and show that it has reasonable predictive power for initial estimates of the force response, displaying excellent agreement with experimental force curves. We also present an analysis of the force sensitivity of an example transducer system to demonstrate identification of synthetic protocols based on desired mechanical properties. These results highlight the usefulness of this simple model as an aid for the design of a new class of compact and tunable nanomechanical force transducers.

  4. An agent-based model for elasto-plastic mechanical interactions between cells, basement membrane and extracellular matrix.

    PubMed

    D'Antonio, Gianluca; Macklin, Paul; Preziosi, Luigi

    2013-02-01

    The basement membrane (BM) and extracellular matrix (ECM) play critical roles in developmental and cancer biology, and are of great interest in biomathematics. We introduce a model of mechanical cell-BM-ECM interactions that extends current (visco)elastic models (e.g. [8,16]), and connects to recent agent-based cell models (e.g. [2,3,20,26]). We model the BM as a linked series of Hookean springs, each with time-varying length, thickness, and spring constant. Each BM spring node exchanges adhesive and repulsive forces with the cell agents using potential functions. We model elastic BM-ECM interactions with analogous ECM springs. We introduce a new model of plastic BM and ECM reorganization in response to prolonged strains, and new constitutive relations that incorporate molecular-scale effects of plasticity into the spring constants. We find that varying the balance of BM and ECM elasticity alters the node spacing along cell boundaries, yielding a nonuniform BM thickness. Uneven node spacing generates stresses that are relieved by plasticity over long times. We find that elasto-viscoplastic cell shape response is critical to relieving uneven stresses in the BM. Our modeling advances and results highlight the importance of rigorously modeling of cell-BM-ECM interactions in clinically important conditions with significant membrane deformations and time-varying membrane properties, such as aneurysms and progression from in situ to invasive carcinoma.

  5. Agent-based modeling traction force mediated compaction of cell-populated collagen gels using physically realistic fibril mechanics.

    PubMed

    Reinhardt, James W; Gooch, Keith J

    2014-02-01

    Agent-based modeling was used to model collagen fibrils, composed of a string of nodes serially connected by links that act as Hookean springs. Bending mechanics are implemented as torsional springs that act upon each set of three serially connected nodes as a linear function of angular deflection about the central node. These fibrils were evaluated under conditions that simulated axial extension, simple three-point bending and an end-loaded cantilever. The deformation of fibrils under axial loading varied <0.001% from the analytical solution for linearly elastic fibrils. For fibrils between 100 μm and 200 μm in length experiencing small deflections, differences between simulated deflections and their analytical solutions were <1% for fibrils experiencing three-point bending and <7% for fibrils experiencing cantilever bending. When these new rules for fibril mechanics were introduced into a model that allowed for cross-linking of fibrils to form a network and the application of cell traction force, the fibrous network underwent macroscopic compaction and aligned between cells. Further, fibril density increased between cells to a greater extent than that observed macroscopically and appeared similar to matrical tracks that have been observed experimentally in cell-populated collagen gels. This behavior is consistent with observations in previous versions of the model that did not allow for the physically realistic simulation of fibril mechanics. The significance of the torsional spring constant value was then explored to determine its impact on remodeling of the simulated fibrous network. Although a stronger torsional spring constant reduced the degree of quantitative remodeling that occurred, the inclusion of torsional springs in the model was not necessary for the model to reproduce key qualitative aspects of remodeling, indicating that the presence of Hookean springs is essential for this behavior. These results suggest that traction force mediated matrix

  6. Electrophilic assistance to the cleavage of an RNA model phopshodiester via specific and general base-catalyzed mechanisms.

    PubMed

    Corona-Martínez, David Octavio; Gomez-Tagle, Paola; Yatsimirsky, Anatoly K

    2012-10-19

    Kinetics of transesterification of the RNA model substrate 2-hydroxypropyl 4-nitrophenyl phosphate promoted by Mg(2+) and Ca(2+), the most common biological metals acting as cofactors for nuclease enzymes and ribozymes, as well as by Co(NH(3))(6)(3+), Co(en)(3)(3+), Li(+), and Na(+) cations, often employed as mechanistic probes, was studied in 80% v/v (50 mol %) aqueous DMSO, a medium that allows one to discriminate easily specific base (OH(-)-catalyzed) and general base (buffer-catalyzed) reaction paths. All cations assist the specific base reaction, but only Mg(2+) and Na(+) assist the general base reaction. For Mg(2+)-assisted reactions, the solvent deuterium isotope effects are 1.23 and 0.25 for general base and specific base mechanisms, respectively. Rate constants for Mg(2+)-assisted general base reactions measured with different bases fit the Brønsted correlation with a slope of 0.38, significantly lower than the slope for the unassisted general base reaction (0.77). Transition state binding constants for catalysts in the specific base reaction (K(‡)(OH)) both in aqueous DMSO and pure water correlate with their binding constants to 4-nitrophenyl phosphate dianion (K(NPP)) used as a minimalist transition state model. It was found that K(‡)(OH) ≈ K(NPP) for "protic" catalysts (Co(NH(3))(6)(3+), Co(en)(3)(3+), guanidinium), but K(‡)(OH) ≫ K(NPP) for Mg(2+) and Ca(2+) acting as Lewis acids. It appears from results of this study that Mg(2+) is unique in its ability to assist efficiently the general base-catalyzed transesterification often occurring in active sites of nuclease enzymes and ribozymes.

  7. A physically-based continuum damage mechanics model for numerical prediction of damage growth in laminated composite plates

    NASA Astrophysics Data System (ADS)

    Williams, Kevin Vaughan

    Rapid growth in use of composite materials in structural applications drives the need for a more detailed understanding of damage tolerant and damage resistant design. Current analytical techniques provide sufficient understanding and predictive capabilities for application in preliminary design, but current numerical models applicable to composites are few and far between and their development into well tested, rigorous material models is currently one of the most challenging fields in composite materials. The present work focuses on the development, implementation, and verification of a plane-stress continuum damage mechanics based model for composite materials. A physical treatment of damage growth based on the extensive body of experimental literature on the subject is combined with the mathematical rigour of a continuum damage mechanics description to form the foundation of the model. The model has been implemented in the LS-DYNA3D commercial finite element hydrocode and the results of the application of the model are shown to be physically meaningful and accurate. Furthermore it is demonstrated that the material characterization parameters can be extracted from the results of standard test methodologies for which a large body of published data already exists for many materials. Two case studies are undertaken to verify the model by comparison with measured experimental data. The first series of analyses demonstrate the ability of the model to predict the extent and growth of damage in T800/3900-2 carbon fibre reinforced polymer (CFRP) plates subjected to normal impacts over a range of impact energy levels. The predicted force-time and force-displacement response of the panels compare well with experimental measurements. The damage growth and stiffness reduction properties of the T800/3900-2 CFRP are derived using published data from a variety of sources without the need for parametric studies. To further demonstrate the physical nature of the model, a IM6

  8. From Agents to Continuous Change via Aesthetics: Learning Mechanics with Visual Agent-Based Computational Modeling

    ERIC Educational Resources Information Center

    Sengupta, Pratim; Farris, Amy Voss; Wright, Mason

    2012-01-01

    Novice learners find motion as a continuous process of change challenging to understand. In this paper, we present a pedagogical approach based on agent-based, visual programming to address this issue. Integrating agent-based programming, in particular, Logo programming, with curricular science has been shown to be challenging in previous research…

  9. A piezoelectric six-DOF vibration energy harvester based on parallel mechanism: dynamic modeling, simulation, and experiment

    NASA Astrophysics Data System (ADS)

    Yuan, G.; Wang, D. H.

    2017-03-01

    Multi-directional and multi-degree-of-freedom (multi-DOF) vibration energy harvesting are attracting more and more research interest in recent years. In this paper, the principle of a piezoelectric six-DOF vibration energy harvester based on parallel mechanism is proposed to convert the energy of the six-DOF vibration to single-DOF vibrations of the limbs on the energy harvester and output voltages. The dynamic model of the piezoelectric six-DOF vibration energy harvester is established to estimate the vibrations of the limbs. On this basis, a Stewart-type piezoelectric six-DOF vibration energy harvester is developed and explored. In order to validate the established dynamic model and the analysis results, the simulation model of the Stewart-type piezoelectric six-DOF vibration energy harvester is built and tested with different vibration excitations by SimMechanics, and some preliminary experiments are carried out. The results show that the vibration of the limbs on the piezoelectric six-DOF vibration energy harvester can be estimated by the established dynamic model. The developed Stewart-type piezoelectric six-DOF vibration energy harvester can harvest the energy of multi-directional linear vibration and multi-axis rotating vibration with resonance frequencies of 17 Hz, 25 Hz, and 47 Hz. Moreover, the resonance frequencies of the developed piezoelectric six-DOF vibration energy harvester are not affected by the direction changing of the vibration excitation.

  10. Development of a physiologically based pharmacokinetic/pharmacodynamic model to identify mechanisms contributing to entacapone low bioavailability.

    PubMed

    Alqahtani, Saeed; Kaddoumi, Amal

    2015-12-01

    Entacapone is an inhibitor of catechol-O-methyltransferase (COMT) and is being used to extend the therapeutic effect of levodopa in patients with advanced and fluctuating Parkinson's disease. Entacapone has low and variable oral bioavailability and the underlying mechanism(s) for this behavior have not been studied. To explain such behavior and to characterize the dynamic changes in the metabolism of entacapone, a physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) model was developed integrating in silico, in vitro and in vivo pharmacokinetic data. The model was developed and verified in healthy volunteers and subsequently expanded to predict the pharmacokinetic parameters of entacapone phosphate, a prodrug of entacapone, and to assess the impact of hepatic impairment on the pharmacokinetics of entacapone. Low and inter-individual variability in bioavailability could be attributed to the extensive first-pass metabolism by UGTs in the liver and, to a lesser extent, the small intestine. The predictive performance of this model was acceptable with predicted Cmax , AUC and PD parameters lying within 20% of the observed data. The model indicates that the low bioavailability could be attributed to the extensive first-pass effect of entacapone.

  11. Confocal microscopy-based three-dimensional cell-specific modeling for large deformation analyses in cellular mechanics.

    PubMed

    Slomka, Noa; Gefen, Amit

    2010-06-18

    This study introduces a new confocal microscopy-based three-dimensional cell-specific finite element (FE) modeling methodology for simulating cellular mechanics experiments involving large cell deformations. Three-dimensional FE models of undifferentiated skeletal muscle cells were developed by scanning C2C12 myoblasts using a confocal microscope, and then building FE model geometries from the z-stack images. Strain magnitudes and distributions in two cells were studied when the cells were subjected to compression and stretching, which are used in pressure ulcer and deep tissue injury research to induce large cell deformations. Localized plasma membrane and nuclear surface area (NSA) stretches were observed for both the cell compression and stretching simulation configurations. It was found that in order to induce large tensile strains (>5%) in the plasma membrane and NSA, one needs to apply more than approximately 15% of global cell deformation in cell compression tests, or more than approximately 3% of tensile strains in the elastic plate substrate in cell stretching experiments. Utilization of our modeling can substantially enrich experimental cellular mechanics studies in classic cell loading designs that typically involve large cell deformations, such as static and cyclic stretching, cell compression, micropipette aspiration, shear flow and hydrostatic pressure, by providing magnitudes and distributions of the localized cellular strains specific to each setup and cell type, which could then be associated with the applied stimuli.

  12. Radiation and mechanical unloading effects on mouse vertebral bone: Ground-based models of the spaceflight environment

    NASA Astrophysics Data System (ADS)

    Alwood, Joshua Stewart

    Astronauts on long-duration space missions experience increased ionizing radiation background levels and occasional acute doses of ionizing radiation from solar particle events, in addition to biological challenges introduced by weightlessness. Previous research indicates that cancer radiotherapy damages bone marrow cell populations and reduces mechanical strength of bone. However, the cumulative doses in radiotherapy are an order of magnitude or greater than dose predictions for long-duration space missions. Further detriments to the skeletal system are the disuse and mechanical unloading experienced during weightlessness, which causes osteopenia in weight-bearing cancellous bone (a sponge-like bony network of rods, plates and voids) and cortical bone (dense, compact bone). Studies of radiation exposure utilizing spaceflight-relevant types and doses, and in combination with mechanical unloading, have received little attention. Motivated by the future human exploration of the solar system, the effects of acute and increased background radiation on astronaut skeletal health are important areas of study in order to prevent osteopenic deterioration and, ultimately, skeletal fracture. This dissertation addresses how spaceflight-relevant radiation affects bone microarchitecture and mechanical properties in the cancellous-rich vertebrae and compares results to that of mechanical unloading. In addition, a period of re-ambulation is used to test whether animals recover skeletal tissue after irradiation. Whether radiation exposure displays synergism with mechanical unloading is further investigated. Finite element structural and statistical analyses are used to investigate how changes in architecture affect mechanical stress within the vertebra and to interpret the mechanical testing results. In this dissertation, ground-based models provide evidence that ionizing radiation, both highly energetic gamma-rays and charged iron ions, resulted in a persistent loss of cancellous

  13. A Physically-Based and Distributed Tool for Modeling the Hydrological and Mechanical Processes of Shallow Landslides

    NASA Astrophysics Data System (ADS)

    Arnone, E.; Noto, L. V.; Dialynas, Y. G.; Caracciolo, D.; Bras, R. L.

    2015-12-01

    This work presents the capabilities of a model, i.e. the tRIBS-VEGGIE-Landslide, in two different versions, i.e. developed within a probabilistic framework and coupled with a root cohesion module. The probabilistic model treats geotechnical and soil retention curve parameters as random variables across the basin and estimates theoretical probability distributions of slope stability and the associated "factor of safety" commonly used to describe the occurrence of shallow landslides. The derived distributions are used to obtain the spatio-temporal dynamics of probability of failure, conditioned on soil moisture dynamics at each watershed location. The framework has been tested in the Luquillo Experimental Forest (Puerto Rico) where shallow landslides are common. In particular, the methodology was used to evaluate how the spatial and temporal patterns of precipitation, whose variability is significant over the basin, affect the distribution of probability of failure. Another version of the model accounts for the additional cohesion exerted by vegetation roots. The approach is to use the Fiber Bundle Model (FBM) framework that allows for the evaluation of the root strength as a function of the stress-strain relationships of bundles of fibers. The model requires the knowledge of the root architecture to evaluate the additional reinforcement from each root diameter class. The root architecture is represented with a branching topology model based on Leonardo's rule. The methodology has been tested on a simple case study to explore the role of both hydrological and mechanical root effects. Results demonstrate that the effects of root water uptake can at times be more significant than the mechanical reinforcement; and that the additional resistance provided by roots depends heavily on the vegetation root structure and length.

  14. A model-based observer for state and stress estimation in structural and mechanical systems: Experimental validation

    NASA Astrophysics Data System (ADS)

    Erazo, Kalil; Hernandez, Eric M.

    2014-02-01

    In this paper we present the results from a validation study of a recently proposed model-based state observer for structural and mechanical systems. The observer uses a finite element model of the structure and noise contaminated measurements to estimate the state and stress time histories at arbitrary locations in the structure of interest. The initial conditions and unknown excitations are described by random vectors and random processes with known covariance and power spectral density. A laboratory model consisting of an aluminum cantilever beam was used to perform the experiment. Two types of loading conditions were tested: an impact hammer test and a band limited excitation delivered through a shaker. The results obtained with the proposed observer are compared to the measured stress at the locations of interest, and to estimates obtained using well-established estimation methods such as Luenberger observers and the Kalman filter. The main finding is that for all experiments conducted the proposed model-based observer yielded estimates with higher or comparable accuracy to all other methods considered, with the advantage of requiring significantly less computational effort and with a more direct and transparent implementation.

  15. Mechanics and hydraulics of unsaturated soils: what makes interfaces an indispensable part of a physically-based model

    NASA Astrophysics Data System (ADS)

    Nikooee, E.; Hassanizadeh, S. M.

    2014-12-01

    The foundations of the current theories for hydraulics and mechanics of unsaturated soils have been mainly based on the empirically introduced equations. There are various characteristics of unsaturated soils for which lots of different empirical equations have been proposed such as hydraulic conductivity, water retention curve, and effective stress parameter. One of the remarkable challenges which all current models face is hysteresis, i.e., for a certain matric suction, values of saturation, hydraulic conductivity and effective stress parameter in drying state and wetting are different. Conventional models of hydraulic and mechanical behaviour of unsaturated soils try to account for the hysteresis phenomenon by means of different empirical equations for each hydraulic path. Hassanizadeh and Gray (1993) claimed that the hysteresis in capillary pressure-saturation curves can be modelled through the inclusion of air-water interfaces as a new independent variable [1]. It has recently been stated that the same conjecture can be made for suction stress [2]. Therefore, it seems to better portray hydraulic and mechanical behaviour of unsaturated soils, interfaces are required as an indispensable part of the framework [3, 4]. This presentation aims at introducing the drawbacks of current theories of hydraulics and mechanics of unsaturated soils. For this purpose, the role of interfaces in the mechanics and hydraulics of unsaturated soils is explained and different possibilities to account for the contribution of interfaces are discussed. Finally, current challenges and future research directions are set forth. References[1] Hassanizadeh, S.M. & Gray, W.G.: Thermodynamic basis of capillary pressure in porous media. Water Resour.Res. 29(1993), 3389-3405.[2] Nikooee, E., Habibagahi, G., Hassanizadeh, S.M. & Ghahramani, A.: Effective Stress in unsaturated Soils: a thermodynamic approach based on the interfacial energy and hydromechanical coupling. Transport porous Med. 96

  16. Tuned and Balanced Redistributed Charge Scheme for Combined Quantum Mechanical and Molecular Mechanical (QM/MM) Methods and Fragment Methods: Tuning Based on the CM5 Charge Model.

    PubMed

    Wang, Bo; Truhlar, Donald G

    2013-02-12

    Tuned and balanced redistributed charge schemes have been developed for modeling the electrostatic fields of bonds that are cut by a quantum mechanical-molecular mechanical boundary in combined quantum mechanical and molecular mechanical (QM/MM) methods. First, the charge is balanced by adjusting the charge on the MM boundary atom to conserve the total charge of the entire QM/MM system. In the balanced smeared redistributed charge (BSRC) scheme, the adjusted MM boundary charge is smeared with a smearing width of 1.0 Å and is distributed in equal portions to the midpoints of the bonds between the MM boundary atom and the MM atoms bonded to it; in the balanced redistributed charge-2 (BRC2) scheme, the adjusted MM boundary charge is distributed as point charges in equal portions to the MM atoms that are bonded to the MM boundary atom. The QM subsystem is capped by a fluorine atom that is tuned to reproduce the sum of partial atomic charges of the uncapped portion of the QM subsystem. The new aspect of the present study is a new way to carry out the tuning process; in particular, the CM5 charge model, rather than the Mulliken population analysis applied in previous studies, is used for tuning the capping atom that terminates the dangling bond of the QM region. The mean unsigned error (MUE) of the QM/MM deprotonation energy for a 15-system test suite of deprotonation reactions is 2.3 kcal/mol for the tuned BSRC scheme (TBSRC) and 2.4 kcal/mol for the tuned BRC2 scheme (TBRC2). As was the case for the original tuning method based on Mulliken charges, the new tuning method performs much better than using conventional hydrogen link atoms, which have an MUE on this test set of about 7 kcal/mol. However, the new scheme eliminates the need to use small basis sets, which can be problematic, and it allows one to be more consistent by tuning the parameters with whatever basis set is appropriate for applications. (Alternatively, since the tuning parameters and partial charges

  17. Thermo-hydro-mechanical modeling and analysis of cement-based energy storages for small-scale dwellings

    NASA Astrophysics Data System (ADS)

    Hailemariam, Henok; Wuttke, Frank

    2016-04-01

    One of the common technologies for balancing the energy demand and supply in district heating, domestic hot water production, thermal power plants and thermal process industries in general is thermal energy storage. Thermal energy storage, in particular sensible heat storage as compared to latent heat storage and thermo-chemical storage, has recently gained much interest in the renewable energy storage sector due to its comparatively low cost and technical development. Sensible heat storages work on the principle of storing thermal energy by raising or lowering the temperature of liquid (commonly water) or solid media, and do not involve material phase change or conversion of thermal energy by chemical reactions or adsorption processes as in latent heat and thermo-chemical storages, respectively. In this study, the coupled thermo-hydro-mechanical behaviour of a cement-based thermal energy storage system for domestic applications has been modeled in both saturated as well as unsaturated conditions using the Finite Element method along with an extensive experimental analysis program for parameter detection. For this purpose, a prototype model is used with three well-known thermal energy storage materials, and the temperature and heat distribution of the system were investigated under specific thermo-hydro-mechanical conditions. Thermal energy samples with controlled water to solids ratio and stored in water for up to 28 days were used for the experimental program. The determination of parameters included: thermal conductivity, specific heat capacity and linear coefficient of thermal expansion (CTE) using a transient line-source measurement technique as well as a steady-state thermal conductivity and expansion meter; mechanical strength parameters such as uni-axial strength, young's modulus of elasticity, poisson's ratio and shear parameters using uniaxial, oedometer and triaxial tests; and hydraulic properties such as hydraulic permeability or conductivity under

  18. Multiscale modelling of DNA mechanics

    NASA Astrophysics Data System (ADS)

    Dršata, Tomáš; Lankaš, Filip

    2015-08-01

    Mechanical properties of DNA are important not only in a wide range of biological processes but also in the emerging field of DNA nanotechnology. We review some of the recent developments in modeling these properties, emphasizing the multiscale nature of the problem. Modern atomic resolution, explicit solvent molecular dynamics simulations have contributed to our understanding of DNA fine structure and conformational polymorphism. These simulations may serve as data sources to parameterize rigid base models which themselves have undergone major development. A consistent buildup of larger entities involving multiple rigid bases enables us to describe DNA at more global scales. Free energy methods to impose large strains on DNA, as well as bead models and other approaches, are also briefly discussed.

  19. Understanding Evapotranspiration Trends and their Driving Mechanisms: An investigation across CONUS based on numerical modeling

    NASA Astrophysics Data System (ADS)

    Parr, D.; Wang, G.; Fu, C.

    2015-12-01

    As shown by climate models, increasing global temperatures and enhanced greenhouse gas concentration such as CO2 have had major effects on the dynamics of the hydrologic cycle and the surface energy budget, in particular, on evapotranspiration (ET). ET has significant decadal variations whether it be regionally or globally and variations of ET have major environmental and socioeconomic impacts. A number of recent studies have found a global increase in annual mean ET around 7mm per year per decade from about 1982 to the late 1990s. These results correspond with what is expected from an intensification of the hydrological cycle. However, the increasing ET trend did not continue after 1998 and from 1998-2008 this global trend was replaced with a decreasing trend of similar magnitude. This study uses numerical modeling to investigate if similar changing ET trends emerge in the continental U.S and part of northern Mexico. After validating model simulated evaporative fluxes and comparing spatial patterns to the aforementioned studies, various changing trends of different signs are identified across the U.S., and specific regions with strong signals of change are chosen for further examination with the purpose of identifying the root causes of these changing trends and which variables are most influential towards change. Experimental simulations conducted to isolate the most influential factors towards ET reveal that precipitation amount as well as its characteristics have the greatest impact on the ET trends discovered, with other factors like wind and air temperatures displaying less influence over inter-annual trends. This study helps better understand terrestrial ET and it's interactions which will help facilitate better predictions of change in surface climate such as heatwaves and droughts as well as impacts on water resources.

  20. Progress in Polarimetric Modeling of Comet Dust Based on its Mechanical Characteristics

    NASA Astrophysics Data System (ADS)

    Kolokolova, Lioudmila; Skorov, Yuri; Blum, Jürgen; Schmidt, Heinrich

    2013-04-01

    Model of comet dust as aggregates of submicron particles (monomers) has proved its reliability by providing a good qualitative fit to the observational data in the visible, near- and thermal infrared. Especially sensitive to the dust properties appeared to be polarization of the scattered light. It provides helpful information concerning structural characteristics of aggregates especially if we combine polarimetric data in the visible and near-infrared. Using Multiple Sphere T-Matrix code (MSTM)by Mackowski and Mishchenko (JQSRT, 112, 2182, 2011) we simulated light scattering by ballistic particle-cluster (BPCA) and cluster-cluster (BCCA) aggregates. It was found that the dependence of polarization on phase angle and wavelength changes significantly at changes in aggregate porosity and size. Comparison with the cometary observations allowed narrowing down the range of porosity of comet dust particles. It was shown that in the case of aggregates made of identical spherical monomers a better fit to the observational data can be achieved if we consider aggregates with the porosity intermediate between the porosity of BPCA and BCCA. In this study we explore aggregates of such an intermediate porosity, modeling them as aggregates of polydisperse monomers or as hierarchic aggregates, i.e. particles resulted from agglomeration of small aggregates. These aggregates have been proved to be a good model to reproduce tensile strength of upper layers of cometary nucleus. Their light-scattering, specifically polarimetric, characteristics reveal porosity and structure of the near-nuclear cometary dust. This, in turn, can shed light on the formation of comets.

  1. A mechanism-based binding model for the population pharmacokinetics and pharmacodynamics of omalizumab

    PubMed Central

    Hayashi, Naoto; Tsukamoto, Yuko; Sallas, William M; Lowe, Philip J

    2007-01-01

    Aim Omalizumab, a humanized IgG monoclonal antibody that binds to human immunoglobulin E (IgE), interrupts the allergic cascade in asthmatic patients. The aim was to compare simultaneously drug exposure and IgE biomarker responses in Japanese and White patient populations. Methods An instantaneous equilibrium drug–ligand binding and turnover population model was built from 202 Japanese patients. A posterior predictive evaluation for the steady-state distributions of omalizumab and IgE was then carried out against 531 White patients. Results The mean parameters estimated from the Japanese patients were as follows: omalizumab clearance 7.32 ± 0.153 ml h−1, IgE clearance 71.0 ± 4.68 ml h−1 and the difference between that for omalizumab and the complex 5.86 ± 0.920 ml h−1, the volume of distribution for omalizumab and IgE 5900 ± 107 ml, and that for the complex 3630 ± 223 ml, the rate of IgE production 30.3 ± 2.04 µg h−1. Half-lives of IgG (23 days) and IgE (2.4 days) were close to previous reports. The dissociation constant for binding, 1.07 nM, was similar to in vitro values. Clearance and volume of distribution for omalizumab varied with bodyweight, whereas the clearance and rate of production of IgE were predicted accurately by baseline IgE. Overall, these covariates explained much of the interindividual variability. Conclusions The predictiveness of the Japanese model was confirmed by Monte-Carlo simulations for a White population, also providing evidence that the pharmacokinetics of omalizumab and IgE were similar in these two populations. Furthermore, the model enabled the estimation of not only omalizumab disposition parameters, but also the binding with and the rate of production, distribution and elimination of its target, IgE. PMID:17096680

  2. Interface transferring mechanism and error modification of FRP-OFBG strain sensor based on standard linear viscoelastic model

    NASA Astrophysics Data System (ADS)

    Li, Jilong; Zhou, Zhi; Ou, Jinping

    2006-03-01

    This paper presents the interface transferring mechanism and error modification of the Fiber Reinforced Polymer-Optical Fiber Bragg Grating (FRP-OFBG) sensing tendons, which including GFRP (Glass Fiber Reinforced Polymer) and CFRP (Carbon Fiber Reinforced Polymer), using standard linear viscoelastic model. The optical fiber is made up of glass, quartz or plastic, et al, which creep strain is very small at room temperature. So the tensile creep compliance of optical fiber is independent of time at room temperature. On the other hand, the FRP (GFRP or CFRP) is composed of a kind of polymeric matrix (epoxy resins or the others) with glass, carbon or aramid fibers, which shear creep strain is dependent of time at room temperature. Hence, the standard linear viscoelastic model is employed to describe the shear creep compliance of FRP along the fiber direction. The expression of interface strain transferring mechanism of FRP-OFBG sensors is derived based on the linear viscoelastic theory and the analytic solution of the error rate is given by the inverse Laplace transform. The effects of FRP viscoelasticity on the error rate of FRP-OFBG sensing tendons are included in the above expression. And the transient and steady-state error modified coefficient of FRP-OFBG sensors are obtained using initial value and final value theorems. Finally, a calculated example is given to explain the correct of theoretical prediction.

  3. Automated quantum mechanical total line shape fitting model for quantitative NMR-based profiling of human serum metabolites.

    PubMed

    Mihaleva, Velitchka V; Korhonen, Samuli-Petrus; van Duynhoven, John; Niemitz, Mathias; Vervoort, Jacques; Jacobs, Doris M

    2014-05-01

    An automated quantum mechanical total line shape (QMTLS) fitting model was implemented for quantitative nuclear magnetic resonance (NMR)-based profiling of 42 metabolites in ultrafiltrated human serum samples. Each metabolite was described by a set of chemical shifts, J-couplings, and line widths. These parameters were optimized for each metabolite in each sample by iteratively minimizing the difference between the calculated and the experimental spectrum. In total, 92.0 to 98.1 % of the signal intensities in the experimental spectrum could be explained by the calculated spectrum. The model was validated by comparison to signal integration of metabolites with isolated signals and by means of standard additions. Metabolites present at average concentration higher than 50 μM were quantified with average absolute relative error less than 10 % when using different initial parameters for the fitting procedure. Furthermore, the biological applicability of the QMTLS model was demonstrated on 287 samples from an intervention study in 37 human volunteers undergoing an exercise challenge. Our automated QMTLS model was able to cope with the large dynamic range of metabolite concentrations in serum and proved to be suitable for high-throughput analysis.

  4. Mechanism of contact angle saturation and an energy-based model for electrowetting

    NASA Astrophysics Data System (ADS)

    Rui, Zhao; Zhong-Cheng, Liang

    2016-06-01

    Electrowetting, as a well-known approach to increasing droplet wettability on a solid surface by electrical bias, has broad applications. However, it is limited by contact angle saturation at large voltage. Although several debated hypotheses have been proposed to describe it, the physical origin of contact angle saturation still remains obscure. In this work, the physical factors responsible for the onset of contact angle saturation are explored, and the correlated theoretical models are established to characterize electrowetting behavior. Combination of the proper 3-phase system employed succeeds in dropping the saturating contact angle below 25°, and validates that the contact angle saturation is not a result of device-related imperfection. Project supported by the Fund from the Research Center of Optical Communications Engineering & Technology, Jiangsu Province, China (Grant No. ZSF0402).

  5. AFM-Based Mechanical Nanomanipulation

    NASA Astrophysics Data System (ADS)

    Landolsi, Fakhreddine

    2011-12-01

    Advances in several research areas increase the need for more sophisticated fabrication techniques and better performing materials. Tackling this problem from a bottom-up perspective is currently an active field of research. The bottom-up fabrication procedure offers sub-nanometer accurate manipulation. At this time, candidates to achieve nanomanipulation include chemical (self-assembly), biotechnology methods (DNA-based), or using controllable physical forces (e.g. electrokinetic forces, mechanical forces). In this thesis, new methods and techniques for mechanical nanomanipulation using probe force interaction are developed. The considered probes are commonly used in Atomic Force Microscopes (AFMs) for high resolution imaging. AFM-based mechanical nanomanipulation will enable arranging nanoscale entities such as nanotubes and molecules in a precise and controlled manner to assemble and produce novel devices and systems at the nanoscale. The novelty of this research stems from the development of new modeling of the physics and mechanics of the tip interaction with nanoscale entities, coupled with the development of new smart cantilevers with multiple degrees of freedom. The gained knowledge from the conducted simulations and analysis is expected to enable true precision and repeatability of nanomanipulation tasks which is not feasible with existing methods and technologies.

  6. A tribo-mechanical analysis of PVA-based building-blocks for implementation in a 2-layered skin model.

    PubMed

    Morales Hurtado, M; de Vries, E G; Zeng, X; van der Heide, E

    2016-09-01

    Poly(vinyl) alcohol hydrogel (PVA) is a well-known polymer widely used in the medical field due to its biocompatibility properties and easy manufacturing. In this work, the tribo-mechanical properties of PVA-based blocks are studied to evaluate their suitability as a part of a structure simulating the length scale dependence of human skin. Thus, blocks of pure PVA and PVA mixed with Cellulose (PVA-Cel) were synthesised via freezing/thawing cycles and their mechanical properties were determined by Dynamic Mechanical Analysis (DMA) and creep tests. The dynamic tests addressed to elastic moduli between 38 and 50kPa for the PVA and PVA-Cel, respectively. The fitting of the creep compliance tests in the SLS model confirmed the viscoelastic behaviour of the samples with retardation times of 23 and 16 seconds for the PVA and PVA-Cel, respectively. Micro indentation tests were also achieved and the results indicated elastic moduli in the same range of the dynamic tests. Specifically, values between 45-55 and 56-81kPa were obtained for the PVA and PVA-Cel samples, respectively. The tribological results indicated values of 0.55 at low forces for the PVA decreasing to 0.13 at higher forces. The PVA-Cel blocks showed lower friction even at low forces with values between 0.2 and 0.07. The implementation of these building blocks in the design of a 2-layered skin model (2LSM) is also presented in this work. The 2LSM was stamped with four different textures and their surface properties were evaluated. The hydration of the 2LSM was also evaluated with a corneometer and the results indicated a gradient of hydration comparable to the human skin.

  7. Evaluation of model-based methods in estimating respiratory mechanics in the presence of variable patient effort.

    PubMed

    Redmond, Daniel P; Chiew, Yeong Shiong; Major, Vincent; Chase, J Geoffrey

    2016-09-23

    Monitoring of respiratory mechanics is required for guiding patient-specific mechanical ventilation settings in critical care. Many models of respiratory mechanics perform poorly in the presence of variable patient effort. Typical modelling approaches either attempt to mitigate the effect of the patient effort on the airway pressure waveforms, or attempt to capture the size and shape of the patient effort. This work analyses a range of methods to identify respiratory mechanics in volume controlled ventilation modes when there is patient effort. The models are compared using 4 Datasets, each with a sample of 30 breaths before, and 2-3 minutes after sedation has been administered. The sedation will reduce patient efforts, but the underlying pulmonary mechanical properties are unlikely to change during this short time. Model identified parameters from breathing cycles with patient effort are compared to breathing cycles that do not have patient effort. All models have advantages and disadvantages, so model selection may be specific to the respiratory mechanics application. However, in general, the combined method of iterative interpolative pressure reconstruction, and stacking multiple consecutive breaths together has the best performance over the Dataset. The variability of identified elastance when there is patient effort is the lowest with this method, and there is little systematic offset in identified mechanics when sedation is administered.

  8. Development of a mechanism-based pharmacokinetic/pharmacodynamic model to characterize the thermoregulatory effects of serotonergic drugs in mice.

    PubMed

    Jiang, Xi-Ling; Shen, Hong-Wu; Mager, Donald E; Schmidt, Stephan; Yu, Ai-Ming

    2016-09-01

    We have shown recently that concurrent harmaline, a monoamine oxidase-A inhibitor (MAOI), potentiates serotonin (5-HT) receptor agonist 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT)-induced hyperthermia. The objective of this study was to develop an integrated pharmacokinetic/pharmacodynamic (PK/PD) model to characterize and predict the thermoregulatory effects of such serotonergic drugs in mice. Physiological thermoregulation was described by a mechanism-based indirect-response model with adaptive feedback control. Harmaline-induced hypothermia and 5-MeO-DMT-elicited hyperthermia were attributable to the loss of heat through the activation of 5-HT1A receptor and thermogenesis via the stimulation of 5-HT2A receptor, respectively. Thus serotonergic 5-MeO-DMT-induced hyperthermia was readily distinguished from handling/injection stress-provoked hyperthermic effects. This PK/PD model was able to simultaneously describe all experimental data including the impact of drug-metabolizing enzyme status on 5-MeO-DMT and harmaline PK properties, and drug- and stress-induced simple hypo/hyperthermic and complex biphasic effects. Furthermore, the modeling results revealed a 4-fold decrease of apparent SC50 value (1.88-0.496 µmol/L) for 5-MeO-DMT when harmaline was co-administered, providing a quantitative assessment for the impact of concurrent MAOI harmaline on 5-MeO-DMT-induced hyperthermia. In addition, the hyperpyrexia caused by toxic dose combinations of harmaline and 5-MeO-DMT were linked to the increased systemic exposure to harmaline rather than 5-MeO-DMT, although the body temperature profiles were mispredicted by the model. The results indicate that current PK/PD model may be used as a new conceptual framework to define the impact of serotonergic agents and stress factors on thermoregulation.

  9. 3D MRI-based anisotropic FSI models with cyclic bending for human coronary atherosclerotic plaque mechanical analysis.

    PubMed

    Tang, Dalin; Yang, Chun; Kobayashi, Shunichi; Zheng, Jie; Woodard, Pamela K; Teng, Zhongzhao; Billiar, Kristen; Bach, Richard; Ku, David N

    2009-06-01

    Heart attack and stroke are often caused by atherosclerotic plaque rupture, which happens without warning most of the time. Magnetic resonance imaging (MRI)-based atherosclerotic plaque models with fluid-structure interactions (FSIs) have been introduced to perform flow and stress/strain analysis and identify possible mechanical and morphological indices for accurate plaque vulnerability assessment. For coronary arteries, cyclic bending associated with heart motion and anisotropy of the vessel walls may have significant influence on flow and stress/strain distributions in the plaque. FSI models with cyclic bending and anisotropic vessel properties for coronary plaques are lacking in the current literature. In this paper, cyclic bending and anisotropic vessel properties were added to 3D FSI coronary plaque models so that the models would be more realistic for more accurate computational flow and stress/strain predictions. Six computational models using one ex vivo MRI human coronary plaque specimen data were constructed to assess the effects of cyclic bending, anisotropic vessel properties, pulsating pressure, plaque structure, and axial stretch on plaque stress/strain distributions. Our results indicate that cyclic bending and anisotropic properties may cause 50-800% increase in maximum principal stress (Stress-P1) values at selected locations. The stress increase varies with location and is higher when bending is coupled with axial stretch, nonsmooth plaque structure, and resonant pressure conditions (zero phase angle shift). Effects of cyclic bending on flow behaviors are more modest (9.8% decrease in maximum velocity, 2.5% decrease in flow rate, 15% increase in maximum flow shear stress). Inclusion of cyclic bending, anisotropic vessel material properties, accurate plaque structure, and axial stretch in computational FSI models should lead to a considerable improvement of accuracy of computational stress/strain predictions for coronary plaque vulnerability

  10. A statistical model for Windstorm Variability over the British Isles based on Large-scale Atmospheric and Oceanic Mechanisms

    NASA Astrophysics Data System (ADS)

    Kirchner-Bossi, Nicolas; Befort, Daniel J.; Wild, Simon B.; Ulbrich, Uwe; Leckebusch, Gregor C.

    2016-04-01

    Time-clustered winter storms are responsible for a majority of the wind-induced losses in Europe. Over last years, different atmospheric and oceanic large-scale mechanisms as the North Atlantic Oscillation (NAO) or the Meridional Overturning Circulation (MOC) have been proven to drive some significant portion of the windstorm variability over Europe. In this work we systematically investigate the influence of different large-scale natural variability modes: more than 20 indices related to those mechanisms with proven or potential influence on the windstorm frequency variability over Europe - mostly SST- or pressure-based - are derived by means of ECMWF ERA-20C reanalysis during the last century (1902-2009), and compared to the windstorm variability for the European winter (DJF). Windstorms are defined and tracked as in Leckebusch et al. (2008). The derived indices are then employed to develop a statistical procedure including a stepwise Multiple Linear Regression (MLR) and an Artificial Neural Network (ANN), aiming to hindcast the inter-annual (DJF) regional windstorm frequency variability in a case study for the British Isles. This case study reveals 13 indices with a statistically significant coupling with seasonal windstorm counts. The Scandinavian Pattern (SCA) showed the strongest correlation (0.61), followed by the NAO (0.48) and the Polar/Eurasia Pattern (0.46). The obtained indices (standard-normalised) are selected as predictors for a windstorm variability hindcast model applied for the British Isles. First, a stepwise linear regression is performed, to identify which mechanisms can explain windstorm variability best. Finally, the indices retained by the stepwise regression are used to develop a multlayer perceptron-based ANN that hindcasted seasonal windstorm frequency and clustering. Eight indices (SCA, NAO, EA, PDO, W.NAtl.SST, AMO (unsmoothed), EA/WR and Trop.N.Atl SST) are retained by the stepwise regression. Among them, SCA showed the highest linear

  11. Effective electric fields along realistic DTI-based neural trajectories for modelling the stimulation mechanisms of TMS.

    PubMed

    De Geeter, N; Crevecoeur, G; Leemans, A; Dupré, L

    2015-01-21

    In transcranial magnetic stimulation (TMS), an applied alternating magnetic field induces an electric field in the brain that can interact with the neural system. It is generally assumed that this induced electric field is the crucial effect exciting a certain region of the brain. More specifically, it is the component of this field parallel to the neuron's local orientation, the so-called effective electric field, that can initiate neuronal stimulation. Deeper insights on the stimulation mechanisms can be acquired through extensive TMS modelling. Most models study simple representations of neurons with assumed geometries, whereas we embed realistic neural trajectories computed using tractography based on diffusion tensor images. This way of modelling ensures a more accurate spatial distribution of the effective electric field that is in addition patient and case specific. The case study of this paper focuses on the single pulse stimulation of the left primary motor cortex with a standard figure-of-eight coil. Including realistic neural geometry in the model demonstrates the strong and localized variations of the effective electric field between the tracts themselves and along them due to the interplay of factors such as the tract's position and orientation in relation to the TMS coil, the neural trajectory and its course along the white and grey matter interface. Furthermore, the influence of changes in the coil orientation is studied. Investigating the impact of tissue anisotropy confirms that its contribution is not negligible. Moreover, assuming isotropic tissues lead to errors of the same size as rotating or tilting the coil with 10 degrees. In contrast, the model proves to be less sensitive towards the not well-known tissue conductivity values.

  12. Effective electric fields along realistic DTI-based neural trajectories for modelling the stimulation mechanisms of TMS

    NASA Astrophysics Data System (ADS)

    De Geeter, N.; Crevecoeur, G.; Leemans, A.; Dupré, L.

    2015-01-01

    In transcranial magnetic stimulation (TMS), an applied alternating magnetic field induces an electric field in the brain that can interact with the neural system. It is generally assumed that this induced electric field is the crucial effect exciting a certain region of the brain. More specifically, it is the component of this field parallel to the neuron’s local orientation, the so-called effective electric field, that can initiate neuronal stimulation. Deeper insights on the stimulation mechanisms can be acquired through extensive TMS modelling. Most models study simple representations of neurons with assumed geometries, whereas we embed realistic neural trajectories computed using tractography based on diffusion tensor images. This way of modelling ensures a more accurate spatial distribution of the effective electric field that is in addition patient and case specific. The case study of this paper focuses on the single pulse stimulation of the left primary motor cortex with a standard figure-of-eight coil. Including realistic neural geometry in the model demonstrates the strong and localized variations of the effective electric field between the tracts themselves and along them due to the interplay of factors such as the tract’s position and orientation in relation to the TMS coil, the neural trajectory and its course along the white and grey matter interface. Furthermore, the influence of changes in the coil orientation is studied. Investigating the impact of tissue anisotropy confirms that its contribution is not negligible. Moreover, assuming isotropic tissues lead to errors of the same size as rotating or tilting the coil with 10 degrees. In contrast, the model proves to be less sensitive towards the not well-known tissue conductivity values.

  13. The Conceptual Mechanism for Viable Organizational Learning Based on Complex System Theory and the Viable System Model

    ERIC Educational Resources Information Center

    Sung, Dia; You, Yeongmahn; Song, Ji Hoon

    2008-01-01

    The purpose of this research is to explore the possibility of viable learning organizations based on identifying viable organizational learning mechanisms. Two theoretical foundations, complex system theory and viable system theory, have been integrated to provide the rationale for building the sustainable organizational learning mechanism. The…

  14. Mechanics based model for predicting structure-induced rolling resistance (SRR) of the tire-pavement system

    NASA Astrophysics Data System (ADS)

    Shakiba, Maryam; Ozer, Hasan; Ziyadi, Mojtaba; Al-Qadi, Imad L.

    2016-11-01

    The structure-induced rolling resistance of pavements, and its impact on vehicle fuel consumption, is investigated in this study. The structural response of pavement causes additional rolling resistance and fuel consumption of vehicles through deformation of pavement and various dissipation mechanisms associated with inelastic material properties and damping. Accurate and computationally efficient models are required to capture these mechanisms and obtain realistic estimates of changes in vehicle fuel consumption. Two mechanistic-based approaches are currently used to calculate vehicle fuel consumption as related to structural rolling resistance: dissipation-induced and deflection-induced methods. The deflection-induced approach is adopted in this study, and realistic representation of pavement-vehicle interactions (PVIs) is incorporated. In addition to considering viscoelastic behavior of asphalt concrete layers, the realistic representation of PVIs in this study includes non-uniform three-dimensional tire contact stresses and dynamic analysis in pavement simulations. The effects of analysis type, tire contact stresses, pavement viscoelastic properties, pavement damping coefficients, vehicle speed, and pavement temperature are then investigated.

  15. Effect of geometric size on mechanical properties of dielectric elastomers based on an improved visco-hyperelastic film model

    NASA Astrophysics Data System (ADS)

    Chang, Mengzhou; Wang, Zhenqing; Tong, Liyong; Liang, Wenyan

    2017-03-01

    Dielectric polymers show complex mechanical behaviors with different boundary conditions, geometry size and pre-stress. A viscoelastic model suitable for inhomogeneous deformation is presented integrating the Kelvin-Voigt model in a new form in this work. For different types of uniaxial tensile test loading along the length direction of sample, single-step-relaxation tests, loading–unloading tests and tensile–creep–relaxation tests the improved model provides a quite favorable comparison with the experiment results. Moreover, The mechanical properties of test sample with several length–width ratios under different boundary conditions are also invested. The influences of the different boundary conditions are calculated with a stress applied on the boundary point and the result show that the fixed boundary will increase the stress compare with homogeneous deformation. In modeling the effect of pre-stress in the shear test, three pre-stressed mode are discussed. The model validation on the general mechanical behavior shows excellent predictive capability.

  16. Origami based Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Lv, Cheng; Krishnaraju, Deepakshyam; Konjevod, Goran; Yu, Hongyu; Jiang, Hanqing

    2014-08-01

    We describe mechanical metamaterials created by folding flat sheets in the tradition of origami, the art of paper folding, and study them in terms of their basic geometric and stiffness properties, as well as load bearing capability. A periodic Miura-ori pattern and a non-periodic Ron Resch pattern were studied. Unexceptional coexistence of positive and negative Poisson's ratio was reported for Miura-ori pattern, which are consistent with the interesting shear behavior and infinity bulk modulus of the same pattern. Unusually strong load bearing capability of the Ron Resch pattern was found and attributed to the unique way of folding. This work paves the way to the study of intriguing properties of origami structures as mechanical metamaterials.

  17. Origami based Mechanical Metamaterials

    PubMed Central

    Lv, Cheng; Krishnaraju, Deepakshyam; Konjevod, Goran; Yu, Hongyu; Jiang, Hanqing

    2014-01-01

    We describe mechanical metamaterials created by folding flat sheets in the tradition of origami, the art of paper folding, and study them in terms of their basic geometric and stiffness properties, as well as load bearing capability. A periodic Miura-ori pattern and a non-periodic Ron Resch pattern were studied. Unexceptional coexistence of positive and negative Poisson's ratio was reported for Miura-ori pattern, which are consistent with the interesting shear behavior and infinity bulk modulus of the same pattern. Unusually strong load bearing capability of the Ron Resch pattern was found and attributed to the unique way of folding. This work paves the way to the study of intriguing properties of origami structures as mechanical metamaterials. PMID:25099402

  18. Models projecting the fate of fish populations under climate change need to be based on valid physiological mechanisms.

    PubMed

    Lefevre, Sjannie; McKenzie, David J; Nilsson, Göran E

    2017-02-06

    Some recent modelling papers projecting smaller fish sizes and catches in a warmer future are based on erroneous assumptions regarding (i) the scaling of gills with body mass and (ii) the energetic cost of 'maintenance'. Assumption (i) posits that insurmountable geometric constraints prevent respiratory surface areas from growing as fast as body volume. It is argued that these constraints explain allometric scaling of energy metabolism, whereby larger fishes have relatively lower mass-specific metabolic rates. Assumption (ii) concludes that when fishes reach a certain size, basal oxygen demands will not be met, because of assumption (i). We here demonstrate unequivocally, by applying accepted physiological principles with reference to the existing literature, that these assumptions are not valid. Gills are folded surfaces, where the scaling of surface area to volume is not constrained by spherical geometry. The gill surface area can, in fact, increase linearly in proportion to gill volume and body mass. We cite the large body of evidence demonstrating that respiratory surface areas in fishes reflect metabolic needs, not vice versa, which explains the large interspecific variation in scaling of gill surface areas. Finally, we point out that future studies basing their predictions on models should incorporate factors for scaling of metabolic rate and for temperature effects on metabolism, which agree with measured values, and should account for interspecific variation in scaling and temperature effects. It is possible that some fishes will become smaller in the future, but to make reliable predictions the underlying mechanisms need to be identified and sought elsewhere than in geometric constraints on gill surface area. Furthermore, to ensure that useful information is conveyed to the public and policymakers about the possible effects of climate change, it is necessary to improve communication and congruity between fish physiologists and fisheries scientists.

  19. Finite Element Simulation of Mechanical Behavior of TRIP800 Steel Under Different Loading Conditions Using an Advanced Microstructure-Based Model

    NASA Astrophysics Data System (ADS)

    Hosseinabadi, F.; Rezaee-Bazzaz, A.; Mazinani, M.

    2017-02-01

    The mechanical behavior of a low alloy multiphase TRIP steel has been predicted by an advanced microstructure-based finite element method. A representative volume element chosen based on the actual microstructure has been utilized for simulating the mechanical behavior of the studied steel. The parameters describing the martensitic transformation kinetics have been estimated using both crystallographic and thermodynamic theories of martensitic transformation. The mechanical behavior of each of the constituent phases required for the prediction of mechanical behavior of the studied material has been extracted from those reported in the literature. Comparison of the predicted mechanical behavior of the investigated TRIP800 steel with those reported in the literature shows that there is good agreement between simulated and experimental results. Therefore, it can be said that, the utilized microstructure-based model can be used for the prediction of both mechanical and transformation behaviors of the TRIP800 steels. It is worth noting that all of the parameters used in the model, except the sensitivity of the martensitic transformation to the stress state, can be estimated theoretically; thus, the number of parameters obtained by correlating the simulated and experimental results reduces to one. This is the unique characteristic of the utilized model, which makes the application of the model for simulation of the mechanical behavior of TRIP steels simpler than that of the similar ones.

  20. Correspondence between AXAF TMA X-ray performance and models based upon mechanical and visible light measurements

    NASA Technical Reports Server (NTRS)

    Van Speybroeck, L.; Mckinnon, P. J.; Murray, S. S.; Primini, F. A.; Schwartz, D. A.; Zombeck, M. V.; Dailey, C. C.; Reily, J. C.; Weisskopf, M. C.; Wyman, C. L.

    1986-01-01

    The AXAF Technology Mirror Assembly (TMA) was characterized prior to X-ray testing by properties measured mechanically or with visible light; these include alignment offsets, roundness and global-axial-slope errors, axial-figure errors with characteristic lengths greater than about five mm, and surface roughness with scale lengths between about 0.005 and 0.5 mm. The X-ray data of Schwartz et al. (1985) are compared with predictions based upon the mechanical and visible light measurements.

  1. Genome-based, mechanism-driven computational modeling of risks of ionizing radiation: The next frontier in genetic risk estimation?

    PubMed

    Sankaranarayanan, K; Nikjoo, H

    2015-01-01

    Research activity in the field of estimation of genetic risks of ionizing radiation to human populations started in the late 1940s and now appears to be passing through a plateau phase. This paper provides a background to the concepts, findings and methods of risk estimation that guided the field through the period of its growth to the beginning of the 21st century. It draws attention to several key facts: (a) thus far, genetic risk estimates have been made indirectly using mutation data collected in mouse radiation studies; (b) important uncertainties and unsolved problems remain, one notable example being that we still do not know the sensitivity of human female germ cells to radiation-induced mutations; and (c) the concept that dominated the field thus far, namely, that radiation exposures to germ cells can result in single gene diseases in the descendants of those exposed has been replaced by the concept that radiation exposure can cause DNA deletions, often involving more than one gene. Genetic risk estimation now encompasses work devoted to studies on DNA deletions induced in human germ cells, their expected frequencies, and phenotypes and associated clinical consequences in the progeny. We argue that the time is ripe to embark on a human genome-based, mechanism-driven, computational modeling of genetic risks of ionizing radiation, and we present a provisional framework for catalyzing research in the field in the 21st century.

  2. Mechanism-based modeling of rebound tachycardia after chronic l-propranolol infusion in spontaneous hypertensive rats.

    PubMed

    Brynne, L; Paalzow, L K; Karlsson, M O

    1999-08-01

    The aims of the study were to characterize the rate and extent of the rebound effect after abrupt cessation of a chronic exposure of l-propranolol in spontaneous hypertensive rats, using exercise-induced tachycardia as a pharmacodynamic endpoint. Thirty-two spontaneous hypertensive rats were randomized to receive either placebo or 4 or 8 mg/kg/day s.c. infusion of l-propranolol for 11 days using osmotic minipumps. The heart rate was measured after standardized physical exercise before and during drug exposure and over 12 days after cessation, using a computerized tail-cuff method. Blood samples were collected after each effect measurement during the infusion. A similar reduction in exercise tachycardia was registered for the two doses. No apparent tolerance development was found, but both doses showed a clear rebound effect of similar extent and intensity. The maximal rebound effect was observed on the second day after cessation and was found to have a duration of about 6 days. A mechanism-based model was developed to describe the rate and extent of changes in beta-adrenoceptor up- and down-regulation with increased sensitivity of the transducer complex. The half-life of disappearance of up-regulated beta-adrenoceptors was estimated to be 2.0 days (1.0-3.9 days). The effect-versus-time data was analyzed by nonlinear mixed-effect modeling with the program NONMEM. A dose-dependent reduction in the growth of body weight was observed during drug treatment, which was reversible. A dose- and time-dependent increase in the alpha(1)-acid glycoprotein concentration was also observed.

  3. A musculo-mechanical model of esophageal transport based on an immersed boundary-finite element approach

    NASA Astrophysics Data System (ADS)

    Kou, Wenjun; Griffith, Boyce E.; Pandolfino, John E.; Kahrilas, Peter J.; Patankar, Neelesh A.

    2015-11-01

    This work extends a fiber-based immersed boundary (IB) model of esophageal transport by incorporating a continuum model of the deformable esophageal wall. The continuum-based esophagus model adopts finite element approach that is capable of describing more complex and realistic material properties and geometries. The leakage from mismatch between Lagrangian and Eulerian meshes resulting from large deformations of the esophageal wall is avoided by careful choice of interaction points. The esophagus model, which is described as a multi-layered, fiber-reinforced nonlinear elastic material, is coupled to bolus and muscle-activation models using the IB approach to form the esophageal transport model. Cases of esophageal transport with different esophagus models are studied. Results on the transport characteristics, including pressure field and esophageal wall kinematics and stress, are analyzed and compared. Support from NIH grant R01 DK56033 and R01 DK079902 is gratefully acknowledged. BEG is supported by NSF award ACI 1460334.

  4. Mechanics Model of Plug Welding

    NASA Technical Reports Server (NTRS)

    Zuo, Q. K.; Nunes, A. C., Jr.

    2015-01-01

    An analytical model has been developed for the mechanics of friction plug welding. The model accounts for coupling of plastic deformation (material flow) and thermal response (plastic heating). The model predictions of the torque, energy, and pull force on the plug were compared to the data of a recent experiment, and the agreements between predictions and data are encouraging.

  5. Modelling the graphite fracture mechanisms

    SciTech Connect

    Jacquemoud, C.; Marie, S.; Nedelec, M.

    2012-07-01

    In order to define a design criterion for graphite components, it is important to identify the physical phenomena responsible for the graphite fracture, to include them in a more effective modelling. In a first step, a large panel of experiments have been realised in order to build up an important database; results of tensile tests, 3 and 4 point bending tests on smooth and notched specimens have been analysed and have demonstrated an important geometry related effects on the behavior up to fracture. Then, first simulations with an elastic or an elastoplastic bilinear constitutive law have not made it possible to simulate the experimental fracture stress variations with the specimen geometry, the fracture mechanisms of the graphite being at the microstructural scale. That is the reason why a specific F.E. model of the graphite structure has been developed in which every graphite grain has been meshed independently, the crack initiation along the basal plane of the particles as well as the crack propagation and coalescence have been modelled too. This specific model has been used to test two different approaches for fracture initiation: a critical stress criterion and two criteria of fracture mechanic type. They are all based on crystallographic considerations as a global critical stress criterion gave unsatisfactory results. The criteria of fracture mechanic type being extremely unstable and unable to represent the graphite global behaviour up to the final collapse, the critical stress criterion has been preferred to predict the results of the large range of available experiments, on both smooth and notched specimens. In so doing, the experimental observations have been correctly simulated: the geometry related effects on the experimental fracture stress dispersion, the specimen volume effects on the macroscopic fracture stress and the crack propagation at a constant stress intensity factor. In addition, the parameters of the criterion have been related to

  6. Mechanisms of Hydrocarbon Based Polymer Etch

    NASA Astrophysics Data System (ADS)

    Lane, Barton; Ventzek, Peter; Matsukuma, Masaaki; Suzuki, Ayuta; Koshiishi, Akira

    2015-09-01

    Dry etch of hydrocarbon based polymers is important for semiconductor device manufacturing. The etch mechanisms for oxygen rich plasma etch of hydrocarbon based polymers has been studied but the mechanism for lean chemistries has received little attention. We report on an experimental and analytic study of the mechanism for etching of a hydrocarbon based polymer using an Ar/O2 chemistry in a single frequency 13.56 MHz test bed. The experimental study employs an analysis of transients from sequential oxidation and Ar sputtering steps using OES and surface analytics to constrain conceptual models for the etch mechanism. The conceptual model is consistent with observations from MD studies and surface analysis performed by Vegh et al. and Oehrlein et al. and other similar studies. Parameters of the model are fit using published data and the experimentally observed time scales.

  7. Using isotope-based climate proxies and model simulations to diagnose drought mechanisms in the western US

    NASA Astrophysics Data System (ADS)

    Buenning, N. H.; Kanner, L. C.; Stott, L. D.; Yoshimura, K.

    2012-12-01

    Wintertime precipitation in the western US is a significant aspect of the region's water resources because of the ability of mountain snowpack to naturally store cold season precipitation and release the moisture via snowmelt and runoff. Protracted periods of drought in the western US are typically a result of decreases in precipitation during winter months. The use of the 18O/16O composition of precipitation (δ18Op) could prove valuable in determining mechanisms responsible for past drought because the isotopes track changes in moisture source on synoptic timescales and condensation height on subannual timescales. It has also been hypothesized that δ18Op reflects the fraction of precipitation that falls as snow within a given season. Consequently, δ18Op (as may be recorded in proxies such as tree cellulose) could provide climatic information that cannot be obtained from other proxies such as tree-ring widths. This study uses isotope based climate proxies from tree cellulose to better understand the cause of past declines in winter precipitation in the western US. In particular, we examine interannual variations in the 18O/16O composition of tree cellulose (δ18Oc) taken from 5 bristlecone pine trees in the White Mountains of eastern California, which capture precipitation δ18O values. Simulations of the Isotope-incorporated Global Spectral Model (IsoGSM) are used to interpret the cellulose isotope record. The simulations reveal that interannual δ18Op variations are strongly influenced by condensation height, and secondarily impacted by moisture source. Possible dynamical mechanisms that lead to dry intervals are assessed using this interpretation of the bristlecone δ18Oc records. For example, one of the most robust features of the 5 chronologies is a local minimum in δ18Oc during 1970, which was a year prior to drought (1971-1972). Indeed, results from IsoGSM "tagging" simulations suggest that δ18Oc rose during the drought years because moisture condensed

  8. Mechanism test bed. Flexible body model report

    NASA Technical Reports Server (NTRS)

    Compton, Jimmy

    1991-01-01

    The Space Station Mechanism Test Bed is a six degree-of-freedom motion simulation facility used to evaluate docking and berthing hardware mechanisms. A generalized rigid body math model was developed which allowed the computation of vehicle relative motion in six DOF due to forces and moments from mechanism contact, attitude control systems, and gravity. No vehicle size limitations were imposed in the model. The equations of motion were based on Hill's equations for translational motion with respect to a nominal circular earth orbit and Newton-Euler equations for rotational motion. This rigid body model and supporting software were being refined.

  9. Dynamic mechanical response and a constitutive model of Fe-based high temperature alloy at high temperatures and strain rates.

    PubMed

    Su, Xiang; Wang, Gang; Li, Jianfeng; Rong, Yiming

    2016-01-01

    The effects of strain rate and temperature on the dynamic behavior of Fe-based high temperature alloy was studied. The strain rates were 0.001-12,000 s(-1), at temperatures ranging from room temperature to 800 °C. A phenomenological constitutive model (Power-Law constitutive model) was proposed considering adiabatic temperature rise and accurate material thermal physical properties. During which, the effects of the specific heat capacity on the adiabatic temperature rise was studied. The constitutive model was verified to be accurate by comparison between predicted and experimental results.

  10. Monitoring of intratidal lung mechanics: a Graphical User Interface for a model-based decision support system for PEEP-titration in mechanical ventilation.

    PubMed

    Buehler, S; Lozano-Zahonero, S; Schumann, S; Guttmann, J

    2014-12-01

    In mechanical ventilation, a careful setting of the ventilation parameters in accordance with the current individual state of the lung is crucial to minimize ventilator induced lung injury. Positive end-expiratory pressure (PEEP) has to be set to prevent collapse of the alveoli, however at the same time overdistension should be avoided. Classic approaches of analyzing static respiratory system mechanics fail in particular if lung injury already prevails. A new approach of analyzing dynamic respiratory system mechanics to set PEEP uses the intratidal, volume-dependent compliance which is believed to stay relatively constant during one breath only if neither atelectasis nor overdistension occurs. To test the success of this dynamic approach systematically at bedside or in an animal study, automation of the computing steps is necessary. A decision support system for optimizing PEEP in form of a Graphical User Interface (GUI) was targeted. Respiratory system mechanics were analyzed using the gliding SLICE method. The resulting shapes of the intratidal compliance-volume curve were classified into one of six categories, each associated with a PEEP-suggestion. The GUI should include a graphical representation of the results as well as a quality check to judge the reliability of the suggestion. The implementation of a user-friendly GUI was successfully realized. The agreement between modelled and measured pressure data [expressed as root-mean-square (RMS)] tested during the implementation phase with real respiratory data from two patient studies was below 0.2 mbar for data taken in volume controlled mode and below 0.4 mbar for data taken in pressure controlled mode except for two cases with RMS < 0.6 mbar. Visual inspections showed, that good and medium quality data could be reliably identified. The new GUI allows visualization of intratidal compliance-volume curves on a breath-by-breath basis. The automatic categorisation of curve shape into one of six shape

  11. An absorption mechanism and polarity-induced viscosity model for CO2 capture using hydroxypyridine-based ionic liquids.

    PubMed

    An, Xiaowei; Du, Xiao; Duan, Donghong; Shi, Lijuan; Hao, Xiaogang; Lu, Houfang; Guan, Guoqing; Peng, Changjun

    2017-01-04

    A series of new hydroxypyridine-based ionic liquids (ILs) are synthesized and applied in CO2 capture through chemical absorption, in which one IL, i.e., tetrabutylphosphonium 2-hydroxypyridine ([P4444][2-Op]), shows a viscosity as low as 193 cP with an absorption capacity as high as 1.20 mol CO2 per mol IL. Because the traditional anion-CO2 absorption mechanism cannot provide an explanation for the influences of cations and temperature on CO2 absorption capacity, herein, a novel cation-participating absorption mechanism based on the proton transfer is proposed to explain the high absorption capacity and the existence of a turning point of absorption capacity with the increase of temperature for the capture of CO2 using [P4444][n-Op] (n = 2, 3, 4) ILs. Also, the relationship between the viscosity of ILs and the linear interaction energy is proposed for the first time, which can guide how to design and synthesize ILs with low viscosity. Quantum chemistry calculations, which are based on the comprehensive analysis of dipole moment, cation-anion interaction energy and surface electrostatic potential, indicate that the different viscosities of hydroxypyridine-based ILs and the changes after CO2 absorption mainly resulted from the different distribution of negative charges in the anion.

  12. Fundamental Study on Applicability of Powder-Based 3D Printer for Physical Modeling in Rock Mechanics

    NASA Astrophysics Data System (ADS)

    Fereshtenejad, Sayedalireza; Song, Jae-Joon

    2016-06-01

    Applications of 3D printing technology become more widespread in many research fields because of its rapid development and valuable capabilities. In rock mechanics and mining engineering, this technology has the potential to become a useful tool that might help implement a number of research studies previously considered impractical. Most commercial 3D printers cannot print prototypes with mechanical properties that match precisely those of natural rock samples. Therefore, some additional enhancements are required for 3D printers to be effectively utilized for rock mechanics applications. In this study, we printed and studied specimens using a powder-based commercial ZPrinter® 450 with ZP® 150 powder and Zb® 63 binder used as raw materials. The specimens printed by this 3D printer exhibited relatively low strength and ductile behavior, implying that it needs further improvements. Hence, we focused on several ways to determine the best combination of printing options and post-processing including the effects of the printing direction, printing layer thickness, binder saturation level, and heating process on the uniaxial compressive strength (UCS) and stress-strain behavior of the printed samples. The suggested procedures have demonstrated their effectiveness by obtaining the printed samples that behave similarly to the natural rocks with low UCS. Although our optimization methods were particularly successful, further improvements are required to expand 3D printer application in the area of rock mechanics.

  13. Neural mechanisms underlying the effects of face-based affective signals on memory for faces: a tentative model

    PubMed Central

    Tsukiura, Takashi

    2012-01-01

    In our daily lives, we form some impressions of other people. Although those impressions are affected by many factors, face-based affective signals such as facial expression, facial attractiveness, or trustworthiness are important. Previous psychological studies have demonstrated the impact of facial impressions on remembering other people, but little is known about the neural mechanisms underlying this psychological process. The purpose of this article is to review recent functional MRI (fMRI) studies to investigate the effects of face-based affective signals including facial expression, facial attractiveness, and trustworthiness on memory for faces, and to propose a tentative concept for understanding this affective-cognitive interaction. On the basis of the aforementioned research, three brain regions are potentially involved in the processing of face-based affective signals. The first candidate is the amygdala, where activity is generally modulated by both affectively positive and negative signals from faces. Activity in the orbitofrontal cortex (OFC), as the second candidate, increases as a function of perceived positive signals from faces; whereas activity in the insular cortex, as the third candidate, reflects a function of face-based negative signals. In addition, neuroscientific studies have reported that the three regions are functionally connected to the memory-related hippocampal regions. These findings suggest that the effects of face-based affective signals on memory for faces could be modulated by interactions between the regions associated with the processing of face-based affective signals and the hippocampus as a memory-related region. PMID:22837740

  14. A density-functional-theory-based finite element model to study the mechanical properties of zigzag phosphorene nanotubes

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Shahnazari, A.; Rouhi, S.

    2017-04-01

    In this paper, the density functional theory calculations are used to obtain the elastic properties of zigzag phosphorene nanotubes. Besides, based on the similarity between phosphorene nanotubes and a space-frame structure, a three-dimensional finite element model is proposed in which the atomic bonds are simulated by beam elements. The results of density functional theory are employed to compute the properties of the beam elements. Finally, using the proposed finite element model, the elastic modulus of the zigzag phosphorene nanotubes is computed. It is shown that phosphorene nanotubes with larger radii have larger Young's modulus. Comparing the results of finite element model with those of density functional theory, it is concluded that the proposed model can predict the elastic modulus of phosphorene nanotubes with a good accuracy.

  15. Generation mechanism of slow earthquakes: Numerical analysis based on a dynamic model with brittle-ductile mixed fault heterogeneity

    NASA Astrophysics Data System (ADS)

    Nakata, Ryoko; Ando, Ryosuke; Hori, Takane; Ide, Satoshi

    2011-08-01

    Various characteristics have been discovered for small, slow earthquakes occurring along subduction zones, which are deep nonvolcanic tremor, low-frequency earthquakes (LFEs), and very low frequency earthquakes (VLFs). In this study, we model these slow earthquakes using a dynamic model consisting of a cluster of frictionally unstable patches on a stable background. The controlling parameters in our model are related to the patch distribution and the viscosity of both the patches and the background. By decreasing patch density or increasing viscosity, we observed the transition in rupture propagation mechanism, that is, from fast elastodynamic interactions characterized by an elastic wave propagation to slow diffusion limited by viscous relaxation times of traction on fault patches and/or background. Some sets of these geometrical and frictional parameters collectively explain the moment rate functions, source spectra, and scaled energy of observed slow earthquakes. In addition, we successfully explain both parabolic and constant velocity migrations in the case of the diffusion-limited rupture. Therefore, the observed various characteristics of tremor, LFEs, VLFs, and, potentially, slow slip events, may be essentially explained by our simple model with a few parameters describing source structures and frictional properties of brittle-ductile transition zones along plate boundaries.

  16. A model-based approach to investigating the pathophysiological mechanisms of hypertension and response to antihypertensive therapies: extending the Guyton model.

    PubMed

    Hallow, K Melissa; Lo, Arthur; Beh, Jeni; Rodrigo, Manoj; Ermakov, Sergey; Friedman, Stuart; de Leon, Hector; Sarkar, Anamika; Xiong, Yuan; Sarangapani, Ramesh; Schmidt, Henning; Webb, Randy; Kondic, Anna Georgieva

    2014-05-01

    Reproducibly differential responses to different classes of antihypertensive agents are observed among hypertensive patients and may be due to interindividual differences in hypertension pathology. Computational models provide a tool for investigating the impact of underlying disease mechanisms on the response to antihypertensive therapies with different mechanisms of action. We present the development, calibration, validation, and application of an extension of the Guyton/Karaaslan model of blood pressure regulation. The model incorporates a detailed submodel of the renin-angiotensin-aldosterone system (RAAS), allowing therapies that target different parts of this pathway to be distinguished. Literature data on RAAS biomarker and blood pressure responses to different classes of therapies were used to refine the physiological actions of ANG II and aldosterone on renin secretion, renal vascular resistance, and sodium reabsorption. The calibrated model was able to accurately reproduce the RAAS biomarker and blood pressure responses to combinations of dual-RAAS agents, as well as RAAS therapies in combination with diuretics or calcium channel blockers. The final model was used to explore the impact of underlying mechanisms of hypertension on the blood pressure response to different classes of antihypertensive agents. Simulations indicate that the underlying etiology of hypertension can impact the magnitude of response to a given class of therapy, making a patient more sensitive to one class and less sensitive others. Given that hypertension is usually the result of multiple mechanisms, rather than a single factor, these findings yield insight into why combination therapy is often required to adequately control blood pressure.

  17. Identification of the primary mechanism of action of an insulin secretagogue from meal test data in healthy volunteers based on an integrated glucose-insulin model.

    PubMed

    Choy, Steve; Hénin, Emilie; van der Walt, Jan-Stefan; Kjellsson, Maria C; Karlsson, Mats O

    2013-02-01

    The integrated glucose-insulin (IGI) model is a previously developed semi-mechanistic model that incorporates control mechanisms for the regulation of glucose production, insulin secretion, and glucose uptake. It has been shown to adequately describe insulin and glucose profiles in both type 2 diabetics and healthy volunteers following various glucose tolerance tests. The aim of this study was to investigate the ability of the IGI model to correctly identify the primary mechanism of action of glibenclamide (Gb), based on meal tolerance test (MTT) data in healthy volunteers. IGI models with different mechanism of drug action were applied to data from eight healthy volunteers participating in a randomized crossover study with five single-dose tests (placebo and four drug arms). The study participants were given 3.5 mg of Gb, intravenously or orally, or 3.5 mg of the two main metabolites M1 and M2 intravenously, 0.5 h prior to a standardized breakfast with energy content of 1800 kJ. Simultaneous analysis of all data by nonlinear mixed effect modeling was performed using NONMEM(®). Drug effects that increased insulin secretion resulted in the best model fit, thus identifying the primary mechanism of action of Gb and metabolites as insulin secretagogues. The model also quantified the combined effect of Gb, M1 and M2 to have a fourfold maximal increase on endogenous insulin secretion, with an EC(50) of 169.1 ng mL(-1) for Gb, 151.4 ng mL(-1) for M1 and 267.1 ng mL(-1) for M2. The semi-mechanistic IGI model was successfully applied to MTT data and identified the primary mechanism of action for Gb, quantifying its effects on glucose and insulin time profiles.

  18. Spinal mechanisms may provide a combination of intermittent and continuous control of human posture: predictions from a biologically based neuromusculoskeletal model.

    PubMed

    Elias, Leonardo Abdala; Watanabe, Renato Naville; Kohn, André Fabio

    2014-11-01

    Several models have been employed to study human postural control during upright quiet stance. Most have adopted an inverted pendulum approximation to the standing human and theoretical models to account for the neural feedback necessary to keep balance. The present study adds to the previous efforts in focusing more closely on modelling the physiological mechanisms of important elements associated with the control of human posture. This paper studies neuromuscular mechanisms behind upright stance control by means of a biologically based large-scale neuromusculoskeletal (NMS) model. It encompasses: i) conductance-based spinal neuron models (motor neurons and interneurons); ii) muscle proprioceptor models (spindle and Golgi tendon organ) providing sensory afferent feedback; iii) Hill-type muscle models of the leg plantar and dorsiflexors; and iv) an inverted pendulum model for the body biomechanics during upright stance. The motor neuron pools are driven by stochastic spike trains. Simulation results showed that the neuromechanical outputs generated by the NMS model resemble experimental data from subjects standing on a stable surface. Interesting findings were that: i) an intermittent pattern of muscle activation emerged from this posture control model for two of the leg muscles (Medial and Lateral Gastrocnemius); and ii) the Soleus muscle was mostly activated in a continuous manner. These results suggest that the spinal cord anatomy and neurophysiology (e.g., motor unit types, synaptic connectivities, ordered recruitment), along with the modulation of afferent activity, may account for the mixture of intermittent and continuous control that has been a subject of debate in recent studies on postural control. Another finding was the occurrence of the so-called "paradoxical" behaviour of muscle fibre lengths as a function of postural sway. The simulations confirmed previous conjectures that reciprocal inhibition is possibly contributing to this effect, but on the

  19. Standardization of seismic tomographic models and earthquake focal mechanisms data sets based on web technologies, visualization with keyhole markup language

    NASA Astrophysics Data System (ADS)

    Postpischl, Luca; Danecek, Peter; Morelli, Andrea; Pondrelli, Silvia

    2011-01-01

    We present two projects in seismology that have been ported to web technologies, which provide results in Keyhole Markup Language (KML) visualization layers. These use the Google Earth geo-browser as the flexible platform that can substitute specialized graphical tools to perform qualitative visual data analyses and comparisons. The Network of Research Infrastructures for European Seismology (NERIES) Tomographic Earth Model Repository contains data sets from over 20 models from the literature. A hierarchical structure of folders that represent the sets of depths for each model is implemented in KML, and this immediately results into an intuitive interface for users to navigate freely and to compare tomographic plots. The KML layer for the European-Mediterranean Regional Centroid-Moment Tensor Catalog displays the focal mechanism solutions or moderate-magnitude Earthquakes from 1997 to the present. Our aim in both projects was to also propose standard representations of scientific data sets. Here, the general semantic approach of an XML framework has an important impact that must be further explored, although we find the KML syntax to more emphasis on aspects of detailed visualization. We have thus used, and propose the use of, Javascript Object Notation (JSON), another semantic notation that stems from the web-development community that provides a compact, general-purpose, data-exchange format.

  20. Structural hysteresis model of transmitting mechanical systems

    NASA Astrophysics Data System (ADS)

    Ruderman, M.; Bertram, T.

    2015-02-01

    We present a structural hysteresis model which describes the dynamic behavior of transmitting mechanical systems with a hysteretic spring and damped bedstop element, both connected in series. From the application point view this approach can be used for predicting the transmitted mechanical force based only on the known kinematic excitation. Using the case study of an elastic gear transmission we show and identify a hysteresis response which multivariate behavior depends on an internal state of the bedstop motion.

  1. 3D Progressive Damage Modeling for Laminated Composite Based on Crack Band Theory and Continuum Damage Mechanics

    NASA Technical Reports Server (NTRS)

    Wang, John T.; Pineda, Evan J.; Ranatunga, Vipul; Smeltzer, Stanley S.

    2015-01-01

    A simple continuum damage mechanics (CDM) based 3D progressive damage analysis (PDA) tool for laminated composites was developed and implemented as a user defined material subroutine to link with a commercially available explicit finite element code. This PDA tool uses linear lamina properties from standard tests, predicts damage initiation with an easy-to-implement Hashin-Rotem failure criteria, and in the damage evolution phase, evaluates the degradation of material properties based on the crack band theory and traction-separation cohesive laws. It follows Matzenmiller et al.'s formulation to incorporate the degrading material properties into the damaged stiffness matrix. Since nonlinear shear and matrix stress-strain relations are not implemented, correction factors are used for slowing the reduction of the damaged shear stiffness terms to reflect the effect of these nonlinearities on the laminate strength predictions. This CDM based PDA tool is implemented as a user defined material (VUMAT) to link with the Abaqus/Explicit code. Strength predictions obtained, using this VUMAT, are correlated with test data for a set of notched specimens under tension and compression loads.

  2. Transport Mechanisms and Quality Changes During Frying of Chicken Nuggets--Hybrid Mixture Theory Based Modeling and Experimental Verification.

    PubMed

    Bansal, Harkirat S; Takhar, Pawan S; Alvarado, Christine Z; Thompson, Leslie D

    2015-12-01

    Hybrid mixture theory (HMT) based 2-scale fluid transport relations of Takhar coupled with a multiphase heat transfer equation were solved to model water, oil and gas movement during frying of chicken nuggets. A chicken nugget was treated as a heterogeneous material consisting of meat core with wheat-based coating. The coupled heat and fluid transfer equations were solved using the finite element method. Numerical simulations resulted in data on spatial and temporal profiles for moisture, rate of evaporation, temperature, oil, pore pressure, pressure in various phases, and coefficient of elasticity. Results showed that most of the oil stayed in the outer 1.5 mm of the coating region. Temperature values greater than 100 °C were observed in the coating after 30 s of frying. Negative gage-pore pressure (p(w) < p(g)) magnitudes were observed in simulations, which is in agreement with experimental observations of Sandhu and others. It is hypothesized that high water-phase capillary pressure (p(c) > p(g)) in the hydrophilic matrix causes p(w) < p(g), which further results in negative pore pressure. The coefficient of elasticity was the highest at the surface (2.5 × 10(5) Pa) for coating and the interface of coating and core (6 × 10(5) Pa). Kinetics equation for color change obtained from experiments was coupled with the HMT based model to predict the color (L, a, and b) as a function of frying time.

  3. Determination of the mechanical and physical properties of cartilage by coupling poroelastic-based finite element models of indentation with artificial neural networks.

    PubMed

    Arbabi, Vahid; Pouran, Behdad; Campoli, Gianni; Weinans, Harrie; Zadpoor, Amir A

    2016-03-21

    One of the most widely used techniques to determine the mechanical properties of cartilage is based on indentation tests and interpretation of the obtained force-time or displacement-time data. In the current computational approaches, one needs to simulate the indentation test with finite element models and use an optimization algorithm to estimate the mechanical properties of cartilage. The modeling procedure is cumbersome, and the simulations need to be repeated for every new experiment. For the first time, we propose a method for fast and accurate estimation of the mechanical and physical properties of cartilage as a poroelastic material with the aid of artificial neural networks. In our study, we used finite element models to simulate the indentation for poroelastic materials with wide combinations of mechanical and physical properties. The obtained force-time curves are then divided into three parts: the first two parts of the data is used for training and validation of an artificial neural network, while the third part is used for testing the trained network. The trained neural network receives the force-time curves as the input and provides the properties of cartilage as the output. We observed that the trained network could accurately predict the properties of cartilage within the range of properties for which it was trained. The mechanical and physical properties of cartilage could therefore be estimated very fast, since no additional finite element modeling is required once the neural network is trained. The robustness of the trained artificial neural network in determining the properties of cartilage based on noisy force-time data was assessed by introducing noise to the simulated force-time data. We found that the training procedure could be optimized so as to maximize the robustness of the neural network against noisy force-time data.

  4. Investigation of the mechanical behavior of kangaroo humeral head cartilage tissue by a porohyperelastic model based on the strain-rate-dependent permeability.

    PubMed

    Thibbotuwawa, Namal; Oloyede, Adekunle; Senadeera, Wijitha; Li, Tong; Gu, YuanTong

    2015-11-01

    Solid-interstitial fluid interaction, which depends on tissue permeability, is significant to the strain-rate-dependent mechanical behavior of humeral head (shoulder) cartilage. Due to anatomical and biomechanical similarities to that of the human shoulder, kangaroos present a suitable animal model. Therefore, indentation experiments were conducted on kangaroo shoulder cartilage tissues from low (10(-4)/s) to moderately high (10(-2)/s) strain-rates. A porohyperelastic model was developed based on the experimental characterization; and a permeability function that takes into account the effect of strain-rate on permeability (strain-rate-dependent permeability) was introduced into the model to investigate the effect of rate-dependent fluid flow on tissue response. The prediction of the model with the strain-rate-dependent permeability was compared with those of the models using constant permeability and strain-dependent permeability. Compared to the model with constant permeability, the models with strain-dependent and strain-rate-dependent permeability were able to better capture the experimental variation at all strain-rates (p < 0.05). Significant differences were not identified between models with strain-dependent and strain-rate-dependent permeability at strain-rate of 5 × 10(-3)/s (p = 0.179). However, at strain-rate of 10(-2)/s, the model with strain-rate-dependent permeability was significantly better at capturing the experimental results (p < 0.005). The findings thus revealed the significance of rate-dependent fluid flow on tissue behavior at large strain-rates, which provides insights into the mechanical deformation mechanisms of cartilage tissues.

  5. New probabilistic fracture mechanics approach with neural network-based crack modeling: Its application to multiple cracks problem

    SciTech Connect

    Yoshimura, Shinobu; Lee, J.S.; Yagawa, Genki; Sugioka, Kiyoshi; Kawai, Tadahiko

    1995-11-01

    Studies on efficient utilization and life extension of operating nuclear power plants (NPPs) have become increasingly important since ages of the first-generation NPPs are approaching their design lives. In order to predict a remaining life of each plant, it is necessary to select those critical components that strongly influence the plant life, and to evaluate their remaining lives by considering aging effects of materials and other factors. This paper proposes a new method to incorporate sophisticated crack models, such as interaction and coalescence of multiple surface cracks, into probabilistic fracture mechanism (PFM) computer programs using neural networks. First, hundreds of finite element (FE) calculations of a plate containing multiple surface cracks are performed by parametrically changing crack parameters such as sizes and locations. A fully automated 3D FE analysis system is effectively utilized here. Second, the back-propagation neural network is trained using the FE solutions, i.e. crack parameters vs. their corresponding stress intensity factors (SIFs). After a sufficient number of training iterations, the network attains an ability to promptly output SIFs for arbitrary combinations of crack parameters. The well trained network is then incorporated into the parallel PFM program which runs on one of massively parallel computers composed of 512 processing units. To demonstrate its fundamental performances, the present computer program is applied to evaluate failure probabilities of aged reactor pressure vessels considering interaction and coalescence of two dissimilar semi-elliptical surface cracks.

  6. Modeling the mechanical response of PBX 9501

    SciTech Connect

    Ragaswamy, Partha; Lewis, Matthew W; Liu, Cheng; Thompson, Darla G

    2010-01-01

    An engineering overview of the mechanical response of Plastic-Bonded eXplosives (PBXs), specifically PBX 9501, will be provided with emphasis on observed mechanisms associated with different types of mechanical testing. Mechanical tests in the form of uniaxial tension, compression, cyclic loading, creep (compression and tension), and Hopkinson bar show strain rate and temperature dependence. A range of mechanical behavior is observed which includes small strain recoverable response in the form of viscoelasticity; change in stiffness and softening beyond peak strength due to damage in the form microcracks, debonding, void formation and the growth of existing voids; inelastic response in the form of irrecoverable strain as shown in cyclic tests, and viscoelastic creep combined with plastic response as demonstrated in creep and recovery tests. The main focus of this paper is to elucidate the challenges and issues involved in modeling the mechanical behavior of PBXs for simulating thermo-mechanical responses in engineering components. Examples of validation of a constitutive material model based on a few of the observed mechanisms will be demonstrated against three point bending, split Hopkinson pressure bar and Brazilian disk geometry.

  7. Mechanisms for similarity based cooperation

    NASA Astrophysics Data System (ADS)

    Traulsen, A.

    2008-06-01

    Cooperation based on similarity has been discussed since Richard Dawkins introduced the term “green beard” effect. In these models, individuals cooperate based on an aribtrary signal (or tag) such as the famous green beard. Here, two different models for such tag based cooperation are analysed. As neutral drift is important in both models, a finite population framework is applied. The first model, which we term “cooperative tags” considers a situation in which groups of cooperators are formed by some joint signal. Defectors adopting the signal and exploiting the group can lead to a breakdown of cooperation. In this case, conditions are derived under which the average abundance of the more cooperative strategy exceeds 50%. The second model considers a situation in which individuals start defecting towards others that are not similar to them. This situation is termed “defective tags”. It is shown that in this case, individuals using tags to cooperate exclusively with their own kind dominate over unconditional cooperators.

  8. Mechanism underlying the bio-effects of an electromagnetic field based on the Huang-Ferrell model.

    PubMed

    Geng, D Y; Hu, G; Wang, L; Jia, N; Wang, F X

    2016-06-27

    To understand the beneficial and harmful bio-effects of extremely low frequency electromagnetic fields, we studied the MAPK/ERK signaling pathway based on the Huang-Ferrell model. The sensitivity analysis method was used to study the influence of the model parameters on the activity of ERK, and to further investigate the key biochemical reactions and proteins. The results of the simulation show that an increase in the reaction rate of MAPK/ERK kinase had little effect on ERK activation and the steady-state molecular number. However, a decrease in the reaction rate of MAPK/ERK kinase significantly affected the trigger time of ERK activation and decreased the steady-state molecular number. Together with the biological significance of ERK activity, our findings indicate that the effects of electromagnetic fields are a result of the decrease in the reaction rate of MAPK/ERK kinase, which eventually determines whether these effects cause physical damage or are beneficial in treatment.

  9. Nonlocal models in continuum mechanics

    SciTech Connect

    Johnson, N.L.; Phan-Thien, N.

    1993-09-01

    The recent appearance of nonlocal methods is examined in the light of traditional continuum mechanics. A comparison of nonlocal approaches in the fields of solid and fluid mechanics reveals that no consistent definition of a nonlocal theory has been used. We suggest a definition based on the violation of the principle of local action in continuum mechanics. From the consideration of the implications of a nonlocal theory based on this definition, we conclude that constitutive relations with nonlocal terms can confuse the traditional separation of the roles between conservation laws and constitutive relations. The diversity of motivations for the nonlocal approaches are presented, resulting primarily from deficiencies in numerical solutions to practical problems. To illustrate these concepts, the history of nonlocal terms in the field of viscoelastic fluids is reviewed. A specific example of a viscoelastic constitutive relation that contains a stress diffusion term is applied to a simple shear flow and found not to be a physical description of any known fluid. We conclude by listing questions that should be asked of nonlocal approaches.

  10. Modeling of fluid injection and withdrawal induced fault activation using discrete element based hydro-mechanical and dynamic coupled simulator

    NASA Astrophysics Data System (ADS)

    Yoon, Jeoung Seok; Zang, Arno; Zimmermann, Günter; Stephansson, Ove

    2016-04-01

    Operation of fluid injection into and withdrawal from the subsurface for various purposes has been known to induce earthquakes. Such operations include hydraulic fracturing for shale gas extraction, hydraulic stimulation for Enhanced Geothermal System development and waste water disposal. Among these, several damaging earthquakes have been reported in the USA in particular in the areas of high-rate massive amount of wastewater injection [1] mostly with natural fault systems. Oil and gas production have been known to induce earthquake where pore fluid pressure decreases in some cases by several tens of Mega Pascal. One recent seismic event occurred in November 2013 near Azle, Texas where a series of earthquakes began along a mapped ancient fault system [2]. It was studied that a combination of brine production and waste water injection near the fault generated subsurface pressures sufficient to induced earthquakes on near-critically stressed faults. This numerical study aims at investigating the occurrence mechanisms of such earthquakes induced by fluid injection [3] and withdrawal by using hydro-geomechanical coupled dynamic simulator (Itasca's Particle Flow Code 2D). Generic models are setup to investigate the sensitivity of several parameters which include fault orientation, frictional properties, distance from the injection well to the fault, amount of fluid withdrawal around the injection well, to the response of the fault systems and the activation magnitude. Fault slip movement over time in relation to the diffusion of pore pressure is analyzed in detail. Moreover, correlations between the spatial distribution of pore pressure change and the locations of induced seismic events and fault slip rate are investigated. References [1] Keranen KM, Weingarten M, Albers GA, Bekins BA, Ge S, 2014. Sharp increase in central Oklahoma seismicity since 2008 induced by massive wastewater injection, Science 345, 448, DOI: 10.1126/science.1255802. [2] Hornbach MJ, DeShon HR

  11. A Mechanism-Based Model for the Prediction of the Metabolic Sites of Steroids Mediated by Cytochrome P450 3A4.

    PubMed

    Dai, Zi-Ru; Ai, Chun-Zhi; Ge, Guang-Bo; He, Yu-Qi; Wu, Jing-Jing; Wang, Jia-Yue; Man, Hui-Zi; Jia, Yan; Yang, Ling

    2015-06-30

    Early prediction of xenobiotic metabolism is essential for drug discovery and development. As the most important human drug-metabolizing enzyme, cytochrome P450 3A4 has a large active cavity and metabolizes a broad spectrum of substrates. The poor substrate specificity of CYP3A4 makes it a huge challenge to predict the metabolic site(s) on its substrates. This study aimed to develop a mechanism-based prediction model based on two key parameters, including the binding conformation and the reaction activity of ligands, which could reveal the process of real metabolic reaction(s) and the site(s) of modification. The newly established model was applied to predict the metabolic site(s) of steroids; a class of CYP3A4-preferred substrates. 38 steroids and 12 non-steroids were randomly divided into training and test sets. Two major metabolic reactions, including aliphatic hydroxylation and N-dealkylation, were involved in this study. At least one of the top three predicted metabolic sites was validated by the experimental data. The overall accuracy for the training and test were 82.14% and 86.36%, respectively. In summary, a mechanism-based prediction model was established for the first time, which could be used to predict the metabolic site(s) of CYP3A4 on steroids with high predictive accuracy.

  12. Modeling mechanical signals on the surface of µCT and CAD based rapid prototype scaffold models to predict (early stage) tissue development.

    PubMed

    Hendrikson, W J; van Blitterswijk, C A; Verdonschot, N; Moroni, L; Rouwkema, J

    2014-09-01

    In the field of tissue engineering, mechano-regulation theories have been applied to help predict tissue development in tissue engineering scaffolds in the past. For this, finite element models (FEMs) were used to predict the distribution of strains within a scaffold. However, the strains reported in these studies are volumetric strains of the material or strains developed in the extracellular matrix occupying the pore space. The initial phase of cell attachment and growth on the biomaterial surface has thus far been neglected. In this study, we present a model that determines the magnitude of biomechanical signals on the biomaterial surface, enabling us to predict cell differentiation stimulus values at this initial stage. Results showed that magnitudes of the 2D strain--termed surface strain--were lower when compared to the 3D volumetric strain or the conventional octahedral shear strain as used in current mechano-regulation theories. Results of both µCT and CAD derived FEMs from the same scaffold were compared. Strain and fluid shear stress distributions, and subsequently the cell differentiation stimulus, were highly dependent on the pore shape. CAD models were not able to capture the distributions seen in the µCT FEM. The calculated mechanical stimuli could be combined with current mechanobiological models resulting in a tool to predict cell differentiation in the initial phase of tissue engineering. Although experimental data is still necessary to properly link mechanical signals to cell behavior in this specific setting, this model is an important step towards optimizing scaffold architecture and/or stimulation regimes.

  13. Endocrine disrupting chemicals in fish: developing exposure indicators and predictive models of effects based on mechanism of action

    EPA Science Inventory

    Knowledge of possible toxic mechanisms/modes of action (MOA) of chemicals can provide valuable insights as to appropriate methods for assessing exposure and effects, such as reducing uncertainties related to extrapolation across species, endpoints and chemical structure. However,...

  14. Metal Ion Modeling Using Classical Mechanics.

    PubMed

    Li, Pengfei; Merz, Kenneth M

    2017-02-08

    Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.

  15. Metal Ion Modeling Using Classical Mechanics

    PubMed Central

    2017-01-01

    Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems. PMID:28045509

  16. A chemo-mechanical free-energy-based approach to model durotaxis and extracellular stiffness-dependent contraction and polarization of cells.

    PubMed

    Shenoy, Vivek B; Wang, Hailong; Wang, Xiao

    2016-02-06

    We propose a chemo-mechanical model based on stress-dependent recruitment of myosin motors to describe how the contractility, polarization and strain in cells vary with the stiffness of their surroundings and their shape. A contractility tensor, which depends on the distribution of myosin motors, is introduced to describe the chemical free energy of the cell due to myosin recruitment. We explicitly include the contributions to the free energy that arise from mechanosensitive signalling pathways (such as the SFX, Rho-Rock and MLCK pathways) through chemo-mechanical coupling parameters. Taking the variations of the total free energy, which consists of the chemical and mechanical components, in accordance with the second law of thermodynamics provides equations for the temporal evolution of the active stress and the contractility tensor. Following this approach, we are able to recover the well-known Hill relation for active stresses, based on the fundamental principles of irreversible thermodynamics rather than phenomenology. We have numerically implemented our free energy-based approach to model spatial distribution of strain and contractility in (i) cells supported by flexible microposts, (ii) cells on two-dimensional substrates, and (iii) cells in three-dimensional matrices. We demonstrate how the polarization of the cells and the orientation of stress fibres can be deduced from the eigenvalues and eigenvectors of the contractility tensor. Our calculations suggest that the chemical free energy of the cell decreases with the stiffness of the extracellular environment as the cytoskeleton polarizes in response to stress-dependent recruitment of molecular motors. The mechanical energy, which includes the strain energy and motor potential energy, however, increases with stiffness, but the overall energy is lower for cells in stiffer environments. This provides a thermodynamic basis for durotaxis, whereby cells preferentially migrate towards stiffer regions of the

  17. Mechanism of general acid-base catalysis in transesterification of an RNA model phosphodiester studied with strongly basic catalysts.

    PubMed

    Corona-Martínez, David O; Taran, Olga; Yatsimirsky, Anatoly K

    2010-02-21

    Using 80% vol aqueous DMSO as the reaction medium for transesterification of an RNA model substrate 2-hydroxypropyl 4-nitrophenyl phosphate allows one to observe catalysis in buffer mixtures composed of highly basic components such as guanidines, amidines or alkylamines, which provide up to 10(3)-fold accelerations over the background reaction in the 0.01-0.1 M concentration range. The rate law k(obs) = k(1)[B] + k(2)[B][BH(+)] was established indicating contributions from both simple general base catalysis and the reaction involving concerted action of neutral (B) and protonated (BH(+)) forms of the buffer. The catalytic efficiency of guanidinium and amidinium cations is 10 times larger than that of more acidic ammonium cations. Rate constants k(1) and k(2) obey the Brønsted equations with the slopes 0.77 and 0.69 respectively. Proton inventory for k(2) (B = guanidine) in D(2)O/H(2)O mixtures gives two fractionation factors phi(1) = 0.48 and phi(2) = 1.26 for normal and inverse isotope effects respectively. The former results from the proton transfer to B and the latter from the binding of guanidinium cation to the phosphate group as follows from observation of an inverse solvent isotope effect for the binding of guanidinium and amidinium cations to a phosphodiester anion. The results of kinetic studies together with analysis of transition state stabilization free energies for guanidinium and amidinium cations show that the protonated buffer component acts via electrostatic transition state stabilization rather than proton transfer, which may be possible for a guanidinium assisted hydroxide catalyzed reaction.

  18. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the family of Cucurbitaceae, cucumber (Cucumis sativus) is the only species with 14 chromosomes. The majority of the remaining species, including melon and the sister species of cucumber, C. hystrix, have 24 chromosomes. To understand the underlying mechanisms of chromosome reduction from n=12 to...

  19. Externally predictive quantitative modeling of supercooled liquid vapor pressure of polychlorinated-naphthalenes through electron-correlation based quantum-mechanical descriptors.

    PubMed

    Vikas; Chayawan

    2014-01-01

    For predicting physico-chemical properties related to environmental fate of molecules, quantitative structure-property relationships (QSPRs) are valuable tools in environmental chemistry. For developing a QSPR, molecular descriptors computed through quantum-mechanical methods are generally employed. The accuracy of a quantum-mechanical method, however, rests on the amount of electron-correlation estimated by the method. In this work, single-descriptor QSPRs for supercooled liquid vapor pressure of chloronaphthalenes and polychlorinated-naphthalenes are developed using molecular descriptors based on the electron-correlation contribution of the quantum-mechanical descriptor. The quantum-mechanical descriptors for which the electron-correlation contribution is analyzed include total-energy, mean polarizability, dipole moment, frontier orbital (HOMO/LUMO) energy, and density-functional theory (DFT) based descriptors, namely, absolute electronegativity, chemical hardness, and electrophilicity index. A total of 40 single-descriptor QSPRs were developed using molecular descriptors computed with advanced semi-empirical (SE) methods, namely, RM1, PM7, and ab intio methods, namely, Hartree-Fock and DFT. The developed QSPRs are validated using state-of-the-art external validation procedures employing an external prediction set. From the comparison of external predictivity of the models, it is observed that the single-descriptor QSPRs developed using total energy and correlation energy are found to be far more robust and predictive than those developed using commonly employed descriptors such as HOMO/LUMO energy and dipole moment. The work proposes that if real external predictivity of a QSPR model is desired to be explored, particularly, in terms of intra-molecular interactions, correlation-energy serves as a more appropriate descriptor than the polarizability. However, for developing QSPRs, computationally inexpensive advanced SE methods such as PM7 can be more reliable than

  20. Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma:Connectome Neurotrauma Mechanics

    DTIC Science & Technology

    2012-08-16

    the- art finite element model of the human head, developed for a single individual directly from MRI, impacted on the forehead region. The local finite...Breakspear M, Deco G, McIntosh AR (2010) Towards the virtual brain: Network modeling of the intact and the damaged brain. Arch Ital Biol 148: 189–205

  1. Simulation modeling based method for choosing an effective set of fault tolerance mechanisms for real-time avionics systems

    NASA Astrophysics Data System (ADS)

    Bakhmurov, A. G.; Balashov, V. V.; Glonina, A. B.; Pashkov, V. N.; Smeliansky, R. L.; Volkanov, D. Yu.

    2013-12-01

    In this paper, the reliability allocation problem (RAP) for real-time avionics systems (RTAS) is considered. The proposed method for solving this problem consists of two steps: (i) creation of an RTAS simulation model at the necessary level of abstraction and (ii) application of metaheuristic algorithm to find an optimal solution (i. e., to choose an optimal set of fault tolerance techniques). When during the algorithm execution it is necessary to measure the execution time of some software components, the simulation modeling is applied. The procedure of simulation modeling also consists of the following steps: automatic construction of simulation model of the RTAS configuration and running this model in a simulation environment to measure the required time. This method was implemented as an experimental software tool. The tool works in cooperation with DYANA simulation environment. The results of experiments with the implemented method are presented. Finally, future plans for development of the presented method and tool are briefly described.

  2. ToTCompute: A Novel EEG-Based TimeOnTask Threshold Computation Mechanism for Engagement Modelling and Monitoring

    ERIC Educational Resources Information Center

    Ghergulescu, Ioana; Muntean, Cristina Hava

    2016-01-01

    Engagement influences participation, progression and retention in game-based e-learning (GBeL). Therefore, GBeL systems should engage the players in order to support them to maximize their learning outcomes, and provide the players with adequate feedback to maintain their motivation. Innovative engagement monitoring solutions based on players'…

  3. Mechanisms of β-Adrenergic Modulation of IKs in the Guinea-Pig Ventricle: Insights from Experimental and Model-Based Analysis

    PubMed Central

    Severi, Stefano; Corsi, Cristiana; Rocchetti, Marcella; Zaza, Antonio

    2009-01-01

    Detailed understanding of IKs gating complexity may provide clues regarding the mechanisms of repolarization instability and the resulting arrhythmias. We developed and tested a kinetic model to interpret physiologically relevant IKs properties, including pause-dependence and modulation by β-adrenergic receptors (β-AR). IKs gating was evaluated in guinea-pig ventricular myocytes at 36°C in control and during β-AR stimulation (0.1 μmol/L isoprenaline (ISO)). We tested voltage dependence of steady-state conductance (Gss), voltage dependence of activation and deactivation time constants (τact, τdeact), and pause-dependence of τact during repetitive activations (τreact). The IKs model was developed from the Silva and Rudy formulation. Parameters were optimized on control and ISO experimental data, respectively. ISO strongly increased Gss and its voltage dependence, changed the voltage dependence of τact and τdeact, and modified the pause-dependence of τreact. A single set of model parameters reproduced all experimental data in control. Modification of only three transition rates led to a second set of parameters suitable to fit all ISO data. Channel unitary conductance and density were unchanged in the model, thus implying increased open probability as the mechanism of ISO-induced Gss enhancement. The new IKs model was applied to analyze ISO effect on repolarization rate-dependence. IKs kinetics and its β-AR modulation were entirely reproduced by a single Markov chain of transitions (for each channel monomer). Model-based analysis suggests that complete opening of IKs channels within a physiological range of potentials requires concomitant β-AR stimulation. Transient redistribution of state occupancy, in addition to direct modulation of transition rates, may underlie β-AR modulation of IKs time dependence. PMID:19413992

  4. Modelling RNA folding under mechanical tension

    PubMed Central

    VIEREGG, JEFFREY R.; TINOCO, IGNACIO

    2006-01-01

    We investigate the thermodynamics and kinetics of RNA unfolding and refolding under mechanical tension. The hierarchical nature of RNA structure and the existence of thermodynamic parameters for base pair formation based on nearest-neighbour interactions allows modelling of sequence-dependent folding dynamics for any secondary structure. We calculate experimental observables such as the transition force for unfolding, the end-to-end distribution function and its variance, as well as kinetic information, for a representative RNA sequence and for a sequence containing two homopolymer segments: A.U and G.C. PMID:16969426

  5. Collagen thermal denaturation study for thermal angioplasty based on modified kinetic model: relation between the artery mechanical properties and collagen denaturation rate

    NASA Astrophysics Data System (ADS)

    Shimazaki, N.; Hayashi, T.; Kunio, M.; Arai, T.

    2010-02-01

    We have been developing the novel short-term heating angioplasty in which sufficient artery lumen-dilatation was attained with thermal softening of collagen fiber in artery wall. In the present study, we investigated on the relation between the mechanical properties of heated artery and thermal denaturation fractures of arterial collagen in ex vivo. We employed Lumry-Eyring model to estimate temperature- and time-dependent thermal denaturation fractures of arterial collagen fiber during heating. We made a kinetic model of arterial collagen thermal denaturation by adjustment of K and k in this model, those were the equilibrium constant of reversible denaturation and the rate constant of irreversible denaturation. Meanwhile we demonstrated that the change of reduced scattering coefficient of whole artery wall during heating reflected the reversible denaturation of the collagen in artery wall. Based on this phenomenon, the K was determined experimentally by backscattered light intensity measurement (at 633nm) of extracted porcine carotid artery during temperature elevation and descending (25°C-->80°C-->25°C). We employed the value of according to our earlier report in which the time-and temperature- dependent irreversible denaturation amount of the artery collagen fiber that was assessed by the artery birefringence. Then, the time- and temperature- dependent reversible (irreversible) denaturation fraction defined as the reversible ((irreversible) denatured collagen amount) / (total collagen amount) was calculated by the model. Thermo-mechanical analysis of artery wall was performed to compare the arterial mechanical behaviors (softening, shrinkage) during heating with the calculated denaturation fraction with the model. In any artery temperature condition in 70-80°, the irreversible denaturation fraction at which the artery thermal shrinkage started was estimated to be around 20%. On the other hand, the calculated irreversible denaturation fraction remained below

  6. Exploring the mechanisms of ecological land change based on the spatial autoregressive model: a case study of the Poyang Lake Eco-Economic Zone, China.

    PubMed

    Xie, Hualin; Liu, Zhifei; Wang, Peng; Liu, Guiying; Lu, Fucai

    2013-12-31

    Ecological land is one of the key resources and conditions for the survival of humans because it can provide ecosystem services and is particularly important to public health and safety. It is extremely valuable for effective ecological management to explore the evolution mechanisms of ecological land. Based on spatial statistical analyses, we explored the spatial disparities and primary potential drivers of ecological land change in the Poyang Lake Eco-economic Zone of China. The results demonstrated that the global Moran's I value is 0.1646 during the 1990 to 2005 time period and indicated significant positive spatial correlation (p < 0.05). The results also imply that the clustering trend of ecological land changes weakened in the study area. Some potential driving forces were identified by applying the spatial autoregressive model in this study. The results demonstrated that the higher economic development level and industrialization rate were the main drivers for the faster change of ecological land in the study area. This study also tested the superiority of the spatial autoregressive model to study the mechanisms of ecological land change by comparing it with the traditional linear regressive model.

  7. Bio-Chemo-Mechanical Models of Vascular Mechanics.

    PubMed

    Kim, Jungsil; Wagenseil, Jessica E

    2015-07-01

    Models of vascular mechanics are necessary to predict the response of an artery under a variety of loads, for complex geometries, and in pathological adaptation. Classic constitutive models for arteries are phenomenological and the fitted parameters are not associated with physical components of the wall. Recently, microstructurally-linked models have been developed that associate structural information about the wall components with tissue-level mechanics. Microstructurally-linked models are useful for correlating changes in specific components with pathological outcomes, so that targeted treatments may be developed to prevent or reverse the physical changes. However, most treatments, and many causes, of vascular disease have chemical components. Chemical signaling within cells, between cells, and between cells and matrix constituents affects the biology and mechanics of the arterial wall in the short- and long-term. Hence, bio-chemo-mechanical models that include chemical signaling are critical for robust models of vascular mechanics. This review summarizes bio-mechanical and bio-chemo-mechanical models with a focus on large elastic arteries. We provide applications of these models and challenges for future work.

  8. Teaching Mathematical Modelling in a Design Context: A Methodology Based on the Mechanical Analysis of a Domestic Cancrusher.

    ERIC Educational Resources Information Center

    Pace, Sydney

    2000-01-01

    Presents a methodology for teaching mathematical modeling skills to A-level students. Gives an example illustrating how mathematics teachers and design teachers can take joint perspective in devising learning opportunities that develop mathematical and design skills concurrently. (Contains 14 references.) (Author/ASK)

  9. Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics

    DTIC Science & Technology

    2012-08-16

    study the effects of localized structural damage or lesions. In the presented work, lesions are simulated by using a state-of-the- art finite element...Breakspear M, Deco G, McIntosh AR (2010) Towards the virtual brain: Network modeling of the intact and the damaged brain. Arch Ital Biol 148: 189–205. 42

  10. Endocrine Disrupting Chemicals in Fish: Developing Exposure Indicators and Predictive Models of Effects Based on Mechanism of Action

    EPA Science Inventory

    In this paper we provide an overview and illustrative results from a large, integrated project that assesses the effects of endocrine-disrupting chemicals (EDCs) on two small fish models, the fathead minnow (Pimephales promelas) and zebrafish (Danio rerio). For this work a syste...

  11. Mechanism-based pharmacokinetic-pharmacodynamic modeling of salvianolic acid A effects on plasma xanthine oxidase activity and uric acid levels in acute myocardial infarction rats.

    PubMed

    Wang, Haidong; Li, Xi; Zhang, Wenting; Liu, Yao; Wang, Shijun; Liu, Xiaoquan; He, Hua

    2017-03-01

    1. Salvianolic acid A (SalA) was found to attenuate plasma uric acid (UA) concentration and xanthine oxidase (XO) activity in acute myocardial infraction (AMI) rats, which was characterized with developed mechanism-based pharmacokinetic-pharmacodynamic (PK-PD) model. 2. AMI was induced in rats by coronary artery ligation. Surviving AMI rats received a single intravenous dose of 5 mg/kg of SalA and normal saline. The plasma SalA concentrations were determined by HPLC-MS/MS method. The plasma UA concentrations were determined by HPLC method and plasma XO activity were measured spectrophotometrically. An integrated mathematical model characterized the relationship between plasma UA and SalA. 3. Pharmacokinetics was described using two-compartment model for SalA with linear metabolic process. In post-AMI rats, XO activity and UA concentrations were increased, while SalA dosing palliated this increase. These effects were well captured by using two series of transduction models, simulating the delay of inhibition on XO driven by SalA and UA elevation resulted from the multiple factors, respectively. 4. The effect was well described by the developed PK-PD model, indicating that SalA can exert cardiovascular protective effects by decreasing elevated plasma UA levels induced by AMI.

  12. Magneto-mechanical modeling study of CO-based amorphous micro- and nanowires for acoustic sensing medical applications

    NASA Astrophysics Data System (ADS)

    Atitoaie, Alexandru; Stancu, Alexandru; Ovari, Tibor-Adrian; Lupu, Nicoleta; Chiriac, Horia

    2016-04-01

    Magnetic nanowires are potential candidates for substituting, within enhanced cochlear implants, the role played by hair cilia from the inner ear, which are responsible for the transduction of acoustic vibrations into electric signals. The sound waves pressure that is bending the magnetic wires induces stresses that are leading to changes in magnetic properties, such as magnetization and permeability. These changes can be detected by a GMR sensor placed below the nanowire array or, in the case of different designs, by a pick-up coil wrapped around the fixed-end of the wires. For the latter case, we are studying the stress distributions caused by bending deformations using the COMSOL finite element software package. We are also proposing a theoretical method for the evaluation of magnetic permeability variation vs. induced stress dependence. The study is performed on CoFeSiB amorphous micro- and nanowires subjected to mechanical perturbations similar to the ones produced by sound pressure waves.

  13. Familial Dysautonomia: Mechanisms and Models

    PubMed Central

    Dietrich, Paula; Dragatsis, Ioannis

    2016-01-01

    Abstract Hereditary Sensory and Autonomic Neuropathies (HSANs) compose a heterogeneous group of genetic disorders characterized by sensory and autonomic dysfunctions. Familial Dysautonomia (FD), also known as HSAN III, is an autosomal recessive disorder that affects 1/3,600 live births in the Ashkenazi Jewish population. The major features of the disease are already present at birth and are attributed to abnormal development and progressive degeneration of the sensory and autonomic nervous systems. Despite clinical interventions, the disease is inevitably fatal. FD is caused by a point mutation in intron 20 of the IKBKAP gene that results in severe reduction in expression of IKAP, its encoded protein. In vitro and in vivo studies have shown that IKAP is involved in multiple intracellular processes, and suggest that failed target innervation and/or impaired neurotrophic retrograde transport are the primary causes of neuronal cell death in FD. However, FD is far more complex, and appears to affect several other organs and systems in addition to the peripheral nervous system. With the recent generation of mouse models that recapitulate the molecular and pathological features of the disease, it is now possible to further investigate the mechanisms underlying different aspects of the disorder, and to test novel therapeutic strategies. PMID:27561110

  14. Threat processing: models and mechanisms.

    PubMed

    Bentz, Dorothée; Schiller, Daniela

    2015-01-01

    The experience of fear is closely linked to the survival of species. Fear can be conceptualized as a brain state that orchestrates defense reactions to threats. To avoid harm, an organism must be equipped with neural circuits that allow learning, detecting, and rapidly responding to threats. Past experience with threat can transform neutral stimuli present at the time of experience into learned threat-related stimuli via associative learning. Pavlovian threat conditioning is the central experimental paradigm to study associative learning. Once learned, these stimulus-response associations are not always expressed depending on context or new experiences with the conditioned stimuli. Neural circuits mediating threat learning have the inherent plasticity to adapt to changing environmental threats. Encounters devoid of danger pave the way for extinction or reconsolidation to occur. Extinction and reconsolidation can both lead to changes in the expression of threat-induced defense responses, but differ in stability and have a different neural basis. This review presents the behavioral models and the system-level neural mechanisms in animals and humans of threat learning and modulation.

  15. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis.

    PubMed

    Yang, Luming; Koo, Dal-Hoe; Li, Dawei; Zhang, Tao; Jiang, Jiming; Luan, Feishi; Renner, Susanne S; Hénaff, Elizabeth; Sanseverino, Walter; Garcia-Mas, Jordi; Casacuberta, Josep; Senalik, Douglas A; Simon, Philipp W; Chen, Jinfeng; Weng, Yiqun

    2014-01-01

    In the large Cucurbitaceae genus Cucumis, cucumber (C. sativus) is the only species with 2n = 2x = 14 chromosomes. The majority of the remaining species, including melon (C. melo) and the sister species of cucumber, C. hystrix, have 2n = 2x = 24 chromosomes, implying a reduction from n = 12 to n = 7. To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. We identified 14 inversions and a C. hystrix lineage-specific reciprocal inversion between C. hystrix and melon. The results reveal the location and orientation of 53 C. hystrix syntenic blocks on the seven cucumber chromosomes, and allow us to infer at least 59 chromosome rearrangement events that led to the seven cucumber chromosomes, including five fusions, four translocations, and 50 inversions. The 12 inferred chromosomes (AK1-AK12) of an ancestor similar to melon and C. hystrix had strikingly different evolutionary fates, with cucumber chromosome C1 apparently resulting from insertion of chromosome AK12 into the centromeric region of translocated AK2/AK8, cucumber chromosome C3 originating from a Robertsonian-like translocation between AK4 and AK6, and cucumber chromosome C5 originating from fusion of AK9 and AK10. Chromosomes C2, C4 and C6 were the result of complex reshuffling of syntenic blocks from three (AK3, AK5 and AK11), three (AK5, AK7 and AK8) and five (AK2, AK3, AK5, AK8 and AK11) ancestral chromosomes, respectively, through 33 fusion, translocation and inversion events. Previous results (Huang, S., Li, R., Zhang, Z. et al., , Nat. Genet. 41, 1275-1281; Li, D., Cuevas, H.E., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z., Weng, Y. 2011a, BMC Genomics, 12, 396) showing that cucumber C7 stayed largely intact during the entire evolution of Cucumis are supported. Results from this study allow a fine-scale understanding of the

  16. Model of a mechanical clock escapement

    NASA Astrophysics Data System (ADS)

    Moline, David; Wagner, John; Volk, Eugene

    2012-07-01

    The mechanical tower clock originated in Europe during the 14th century to sound hourly bells and later display hands on a dial. An important innovation was the escapement mechanism, which converts stored energy into oscillatory motion for fixed time intervals through the pendulum swing. Previous work has modeled the escapement mechanism in terms of inelastic and elastic collisions. We derive and experimentally verify a theoretical model in terms of impulsive differential equations for the Graham escapement mechanism in a Seth Thomas tower clock. The model offers insight into the clock's mechanical behavior and the functionality of the deadbeat escapement mechanism.

  17. Multiscale mechanical modeling of soft biological tissues

    NASA Astrophysics Data System (ADS)

    Stylianopoulos, Triantafyllos

    2008-10-01

    Soft biological tissues include both native and artificial tissues. In the human body, tissues like the articular cartilage, arterial wall, and heart valve leaflets are examples of structures composed of an underlying network of collagen fibers, cells, proteins and molecules. Artificial tissues are less complex than native tissues and mainly consist of a fiber polymer network with the intent of replacing lost or damaged tissue. Understanding of the mechanical function of these materials is essential for many clinical treatments (e.g. arterial clamping, angioplasty), diseases (e.g. arteriosclerosis) and tissue engineering applications (e.g. engineered blood vessels or heart valves). This thesis presents the derivation and application of a multiscale methodology to describe the macroscopic mechanical function of soft biological tissues incorporating directly their structural architecture. The model, which is based on volume averaging theory, accounts for structural parameters such as the network volume fraction and orientation, the realignment of the fibers in response to strain, the interactions among the fibers and the interactions between the fibers and the interstitial fluid in order to predict the overall tissue behavior. Therefore, instead of using a constitutive equation to relate strain to stress, the tissue microstructure is modeled within a representative volume element (RVE) and the macroscopic response at any point in the tissue is determined by solving a micromechanics problem in the RVE. The model was applied successfully to acellular collagen gels, native blood vessels, and electrospun polyurethane scaffolds and provided accurate predictions for permeability calculations in isotropic and oriented fiber networks. The agreement of model predictions with experimentally determined mechanical properties provided insights into the mechanics of tissues and tissue constructs, while discrepancies revealed limitations of the model framework.

  18. Scenario-based modelling of mass transfer mechanisms at a petroleum contaminated field site-numerical implications.

    PubMed

    Vasudevan, M; Nambi, Indumathi M; Suresh Kumar, G

    2016-06-15

    Knowledge about distribution of dissolved plumes and their influencing factors is essential for risk assessment and remediation of light non-aqueous phase liquid contamination in groundwater. Present study deals with the applicability of numerical model for simulating various hydro-geological scenarios considering non-uniform source distribution at a petroleum contaminated site in Chennai, India. The complexity associated with the hydrogeology of the site has limited scope for on-site quantification of petroleum pipeline spillage. The change in fuel composition under mass-transfer limited conditions was predicted by simultaneously comparing deviations in aqueous concentrations and activity coefficients (between Raoult's law and analytical approaches). The effects of source migration and weathering on the dissolution of major soluble fractions of petroleum fuel were also studied in relation to the apparent change in their activity coefficients and molar fractions. The model results were compared with field observations and found that field conditions were favourable for biodegradation, especially for the aromatic fraction (benzene and toluene (nearly 95% removal), polycyclic aromatic hydrocarbons (up to 65% removal) and xylene (nearly 45% removal). The results help to differentiate the effect of compositional non-ideality from rate-limited dissolution towards tailing of less soluble compounds (alkanes and trimethylbenzene). Although the effect of non-ideality decreased with distance from the source, the assumption of spatially varying residual saturation could effectively illustrate post-spill scenario by estimating the consequent decrease in mass transfer rate.

  19. Molecular analysis and modeling of inactivation of human CYP2D6 by four mechanism based inactivators.

    PubMed

    Livezey, Mara; Nagy, Leslie D; Diffenderfer, Laura E; Arthur, Evan J; Hsi, David J; Holton, Jeffrey M; Furge, Laura Lowe

    2012-03-01

    Human cytochrome P450 2D6 (CYP2D6) is involved in metabolism of approximately 25% of pharmaceutical drugs. Inactivation of CYP2D6 can lead to adverse drug interactions. Four inactivators of CYP2D6 have previously been identified: 5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine(SCH66712), (1-[(2-ethyl- 4-methyl-1H-imidazol-5-yl)-methyl]-4-[4-(trifluoromethyl)-2-pyridinyl]piperazine(EMTPP), paroxetine, and 3,4- methylenedioxymethamphetamine (MDMA). All four contain planar, aromatic groups as well as basic nitrogens common to CYP2D6 substrates. SCH66712 and EMTPP also contain piperazine groups and substituted imidazole rings that are common in pharmaceutical agents, though neither of these compounds is clinically relevant. Paroxetine and MDMA contain methylenedioxyphenyls. SCH66712 and EMTPP are both known protein adductors while paroxetine and MDMA are probable heme modifiers. The current study shows that each inactivator displays Type I binding with Ks values that vary by 2-orders of magnitude with lower Ks values associated with greater inactivation. Comparison of KI, kinact, and partition ratio values shows SCH66712 is the most potent inactivator. Molecular modeling experiments using AutoDock identify Phe120 as a key interaction for all four inactivators with face-to-face and edge-to-face pi interactions apparent. Distance between the ligand and heme iron correlates with potency of inhibition. Ligand conformations were scored according to their binding energies as calculated by AutoDock and correlation was observed between molecular models and Ks values.

  20. MOLECULAR ANALYSIS AND MODELING OF INACTIVATION OF HUMAN CYP2D6 BY FOUR MECHANISM BASED INACTIVATORS

    PubMed Central

    Livezey, Mara; Nagy, Leslie D.; Diffenderfer, Laura E.; Arthur, Evan J.; Hsi, David J.; Holton, Jeffrey M.; Furge, Laura Lowe

    2014-01-01

    Human cytochrome P450 2D6 (CYP2D6) is involved in metabolism of approximately 25% of pharmaceutical drugs. Inactivation of CYP2D6 can lead to adverse drug interactions. Four inactivators of CYP2D6 have previously been identified: 5-Fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine (SCH66712), (1-[(2-ethyl-4-methyl-1H(-EMTPP-imidazol-5-yl)-methyl]-4-[4-(trifluoromethyl)-2-pyridinyl]piperazine (EMTPP), paroxetine, and 3,4-methylenedioxymethamphetamine (MDMA). All four contain planar, aromatic groups as well as basic nitrogens common to CYP2D6 substrates. SCH66712 and EMTPP also contain piperazine groups and substituted imidazole rings that are common in pharmaceutical agents, though neither of these compounds is clinically relevant. Paroxetine and MDMA contain methylenedioxyphenyls. SCH66712 and EMTPP are both known protein adductors while paroxetine and MDMA are probable heme modifiers. The current study shows that each inactivator displays Type I binding with Ks values that vary by 2-orders of magnitude with lower Ks values associated with greater inactivation. Comparison of KI, kinact, and partition ratio values shows SCH66712 is the most potent inactivator. Molecular modeling experiments using AutoDock identify Phe120 as a key interaction for all four inactivators with face-to-face and edge-to-face pi interactions apparent. Distance between the ligand and heme iron correlates with potency of inhibition. Ligand conformations were scored according to their binding energies as calculated by AutoDock and correlation was observed between molecular models and Ks values. PMID:22372551

  1. Mathematical Modeling in Continuum Mechanics

    NASA Astrophysics Data System (ADS)

    Temam, Roger; Miranville, Alain

    2005-06-01

    Temam and Miranville present core topics within the general themes of fluid and solid mechanics. The brisk style allows the text to cover a wide range of topics including viscous flow, magnetohydrodynamics, atmospheric flows, shock equations, turbulence, nonlinear solid mechanics, solitons, and the nonlinear Schrödinger equation. This second edition will be a unique resource for those studying continuum mechanics at the advanced undergraduate and beginning graduate level whether in engineering, mathematics, physics or the applied sciences. Exercises and hints for solutions have been added to the majority of chapters, and the final part on solid mechanics has been substantially expanded. These additions have now made it appropriate for use as a textbook, but it also remains an ideal reference book for students and anyone interested in continuum mechanics.

  2. Albumin and Uptake of Drugs in Cells: Additional Validation Exercises of a Recently Published Equation that Quantifies the Albumin-Facilitated Uptake Mechanism(s) in Physiologically Based Pharmacokinetic and Pharmacodynamic Modeling Research.

    PubMed

    Poulin, Patrick; Haddad, Sami

    2015-12-01

    correction while the experimental data are generated either without albumin or with varied albumin concentrations, in order to predict more accurately the in vivo conditions in physiologically-based pharmacokinetic and pharmacodynamic (PBPK/PD) modeling research. Overall, the protein-facilitated uptake mechanism(s) could be another paradigm shift in addition to a previous paradigm related to the pH gradient effect.

  3. Determination of focal mechanisms of intermediate-magnitude earthquakes in Mexico, based on Greens functions calculated for a 3D Earth model

    NASA Astrophysics Data System (ADS)

    Rodrigo Rodríguez Cardozo, Félix; Hjörleifsdóttir, Vala

    2015-04-01

    One important ingredient in the study of the complex active tectonics in Mexico is the analysis of earthquake focal mechanisms, or the seismic moment tensor. They can be determined trough the calculation of Green functions and subsequent inversion for moment-tensor parameters. However, this calculation is gets progressively more difficult as the magnitude of the earthquakes decreases. Large earthquakes excite waves of longer periods that interact weakly with laterally heterogeneities in the crust. For these earthquakes, using 1D velocity models to compute the Greens fucntions works well. The opposite occurs for smaller and intermediate sized events, where the relatively shorter periods excited interact strongly with lateral heterogeneities in the crust and upper mantle and requires more specific or regional 3D models. In this study, we calculate Greens functions for earthquakes in Mexico using a laterally heterogeneous seismic wave speed model, comprised of mantle model S362ANI (Kustowski et al 2008) and crustal model CRUST 2.0 (Bassin et al 1990). Subsequently, we invert the observed seismograms for the seismic moment tensor using a method developed by Liu et al (2004) an implemented by Óscar de La Vega (2014) for earthquakes in Mexico. By following a brute force approach, in which we include all observed Rayleigh and Love waves of the Mexican National Seismic Network (Servicio Sismológico Naciona, SSN), we obtain reliable focal mechanisms for events that excite a considerable amount of low frequency waves (Mw > 4.8). However, we are not able to consistently estimate focal mechanisms for smaller events using this method, due to high noise levels in many of the records. Excluding the noisy records, or noisy parts of the records manually, requires interactive edition of the data, using an efficient tool for the editing. Therefore, we developed a graphical user interface (GUI), based on python and the python library ObsPy, that allows the edition of observed and

  4. Toxic heavy metal capture using a novel electronic waste-based material-mechanism, modeling and comparison.

    PubMed

    Hadi, Pejman; Barford, John; McKay, Gordon

    2013-08-06

    In the modern communication era, the disposal of printed circuit boards is ecologically of dire concern on a global scale. The two prevalent methods applied for the disposal of this waste are either incineration or landfilling both of which are viewed with skepticism due to their negative environmental impact. Activation of the nonmetallic fraction of this waste leads to the development of a mesoporous material with highly functional groups which can potentially be applied for heavy metal uptake. The removal of copper, lead, and zinc was studied employing a cost-effective novel adsorbent based on waste printed circuit boards. The results indicate that the modification of the original e-waste material has a considerable effect on its surface area enhancement. Adsorption experiments revealed that the modified novel material had uptake capacities of 2.9 mmol Cu, 3.4 mmol Pb, and 2.0 mmol Zn per each gram of the adsorbent which are significantly higher values than its commercial counterparts used in industry.

  5. A mechanical model of overnight hair curling.

    PubMed

    Xiao, Hang; Chen, Xi

    2015-09-01

    Based on the observation of overnight hair curling procedure, we establish a mechanical model to describe the temporary wave formation of straight hair (initial curvature is zero), which incorporates the contact between hair and hair roller. Systematic studies are carried out to explore the effects of radius ratio between hair and hair roller, hair's average axial strain, creep time, Poisson's ratio and gravity on the curl retention. The variation of curl retention with respect to time obtained from our numerical model is validated by a simple theoretical model and by overnight curling experiments on hair samples. The results of simulation show that overnight hair curling is suitable to create a wavy hairstyle within about 7 hours, while the combined usage with hair fixatives enables a wavy hairstyle with desired curvature that lasts for a day or more.

  6. Characterization of the mechanical properties of a new grade of ultra high molecular weight polyethylene and modeling with the viscoplasticity based on overstress.

    PubMed

    Khan, Fazeel; Yeakle, Colin; Gomaa, Said

    2012-02-01

    Enhancements to the service life and performance of orthopedic implants used in total knee and hip replacement procedures can be achieved through optimization of design and the development of superior biocompatible polymeric materials. The introduction of a new or modified polymer must, naturally, be preceded by a rigorous testing program. This paper presents the assessment of the mechanical properties of a new filled grade of ultra high molecular weight polyethylene (UHMWPE) designated AOX(TM) and developed by DePuy Orthopaedics Inc. The deformation behavior was investigated through a series of tensile and compressive tests including strain rate sensitivity, creep, relaxation, and recovery. The polymer was found to exhibit rate-reversal behavior for certain loading histories: strain rate during creep with a compressive stress can be negative, positive, or change between the two during a test. Analogous behavior occurs during relaxation as well. This behavior lies beyond the realm of most numerical models used to computationally investigate and improve part geometry through finite element analysis of components. To address this shortcoming, the viscoplasticity theory based on overstress (VBO) has been suitably modified to capture these trends. VBO is a state variable based model in a differential formulation. Numerical simulation and prediction of all of the aforementioned tests, including good reproduction of the rate reversal behavior, is presented in this study.

  7. Modeling of hydro-thermo-mechanical behavior of Nafion NRE212 for Polymer Electrolyte Membrane Fuel Cells using the Finite Viscoplasticity Theory Based on Overstress for Polymers (FVBOP)

    NASA Astrophysics Data System (ADS)

    Colak, Ozgen U.; Acar, Alperen

    2013-08-01

    The primary aim of this work is to present the modifications made to the Finite Viscoplasticity Theory Based on Overstress for Polymers (FVBOP). This is a unified state variable theory and the proposed changes are designed to account for humidity and temperature effects relevant to the modeling of the hydrothermal deformation behavior of ionomer membranes used in Polymer Electrolyte Membrane Fuel Cells (PEMFC). Towards that end, the flow function, which is responsible for conferring rate dependency in FVBOP, is modified. A secondary objective of this work was to investigate the feasibility of using the storage modulus obtained by Dynamic Mechanical Analysis (DMA) in place of the elasticity modulus obtained from conventional tensile/compressive tests, and find the correlation between the storage modulus and the elasticity modulus. The numerical simulations were juxtaposed against data from tensile monotonic loading and unloading experiments on perfluorosulfonic acid (PFSA) membrane Nafion NRE212 samples which are used extensively as a membrane material in PEMFC. The deformation behavior was modeled at four different temperatures (298, 323, 338, and 353 K—all values below the glass transition temperature of Nafion) and at three water content levels (3, 7 and 8 % swelling). The effects of strain rate, temperature, and hydration were captured well with the modified FVBOP model.

  8. Mechanical Model Development for Composite Structural Supercapacitors

    NASA Technical Reports Server (NTRS)

    Ricks, Trenton M.; Lacy, Thomas E., Jr.; Santiago, Diana; Bednarcyk, Brett A.

    2016-01-01

    Novel composite structural supercapacitor concepts have recently been developed as a means both to store electrical charge and to provide modest mechanical load carrying capability. Double-layer composite supercapacitors are often fabricated by impregnating a woven carbon fiber fabric, which serves as the electrodes, with a structural polymer electrolyte. Polypropylene or a glass fabric is often used as the separator material. Recent research has been primarily limited to evaluating these composites experimentally. In this study, mechanical models based on the Multiscale Generalized Method of Cells (MSGMC) were developed and used to calculate the shear and tensile properties and response of two composite structural supercapacitors from the literature. The modeling approach was first validated against traditional composite laminate data. MSGMC models for composite supercapacitors were developed, and accurate elastic shear/tensile properties were obtained. It is envisioned that further development of the models presented in this work will facilitate the design of composite components for aerospace and automotive applications and can be used to screen candidate constituent materials for inclusion in future composite structural supercapacitor concepts.

  9. Demonstrating the Stretch Reflex: A Mechanical Model.

    ERIC Educational Resources Information Center

    Batavia, Mitchell; McDonough, Andrew L.

    2000-01-01

    Explains the concept of stretch reflexes to students using a mechanical model. The model provides a dynamic multisensory experience using movement, light, and sound. Describes the construction design. (SAH)

  10. Individual-based energetic model suggests bottom up mechanisms for the impact of coastal hypoxia on Pacific harbor seal (Phoca vitulina richardii) foraging behavior.

    PubMed

    Steingass, Sheanna; Horning, Markus

    2017-03-07

    Wind-driven coastal hypoxia represents an environmental stressor that has the potential to drive redistribution of gilled marine organisms, and thereby indirectly affect the foraging characteristics of air-breathing upper trophic-level predators. We used a conceptual individual-based model to simulate effects of coastal hypoxia on the spatial foraging behavior and efficiency of a marine mammal, the Pacific harbor seal (Phoca vitulina richardii) on the Oregon coast. Habitat compression of fish was simulated at varying intensities of hypoxia. Modeled hypoxia affected up to 80% of the water column and half of prey species' horizontal habitat. Pacific sand lance (Ammodytes hexapterus), Pacific herring (Clupea pallasii), and English sole (Parophrys vetulus) were selected as representative harbor seal prey species. Model outputs most affected by coastal hypoxia were seal travel distance to foraging sites, time spent at depth during foraging dives, and daily energy balance. For larger seals, English sole was the most optimal prey during normoxia, however during moderate to severe hypoxia Pacific sand lance was the most beneficial prey. For smaller seals, Pacific herring was the most efficient prey species during normoxia, but sand lance became more efficient as hypoxia increased. Sand lance represented the highest increase in foraging efficiency during severe hypoxic events for all seals. Results suggest that during increasing hypoxia, smaller adult harbor seals could benefit by shifting from foraging on larger neritic schooling fishes to foraging closer inshore on less energetically-dense forage fish. Larger adult seals may benefit by shifting from foraging on groundfish to smaller, schooling neritic fishes as hypoxia increases. The model suggests a mechanism by which hypoxia may result in increased foraging efficiency of Pacific harbor seals, and therefore increased rates of predation on coastal fishes on the continental shelf during hypoxic events.

  11. Statistical mechanics based on fractional classical and quantum mechanics

    SciTech Connect

    Korichi, Z.; Meftah, M. T.

    2014-03-15

    The purpose of this work is to study some problems in statistical mechanics based on the fractional classical and quantum mechanics. At first stage we have presented the thermodynamical properties of the classical ideal gas and the system of N classical oscillators. In both cases, the Hamiltonian contains fractional exponents of the phase space (position and momentum). At the second stage, in the context of the fractional quantum mechanics, we have calculated the thermodynamical properties for the black body radiation, studied the Bose-Einstein statistics with the related problem of the condensation and the Fermi-Dirac statistics.

  12. Modelling the molecular mechanisms of aging.

    PubMed

    Mc Auley, Mark T; Guimera, Alvaro Martinez; Hodgson, David; Mcdonald, Neil; Mooney, Kathleen M; Morgan, Amy E; Proctor, Carole J

    2017-02-28

    The aging process is driven at the cellular level by random molecular damage that slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the aging process. The complexity of the aging process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards and discusses many specific examples of models that have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field.

  13. Modelling the molecular mechanisms of aging

    PubMed Central

    Mc Auley, Mark T.; Guimera, Alvaro Martinez; Hodgson, David; Mcdonald, Neil; Mooney, Kathleen M.; Morgan, Amy E.

    2017-01-01

    The aging process is driven at the cellular level by random molecular damage that slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the aging process. The complexity of the aging process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards and discusses many specific examples of models that have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field. PMID:28096317

  14. Mechanism and modeling of interphase boundary precipitation

    NASA Astrophysics Data System (ADS)

    Meng, Weigang

    Part 1. Mechanism of interphase boundary carbide precipitation in pearlite. Carbide precipitation, containing microalloying elements such as V, Ti, Nb, has been used in steels for decades to increase their yield strength. One mode of the carbide precipitation is InterPhase Boundary (IPR) carbide precipitation. The morphology consists of characteristically aligned rows (planar sheets in three dimension, a special type of "lamellar" structure) or curved rows (non-planar sheets in 3D) of carbides which are associated with the growth interface in both proeutectoid and pearlitic ferrite. The exact mechanism of IPB carbide precipitation is still questioned. IPB vanadium carbide (VC) precipitation at temperatures between 750sp°C and 600sp°C has been investigated by Transmission Electron Microscopy (TEM) in an Fe-C-V steel. The intersection of two sets of VC sheets (both planar and non-planar) within the same proeutectoid ferrite grain reveals the existence of "steps", which is strong evidence in support of the multi-ledge/structural ledge formation mechanism for both planar and non-planar sheets of VC. The formation of IPB carbides can be explained by the multi-ledge/structural ledge mechanism of Aaronson et al. which states that the ferrite/VC transformation occurs through the lateral migration of steps, which are likely inclined to each other and contain structural ledges. It is demonstrated that the IPB vanadium carbide precipitation in pearlite is very similar to that in proeutectoid ferrite. Direction steps at the interlamellar interface are frequently found to intersect with the VC rows. Based on this new evidence and previous work by Hackney, Zhou and Shiflet a shared ledge and a multi-ledge mechanism are proposed for the formation of planar and curved sheets of carbides in pearlite, respectively. A bowing or quasi-ledge mechanism for IPB carbide precipitation in pearlite is an alternate mechanism that will be discussed. Analysis is based within the context of

  15. Neurocomputational Nosology: Malfunctions of Models and Mechanisms.

    PubMed

    Barack, David L; Platt, Michael L

    2016-01-01

    Executive dysfunctions, psychopathologies arising from problems in the control and regulation of behavior, can occur as a result of the faulty execution of formal information processing models or as a result of malfunctioning neural mechanisms. The models correspond to the formal descriptions of how signals in the environment must be transformed in order to behave adaptively, and the mechanisms correspond to the signal transformations that nervous systems implement in order to execute those cognitive functions. Mechanisms in the form of repeated patterns of neural dynamics execute information processing models. Two distinct modes of malfunction can occur when neural dynamics execute models of information processing. The processing models describing behavior may fail to be executed correctly by neural mechanisms. Or, the neural mechanisms may malfunction, failing to implement the right computation. As an example of malfunctioning models in executive cognition, purported failures of rule following can be understood as failures to appropriately execute a suite of processing models. As an example of malfunctioning mechanisms of executive cognition, maladaptive behavior resulting from dysfunction in the medial prefrontal cortex (mPFC) can be understood as failures in the signal transformations carried out therein. The purpose of these examples is to illustrate the potential benefits of considering models and mechanisms in the diagnosis and etiology of neuropsychological illness and dysfunction, especially disorders of executive cognition.

  16. Neurocomputational Nosology: Malfunctions of Models and Mechanisms

    PubMed Central

    Barack, David L.; Platt, Michael L.

    2016-01-01

    Executive dysfunctions, psychopathologies arising from problems in the control and regulation of behavior, can occur as a result of the faulty execution of formal information processing models or as a result of malfunctioning neural mechanisms. The models correspond to the formal descriptions of how signals in the environment must be transformed in order to behave adaptively, and the mechanisms correspond to the signal transformations that nervous systems implement in order to execute those cognitive functions. Mechanisms in the form of repeated patterns of neural dynamics execute information processing models. Two distinct modes of malfunction can occur when neural dynamics execute models of information processing. The processing models describing behavior may fail to be executed correctly by neural mechanisms. Or, the neural mechanisms may malfunction, failing to implement the right computation. As an example of malfunctioning models in executive cognition, purported failures of rule following can be understood as failures to appropriately execute a suite of processing models. As an example of malfunctioning mechanisms of executive cognition, maladaptive behavior resulting from dysfunction in the medial prefrontal cortex (mPFC) can be understood as failures in the signal transformations carried out therein. The purpose of these examples is to illustrate the potential benefits of considering models and mechanisms in the diagnosis and etiology of neuropsychological illness and dysfunction, especially disorders of executive cognition. PMID:27199835

  17. Indentation analysis of nano-particle using nano-contact mechanics models during nano-manipulation based on atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Daeinabi, Khadijeh; Korayem, Moharam Habibnejad

    2011-03-01

    Atomic force microscopy is applied to measure intermolecular forces and mechanical properties of materials, nano-particle manipulation, surface scanning and imaging with atomic accuracy in the nano-world. During nano-manipulation process, contact forces cause indentation in contact area between nano-particle and tip/substrate which is considerable at nano-scale and affects the nano-manipulation process. Several nano-contact mechanics models such as Hertz, Derjaguin-Muller-Toporov (DMT), Johnson-Kendall-Roberts-Sperling (JKRS), Burnham-Colton-Pollock (BCP), Maugis-Dugdale (MD), Carpick-Ogletree-Salmeron (COS), Pietrement-Troyon (PT), and Sun et al. have been applied as the continuum mechanics approaches at nano-scale. In this article, indentation depth and contact radius between tip and substrate with nano-particle for both spherical and conical tip shape during nano-manipulation process are analyzed and compared by applying theoretical, semiempirical, and empirical nano-contact mechanics models. The effects of adhesion force, as the main contrast point in different nano-contact mechanics models, on nano-manipulation analysis is investigated for different contact radius, and the critical point is discussed for mentioned models.

  18. Modeling mechanical response of heterogeneous materials

    NASA Astrophysics Data System (ADS)

    Pal, Siladitya

    Heterogeneous materials are ubiquitous in nature and as synthetic materials. These materials provide unique combination of desirable mechanical properties emerging from its heterogeneities at different length scales. Future structural and technological applications will require the development of advanced light weight materials with superior strength and toughness. Cost effective design of the advanced high performance synthetic materials by tailoring their microstructure is the challenge facing the materials design community. Prior knowledge of structure-property relationships for these materials is imperative for optimal design. Thus, understanding such relationships for heterogeneous materials is of primary interest. Furthermore, computational burden is becoming critical concern in several areas of heterogeneous materials design. Therefore, computationally efficient and accurate predictive tools are highly essential. In the present study, we mainly focus on mechanical behavior of soft cellular materials and tough biological material such as mussel byssus thread. Cellular materials exhibit microstructural heterogeneity by interconnected network of same material phase. However, mussel byssus thread comprises of two distinct material phases. A robust numerical framework is developed to investigate the micromechanisms behind the macroscopic response of both of these materials. Using this framework, effect of microstuctural parameters has been addressed on the stress state of cellular specimens during split Hopkinson pressure bar test. A voronoi tessellation based algorithm has been developed to simulate the cellular microstructure. Micromechanisms (microinertia, microbuckling and microbending) governing macroscopic behavior of cellular solids are investigated thoroughly with respect to various microstructural and loading parameters. To understand the origin of high toughness of mussel byssus thread, a Genetic Algorithm (GA) based optimization framework has been

  19. Molecular model with quantum mechanical bonding information.

    PubMed

    Bohórquez, Hugo J; Boyd, Russell J; Matta, Chérif F

    2011-11-17

    The molecular structure can be defined quantum mechanically thanks to the theory of atoms in molecules. Here, we report a new molecular model that reflects quantum mechanical properties of the chemical bonds. This graphical representation of molecules is based on the topology of the electron density at the critical points. The eigenvalues of the Hessian are used for depicting the critical points three-dimensionally. The bond path linking two atoms has a thickness that is proportional to the electron density at the bond critical point. The nuclei are represented according to the experimentally determined atomic radii. The resulting molecular structures are similar to the traditional ball and stick ones, with the difference that in this model each object included in the plot provides topological information about the atoms and bonding interactions. As a result, the character and intensity of any given interatomic interaction can be identified by visual inspection, including the noncovalent ones. Because similar bonding interactions have similar plots, this tool permits the visualization of chemical bond transferability, revealing the presence of functional groups in large molecules.

  20. Mechanical models for slosh of liquid fuel

    NASA Technical Reports Server (NTRS)

    Buseck, R.; Benaroya, H.

    1993-01-01

    This paper concentrates on equilibrium behavior of fluids in low or zero gravity, and sloshing in normal and low gravity. Included are a background and review of the literature, and an introduction to a new equivalent mechanical model.

  1. Transmission of mechanical stresses within the cytoskeleton of adherent cells: a theoretical analysis based on a multi-component cell model.

    PubMed

    Tracqui, Philippe; Ohayon, Jacques

    2004-01-01

    How environmental mechanical forces affect cellular functions is a central problem in cell biology. Theoretical models of cellular biomechanics provide relevant tools for understanding how the contributions of deformable intracellular components and specific adhesion conditions at the cell interface are integrated for determining the overall balance of mechanical forces within the cell. We investigate here the spatial distributions of intracellular stresses when adherent cells are probed by magnetic twisting cytometry. The influence of the cell nucleus stiffness on the simulated nonlinear torque-bead rotation response is analyzed by considering a finite element multi-component cell model in which the cell and its nucleus are considered as different hyperelastic materials. We additionally take into account the mechanical properties of the basal cell cortex, which can be affected by the interaction of the basal cell membrane with the extracellular substrate. In agreement with data obtained on epithelial cells, the simulated behaviour of the cell model relates the hyperelastic response observed at the entire cell scale to the distribution of stresses and strains within the nucleus and the cytoskeleton, up to cell adhesion areas. These results, which indicate how mechanical forces are transmitted at distant points through the cytoskeleton, are compared to recent data imaging the highly localized distribution of intracellular stresses.

  2. Detailed reduction of reaction mechanisms for flame modeling

    NASA Technical Reports Server (NTRS)

    Wang, Hai; Frenklach, Michael

    1991-01-01

    A method for reduction of detailed chemical reaction mechanisms, introduced earlier for ignition system, was extended to laminar premixed flames. The reduction is based on testing the reaction and reaction-enthalpy rates of the 'full' reaction mechanism using a zero-dimensional model with the flame temperature profile as a constraint. The technique is demonstrated with numerical tests performed on the mechanism of methane combustion.

  3. Structured detailed opto-mechanical tolerance modeling

    NASA Astrophysics Data System (ADS)

    Swart, P. C.

    2016-02-01

    Opto-mechanical tolerancing is a complex art, which is often reduced to inadequate tabled data of allowable tilts and decentres. During the process the respective roles of optical- and mechanical designers can become entangled and a source of conflict. A framework of principles is introduced to guide the design team through these murky waters. From these principles the development of a catalogue of models, practices and past precedents are proposed. An example is presented to serve as illustration. The final result is a model, of opto-mechanical tolerances, which allows a structured flow of tolerances into optical performance prediction.

  4. Modeling biofilms with dual extracellular electron transfer mechanisms

    PubMed Central

    Renslow, Ryan; Babauta, Jerome; Kuprat, Andrew; Schenk, Jim; Ivory, Cornelius; Fredrickson, Jim; Beyenal, Haluk

    2013-01-01

    Electrochemically active biofilms have a unique form of respiration in which they utilize solid external materials as terminal electron acceptors for their metabolism. Currently, two primary mechanisms have been identified for long-range extracellular electron transfer (EET): a diffusion- and a conduction-based mechanism. Evidence in the literature suggests that some biofilms, particularly Shewanella oneidensis, produce the requisite components for both mechanisms. In this study, a generic model is presented that incorporates the diffusion- and the conduction-based mechanisms and allows electrochemically active biofilms to utilize both simultaneously. The model was applied to S. oneidensis and Geobacter sulfurreducens biofilms using experimentally generated data found in the literature. Our simulation results show that 1) biofilms having both mechanisms available, especially if they can interact, may have a metabolic advantage over biofilms that can use only a single mechanism; 2) the thickness of G. sulfurreducens biofilms is likely not limited by conductivity; 3) accurate intrabiofilm diffusion coefficient values are critical for current generation predictions; and 4) the local biofilm potential and redox potential are two distinct parameters and cannot be assumed to have identical values. Finally, we determined that simulated cyclic and squarewave voltammetry based on our model are currently not capable of determining the specific percentages of extracellular electron transfer mechanisms in a biofilm. The developed model will be a critical tool for designing experiments to explain EET mechanisms. PMID:24113651

  5. Base Flow Model Validation

    NASA Technical Reports Server (NTRS)

    Sinha, Neeraj; Brinckman, Kevin; Jansen, Bernard; Seiner, John

    2011-01-01

    A method was developed of obtaining propulsive base flow data in both hot and cold jet environments, at Mach numbers and altitude of relevance to NASA launcher designs. The base flow data was used to perform computational fluid dynamics (CFD) turbulence model assessments of base flow predictive capabilities in order to provide increased confidence in base thermal and pressure load predictions obtained from computational modeling efforts. Predictive CFD analyses were used in the design of the experiments, available propulsive models were used to reduce program costs and increase success, and a wind tunnel facility was used. The data obtained allowed assessment of CFD/turbulence models in a complex flow environment, working within a building-block procedure to validation, where cold, non-reacting test data was first used for validation, followed by more complex reacting base flow validation.

  6. Mechanical characterization of seismic base isolation elastomers

    SciTech Connect

    Kulak, R.F.; Hughes, T.H.

    1991-01-01

    From the various devices proposed for seismic isolators, the laminated elastomer bearing is emerging as the preferred device for large buildings/structures, such as nuclear reactor plants. The laminated bearing is constructed from alternating thin layers of elastomer and metallic plates (shims). The elastomer is usually a carbon filled natural rubber that exhibits damping when subjected to shear. Recently, some blends of natural and synthetic rubbers have appeared. Before candidate elastomers can be used in seismic isolation bearings, their response to design-basis loads and beyond- design-basis loads must be determined. This entails the development of constitutive models and and then the determination of associated material parameters through specimen testing. This paper describes the methods used to obtain data for characterizing the mechanical response of elastomers used for seismic isolation. The data provides a data base for use in determining material parameters associated with nonlinear constitutive models. In addition, the paper presents a definition for a damping ratio that does not exhibit the usual reduction at higher strain cycles. 2 refs., 6 figs., 1 tab.

  7. Time-independent Anisotropic Plastic Behavior by Mechanical Subelement Models

    NASA Technical Reports Server (NTRS)

    Pian, T. H. H.

    1983-01-01

    The paper describes a procedure for modelling the anisotropic elastic-plastic behavior of metals in plane stress state by the mechanical sub-layer model. In this model the stress-strain curves along the longitudinal and transverse directions are represented by short smooth segments which are considered as piecewise linear for simplicity. The model is incorporated in a finite element analysis program which is based on the assumed stress hybrid element and the iscoplasticity-theory.

  8. Mechanical model of a single tendon finger

    NASA Astrophysics Data System (ADS)

    Rossi, Cesare; Savino, Sergio

    2013-10-01

    The mechanical model of a single tendon three phalanxes finger is presented. By means of the model both kinematic and dynamical behavior of the finger itself can be studied. This finger is a part of a more complex mechanical system that consists in a four finger grasping device for robots or in a five finger human hand prosthesis. A first prototype has been realized in our department in order to verify the real behavior of the model. Some results of both kinematic and dynamical behavior are presented.

  9. An automated dynamic fracture procedure and a continuum damage mechanics based model for finite element simulations of delamination failure in laminated composites

    NASA Astrophysics Data System (ADS)

    Aminjikarai Vedagiri, Srinivasa Babu

    An active field of research that has developed due to the increasing use of computational techniques like finite element simulations for analysis of highly complex structural mechanics problems and the increasing use of composite laminates in varied industries such as aerospace, automotive, bio-medical, etc. is the development of numerical models to capture the behavior of composite materials. One of the big challenges not yet overcome convincingly in this field is the modeling of delamination failure which is one of the primary modes of damage in composite laminates. Hence, the primary aim of this work is to develop two numerical models for finite element simulations of delamination failure in composite laminates and implement them in the explicit finite element software DYNA3D/LS-DYNA. Dynamic fracture mechanics is an example of a complex structural analysis problem for which finite element simulations seem to be the only possible way to extract detailed information on sophisticated physical quantities of the crack-tip at any instant of time along a highly transient history of fracture. However, general purpose, commercial finite element software which have capabilities to do fracture analyses are still limited in their use to stationary cracks and crack propagation along trajectories known a priori. Therefore, an automated dynamic fracture procedure capable of simulating dynamic propagation of through-thickness cracks in arbitrary directions in linear, isotropic materials without user-intervention is first developed and implemented in DYNA3D for its default 8-node solid (brick) element. Dynamic energy release rate and stress intensity factors are computed in the model using integral expressions particularly well-suited for the finite element method. Energy approach is used to check for crack propagation and the maximum circumferential stress criterion is used to determine the direction of crack growth. Since the re-meshing strategy used to model crack growth

  10. A fully coupled thermal, chemical, mechanical cookoff model

    SciTech Connect

    Hobbs, M.L.; Baer, M.R.; Gross, R.J.

    1994-05-01

    Cookoff modeling of confined energetic materials involves the coupling of thermal, chemical and mechanical effects. In the past, modeling has focussed on the prediction of thermal runaway with little regard to the effects of mechanical behavior of the energetic material. To address the mechanical response of the energetic material, a constitutive submodel has been developed which can be incorporated into thermal-chemical-mechanical analysis. This work presents development of this submodel and its incorporation into a fully coupled one-dimensional, thermal-chemical-mechanical computer code to simulate thermal initiation of energetic materials. Model predictions include temperature, chemical species, stress, strain, solid/gas pressure, solid/gas density, yield function, and gas volume fraction. Sample results from a scaled aluminum tube filled with RDX exposed to a constant temperature bath at 500 K will be displayed. The micromechanical submodel is based on bubble mechanics which describes nucleation, decomposition, and elastic/plastic mechanical behavior. This constitutive material description requires input of temperatures and reacted fraction of the energetic material as provided by the reactive heat flow code, XCHEM, and the mechanical response is predicted using a quasistatic mechanics code, SANTOS. A parametric sensitivity analysis indicates that a small degree of decomposition causes significant pressurization of the energetic material, which implies that cookoff modeling must consider the strong interaction between thermal-chemistry and mechanics. This document consists of view graphs from the poster session.

  11. Mechanism of thioether oxidation over di- and tetrameric ti centres: kinetic and DFT studies based on model Ti-containing polyoxometalates.

    PubMed

    Skobelev, Igor Y; Zalomaeva, Olga V; Kholdeeva, Oxana A; Poblet, Josep M; Carbó, Jorge J

    2015-10-05

    The oxidation of thioethers by the green oxidant aqueous H2 O2 catalysed by the tetratitanium-substituted Polyoxometalate (POM) (Bu4 N)8 [{γ-SiTi2 W10 O36 (OH)2 }2 (μ-O)2 ], as a model catalyst comprising tetrameric titanium centres, was investigated by kinetic modelling and DFT calculations. Several mechanisms of sulfoxidation were evaluated by using methyl phenyl sulfide (PhSMe) as a model substrate in the experiments and dimethyl sulfide in the calculations. The first mechanism assumes that the active hydroperoxo species forms directly through interaction of the Ti2 (μ-OH)2 group in [{γ-SiTi2 W10 O36 (OH)2 }2 (μ-O)2 ](8-) (1 D) with H2 O2 . The second mechanism includes hydrolysis of Ti-O-Ti bonds linking two γ-Keggin units in structure 1 D to produce the monomer [(γ-SiW10 Ti2 O38 H2 )(OH)2 ](4-) (1 M), followed by the formation of an active hydroperoxo species upon interaction of the Ti hydroxo group with H2 O2 . Both kinetic modelling and DFT calculations support the mechanism through the monomeric species that involves the hydrolysis step. According to the DFT studies the activation of H2 O2 by compound 1 M is preferred by 6.5 kcal mol(-1) with respect to anion 1 D due to the more flexible Ti environment of the terminal Ti hydroxo group in 1 M. The calculations also indicate that for the "monomeric" mechanism two pathways are operative: the mono- and the multinuclear pathway. In the mononuclear mechanism, the active group is the terminal TiOH group, whereas in the multinuclear path the active group is the bridging Ti2 (μ-OH) moiety. Moreover, unlike previous studies, the sulfoxidation is preferred through a β-oxygen atom transfer from the Ti hydroperoxo group because the α-oxygen atom transfer leads to an unfavourable seven-fold coordinated Ti environment in the transition state. Finally, we have generalised these results to other Ti-containing POMs: the Ti-monosubstituted α-Keggin ion [α-PTi(OH)W11 O39 ](4-) and the dititanium

  12. 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.

  13. A model for cyclic mechanical reinforcement

    PubMed Central

    Li, Zhenhai; Kong, Fang; Zhu, Cheng

    2016-01-01

    Mechanical force regulates a broad range of molecular interactions in biology. Three types of counterintuitive mechanical regulation of receptor–ligand dissociation have been described. Catch bonds are strengthened by constant forces, as opposed to slip bonds that are weakened by constant forces. The phenomenon that bonds become stronger with prior application of cyclic forces is termed cyclic mechanical reinforcement (CMR). Slip and catch bonds have respectively been explained by two-state models. However, they assume fast equilibration between internal states and hence are inadequate for CMR. Here we propose a three-state model for CMR where both loading and unloading regulate the transition of bonds among the short-lived, intermediate, and long-lived state. Cyclic forces favor bonds in the long-lived state, hence greatly prolonging their lifetimes. The three-state model explains the force history effect and agrees with the experimental CMR effect of integrin α5β1–fibronectin interaction. This model helps decipher the distinctive ways by which molecular bonds are mechanically strengthened: catch bonds by constant forces and CMR by cyclic forces. The different types of mechanical regulation may enable the cell to fine tune its mechanotransduction via membrane receptors. PMID:27786286

  14. Modeling thermal/chemical/mechanical response of energetic materials

    SciTech Connect

    Baer, M.R.; Hobbs, M.L.; Gross, R.J.

    1995-07-01

    An overview of modeling at Sandia National Laboratories is presented which describes coupled thermal, chemical and mechanical response of energetic materials. This modeling addresses cookoff scenarios for safety assessment studies in systems containing energetic materials. Foundation work is discussed which establishes a method for incorporating chemistry and mechanics into multidimensional analysis. Finite element analysis offers the capabilities to simultaneously resolve reactive heat transfer and structural mechanics in complex geometries. Nonlinear conduction heat transfer, with multiple step finite-rate chemistry, is resolved using a thermal finite element code. Rate equations are solved element-by-element using a modified matrix-free stiff solver This finite element software was developed for the simulation of systems requiring large numbers of finite elements. An iterative implicit scheme, based on the conjugate gradient method, is used and a hemi-cube algorithm is employed for the determination of view factors in surface-to-surface radiation transfer The critical link between the reactive heat transfer and mechanics is the introduction of an appropriate constitutive material model providing a stress-strain relationship for quasi-static mechanics analysis. This model is formally derived from bubble nucleation theory, and parameter variations of critical model parameters indicate that a small degree of decomposition leads to significant mechanical response. Coupled thermal/chemical/mechanical analysis is presented which simulates experiments designed to probe cookoff thermal-mechanical response of energetic materials.

  15. Modeling Transport and Flow Regulatory Mechanisms of the Kidney

    PubMed Central

    Layton, Anita T.

    2013-01-01

    The kidney plays an indispensable role in the regulation of whole-organism water balance, electrolyte balance, and acid-base balance, and in the excretion of metabolic wastes and toxins. In this paper, we review representative mathematical models that have been developed to better understand kidney physiology and pathophysiology, including the regulation of glomerular filtration, the regulation of renal blood flow by means of the tubuloglomerular feedback mechanisms and of the myogenic mechanism, the urine concentrating mechanism, and regulation of renal oxygen transport. We discuss how such modeling efforts have significantly expanded our understanding of renal function in both health and disease. PMID:23914303

  16. Secondary Inorganic Soluble Aerosol in Hong Kong: Continuous Measurements, Formation Mechanism Discussion and Improvement of an Observation-Based Model to Study Control Strategies

    NASA Astrophysics Data System (ADS)

    Xue, Jian

    Work in this thesis focuses on half-hourly or hourly measurements of PM2.5 secondary inorganic aerosols (SIA) in two locations in Hong Kong (HK) using a continuous system, PILS (Particle-into-Liquid System) coupled to two ion chromatographs. The high-resolution data sets allow the examination of SIA temporal dynamics in the scale of hours that the filter-based approach is incapable of providing. (1) Impacts of local emissions, regional transports and their interactions on chemical composition and concentrations of PM2.5 SIA and other ionic species were investigated at the Hong Kong University of Science and Technology (HKUST), a receptor site, under three synoptic conditions. (2) Chemical compositions and size characteristics of ionic species were investigated at Tung Chung, a new town area located in the Southwest part of HK. The sampling period was from 17 to 26 December 2009, covering both normal conditions and an aerosol episode. The three major secondary inorganic ions, SO42, NH4+ and NO 3-, accounted for 47 +/- 6% of PM2.5 mass. Further examination of size characteristics of NO3 - shows that fine mode NO3- is more likely to occur in environments when the fine particles are less acidic and the sea-salt aerosol contributions are low. (3) The ionic chemical composition of PM2.5 and meteorological parameters (e.g., temperature, RH) obtained at the HKUST site under all three different synoptic conditions are input into Aerosol Inorganic Model (AIM-III) for estimation of in situ pH through calculation of H+ amount and aerosol liquid water content (LWC). The second part of this thesis work is to improve an observation-based model (OBAMAP) for SIA, which was first developed by Dr. Zibing Yuan (2006) to evaluate the sensitivity of formation of nitrate ad sulfate to changes in the emissions of their precursors (i.e., NOx, SO2, and VOCs). The improvement work includes incorporating updated chemical mechanisms, thermodynamic equilibrium for gas-aerosol phase

  17. Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).

    PubMed

    Konno, Michiko; Sumida, Tomomi; Uchikawa, Emiko; Mori, Yukie; Yanagisawa, Tatsuo; Sekine, Shun-ichi; Yokoyama, Shigeyuki; Yokoyama, Shigeuki

    2009-09-01

    The ATP-pyrophosphate exchange reaction catalyzed by Arg-tRNA, Gln-tRNA and Glu-tRNA synthetases requires the assistance of the cognate tRNA. tRNA also assists Arg-tRNA synthetase in catalyzing the pyrophosphorolysis of synthetic Arg-AMP at low pH. The mechanism by which the 3'-end A76, and in particular its hydroxyl group, of the cognate tRNA is involved with the exchange reaction catalyzed by those enzymes has yet to be established. We determined a crystal structure of a complex of Arg-tRNA synthetase from Pyrococcus horikoshii, tRNA(Arg)(CCU) and an ATP analog with Rfactor = 0.213 (Rfree = 0.253) at 2.0 A resolution. On the basis of newly obtained structural information about the position of ATP bound on the enzyme, we constructed a structural model for a mechanism in which the formation of a hydrogen bond between the 2'-OH group of A76 of tRNA and the carboxyl group of Arg induces both formation of Arg-AMP (Arg + ATP --> Arg-AMP + pyrophosphate) and pyrophosphorolysis of Arg-AMP (Arg-AMP + pyrophosphate --> Arg + ATP) at low pH. Furthermore, we obtained a structural model of the molecular mechanism for the Arg-tRNA synthetase-catalyzed deacylation of Arg-tRNA (Arg-tRNA + AMP --> Arg-AMP + tRNA at high pH), in which the deacylation of aminoacyl-tRNA bound on Arg-tRNA synthetase and Glu-tRNA synthetase is catalyzed by a quite similar mechanism, whereby the proton-donating group (-NH-C+(NH2)2 or -COOH) of Arg and Glu assists the aminoacyl transfer from the 2'-OH group of tRNA to the phosphate group of AMP at high pH.

  18. Thermal shock fracture mechanics analysis of a semi-infinite medium based on the dual-phase-lag heat conduction model

    PubMed Central

    Wang, B.; Li, J. E.; Yang, C.

    2015-01-01

    The generalized lagging behaviour in solids is very important in understanding heat conduction in small-scale and high-rate heating. In this paper, an edge crack in a semi-infinite medium subjected to a heat shock on its surface is studied under the framework of the dual-phase-lag (DPL) heat conduction model. The transient thermal stress in the medium without crack is obtained first. This stress is used as the crack surface traction with an opposite sign to formulate the crack problem. Numerical results of thermal stress intensity factor are obtained as the functions of crack length and thermal shock time. Crack propagation predictions are conducted and results based on the DPL model and those based on the classical Fourier heat conduction model are compared. The thermal shock strength that the medium can sustain without catastrophic failure is established according to the maximum local stress criterion and the stress intensity factor criterion. PMID:25663805

  19. Thermal shock fracture mechanics analysis of a semi-infinite medium based on the dual-phase-lag heat conduction model.

    PubMed

    Wang, B; Li, J E; Yang, C

    2015-02-08

    The generalized lagging behaviour in solids is very important in understanding heat conduction in small-scale and high-rate heating. In this paper, an edge crack in a semi-infinite medium subjected to a heat shock on its surface is studied under the framework of the dual-phase-lag (DPL) heat conduction model. The transient thermal stress in the medium without crack is obtained first. This stress is used as the crack surface traction with an opposite sign to formulate the crack problem. Numerical results of thermal stress intensity factor are obtained as the functions of crack length and thermal shock time. Crack propagation predictions are conducted and results based on the DPL model and those based on the classical Fourier heat conduction model are compared. The thermal shock strength that the medium can sustain without catastrophic failure is established according to the maximum local stress criterion and the stress intensity factor criterion.

  20. Polar auxin transport: models and mechanisms.

    PubMed

    van Berkel, Klaartje; de Boer, Rob J; Scheres, Ben; ten Tusscher, Kirsten

    2013-06-01

    Spatial patterns of the hormone auxin are important drivers of plant development. The observed feedback between the active, directed transport that generates auxin patterns and the auxin distribution that influences transport orientation has rendered this a popular subject for modelling studies. Here we propose a new mathematical framework for the analysis of polar auxin transport and present a detailed mathematical analysis of published models. We show that most models allow for self-organised patterning for similar biological assumptions, and find that the pattern generated is typically unidirectional, unless additional assumptions or mechanisms are incorporated. Our analysis thus suggests that current models cannot explain the bidirectional fountain-type patterns found in plant meristems in a fully self-organised manner, and we discuss future research directions to address the gaps in our understanding of auxin transport mechanisms.

  1. Modeling biofilms with dual extracellular electron transfer mechanisms

    SciTech Connect

    Renslow, Ryan S.; Babauta, Jerome T.; Kuprat, Andrew P.; Schenk, Jim; Ivory, Cornelius; Fredrickson, Jim K.; Beyenal, Haluk

    2013-11-28

    Electrochemically active biofilms have a unique form of respiration in which they utilize solid external materials as their terminal electron acceptor for metabolism. Currently, two primary mechanisms have been identified for long-range extracellular electron transfer (EET): a diffusion- and a conduction-based mechanism. Evidence in the literature suggests that some biofilms, particularly Shewanella oneidensis, produce components requisite for both mechanisms. In this study, a generic model is presented that incorporates both diffusion- and conduction-based mechanisms and allows electrochemically active biofilms to utilize both simultaneously. The model was applied to Shewanella oneidensis and Geobacter sulfurreducens biofilms using experimentally generated data found the literature. Our simulation results showed that 1) biofilms having both mechanisms available, especially if they can interact, may have metabolic advantage over biofilms that can use only a single mechanism; 2) the thickness of Geobacter sulfurreducens biofilms is likely not limited by conductivity; 3) accurate intrabiofilm diffusion coefficient values are critical for current generation predictions; and 4) the local biofilm potential and redox potential are two distinct measurements and cannot be assumed to have identical values. Finally, we determined that cyclic and squarewave voltammetry are currently not good tools to determine the specific percentage of extracellular electron transfer mechanisms used by biofilms. The developed model will be a critical tool in designing experiments to explain EET mechanisms.

  2. Quantum Mechanical Modeling of Ballistic MOSFETs

    NASA Technical Reports Server (NTRS)

    Svizhenko, Alexei; Anantram, M. P.; Govindan, T. R.; Biegel, Bryan (Technical Monitor)

    2001-01-01

    The objective of this project was to develop theory, approximations, and computer code to model quasi 1D structures such as nanotubes, DNA, and MOSFETs: (1) Nanotubes: Influence of defects on ballistic transport, electro-mechanical properties, and metal-nanotube coupling; (2) DNA: Model electron transfer (biochemistry) and transport experiments, and sequence dependence of conductance; and (3) MOSFETs: 2D doping profiles, polysilicon depletion, source to drain and gate tunneling, understand ballistic limit.

  3. Modelling approaches for evaluating multiscale tendon mechanics

    PubMed Central

    Fang, Fei; Lake, Spencer P.

    2016-01-01

    Tendon exhibits anisotropic, inhomogeneous and viscoelastic mechanical properties that are determined by its complicated hierarchical structure and varying amounts/organization of different tissue constituents. Although extensive research has been conducted to use modelling approaches to interpret tendon structure–function relationships in combination with experimental data, many issues remain unclear (i.e. the role of minor components such as decorin, aggrecan and elastin), and the integration of mechanical analysis across different length scales has not been well applied to explore stress or strain transfer from macro- to microscale. This review outlines mathematical and computational models that have been used to understand tendon mechanics at different scales of the hierarchical organization. Model representations at the molecular, fibril and tissue levels are discussed, including formulations that follow phenomenological and microstructural approaches (which include evaluations of crimp, helical structure and the interaction between collagen fibrils and proteoglycans). Multiscale modelling approaches incorporating tendon features are suggested to be an advantageous methodology to understand further the physiological mechanical response of tendon and corresponding adaptation of properties owing to unique in vivo loading environments. PMID:26855747

  4. Modeling mechanical interactions between cancerous mammary acini

    NASA Astrophysics Data System (ADS)

    Wang, Jeffrey; Liphardt, Jan; Rycroft, Chris

    2015-03-01

    The rules and mechanical forces governing cell motility and interactions with the extracellular matrix of a tissue are often critical for understanding the mechanisms by which breast cancer is able to spread through the breast tissue and eventually metastasize. Ex vivo experimentation has demonstrated the the formation of long collagen fibers through collagen gels between the cancerous mammary acini responsible for milk production, providing a fiber scaffolding along which cancer cells can disorganize. We present a minimal mechanical model that serves as a potential explanation for the formation of these collagen fibers and the resultant motion. Our working hypothesis is that cancerous cells induce this fiber formation by pulling on the gel and taking advantage of the specific mechanical properties of collagen. To model this system, we employ a new Eulerian, fixed grid simulation method to model the collagen as a nonlinear viscoelastic material subject to various forces coupled with a multi-agent model to describe individual cancer cells. We find that these phenomena can be explained two simple ideas: cells pull collagen radially inwards and move towards the tension gradient of the collagen gel, while being exposed to standard adhesive and collision forces.

  5. Quantum mechanical hamiltonian models of turing machines

    NASA Astrophysics Data System (ADS)

    Benioff, Paul

    1982-11-01

    Quantum mechanical Hamiltonian models, which represent an aribtrary but finite number of steps of any Turing machine computation, are constructed here on a finite lattice of spin-1/2 systems. Different regions of the lattice correspond to different components of the Turing machine (plus recording system). Successive states of any machine computation are represented in the model by spin configuration states. Both time-independent and time-dependent Hamiltonian models are constructed here. The time-independent models do not dissipate energy or degrade the system state as they evolve. They operate close to the quantum limit in that the total system energy uncertainty/computation speed is close to the limit given by the time-energy uncertainty relation. However, the model evolution is time global and the Hamiltonian is more complex. The time-dependent models do not degrade the system state. Also they are time local and the Hamiltonian is less complex.

  6. Glutamate Transporter Homolog-based Model Predicts That Anion-π Interaction Is the Mechanism for the Voltage-dependent Response of Prestin*

    PubMed Central

    Lovas, Sándor; He, David Z. Z.; Liu, Huizhan; Tang, Jie; Pecka, Jason L.; Hatfield, Marcus P. D.; Beisel, Kirk W.

    2015-01-01

    Prestin is the motor protein of cochlear outer hair cells. Its unique capability to perform direct, rapid, and reciprocal electromechanical conversion depends on membrane potential and interaction with intracellular anions. How prestin senses the voltage change and interacts with anions are still unknown. Our three-dimensional model of prestin using molecular dynamics simulations predicts that prestin contains eight transmembrane-spanning segments and two helical re-entry loops and that tyrosyl residues are the structural specialization of the molecule for the unique function of prestin. Using site-directed mutagenesis and electrophysiological techniques, we confirmed that residues Tyr367, Tyr486, Tyr501, and Tyr508 contribute to anion binding, interacting with intracellular anions through novel anion-π interactions. Such weak interactions, sensitive to voltage and mechanical stimulation, confer prestin with a unique capability to perform electromechanical and mechanoelectric conversions with exquisite sensitivity. This novel mechanism is completely different from all known mechanisms seen in ion channels, transporters, and motor proteins. PMID:26283790

  7. Modeling and experimental research on a removal mechanism during chemical mechanical polishing at the molecular scale

    NASA Astrophysics Data System (ADS)

    Wei, An; Yongwu, Zhao; Yongguang, Wang

    2010-11-01

    In order to understand the fundamentals of the chemical mechanical polishing (CMP) material removal mechanism, the indentation depth of a slurry particle into a wafer surface is determined using the in situ nanomechanical testing system tribo-indenter by Hysitron. It was found that the removal mechanism in CMP is most probably a molecular scale removal theory. Furthermore, a comprehensive mathematical model was modified and used to pinpoint the effects of wafer/pad relative velocity, which has not been modeled previously. The predicted results based on the current model are shown to be consistent with the published experimental data. Results and analysis may lead to further understanding of the microscopic removal mechanism at the molecular scale in addition to its underlying theoretical foundation.

  8. Model based manipulator control

    NASA Technical Reports Server (NTRS)

    Petrosky, Lyman J.; Oppenheim, Irving J.

    1989-01-01

    The feasibility of using model based control (MBC) for robotic manipulators was investigated. A double inverted pendulum system was constructed as the experimental system for a general study of dynamically stable manipulation. The original interest in dynamically stable systems was driven by the objective of high vertical reach (balancing), and the planning of inertially favorable trajectories for force and payload demands. The model-based control approach is described and the results of experimental tests are summarized. Results directly demonstrate that MBC can provide stable control at all speeds of operation and support operations requiring dynamic stability such as balancing. The application of MBC to systems with flexible links is also discussed.

  9. Magnetic suspension based Fourier Transform Infrared Spectrometer mechanism (FTIS)

    NASA Astrophysics Data System (ADS)

    Köker, Ingo; Langenbach, Harald; Schmid, Manfred; Lautier, Jean-Michel

    2005-07-01

    In the frame of an ESTEC technology contract the development of a Magnetically Suspended Fourier Transform Spectrometer Mechanism (FTIS) was carried out. The aim of the development is to avoid the issues found in mechanically suspended systems and to provide an active alignment and disturbance rejection capability for spectrometer applications. In the frame of FTIS an actively controlled suspension system based on the use of magnetic bearings was defined, developed and built as a demonstration model.

  10. Linking Theoretical Decision-making Mechanisms in the Simon Task with Electrophysiological Data: A Model-based Neuroscience Study in Humans.

    PubMed

    Servant, Mathieu; White, Corey; Montagnini, Anna; Burle, Borís

    2016-10-01

    A current challenge for decision-making research is in extending models of simple decisions to more complex and ecological choice situations. Conflict tasks (e.g., Simon, Stroop, Eriksen flanker) have been the focus of much interest, because they provide a decision-making context representative of everyday life experiences. Modeling efforts have led to an elaborated drift diffusion model for conflict tasks (DMC), which implements a superimposition of automatic and controlled decision activations. The DMC has proven to capture the diversity of behavioral conflict effects across various task contexts. This study combined DMC predictions with EEG and EMG measurements to test a set of linking propositions that specify the relationship between theoretical decision-making mechanisms involved in the Simon task and brain activity. Our results are consistent with a representation of the superimposed decision variable in the primary motor cortices. The decision variable was also observed in the EMG activity of response agonist muscles. These findings provide new insight into the neurophysiology of human decision-making. In return, they provide support for the DMC model framework.

  11. Comparing fluid mechanics models with experimental data.

    PubMed

    Spedding, G R

    2003-09-29

    The art of modelling the physical world lies in the appropriate simplification and abstraction of the complete problem. In fluid mechanics, the Navier-Stokes equations provide a model that is valid under most circumstances germane to animal locomotion, but the complexity of solutions provides strong incentive for the development of further, more simplified practical models. When the flow organizes itself so that all shearing motions are collected into localized patches, then various mathematical vortex models have been very successful in predicting and furthering the physical understanding of many flows, particularly in aerodynamics. Experimental models have the significant added convenience that the fluid mechanics can be generated by a real fluid, not a model, provided the appropriate dimensionless groups have similar values. Then, analogous problems can be encountered in making intelligible but independent descriptions of the experimental results. Finally, model predictions and experimental results may be compared if, and only if, numerical estimates of the likely variations in the tested quantities are provided. Examples from recent experimental measurements of wakes behind a fixed wing and behind a bird in free flight are used to illustrate these principles.

  12. Comparing fluid mechanics models with experimental data.

    PubMed Central

    Spedding, G R

    2003-01-01

    The art of modelling the physical world lies in the appropriate simplification and abstraction of the complete problem. In fluid mechanics, the Navier-Stokes equations provide a model that is valid under most circumstances germane to animal locomotion, but the complexity of solutions provides strong incentive for the development of further, more simplified practical models. When the flow organizes itself so that all shearing motions are collected into localized patches, then various mathematical vortex models have been very successful in predicting and furthering the physical understanding of many flows, particularly in aerodynamics. Experimental models have the significant added convenience that the fluid mechanics can be generated by a real fluid, not a model, provided the appropriate dimensionless groups have similar values. Then, analogous problems can be encountered in making intelligible but independent descriptions of the experimental results. Finally, model predictions and experimental results may be compared if, and only if, numerical estimates of the likely variations in the tested quantities are provided. Examples from recent experimental measurements of wakes behind a fixed wing and behind a bird in free flight are used to illustrate these principles. PMID:14561348

  13. Modeling molecular mechanisms in the axon

    NASA Astrophysics Data System (ADS)

    de Rooij, R.; Miller, K. E.; Kuhl, E.

    2016-12-01

    Axons are living systems that display highly dynamic changes in stiffness, viscosity, and internal stress. However, the mechanistic origin of these phenomenological properties remains elusive. Here we establish a computational mechanics model that interprets cellular-level characteristics as emergent properties from molecular-level events. We create an axon model of discrete microtubules, which are connected to neighboring microtubules via discrete crosslinking mechanisms that obey a set of simple rules. We explore two types of mechanisms: passive and active crosslinking. Our passive and active simulations suggest that the stiffness and viscosity of the axon increase linearly with the crosslink density, and that both are highly sensitive to the crosslink detachment and reattachment times. Our model explains how active crosslinking with dynein motors generates internal stresses and actively drives axon elongation. We anticipate that our model will allow us to probe a wide variety of molecular phenomena—both in isolation and in interaction—to explore emergent cellular-level features under physiological and pathological conditions.

  14. Modeling molecular mechanisms in the axon

    NASA Astrophysics Data System (ADS)

    de Rooij, R.; Miller, K. E.; Kuhl, E.

    2017-03-01

    Axons are living systems that display highly dynamic changes in stiffness, viscosity, and internal stress. However, the mechanistic origin of these phenomenological properties remains elusive. Here we establish a computational mechanics model that interprets cellular-level characteristics as emergent properties from molecular-level events. We create an axon model of discrete microtubules, which are connected to neighboring microtubules via discrete crosslinking mechanisms that obey a set of simple rules. We explore two types of mechanisms: passive and active crosslinking. Our passive and active simulations suggest that the stiffness and viscosity of the axon increase linearly with the crosslink density, and that both are highly sensitive to the crosslink detachment and reattachment times. Our model explains how active crosslinking with dynein motors generates internal stresses and actively drives axon elongation. We anticipate that our model will allow us to probe a wide variety of molecular phenomena—both in isolation and in interaction—to explore emergent cellular-level features under physiological and pathological conditions.

  15. Mechanism of the Two-Phase Flow Model for Water and Gas Based on Adsorption and Desorption in Fractured Coal and Rock

    NASA Astrophysics Data System (ADS)

    Chen, Shikuo; Yang, Tianhong; Ranjith, P. G.; Wei, Chenhui

    2017-03-01

    Coalbed methane (CBM) is an important high-efficiency, clean-energy raw material with immense potential for application; however, its occurrence in low-permeability reservoirs limits its application. Hydraulic fracturing has been used in low-permeability CBM exploration and as a new technique for preventing gas hazards in coal mines. Fractures are the main pathways of fluid accumulation and migration, and they exert some control over the stability of rock mass. However, the differences in progression between the original fractures of the coal mass and the new discrete fractures caused by hydraulic fracturing remain unclear, and the unsaturated seepage flows require further study. Therefore, a cross-scale hydraulic fractured rock mass numerical model was developed by using the 3D fractured extrusion coupling variables reconstruction technique. This paper uses fracture surface parameters combined with the fractal dimension and multi-medium theory to provide a high-precision characterization and interpretation of the fracture mechanics. The mechanism of the permeability evolution of fractured coal and rock under stress-releasing mining combined with water injection was studied by considering gas adsorption and desorption as well as the coupling characteristic of seepage-stress in fractured rock masses. Aperture, contact area ratio, and stress in permeability and fracture development have a strong influence on the permeability and seepage path, which in turn control the effective radius by absolute water injection. All of these factors should be considered when studying the structural characteristics of rock masses.

  16. Implementing and Assessing Computational Modeling in Introductory Mechanics

    ERIC Educational Resources Information Center

    Caballero, Marcos D.; Kohlmyer, Matthew A.; Schatz, Michael F.

    2012-01-01

    Students taking introductory physics are rarely exposed to computational modeling. In a one-semester large lecture introductory calculus-based mechanics course at Georgia Tech, students learned to solve physics problems using the VPython programming environment. During the term, 1357 students in this course solved a suite of 14 computational…

  17. Statistical mechanics of ontology based annotations

    NASA Astrophysics Data System (ADS)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.

  18. Models and Mechanisms of Vascular Dementia

    PubMed Central

    Venkat, Poornima; Chopp, Michael; Chen, Jieli

    2015-01-01

    Vascular Dementia (VaD) is the second leading form of dementia after Alzheimer’s disease (AD) plaguing the elderly population. VaD is a progressive disease caused by reduced blood flow to the brain, and it affects cognitive abilities especially executive functioning. VaD is poorly understood and lacks suitable animal models, which constrain the progress on understanding the basis of the disease and developing treatments. This review article discusses VaD, its risk factors, induced cognitive disability, various animal (rodent) models of VaD, pathology, and mechanisms of VaD and treatment options. PMID:25987538

  19. A model for the nonlinear mechanism responsible for cochlear amplification.

    PubMed

    Fessel, Kimberly; Holmes, Mark H

    2014-12-01

    A nonlinear model for the mechanism responsible for the amplification of the sound wave in the ear is derived using the geometric and material properties of the system. The result is a nonlinear beam equation, with the nonlinearity appearing in a coefficient of the equation. Once derived, the beam problem is analyzed for various loading conditions. Based on this analysis it is seen that the mechanism is capable of producing a spatially localized gain, as required by any amplification mechanism, but it is also capable of increasing the spatial contrast in the signal.

  20. In vivo evaluation of bioactive PMMA-based bone cement with unchanged mechanical properties in a load-bearing model on rabbits.

    PubMed

    Fottner, Andreas; Nies, Berthold; Kitanovic, Denis; Steinbrück, Arnd; Hausdorf, Jörg; Mayer-Wagner, Susanne; Pohl, Ulrich; Jansson, Volkmar

    2015-07-01

    Polymethylmethacrylate-based bone cements are widely used for fixation of joint replacements. To improve the long-term outcome, bioactive bone cements are aspired to advance the bone-cement interface. This study evaluated the in vivo properties of a new polymethylmethacrylate-based bioactive bone cement with addition of amphiphilic phosphorylated 2-hydroxyethylmethacrylate. Previous in vitro studies confirmed bioactive properties in cell culture, as well as unchanged mechanical properties are tests according to ISO 5833:2002.Three different variations of the cement (polymethylmethacrylate + phosphorylated 2-hydroxyethylmethacrylate, polymethylmethacrylate + phosphorylated 2-hydroxyethylmethacrylate + CaCl2 and polymethylmethacrylate + phosphorylated 2-hydroxyethylmethacrylate + CaCl2 + Na2CO3) were compared to conventional polymethylmethacrylate cement. To evaluate the properties under load-bearing conditions, a spacer prosthesis was implanted into the femoral diaphysis of 24 rabbits. Additionally, a cement plug was installed into the proximal tibia. After three months, polished sections with Giemsa surface staining were prepared. The bioactivity was determined using the bone affinity index.The sections showed a good osseointegration of the bioactive bone cement without cement cracks under load-bearing conditions. Regarding the bone affinity index, the bioactive bone cement revealed a significantly higher value in the proximal tibia (25.9-37.7%) and around the spacer prosthesis (36.8-58.9%) compared to the conventional polymethylmethacrylate cement (12.8-17.0%).The results confirm the in vivo bioactivity of this bone cement. The absence of cement cracks indicates a sufficient mechanical stability to fix prostheses with this bioactive cement, but for a final assessment long-term tests are necessary.

  1. Parameter identification of hyperelastic material properties of the heel pad based on an analytical contact mechanics model of a spherical indentation.

    PubMed

    Suzuki, Ryo; Ito, Kohta; Lee, Taeyong; Ogihara, Naomichi

    2017-01-01

    Accurate identification of the material properties of the plantar soft tissue is important for computer-aided analysis of foot pathologies and design of therapeutic footwear interventions based on subject-specific models of the foot. However, parameter identification of the hyperelastic material properties of plantar soft tissues usually requires an inverse finite element analysis due to the lack of a practical contact model of the indentation test. In the present study, we derive an analytical contact model of a spherical indentation test in order to directly estimate the material properties of the plantar soft tissue. Force-displacement curves of the heel pads are obtained through an indentation experiment. The experimental data are fit to the analytical stress-strain solution of the spherical indentation in order to obtain the parameters. A spherical indentation approach successfully predicted the non-linear material properties of the heel pad without iterative finite element calculation. The force-displacement curve obtained in the present study was found to be situated lower than those identified in previous studies. The proposed framework for identifying the hyperelastic material parameters may facilitate the development of subject-specific FE modeling of the foot for possible clinical and ergonomic applications.

  2. Numerical modeling of polar mesocyclones generation mechanisms

    NASA Astrophysics Data System (ADS)

    Sergeev, Dennis; Stepanenko, Victor

    2013-04-01

    Polar mesocyclones, commonly referred to as polar lows, remain of great interest due to their complicated dynamics. These mesoscale vortices are small short-living objects that are formed over the observation-sparse high-latitude oceans, and therefore, their evolution can hardly be observed and predicted numerically. The origin of polar mesoscale cyclones is still a matter of uncertainty, though the recent numerical investigations [3] have exposed a strong dependence of the polar mesocyclone development upon the magnitude of baroclinicity. Nevertheless, most of the previous studies focused on the individual polar low (the so-called case studies), with too many factors affecting it simultaneously. None of the earlier studies suggested a clear picture of polar mesocyclone generation within an idealized experiment, where it is possible to look deeper into each single physical process. The present paper concentrates on the initial triggering mechanism of the polar mesocyclone. As it is reported by many researchers, some mesocyclones are formed by the surface forcing, namely the uneven distribution of heat fluxes. That feature is common on the ice boundaries [2], where intense air stream flows from the cold ice surface to the warm sea surface. Hence, the resulting conditions are shallow baroclinicity and strong surface heat fluxes, which provide an arising polar mesocyclone with potential energy source converting it to the kinetic energy of the vortex. It is shown in this paper that different surface characteristics, including thermal parameters and, for example, the shape of an ice edge, determine an initial phase of a polar low life cycle. Moreover, it is shown what initial atmospheric state is most preferable for the formation of a new polar mesocyclone or in maintaining and reinforcing the existing one. The study is based on idealized high-resolution (~2 km) numerical experiment in which baroclinicity, stratification, initial wind profile and disturbance, surface

  3. Information model construction of MES oriented to mechanical blanking workshop

    NASA Astrophysics Data System (ADS)

    Wang, Jin-bo; Wang, Jin-ye; Yue, Yan-fang; Yao, Xue-min

    2016-11-01

    Manufacturing Execution System (MES) is one of the crucial technologies to implement informatization management in manufacturing enterprises, and the construction of its information model is the base of MES database development. Basis on the analysis of the manufacturing process information in mechanical blanking workshop and the information requirement of MES every function module, the IDEF1X method was adopted to construct the information model of MES oriented to mechanical blanking workshop, and a detailed description of the data structure feature included in MES every function module and their logical relationship was given from the point of view of information relationship, which laid the foundation for the design of MES database.

  4. Model-Based Systems

    NASA Technical Reports Server (NTRS)

    Frisch, Harold P.

    2007-01-01

    Engineers, who design systems using text specification documents, focus their work upon the completed system to meet Performance, time and budget goals. Consistency and integrity is difficult to maintain within text documents for a single complex system and more difficult to maintain as several systems are combined into higher-level systems, are maintained over decades, and evolve technically and in performance through updates. This system design approach frequently results in major changes during the system integration and test phase, and in time and budget overruns. Engineers who build system specification documents within a model-based systems environment go a step further and aggregate all of the data. They interrelate all of the data to insure consistency and integrity. After the model is constructed, the various system specification documents are prepared, all from the same database. The consistency and integrity of the model is assured, therefore the consistency and integrity of the various specification documents is insured. This article attempts to define model-based systems relative to such an environment. The intent is to expose the complexity of the enabling problem by outlining what is needed, why it is needed and how needs are being addressed by international standards writing teams.

  5. Mechanical-mathematical modeling for landslide process

    NASA Astrophysics Data System (ADS)

    Svalova, V.

    2009-04-01

    500 m and displacement of a landslide in the plan over 1 m. Last serious activization of a landslide has taken place in 2002 with a motion on 53 cm. Catastrophic activization of the deep blockglide landslide in the area of Khoroshevo in Moscow took place in 2006-2007. A crack of 330 m long appeared in the old sliding circus, along which a new 220 m long creeping block was separated from the plateau and began sinking with a displaced surface of the plateau reaching to 12 m. Such activization of the landslide process was not observed in Moscow since mid XIX century. The sliding area of Khoroshevo was stable during long time without manifestations of activity. Revealing of the reasons of deformation and development of ways of protection from deep landslide motions is extremely actual and difficult problem which decision is necessary for preservation of valuable historical monuments and modern city constructions. The reasons of activization and protective measures are discussed. Structure of monitoring system for urban territories is elaborated. Mechanical-mathematical model of high viscous fluid was used for modeling of matter behavior on landslide slopes. Equation of continuity and an approximated equation of the Navier-Stockes for slow motions in a thin layer were used. The results of modelling give possibility to define the place of highest velocity on landslide surface, which could be the best place for monitoring post position. Model can be used for calibration of monitoring equipment and gives possibility to investigate some fundamental aspects of matter movement on landslide slope.

  6. Mechanism and models for zinc metal morphology in alkaline media

    NASA Technical Reports Server (NTRS)

    May, C. E.; Kautz, H. E.

    1981-01-01

    Based on experimental observations, a mechanism is presented to explain existence of the different morphologies of electrodeposited zinc in alkaline solution. The high current density dendrites appear to be due to more rapid growth on the nonbasal crystallographic planes than on the basal plane. The low current density moss apparently results from dissolution from the nonbasal planes at low cathodic voltages. Electrochemical models were sought which would produce such a phenomenon. The fundamental plating mechanism alone accounts only for different rates on different planes, not for zinc dissolution from a plane in the cathodic region. Fourteen models were explored; two models were in accord with the proposed mechanism. One involves rapid disproportionation of the zinc +1 species on the nonbasal planes. The other involves a redox reaction (corrosion) between the zinc-zincate and hydrogen-water systems.

  7. Mechanical Model of Traditional Thai Massage for Integrated Healthcare.

    PubMed

    Rattanaphan, Salinee; Srichandr, Panya

    2015-01-01

    In this study, a mechanical model was developed, aiming to provide standardized and programmable traditional Thai massage (TTM) therapy to patients. The TTM was modeled and integrated into a mechanical hand (MH) system, and a prototype massage chair was built and tested for user satisfaction. Three fundamental principles of Thai massage were integrated: pull, press, and pin. Based on these principles, the mechanics of Thai massage was studied and a mathematical model was developed to describe the dynamics and conditions for the design and prototyping of an MH. On average, it was found that users were satisfied with the treatment and felt that the treatment was similar to that performed by human hands. According to the interview results, users indicated that they were likely to utilize the MH as an alternative to traditional massage. Therefore, integrated TTM with an MH may help healthcare providers deliver standardized, programmable massage therapy to patients as opposed to variable, inconsistent human massage.

  8. Physical modeling of transverse drainage mechanisms

    NASA Astrophysics Data System (ADS)

    Douglass, J. C.; Schmeeckle, M. W.

    2005-12-01

    Streams that incise across bedrock highlands such as anticlines, upwarps, cuestas, or horsts are termed transverse drainages. Their relevance today involves such diverse matters as highway and dam construction decisions, location of wildlife corridors, better-informed sediment budgets, and detailed studies into developmental histories of late Cenozoic landscapes. The transient conditions responsible for transverse drainage incision have been extensively studied on a case-by-case basis, and the dominate mechanisms proposed include: antecedence, superimposition, overflow, and piracy. Modeling efforts have been limited to antecedence, and such the specific erosional conditions required for transverse drainage incision, with respect to the individual mechanisms, remains poorly understood. In this study, fifteen experiments attempted to simulate the four mechanisms and constructed on a 9.15 m long, 2.1 m wide, and 0.45 m deep stream table. Experiments lasted between 50 and 220 minutes. The stream table was filled with seven tons of sediment consisting of a silt and clay (30%) and a fine to coarse sand (70%) mixture. The physical models highlighted the importance of downstream aggradation with regard to antecedent incision versus possible defeat and diversion. The overflow experiments indicate that retreating knickpoints across a basin outlet produce a high probability of downstream flooding when associated with a deep lake. Misters used in a couple of experiments illustrate a potential complication with regard to headward erosion driven piracy. Relatively level asymmetrically sloped ridges allow for the drainage divide across the ridge to retreat from headward erosion, but hindered when the ridge's apex undulates or when symmetrically sloped. Although these physical models cannot strictly simulate natural transverse drainages, the observed processes, their development over time, and resultant landforms roughly emulate their natural counterparts. Proposed originally from

  9. Mechanical model of an earthquake fault

    NASA Technical Reports Server (NTRS)

    Carlson, J. M.; Langer, J. S.

    1989-01-01

    The dynamic behavior of a simple mechanical model of an earthquake fault is studied. This model, introduced originally by Burridge and Knopoff (1967), consists of an elastically coupled chain of masses in contact with a moving rough surface. The present version of the model retains the full Newtonian dynamics with inertial effects and contains no externally imposed stochasticity or spatial inhomogeneity. The only nonlinear feature is a velocity-weakening stick-slip friction force between the masses and the moving surface. This system is being driven persistently toward a slipping instability and therefore exhibits noisy sequences of earthquakelike events. These events are observed in numerical simulations, and many of their features can be predicted analytically.

  10. A Separable, Dynamically Local Ontological Model of Quantum Mechanics

    NASA Astrophysics Data System (ADS)

    Pienaar, Jacques

    2016-01-01

    A model of reality is called separable if the state of a composite system is equal to the union of the states of its parts, located in different regions of space. Spekkens has argued that it is trivial to reproduce the predictions of quantum mechanics using a separable ontological model, provided one allows for arbitrary violations of `dynamical locality'. However, since dynamical locality is strictly weaker than local causality, this leaves open the question of whether an ontological model for quantum mechanics can be both separable and dynamically local. We answer this question in the affirmative, using an ontological model based on previous work by Deutsch and Hayden. Although the original formulation of the model avoids Bell's theorem by denying that measurements result in single, definite outcomes, we show that the model can alternatively be cast in the framework of ontological models, where Bell's theorem does apply. We find that the resulting model violates local causality, but satisfies both separability and dynamical locality, making it a candidate for the `most local' ontological model of quantum mechanics.

  11. Collision-based mechanics of bipedal hopping.

    PubMed

    Gutmann, Anne K; Lee, David V; McGowan, Craig P

    2013-08-23

    The muscle work required to sustain steady-speed locomotion depends largely upon the mechanical energy needed to redirect the centre of mass and the degree to which this energy can be stored and returned elastically. Previous studies have found that large bipedal hoppers can elastically store and return a large fraction of the energy required to hop, whereas small bipedal hoppers can only elastically store and return a relatively small fraction. Here, we consider the extent to which large and small bipedal hoppers (tammar wallabies, approx. 7 kg, and desert kangaroo rats, approx. 0.1 kg) reduce the mechanical energy needed to redirect the centre of mass by reducing collisions. We hypothesize that kangaroo rats will reduce collisions to a greater extent than wallabies since kangaroo rats cannot elastically store and return as high a fraction of the mechanical energy of hopping as wallabies. We find that kangaroo rats use a significantly smaller collision angle than wallabies by employing ground reaction force vectors that are more vertical and center of mass velocity vectors that are more horizontal and thereby reduce their mechanical cost of transport. A collision-based approach paired with tendon morphometry may reveal this effect more generally among bipedal runners and quadrupedal trotters.

  12. Modeling of rolling element bearing mechanics

    NASA Technical Reports Server (NTRS)

    Greenhill, L. M.

    1991-01-01

    Roller element bearings provide the primary mechanical interface between rotating and nonrotating components in the high performance turbomachinery of the Space Shuttle Main Engine (SSME). Knowledge of bearing behavior under various loading and environmental conditions is essential to predicting and understanding the overall behavior of turbopumps, including rotordynamic stability, critical speeds and bearing life. The objective is to develop mathematical models and computer programs to describe the mechanical behavior of ball and cylinder roller bearings under the loading and environmental conditions encountered in the SSME and future high performance rocket engines. This includes characteristics such as nonlinear load/motion relationships, stiffness and damping, rolling element loads for life prediction, and roller and cage stability.

  13. Model Based Definition

    NASA Technical Reports Server (NTRS)

    Rowe, Sidney E.

    2010-01-01

    In September 2007, the Engineering Directorate at the Marshall Space Flight Center (MSFC) created the Design System Focus Team (DSFT). MSFC was responsible for the in-house design and development of the Ares 1 Upper Stage and the Engineering Directorate was preparing to deploy a new electronic Configuration Management and Data Management System with the Design Data Management System (DDMS) based upon a Commercial Off The Shelf (COTS) Product Data Management (PDM) System. The DSFT was to establish standardized CAD practices and a new data life cycle for design data. Of special interest here, the design teams were to implement Model Based Definition (MBD) in support of the Upper Stage manufacturing contract. It is noted that this MBD does use partially dimensioned drawings for auxiliary information to the model. The design data lifecycle implemented several new release states to be used prior to formal release that allowed the models to move through a flow of progressive maturity. The DSFT identified some 17 Lessons Learned as outcomes of the standards development, pathfinder deployments and initial application to the Upper Stage design completion. Some of the high value examples are reviewed.

  14. Unraveling the binding mechanism of polyoxyethylene sorbitan esters with bovine serum albumin: a novel theoretical model based on molecular dynamic simulations.

    PubMed

    Delgado-Magnero, Karelia H; Valiente, Pedro A; Ruiz-Peña, Miriam; Pérez-Gramatges, Aurora; Pons, Tirso

    2014-04-01

    To gain a better understanding of the interactions governing the binding mechanism of proteins with non-ionic surfactants, the association processes of Tween 20 and Tween 80 with the bovine serum albumin (BSA) protein were investigated using molecular dynamics (MD) simulations. Protein:surfactant molar ratios were chosen according to the critical micelle concentration (CMC) of each surfactant in the presence of BSA. It was found that both the hydrophilic and the hydrophobic groups of the BSA equally contribute to the surface area of interaction with the non-ionic surfactants. A novel theoretical model for the interactions between BSA and these surfactants at the atomic level is proposed, where both surfactants bind to non-specific domains of the BSA three-dimensional structure mainly through their polyoxyethylene groups, by hydrogen bonds and van der Waals interactions. This is well supported by the strong electrostatic and van der Waals interaction energies obtained in the calculations involving surfactant polyoxyethylene groups and different protein regions. The results obtained from the MD simulations suggest that the formation of surfactant clusters over the BSA structure, due to further cooperative self-assembly of Tween molecules, could increase the protein conformational stability. These results extend the current knowledge on molecular interactions between globular proteins and non-ionic surfactants, and contribute to the fine-tuning design of protein formulations using polysorbates as excipients for minimizing the undesirable effects of protein adsorption and aggregation.

  15. Mechanism of base activation of persulfate.

    PubMed

    Furman, Olha S; Teel, Amy L; Watts, Richard J

    2010-08-15

    Base is the most commonly used activator of persulfate for the treatment of contaminated groundwater by in situ chemical oxidation (ISCO). A mechanism for the base activation of persulfate is proposed involving the base-catalyzed hydrolysis of persulfate to hydroperoxide anion and sulfate followed by the reduction of another persulfate molecule by hydroperoxide. Reduction by hydroperoxide decomposes persulfate into sulfate radical and sulfate anion, and hydroperoxide is oxidized to superoxide. The base-catalyzed hydrolysis of persulfate was supported by kinetic analyses of persulfate decomposition at various base:persulfate molar ratios and an increased rate of persulfate decomposition in D(2)O vs H(2)O. Stoichiometric analyses confirmed that hydroperoxide reacts with persulfate in a 1:1 molar ratio. Addition of hydroperoxide to basic persulfate systems resulted in rapid decomposition of the hydroperoxide and persulfate and decomposition of the superoxide probe hexachloroethane. The presence of superoxide was confirmed with scavenging by Cu(II). Electron spin resonance spectroscopy confirmed the generation of sulfate radical, hydroxyl radical, and superoxide. The results of this research are consistent with the widespread reactivity reported for base-activated persulfate when it is used for ISCO.

  16. Diagnosis of Photochemical Ozone Production Rates and Limiting Factors based on Observation-based Modeling Approach over East Asia: Impact of Radical Chemistry Mechanism and Ozone-Control Implications

    NASA Astrophysics Data System (ADS)

    Kanaya, Y.

    2015-12-01

    Growth of tropospheric ozone, causing health and climate impacts, is concerned over East Asia, because emissions of precursors have dramatically increased. Photochemical production rates of ozone and limiting factors, primarily studied for urban locations, have been poorly assessed within a perspective of regional-scale air pollution over East Asia. We performed comprehensive observations of ozone precursors at several locations with regional representativeness and made such assessment based on the observation-based modeling approach. Here, diagnosis at Fukue Island (32.75°N, 128.68°E) remotely located in western Japan (May 2009) is highlighted, where the highest 10% of hourly ozone concentrations reached 72‒118 ppb during May influenced by Asian continental outflow. The average in-situ ozone production rate was estimated to be 6.8 ppb per day, suggesting that in-travel production was still active, while larger buildup must have occurred beforehand. Information on the chemical status of the air mass arriving in Japan is important, because it affects how further ozone production occurs after precursor addition from Japanese domestic emissions. The main limiting factor of ozone production was usually NOx, suggesting that domestic NOx emission control is important in reducing further ozone production and the incidence of warning issuance (>120 ppb). VOCs also increased the ozone production rate, and occasionally (14% of time) became dominant. This analysis implies that the VOC reduction legislation recently enacted should be effective. The uncertainty in the radical chemistry mechanism governing ozone production had a non-negligible impact, but the main conclusion relevant to policy was not altered. When chain termination was augmented by HO2-H2O + NO/NO2 reactions and by heterogeneous loss of HO2 on aerosol particle surfaces, the daily ozone production rate decreased by <24%, and the fraction of hours when the VOC-limited condition occurred varied from 14% to 13

  17. Mechanical Models of Fault-Related Folding

    SciTech Connect

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  18. Fluid mechanical model of the Helmholtz resonator

    NASA Technical Reports Server (NTRS)

    Hersh, A. S.; Walker, B.

    1977-01-01

    A semi-empirical fluid mechanical model of the acoustic behavior of Helmholtz resonators is presented which predicts impedance as a function of the amplitude and frequency of the incident sound pressure field and resonator geometry. The model assumes that the particle velocity approaches the orifice in a spherical manner. The incident and cavity sound fields are connected by solving the governing oscillating mass and momentum conservation equations. The model is in agreement with the Rayleigh slug-mass model at low values of incident sound pressure level. At high values, resistance is predicted to be independent of frequency, proportional to the square root of the amplitude of the incident sound pressure field, and virtually independent of resonator geometry. Reactance is predicted to depend in a very complicated way upon resonator geometry, incident sound pressure level, and frequency. Nondimensional parameters are defined that divide resonator impedance into three categories corresponding to low, moderately low, and intense incident sound pressure amplitudes. The two-microphone method was used to measure the impedance of a variety of resonators. The data were used to refine and verify the model.

  19. A predictive model for artificial mechanical cochlea

    NASA Astrophysics Data System (ADS)

    Ahmed, Riaz U.; Adiba, Afifa; Banerjee, Sourav

    2015-03-01

    To recover the hearing deficiency, cochlea implantation is essential if the inner ear is damaged. Existing implantable cochlea is an electronic device, usually placed outside the ear to receive sound from environment, convert into electric impulses and send to auditory nerve bypassing the damaged cochlea. However, due to growing demand researchers are interested in fabricating artificial mechanical cochlea to overcome the limitations of electronic cochlea. Only a hand full number of research have been published in last couple of years showing fabrication of basilar membrane mimicking the cochlear operations. Basilar membrane plays the most important role in a human cochlea by responding only on sonic frequencies using its varying material properties from basal to apical end. Only few sonic frequencies have been sensed with the proposed models; however no process was discussed on how the frequency selectivity of the models can be improved to sense the entire sonic frequency range. Thus, we argue that a predictive model is the missing-link and is the utmost necessity. Hence, in this study, we intend to develop a multi-scale predictive model for basilar membrane such that sensing potential of the artificial cochlea can be designed and tuned predictively by altering the model parameters.

  20. Influence of Cremophor EL and genetic polymorphisms on the pharmacokinetics of paclitaxel and its metabolites using a mechanism-based model.

    PubMed

    Fransson, Martin N; Gréen, Henrik; Litton, Jan-Eric; Friberg, Lena E

    2011-02-01

    The formulation vehicle Cremophor EL has previously been shown to affect paclitaxel kinetics, but it is not known whether it also affects the kinetics of paclitaxel metabolites. This information may be important for understanding paclitaxel metabolism in vivo and in the investigation of the role of genetic polymorphisms in the metabolizing enzymes CYP2C8 and CYP3A4/CYP3A5 and the ABCB1 transporter. In this study we used the population pharmacokinetic approach to explore the influence of predicted Cremophor EL concentrations on paclitaxel (Taxol) metabolites. In addition, correlations between genetic polymorphisms and enzyme activity with clearance of paclitaxel, its two primary metabolites, 6α-hydroxypaclitaxel and p-3'-hydroxypaclitaxel, and its secondary metabolite, 6α-p-3'-dihydroxypaclitaxel were investigated. Model building was based on 1156 samples from a study with 33 women undergoing paclitaxel treatment for gynecological cancer. Total concentrations of paclitaxel were fitted to a model described previously. One-compartment models characterized unbound metabolite concentrations. Total concentrations of 6α-hydroxypaclitaxel and p-3'-hydroxypaclitaxel were strongly dependent on predicted Cremophor EL concentrations, but this association was not found for 6α-p-3'-dihydroxypaclitaxel. Clearance of 6α-hydroxypaclitaxel (fraction metabolized) was significantly correlated (p < 0.05) to the ABCB1 allele G2677T/A. Individuals carrying the polymorphisms G/A (n = 3) or G/G (n = 5) showed a 30% increase, whereas individuals with polymorphism T/T (n = 8) showed a 27% decrease relative to those with the polymorphism G/T (n = 17). The correlation of G2677T/A with 6α-hydroxypaclitaxel has not been described previously but supports other findings of the ABCB1 transporter playing a part in paclitaxel metabolism.

  1. New Models of Mechanisms for the Motion Transformation

    NASA Astrophysics Data System (ADS)

    Petrović, Tomislav; Ivanov, Ivan

    In this paper two new mechanisms for the motion transformations are presented: screw mechanism for the transformation of one-way circular into two-way linear motion with impulse control and worm-planetary gear train with extremely height gear ratio. Both mechanisms represent new models of construction solutions for which patent protection has been achieved. These mechanisms are based on the application of the differential gearbox with two degrees of freedom. They are characterized by series of kinematic impacts at motion transformation and the possibility of temporary or permanent changes in the structure by subtracting the redundant degree of freedom. Thus the desired characteristic of the motion transformation is achieved. For each mechanism separately the principles of motion and transformation are described and the basic equations that describe the interdependence of geometric and kinematic and kinetic parameters of the system dynamics are given. The basic principles of controlling new mechanisms for motion transformation have been pointed to and the basic constructional performances which may find practical application have been given. The physical models of new systems of motion transformation have been designed and their operation has been presented. Performed experimental researches confirmed the theoretical results and very favorable kinematic characteristics of the mechanisms.

  2. Statistical Mechanical Models of Integer Factorization Problem

    NASA Astrophysics Data System (ADS)

    Nakajima, Chihiro H.; Ohzeki, Masayuki

    2017-01-01

    We formulate the integer factorization problem via a formulation of the searching problem for the ground state of a statistical mechanical Hamiltonian. The first passage time required to find a correct divisor of a composite number signifies the exponential computational hardness. The analysis of the density of states of two macroscopic quantities, i.e., the energy and the Hamming distance from the correct solutions, leads to the conclusion that the ground state (correct solution) is completely isolated from the other low-energy states, with the distance being proportional to the system size. In addition, the profile of the microcanonical entropy of the model has two peculiar features that are each related to two marked changes in the energy region sampled via Monte Carlo simulation or simulated annealing. Hence, we find a peculiar first-order phase transition in our model.

  3. Investigation of mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model and experimental optimization/validation

    NASA Astrophysics Data System (ADS)

    Zhang, Le; Qiao, Minna; Gao, Hongjie; Hu, Bin; Tan, Hua; Zhou, Xiaobo; Li, Chang Ming

    2016-08-01

    Herein, we have developed a novel approach to investigate the mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model, experimental optimization of key parameters and experimental data validation of the predictive power of the model. The advantages of this study are that the impact of mechanical stimulation on bone regeneration in a porous biodegradable CaP scaffold is considered, experimental design is used to investigate the optimal combination of growth factors loaded on the porous biodegradable CaP scaffold to promote bone regeneration and the training, testing and analysis of the model are carried out by using experimental data, a data-mining algorithm and related sensitivity analysis. The results reveal that mechanical stimulation has a great impact on bone regeneration in a porous biodegradable CaP scaffold and the optimal combination of growth factors that are encapsulated in nanospheres and loaded into porous biodegradable CaP scaffolds layer-by-layer can effectively promote bone regeneration. Furthermore, the model is robust and able to predict the development of bone regeneration under specified conditions.

  4. Investigation of mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model and experimental optimization/validation.

    PubMed

    Zhang, Le; Qiao, Minna; Gao, Hongjie; Hu, Bin; Tan, Hua; Zhou, Xiaobo; Li, Chang Ming

    2016-08-21

    Herein, we have developed a novel approach to investigate the mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model, experimental optimization of key parameters and experimental data validation of the predictive power of the model. The advantages of this study are that the impact of mechanical stimulation on bone regeneration in a porous biodegradable CaP scaffold is considered, experimental design is used to investigate the optimal combination of growth factors loaded on the porous biodegradable CaP scaffold to promote bone regeneration and the training, testing and analysis of the model are carried out by using experimental data, a data-mining algorithm and related sensitivity analysis. The results reveal that mechanical stimulation has a great impact on bone regeneration in a porous biodegradable CaP scaffold and the optimal combination of growth factors that are encapsulated in nanospheres and loaded into porous biodegradable CaP scaffolds layer-by-layer can effectively promote bone regeneration. Furthermore, the model is robust and able to predict the development of bone regeneration under specified conditions.

  5. Melanoma Brain Metastasis: Mechanisms, Models, and Medicine.

    PubMed

    Kircher, David A; Silvis, Mark R; Cho, Joseph H; Holmen, Sheri L

    2016-09-02

    The development of brain metastases in patients with advanced stage melanoma is common, but the molecular mechanisms responsible for their development are poorly understood. Melanoma brain metastases cause significant morbidity and mortality and confer a poor prognosis; traditional therapies including whole brain radiation, stereotactic radiotherapy, or chemotherapy yield only modest increases in overall survival (OS) for these patients. While recently approved therapies have significantly improved OS in melanoma patients, only a small number of studies have investigated their efficacy in patients with brain metastases. Preliminary data suggest that some responses have been observed in intracranial lesions, which has sparked new clinical trials designed to evaluate the efficacy in melanoma patients with brain metastases. Simultaneously, recent advances in our understanding of the mechanisms of melanoma cell dissemination to the brain have revealed novel and potentially therapeutic targets. In this review, we provide an overview of newly discovered mechanisms of melanoma spread to the brain, discuss preclinical models that are being used to further our understanding of this deadly disease and provide an update of the current clinical trials for melanoma patients with brain metastases.

  6. Reverse engineering systems models of regulation: discovery, prediction and mechanisms.

    PubMed

    Ashworth, Justin; Wurtmann, Elisabeth J; Baliga, Nitin S

    2012-08-01

    Biological systems can now be understood in comprehensive and quantitative detail using systems biology approaches. Putative genome-scale models can be built rapidly based upon biological inventories and strategic system-wide molecular measurements. Current models combine statistical associations, causative abstractions, and known molecular mechanisms to explain and predict quantitative and complex phenotypes. This top-down 'reverse engineering' approach generates useful organism-scale models despite noise and incompleteness in data and knowledge. Here we review and discuss the reverse engineering of biological systems using top-down data-driven approaches, in order to improve discovery, hypothesis generation, and the inference of biological properties.

  7. Models on the boundary between classical and quantum mechanics.

    PubMed

    Hooft, Gerard 't

    2015-08-06

    Arguments that quantum mechanics cannot be explained in terms of any classical theory using only classical logic seem to be based on sound mathematical considerations: there cannot be physical laws that require 'conspiracy'. It may therefore be surprising that there are several explicit quantum systems where these considerations apparently do not apply. In this report, several such counterexamples are shown. These are quantum models that do have a classical origin. The most curious of these models is superstring theory. So now the question is asked: how can such a model feature 'conspiracy', and how bad is that? Is there conspiracy in the vacuum fluctuations? Arguments concerning Bell's theorem are further sharpened.

  8. Mechanism of Actin-Based Motility

    NASA Astrophysics Data System (ADS)

    Pantaloni, Dominique; Le Clainche, Christophe; Carlier, Marie-France

    2001-05-01

    Spatially controlled polymerization of actin is at the origin of cell motility and is responsible for the formation of cellular protrusions like lamellipodia. The pathogens Listeria monocytogenes and Shigella flexneri, which undergo actin-based propulsion, are acknowledged models of the leading edge of lamellipodia. Actin-based motility of the bacteria or of functionalized microspheres can be reconstituted in vitro from only five pure proteins. Movement results from the regulated site-directed treadmilling of actin filaments, consistent with observations of actin dynamics in living motile cells and with the biochemical properties of the components of the synthetic motility medium.

  9. Instability-based mechanism for body undulations in centipede locomotion.

    PubMed

    Aoi, Shinya; Egi, Yoshimasa; Tsuchiya, Kazuo

    2013-01-01

    Centipedes have many body segments and legs and they generate body undulations during terrestrial locomotion. Centipede locomotion has the characteristic that body undulations are absent at low speeds but appear at faster speeds; furthermore, their amplitude and wavelength increase with increasing speed. There are conflicting reports regarding whether the muscles along the body axis resist or support these body undulations and the underlying mechanisms responsible for the body undulations remain largely unclear. In the present study, we investigated centipede locomotion dynamics using computer simulation with a body-mechanical model and experiment with a centipede-like robot and then conducted dynamic analysis with a simple model to clarify the mechanism. The results reveal that body undulations in these models occur due to an instability caused by a supercritical Hopf bifurcation. We subsequently compared these results with data obtained using actual centipedes. The model and actual centipedes exhibit similar dynamic properties, despite centipedes being complex, nonlinear dynamic systems. Based on our findings, we propose a possible passive mechanism for body undulations in centipedes, similar to a follower force or jackknife instability. We also discuss the roles of the muscles along the body axis in generating body undulations in terms of our physical model.

  10. Instability-based mechanism for body undulations in centipede locomotion

    NASA Astrophysics Data System (ADS)

    Aoi, Shinya; Egi, Yoshimasa; Tsuchiya, Kazuo

    2013-01-01

    Centipedes have many body segments and legs and they generate body undulations during terrestrial locomotion. Centipede locomotion has the characteristic that body undulations are absent at low speeds but appear at faster speeds; furthermore, their amplitude and wavelength increase with increasing speed. There are conflicting reports regarding whether the muscles along the body axis resist or support these body undulations and the underlying mechanisms responsible for the body undulations remain largely unclear. In the present study, we investigated centipede locomotion dynamics using computer simulation with a body-mechanical model and experiment with a centipede-like robot and then conducted dynamic analysis with a simple model to clarify the mechanism. The results reveal that body undulations in these models occur due to an instability caused by a supercritical Hopf bifurcation. We subsequently compared these results with data obtained using actual centipedes. The model and actual centipedes exhibit similar dynamic properties, despite centipedes being complex, nonlinear dynamic systems. Based on our findings, we propose a possible passive mechanism for body undulations in centipedes, similar to a follower force or jackknife instability. We also discuss the roles of the muscles along the body axis in generating body undulations in terms of our physical model.

  11. Mathematical model I. Electron and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Gadre, Nitin Ramchandra

    2011-03-01

    The basic particle electron obeys various theories like electrodynamics, quantum mechanics and special relativity. Particle under different experimental conditions behaves differently, allowing us to observe different characteristics which become basis for these theories. In this paper, we have made an attempt to suggest a classical picture by studying the requirements of these three modern theories. The basic presumption is: There must be certain structural characteristics in a particle like electron which make it obey postulates of modern theories. As it is `difficult' to find structure of electron experimentally, we make a mathematical attempt. For a classical approach, we require well defined systems and we have studied a system with two charged particles, proton and electron in a hydrogen atom. An attempt has been made to give a model to describe electron as seen by the proton. We then discuss how the model can satisfy the requirements of the three modern theories in a classical manner. The paper discusses basic aspects of relativity and electrodynamics. However the focus of the paper is on quantum mechanics.

  12. Cooling of burns: Mechanisms and models.

    PubMed

    Wright, E H; Harris, A L; Furniss, D

    2015-08-01

    The role of cooling in the acute management of burns is widely accepted in clinical practice, and is a cornerstone of basic first aid in burns. This has been underlined in a number of animal models. The mechanism by which it delivers its benefit is poorly understood, but there is a reduction in burns progression over the first 48 h, reduced healing time, and some subjective improvements in scarring when cooling is administered after burning. Intradermal temperature normalises within a matter of seconds to a few minutes, yet the benefits of even delayed cooling persist, implying it is not simply the removal of thermal energy from the damaged tissues. Animal models have used oedema formation, preservation of dermal perfusion, healing time and hair retention as indicators of burns severity, and have shown cooling to improve these indices, but pharmacological or immunological blockade of humoural and cellular mediators of inflammation did not reproduce the benefit of cooling. More recently, some studies of tissue from human and animal burns have shown consistent, reproducible, temporal changes in gene expression in burned tissues. Here, we review the experimental evidence of the role and mechanism of cooling in burns management, and suggest future research directions that may eventually lead to improved treatment outcomes.

  13. A statistical mechanical model for inverse melting

    NASA Astrophysics Data System (ADS)

    Feeney, Melissa R.; Debenedetti, Pablo G.; Stillinger, Frank H.

    2003-08-01

    Inverse melting is the situation in which a liquid freezes when it is heated isobarically. Both helium isotopes exhibit intervals of inverse melting at low temperature, and published data suggests that isotactic poly (4-methylpentene-1) also displays this unusual phase behavior. Here we propose a statistical mechanical model for inverse melting. It is a decorated modification of the Gaussian core model, in which particles possess a spectrum of thermally activated internal states. Excitation leads to a change in a particle's Gaussian interaction parameters, and this can result in a spatially periodic crystal possessing a higher entropy than the fluid with which it coexists. Numerical solution of the model, using integral equations and the hypernetted chain closure for the fluid phase, and the Einstein model for the solid phases, identifies two types of inverse melting. One mimics the behavior of the helium isotopes, for which the higher-entropy crystal is denser than the liquid. The other corresponds to inverse melting in poly(4-methylpentene-1), where the high-entropy crystal is less dense than the liquid with which it coexists.

  14. Mechanical contact by constraints and split-based preconditioning

    SciTech Connect

    Dmitry Karpeyev; Derek Gaston; Jason Hales; Steven Novascone

    2014-03-01

    An accurate implementation of glued mechanical contact was developed in MOOSE based on its Constraint system. This approach results in a superior convergence of elastic structure problems, in particular in BISON. Adaptation of this technique to frictionless and frictional contact models is under way. Additionally, the improved convergence of elastic problems results from the application of the split-based preconditioners to constraint-based systems. This yields a substantial increase in the robustness of elastic solvers when the number of nodes in contact is increased and/or the mesh is refined.

  15. A Hydro-mechanical Model and Analytical Solutions for Geomechanical Modeling of Carbon Dioxide Geological Sequestration

    SciTech Connect

    Xu, Zhijie; Fang, Yilin; Scheibe, Timothy D.; Bonneville, Alain

    2012-05-15

    We present a hydro-mechanical model for geological sequestration of carbon dioxide. The model considers the poroelastic effects by taking into account the coupling between the geomechanical response and the fluid flow in greater detail. The simplified hydro-mechanical model includes the geomechanical part that relies on the linear elasticity, while the fluid flow is based on the Darcy’s law. Two parts were coupled using the standard linear poroelasticity. Analytical solutions for pressure field were obtained for a typical geological sequestration scenario. The model predicts the temporal and spatial variation of pressure field and effects of permeability and elastic modulus of formation on the fluid pressure distribution.

  16. Systematic development of reduced reaction mechanisms for dynamic modeling

    NASA Technical Reports Server (NTRS)

    Frenklach, M.; Kailasanath, K.; Oran, E. S.

    1986-01-01

    A method for systematically developing a reduced chemical reaction mechanism for dynamic modeling of chemically reactive flows is presented. The method is based on the postulate that if a reduced reaction mechanism faithfully describes the time evolution of both thermal and chain reaction processes characteristic of a more complete mechanism, then the reduced mechanism will describe the chemical processes in a chemically reacting flow with approximately the same degree of accuracy. Here this postulate is tested by producing a series of mechanisms of reduced accuracy, which are derived from a full detailed mechanism for methane-oxygen combustion. These mechanisms were then tested in a series of reactive flow calculations in which a large-amplitude sinusoidal perturbation is applied to a system that is initially quiescent and whose temperature is high enough to start ignition processes. Comparison of the results for systems with and without convective flow show that this approach produces reduced mechanisms that are useful for calculations of explosions and detonations. Extensions and applicability to flames are discussed.

  17. Semi-classical modeling of nano-mechanical transistors

    NASA Astrophysics Data System (ADS)

    Scorrano, Alessandro; Carcaterra, Antonio

    2013-08-01

    The introduction of vibration-based Nano Electro-Mechanical Transistors (NEMT) opens a new horizon for mechanics in computer science. NEMT working principle is based on an electrical charge shuttle between two electrodes operated by a vibrating conductor body. Advantages of these novel devices would be very low power dissipation, limited influence of external electromagnetic disturbances, and improved thermal resistance. The paper introduces an analytical model for such a device, in which the matching of a mechanical resonator and an electric circuit is studied: the coupling is provided by capacitance effects, electrostatic force and the quantum tunneling. The approach is quasi-classical, describing the quantum phenomena through a non-linear conductance and using a continuous variable for the charges. Through suitably introduced simplifications, the model is reduced to a set of two differential equations in terms of pillar position and charge. These equations represent the simplest model still preserving the basic phenomenology of the investigated system. Numerical simulations show different possible motion regimes, both in the single- and multiple-module configurations, the latter able to reproduce the conventional transistor functionality. This opens the way to mechanical voltage-driven switches or amplifiers.

  18. Passive ventricular mechanics modelling using MRI of structure and function.

    PubMed

    Wang, V Y; Lam, H I; Ennis, D B; Young, A A; Nash, M P

    2008-01-01

    Patients suffering from dilated cardiomyopathy or myocardial infarction can develop left ventricular (LV) diastolic impairment. The LV remodels its structure and function to adapt to pathophysiological changes in geometry and loading conditions and this remodeling process can alter the passive ventricular mechanics. In order to better understand passive ventricular mechanics, a LV finite element model was developed to incorporate physiological and mechanical information derived from in vivo magnetic resonance imaging (MRI) tissue tagging, in vivo LV cavity pressure recording and ex vivo diffusion tensor MRI (DTMRI) of a canine heart. MRI tissue tagging enables quantitative evaluation of cardiac mechanical function with high spatial and temporal resolution, whilst the direction of maximum water diffusion (the primary eigenvector) in each voxel of a DTMRI directly correlates with the myocardial fibre orientation. This model was customized to the geometry of the canine LV during diastasis by fitting the segmented epicardial and endocardial surface data from tagged MRI using nonlinear finite element fitting techniques. Myofibre orientations, extracted from DTMRI of the same heart, were incorporated into this geometric model using a free form deformation methodology. Pressure recordings, temporally synchronized to the tissue tagging MRI data, were used to simulate the LV deformation during diastole. Simulation of the diastolic LV mechanics allowed us to estimate the stiffness of the passive LV myocardium based on kinematic data obtained from tagged MRI. This integrated physiological model will allow more insight into the regional passive diastolic mechanics of the LV on an individualized basis, thereby improving our understanding of the underlying structural basis of mechanical dysfunction in pathological conditions.

  19. The mechanical behavior of a mammalian lung alveolar duct model.

    PubMed

    Denny, E; Schroter, R C

    1995-08-01

    A model for the mechanical properties of an alveolar duct is analyzed using the finite element method. Its geometry comprises an assemblage of truncated octahedral alveoli surrounding a longitudinal air duct. The amounts and distributions of elastin and collagen fiber bundles, modeled by separate stress-strain laws, are based upon published data for dogs. The surface tension of the air-liquid interface is modeled using an area-dependent relationship. Pressure-volume curves are computed that compare well with experimental data for both saline-filled and air-filled lungs. Pressure-volume curves of the separate elastin and collagen fiber contributions are similar in form to the behavior of saline-filled lungs treated with either elastase or collagenase. A comparison with our earlier model, based upon a single alveolus, shows the duct to have a behavior closer to reported experimental data.

  20. Particle-based methods for multiscale modeling of blood flow in the circulation and in devices: challenges and future directions. Sixth International Bio-Fluid Mechanics Symposium and Workshop March 28-30, 2008 Pasadena, California.

    PubMed

    Yamaguchi, Takami; Ishikawa, Takuji; Imai, Y; Matsuki, N; Xenos, Mikhail; Deng, Yuefan; Bluestein, Danny

    2010-03-01

    A major computational challenge for a multiscale modeling is the coupling of disparate length and timescales between molecular mechanics and macroscopic transport, spanning the spatial and temporal scales characterizing the complex processes taking place in flow-induced blood clotting. Flow and pressure effects on a cell-like platelet can be well represented by a continuum mechanics model down to the order of the micrometer level. However, the molecular effects of adhesion/aggregation bonds are on the order of nanometer. A successful multiscale model of platelet response to flow stresses in devices and the ensuing clotting responses should be able to characterize the clotting reactions and their interactions with the flow. This paper attempts to describe a few of the computational methods that were developed in recent years and became available to researchers in the field. They differ from traditional approaches that dominate the field by expanding on prevailing continuum-based approaches, or by completely departing from them, yielding an expanding toolkit that may facilitate further elucidation of the underlying mechanisms of blood flow and the cellular response to it. We offer a paradigm shift by adopting a multidisciplinary approach with fluid dynamics simulations coupled to biophysical and biochemical transport.

  1. Coupled Thermal-Chemical-Mechanical Modeling of Validation Cookoff Experiments

    SciTech Connect

    ERIKSON,WILLIAM W.; SCHMITT,ROBERT G.; ATWOOD,A.I.; CURRAN,P.D.

    2000-11-27

    The cookoff of energetic materials involves the combined effects of several physical and chemical processes. These processes include heat transfer, chemical decomposition, and mechanical response. The interaction and coupling between these processes influence both the time-to-event and the violence of reaction. The prediction of the behavior of explosives during cookoff, particularly with respect to reaction violence, is a challenging task. To this end, a joint DoD/DOE program has been initiated to develop models for cookoff, and to perform experiments to validate those models. In this paper, a series of cookoff analyses are presented and compared with data from a number of experiments for the aluminized, RDX-based, Navy explosive PBXN-109. The traditional thermal-chemical analysis is used to calculate time-to-event and characterize the heat transfer and boundary conditions. A reaction mechanism based on Tarver and McGuire's work on RDX{sup 2} was adjusted to match the spherical one-dimensional time-to-explosion data. The predicted time-to-event using this reaction mechanism compares favorably with the validation tests. Coupled thermal-chemical-mechanical analysis is used to calculate the mechanical response of the confinement and the energetic material state prior to ignition. The predicted state of the material includes the temperature, stress-field, porosity, and extent of reaction. There is little experimental data for comparison to these calculations. The hoop strain in the confining steel tube gives an estimation of the radial stress in the explosive. The inferred pressure from the measured hoop strain and calculated radial stress agree qualitatively. However, validation of the mechanical response model and the chemical reaction mechanism requires more data. A post-ignition burn dynamics model was applied to calculate the confinement dynamics. The burn dynamics calculations suffer from a lack of characterization of the confinement for the flaw

  2. Modeling the effects of particle deformation in chemical mechanical polishing

    NASA Astrophysics Data System (ADS)

    Chen, Xiaochun; Zhao, Yongwu; Wang, Yongguang

    2012-09-01

    In a chemical mechanical polishing (CMP) process, an active abrasive particle participating in the wear process will contact the pad and the wafer at the same time. The applied polishing load causes the deformation of the pad in the contact interface of the particle and the pad, and the deformation of the wafer in the contact interface of the particle and the wafer. Besides, this force causes the deformation of the abrasive particle. Based on the elastic-plastic micro-contact mechanics and abrasive wear theory, a novel model for material removal rate (MRR) with consideration of the abrasive particle deformation is presented in this paper. The deformation of the abrasive particle, affecting the indentation depth of the particle into the wafer, is quantitatively incorporated into the model. The results and analyses show that the present model is in good agreement with the experimental data.

  3. Seismic metamaterials based on isochronous mechanical oscillators

    SciTech Connect

    Finocchio, G. Garescì, F.; Azzerboni, B.; Casablanca, O.; Chiappini, M.; Ricciardi, G.; Alibrandi, U.

    2014-05-12

    This Letter introduces a seismic metamaterial (SM) composed by a chain of mass-in-mass system able to filter the S-waves of an earthquake. We included the effect of the SM into the mono dimensional model for the soil response analysis. The SM modifies the soil behavior and in presence of an internal damping the amplitude of the soil amplification function is reduced also in a region near the resonance frequency. This SM can be realized by a continuous structure with inside a 3d-matrix of isochronous oscillators based on a sphere rolling over a cycloidal trajectory.

  4. A statistical mechanical model of economics

    NASA Astrophysics Data System (ADS)

    Lubbers, Nicholas Edward Williams

    Statistical mechanics pursues low-dimensional descriptions of systems with a very large number of degrees of freedom. I explore this theme in two contexts. The main body of this dissertation explores and extends the Yard Sale Model (YSM) of economic transactions using a combination of simulations and theory. The YSM is a simple interacting model for wealth distributions which has the potential to explain the empirical observation of Pareto distributions of wealth. I develop the link between wealth condensation and the breakdown of ergodicity due to nonlinear diffusion effects which are analogous to the geometric random walk. Using this, I develop a deterministic effective theory of wealth transfer in the YSM that is useful for explaining many quantitative results. I introduce various forms of growth to the model, paying attention to the effect of growth on wealth condensation, inequality, and ergodicity. Arithmetic growth is found to partially break condensation, and geometric growth is found to completely break condensation. Further generalizations of geometric growth with growth in- equality show that the system is divided into two phases by a tipping point in the inequality parameter. The tipping point marks the line between systems which are ergodic and systems which exhibit wealth condensation. I explore generalizations of the YSM transaction scheme to arbitrary betting functions to develop notions of universality in YSM-like models. I find that wealth vi condensation is universal to a large class of models which can be divided into two phases. The first exhibits slow, power-law condensation dynamics, and the second exhibits fast, finite-time condensation dynamics. I find that the YSM, which exhibits exponential dynamics, is the critical, self-similar model which marks the dividing line between the two phases. The final chapter develops a low-dimensional approach to materials microstructure quantification. Modern materials design harnesses complex

  5. Modelling mechanical characteristics of microbial biofilms by network theory

    PubMed Central

    Ehret, Alexander E.; Böl, Markus

    2013-01-01

    In this contribution, we present a constitutive model to describe the mechanical behaviour of microbial biofilms based on classical approaches in the continuum theory of polymer networks. Although the model is particularly developed for the well-studied biofilms formed by mucoid Pseudomonas aeruginosa strains, it could easily be adapted to other biofilms. The basic assumption behind the model is that the network of extracellular polymeric substances can be described as a superposition of worm-like chain networks, each connected by transient junctions of a certain lifetime. Several models that were applied to biofilms previously are included in the presented approach as special cases, and for small shear strains, the governing equations are those of four parallel Maxwell elements. Rheological data given in the literature are very adequately captured by the proposed model, and the simulated response for a series of compression tests at large strains is in good qualitative agreement with reported experimental behaviour. PMID:23034354

  6. Distinguishing Feedback Mechanisms in Clock Models

    NASA Astrophysics Data System (ADS)

    Golden, Alexander; Lubensky, David

    Biological oscillators are very diverse but can be classified based on dynamical motifs such as type of feedback. The S. Elongatus circadian oscillator is a novel circadian oscillator that can operate at constant protein number by modifying covalent states. It can be reproduced in vitro with only 3 different purified proteins: KaiA, KaiB, and KaiC. We use computational and analytic techniques to compare models of the S. Elongatus post-translational oscillator that rely on positive feedback with models that rely on negative feedback. We show that introducing a protein that binds competitively with KaiA to the KaiB-KaiC complex can distinguish between positive and negative feedback as the primary driver of the rhythm, which has so far been difficult to address experimentally. NSF Grant DMR-1056456.

  7. A monolithic 3D-0D coupled closed-loop model of the heart and the vascular system: Experiment-based parameter estimation for patient-specific cardiac mechanics.

    PubMed

    Hirschvogel, Marc; Bassilious, Marina; Jagschies, Lasse; Wildhirt, Stephen M; Gee, Michael W

    2016-10-15

    A model for patient-specific cardiac mechanics simulation is introduced, incorporating a 3-dimensional finite element model of the ventricular part of the heart, which is coupled to a reduced-order 0-dimensional closed-loop vascular system, heart valve, and atrial chamber model. The ventricles are modeled by a nonlinear orthotropic passive material law. The electrical activation is mimicked by a prescribed parameterized active stress acting along a generic muscle fiber orientation. Our activation function is constructed such that the start of ventricular contraction and relaxation as well as the active stress curve's slope are parameterized. The imaging-based patient-specific ventricular model is prestressed to low end-diastolic pressure to account for the imaged, stressed configuration. Visco-elastic Robin boundary conditions are applied to the heart base and the epicardium to account for the embedding surrounding. We treat the 3D solid-0D fluid interaction as a strongly coupled monolithic problem, which is consistently linearized with respect to 3D solid and 0D fluid model variables to allow for a Newton-type solution procedure. The resulting coupled linear system of equations is solved iteratively in every Newton step using 2  ×  2 physics-based block preconditioning. Furthermore, we present novel efficient strategies for calibrating active contractile and vascular resistance parameters to experimental left ventricular pressure and stroke volume data gained in porcine experiments. Two exemplary states of cardiovascular condition are considered, namely, after application of vasodilatory beta blockers (BETA) and after injection of vasoconstrictive phenylephrine (PHEN). The parameter calibration to the specific individual and cardiovascular state at hand is performed using a 2-stage nonlinear multilevel method that uses a low-fidelity heart model to compute a parameter correction for the high-fidelity model optimization problem. We discuss 2 different low

  8. Thermal-Mechanical Noise Based CMUT Characterization and Sensing

    PubMed Central

    Gurun, Gokce; Hochman, Michael; Hasler, Paul; Degertekin, F. Levent

    2012-01-01

    When capacitive micromachined ultrasonic transducers (CMUTs) are monolithically integrated with custom-designed low-noise electronics, the output noise of the system can be dominated by the CMUT thermal-mechanical noise both in air and in immersion even for devices with low capacitance. Since the thermal-mechanical noise can be related to the electrical admittance of the CMUTs, this provides an effective means of device characterization. This approach yields a novel method to test the functionality and uniformity of CMUT arrays and the integrated electronics where a direct connection to CMUT array element terminals is not available. These measurements can be performed in air at the wafer level, suitable for batch manufacturing and testing. We demonstrate this method on the elements of an 800-μm diameter CMUT-on-CMOS array designed for intravascular imaging in the 10-20 MHz range. Noise measurements in air show the expected resonance behavior and spring softening effects. Noise measurements in immersion for the same array provide useful information on both the acoustic cross talk and radiation properties of the CMUT array elements. The good agreement between a CMUT model based on finite difference and boundary element method and the noise measurements validates the model and indicates that the output noise is indeed dominated by thermal-mechanical noise. The measurement method can be exploited to implement CMUT based passive sensors to measure immersion medium properties, or other parameters affecting the electro-mechanics of the CMUT structure. PMID:22718877

  9. An agent based model of genotype editing

    SciTech Connect

    Rocha, L. M.; Huang, C. F.

    2004-01-01

    This paper presents our investigation on an agent-based model of Genotype Editing. This model is based on several characteristics that are gleaned from the RNA editing system as observed in several organisms. The incorporation of editing mechanisms in an evolutionary agent-based model provides a means for evolving agents with heterogenous post-transcriptional processes. The study of this agent-based genotype-editing model has shed some light into the evolutionary implications of RNA editing as well as established an advantageous evolutionary computation algorithm for machine learning. We expect that our proposed model may both facilitate determining the evolutionary role of RNA editing in biology, and advance the current state of research in agent-based optimization.

  10. Qualitative mechanism models and the rationalization of procedures

    NASA Technical Reports Server (NTRS)

    Farley, Arthur M.

    1989-01-01

    A qualitative, cluster-based approach to the representation of hydraulic systems is described and its potential for generating and explaining procedures is demonstrated. Many ideas are formalized and implemented as part of an interactive, computer-based system. The system allows for designing, displaying, and reasoning about hydraulic systems. The interactive system has an interface consisting of three windows: a design/control window, a cluster window, and a diagnosis/plan window. A qualitative mechanism model for the ORS (Orbital Refueling System) is presented to coordinate with ongoing research on this system being conducted at NASA Ames Research Center.

  11. Mechanical behavior, modeling, and color change of electrospun fiber mats

    NASA Astrophysics Data System (ADS)

    Pedicini, Angelo

    The process of electrospinning and the physical properties of electrospun fibers are presented in this thesis. In electrospinning, polymeric fibers having diameters ranging from 50 nanometers to 1 micrometer are prepared by applying high static charge to a polymer solution. The mechanical properties and molecular morphology of some electrospun polymers are shown to be fundamentally different compared to their bulk analogs. Experimental results indicate that the mechanical behavior of electrospun polyurethane fiber mats is influenced by fiber mat morphology, molecular orientation, and surface flaws on electrospun fibers. This research characterizes the mechanical behavior of randomly oriented electrospun polyurethane mats and sheds light on general differences in behavior between electrospun and bulk materials. Further, the mechanical response of random fiber mats is modeled based on the mechanical characterization of aligned electrospun fibers. Also, empirical models are employed to relate the tensile properties of electrospun materials to their bulk analogs. The crystallinity and melting behavior of a family of electrospun polyesters is studied and provides insight to the rapid cooling and effects on solidification and crystallization of electrospun polymeric fibers. The results indicate a commonly accepted idea in electrospinning, that electrospun fibers result from rapid solvent evaporation and experience quench-like solidification from a jet of polymer solution. A qualitative study illustrates a color change phenomenon in a series of electrospun polymer/solvent systems. Color change is produced by electrospinning, and subsequent heating, and occurs at characteristic temperatures dependent on the polymer system used. These color change systems are also demonstrated as candidates for imageable media.

  12. Extended model of the photoinitiation mechanisms in photopolymer materials

    SciTech Connect

    Liu Shui; Gleeson, Michael R.; Sabol, Dusan; Sheridan, John T.

    2009-11-15

    In order to further improve photopolymer materials for applications such as data storage, a deeper understanding of the photochemical mechanisms which are present during the formation of holographic gratings has become ever more crucial. This is especially true of the photoinitiation processes, since holographic data storage requires multiple sequential short exposures. Previously, models describing the temporal variation in the photosensitizer (dye) concentration as a function of exposure have been presented and applied to two different types of photosensitizer, i.e., Methylene Blue and Erythrosine B, in a polyvinyl alcohol/acrylamide based photopolymer. These models include the effects of photosensitizer recovery and bleaching under certain limiting conditions. In this paper, based on a detailed study of the photochemical reactions, the previous models are further developed to more physically represent these effects. This enables a more accurate description of the time varying dye absorption, recovery, and bleaching, and therefore of the generation of primary radicals in photopolymers containing such dyes.

  13. A mathematical model for material removal and chemical mechanical synergy in chemical mechanical polishing at molecular scale

    NASA Astrophysics Data System (ADS)

    Bai, J.; Zhao, Y. W.; Wang, Y. G.

    2007-08-01

    This paper presents a mathematical material removal model based on the chemical and mechanical synergistic effects in the chemical-mechanical polishing (CMP) process. It seems to explain the transition from a chemically dominant region to a mechanically dominant region. In addition, this model predicts the effects of most variables involved in the CMP process including the processing conditions (velocity, downpressure), pad properties (modulus, hardness and asperity sizes) and slurry characteristics (particle size, concentration and distribution). The results reveal some insights into the micro-contact and wear mechanisms of the CMP process.

  14. Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques.

    PubMed Central

    Malhotra, A; Tan, R K; Harvey, S C

    1994-01-01

    There is a growing body of low-resolution structural data that can be utilized to devise structural models for large RNAs and ribonucleoproteins. These models are routinely built manually. We introduce an automated refinement protocol to utilize such data for building low-resolution three-dimensional models using the tools of molecular mechanics. In addition to specifying the positions of each nucleotide, the protocol provides quantitative estimates of the uncertainties in those positions, i.e., the resolution of the model. In typical applications, the resolution of the models is about 10-20 A. Our method uses reduced representations and allows us to refine three-dimensional structures of systems as big as the 16S and 23S ribosomal RNAs, which are about one to two orders of magnitude larger than nucleic acids that can be examined by traditional all-atom modeling methods. Nonatomic resolution structural data--secondary structure, chemical cross-links, chemical and enzymatic footprinting patterns, protein positions, solvent accessibility, and so on--are combined with known motifs in RNA structure to predict low-resolution models of large RNAs. These structural constraints are imposed on the RNA chain using molecular mechanics-type potential functions with parameters based on the quality of experimental data. Surface potential functions are used to incorporate shape and positional data from electron microscopy image reconstruction experiments into our models. The structures are optimized using techniques of energy refinement to get RNA folding patterns. In addition to providing a consensus model, the method finds the range of models consistent with the data, which allows quantitative evaluation of the resolution of the model. The method also identifies conflicts in the experimental data. Although our protocol is aimed at much larger RNAs, we illustrate these techniques using the tRNA structure as an example and test-bed. Images FIGURE 7 FIGURE 8 PMID:7521223

  15. Correspondence patterns: mechanisms and models of human dynamics.

    PubMed

    Kentsis, Alex

    2006-05-25

    A stochastic queue model of human behaviour developed on the basis of the distribution of timing of tasks, as studied in a sample of e-mail messages at a university and in the written correspondence of Albert Einstein, may not be as simple as it seems. Although this model reproduces the apparently non-Poisson distribution of correspondence delays, its interpretation is more complicated than suggested by Barabási, who claims that humans execute their tasks based on some perceived priority, setting up queues that generate very uneven waiting-time distributions for different tasks. Such an explanation is intuitively appealing in the context of the queue metaphor, but does not exclude other mechanisms. By attributing delays in the correspondence to task priorities, this explanation ignores two important classes of mechanism that also contribute to the apparent distributions of task timings: the semantic content of an individual's correspondence and the social context in which this correspondence occurs.

  16. Implementing and assessing computational modeling in introductory mechanics

    NASA Astrophysics Data System (ADS)

    Caballero, Marcos D.; Kohlmyer, Matthew A.; Schatz, Michael F.

    2012-12-01

    Students taking introductory physics are rarely exposed to computational modeling. In a one-semester large lecture introductory calculus-based mechanics course at Georgia Tech, students learned to solve physics problems using the VPython programming environment. During the term, 1357 students in this course solved a suite of 14 computational modeling homework questions delivered using an online commercial course management system. Their proficiency with computational modeling was evaluated with a proctored assignment involving a novel central force problem. The majority of students (60.4%) successfully completed the evaluation. Analysis of erroneous student-submitted programs indicated that a small set of student errors explained why most programs failed. We discuss the design and implementation of the computational modeling homework and evaluation, the results from the evaluation, and the implications for computational instruction in introductory science, technology, engineering, and mathematics (STEM) courses.

  17. Mechanical stabilization of the Levitron's realistic model

    NASA Astrophysics Data System (ADS)

    Olvera, Arturo; De la Rosa, Abraham; Giordano, Claudia M.

    2016-11-01

    The stability of the magnetic levitation showed by the Levitron was studied by M.V. Berry as a six degrees of freedom Hamiltonian system using an adiabatic approximation. Further, H.R. Dullin found critical spin rate bounds where the levitation persists and R.F. Gans et al. offered numerical results regarding the initial conditions' manifold where this occurs. In the line of this series of works, first, we extend the equations of motion to include dissipation for a more realistic model, and then introduce a mechanical forcing to inject energy into the system in order to prevent the Levitron from falling. A systematic study of the flying time as a function of the forcing parameters is carried out which yields detailed bifurcation diagrams showing an Arnold's tongues structure. The stability of these solutions were studied with the help of a novel method to compute the maximum Lyapunov exponent called MEGNO. The bifurcation diagrams for MEGNO reproduce the same Arnold's tongue structure.

  18. Normal brain ageing: models and mechanisms

    PubMed Central

    Toescu, Emil C

    2005-01-01

    Normal ageing is associated with a degree of decline in a number of cognitive functions. Apart from the issues raised by the current attempts to expand the lifespan, understanding the mechanisms and the detailed metabolic interactions involved in the process of normal neuronal ageing continues to be a challenge. One model, supported by a significant amount of experimental evidence, views the cellular ageing as a metabolic state characterized by an altered function of the metabolic triad: mitochondria–reactive oxygen species (ROS)–intracellular Ca2+. The perturbation in the relationship between the members of this metabolic triad generate a state of decreased homeostatic reserve, in which the aged neurons could maintain adequate function during normal activity, as demonstrated by the fact that normal ageing is not associated with widespread neuronal loss, but become increasingly vulnerable to the effects of excessive metabolic loads, usually associated with trauma, ischaemia or neurodegenerative processes. This review will concentrate on some of the evidence showing altered mitochondrial function with ageing and also discuss some of the functional consequences that would result from such events, such as alterations in mitochondrial Ca2+ homeostasis, ATP production and generation of ROS. PMID:16321805

  19. A Computationally-Efficient, Multi-Mechanism Based Framework for the Comprehensive Modeling of the Evolutionary Behavior of Shape Memory Alloys

    NASA Technical Reports Server (NTRS)

    Saleeb, Atef F.; Vaidyanathan, Raj

    2016-01-01

    The report summarizes the accomplishments made during the 4-year duration of the project. Here, the major emphasis is placed on the different tasks performed by the two research teams; i.e., the modeling activities by the University of Akron (UA) team and the experimental and neutron diffraction studies conducted by the University of Central Florida (UCF) team, during this 4-year period. Further technical details are given in the upcoming sections by UA and UCF for each of the milestones/years (together with the corresponding figures and captions).The project majorly involved the development, validation, and application of a general theoretical model that is capable of capturing the nonlinear hysteretic responses, including pseudoelasticity, shape memory effect, rate-dependency, multi-axiality, asymmetry in tension versus compression response of shape memory alloys. Among the targeted goals for the SMA model was its ability to account for the evolutionary character response (including transient and long term behavior under sustained cycles) for both conventional and high temperature (HT) SMAs, as well as being able to simulate some of the devices which exploit these unique material systems. This required extensive (uniaxial and multi-axial) experiments needed to guide us in calibrating and characterizing the model. Moreover, since the model is formulated on the theoretical notion of internal state variables (ISVs), neutron diffraction experiments were needed to establish the linkage between the micromechanical changes and these ISVs. In addition, the design of the model should allow easy implementation in large scale finite element application to study the behavior of devices making use of these SMA materials under different loading controls. Summary of the activities, progress/achievements made during this period is given below in details for the University of Akron and the University (Section 2.0) of Central Florida (Section 3.0).

  20. Micromechanical Modeling of Impact Damage Mechanisms in Unidirectional Composite Laminates

    NASA Astrophysics Data System (ADS)

    Meng, Qinghua; Wang, Zhenqing

    2016-12-01

    Composite laminates are susceptible to the transverse impact loads resulting in significant damage such as matrix cracking, fiber breakage and delamination. In this paper, a micromechanical model is developed to predict the impact damage of composite laminates based on microstructure and various failure models of laminates. The fiber and matrix are represented by the isotropic and elastic-plastic solid, and their impact failure behaviors are modeled based on shear damage model. The delaminaton failure is modeling by the interface element controlled by cohesive damage model. Impact damage mechanisms of laminate are analyzed by using the micromechanical model proposed. In addition, the effects of impact energy and laminated type on impact damage behavior of laminates are investigated. Due to the damage of the surrounding matrix near the impact point caused by the fiber deformation, the surface damage area of laminate is larger than the area of ​​impact projectile. The shape of the damage area is roughly rectangle or elliptical with the major axis extending parallel to the fiber direction in the surface layer of laminate. The alternating laminated type with two fiber directions is more propitious to improve the impact resistance of laminates.

  1. Model-based software design

    NASA Technical Reports Server (NTRS)

    Iscoe, Neil; Liu, Zheng-Yang; Feng, Guohui; Yenne, Britt; Vansickle, Larry; Ballantyne, Michael

    1992-01-01

    Domain-specific knowledge is required to create specifications, generate code, and understand existing systems. Our approach to automating software design is based on instantiating an application domain model with industry-specific knowledge and then using that model to achieve the operational goals of specification elicitation and verification, reverse engineering, and code generation. Although many different specification models can be created from any particular domain model, each specification model is consistent and correct with respect to the domain model.

  2. Piezoelectric compliant mechanism energy harvesters under large base excitations

    NASA Astrophysics Data System (ADS)

    Ma, Xiaokun; Trolier-McKinstry, Susan; Rahn, Christopher D.

    2016-09-01

    A piezoelectric compliant mechanism (PCM) energy harvester is designed, modeled, and analyzed that consists of a polyvinylidene diflouoride, PVDF unimorph clamped at its base and attached to a compliant mechanism at its tip. The compliant hinge stiffness is carefully tuned to approach a low frequency first mode with an efficient (nearly quadratic) shape that provides a uniform strain distribution. A nonlinear model of the PCM energy harvester under large base excitation is derived to determine the maximum power that can be generated by the device. Experiments with a fabricated PCM energy harvester prototype show that the compliant mechanism introduces a stiffening effect and a much wider bandwidth than a benchmark proof mass cantilever design. The PCM bridge structure self-limits the displacement and maximum strain at large excitations compared with the proof mass cantilever, improving the device robustness. The PCM outperforms the cantilever in both average power and power-strain sensitivity at high accelerations due to the PCM axial stretching effect and its more uniform strain distribution.

  3. Model-Based Reasoning

    ERIC Educational Resources Information Center

    Ifenthaler, Dirk; Seel, Norbert M.

    2013-01-01

    In this paper, there will be a particular focus on mental models and their application to inductive reasoning within the realm of instruction. A basic assumption of this study is the observation that the construction of mental models and related reasoning is a slowly developing capability of cognitive systems that emerges effectively with proper…

  4. Assessing Heat-to-Heat Variations Affecting Mechanism Based Modeling of Hydrogen Environment Cracking (HEAC) in High Strength Alloys for Marine Applications: Monel K-500

    DTIC Science & Technology

    2016-01-28

    misfit strain) with an ordered Ll2 structure composed of Ni atoms at the faces and Al (or Ti) atoms on the corners of the unit cell [42-44]. Due to...local spin density atomic cluster model [99], researchers have postulated that the electronegativity of S changes the local chemical bonding structure ...Hutchings, ANALYSIS OF HYDROGEN- ATOM TRANSPORT IN A 2-PHASE ALLOY, Materials Science and Engineering a- Structural Materials Properties

  5. Quantum Mechanical Models Of The Fermi Shuttle

    SciTech Connect

    Sternberg, James

    2011-06-01

    The Fermi shuttle is a mechanism in which high energy electrons are produced in an atomic collision by multiple collisions with a target and a projectile atom. It is normally explained purely classically in terms of the electron's orbits prescribed in the collision. Common calculations to predict the Fermi shuttle use semi-classical methods, but these methods still rely on classical orbits. In reality such collisions belong to the realm of quantum mechanics, however. In this paper we discuss several purely quantum mechanical calculations which can produce the Fermi shuttle. Being quantum mechanical in nature, these calculations produce these features by wave interference, rather than by classical orbits.

  6. Principles of models based engineering

    SciTech Connect

    Dolin, R.M.; Hefele, J.

    1996-11-01

    This report describes a Models Based Engineering (MBE) philosophy and implementation strategy that has been developed at Los Alamos National Laboratory`s Center for Advanced Engineering Technology. A major theme in this discussion is that models based engineering is an information management technology enabling the development of information driven engineering. Unlike other information management technologies, models based engineering encompasses the breadth of engineering information, from design intent through product definition to consumer application.

  7. Mechanically induced residual stresses: Modelling and characterisation

    NASA Astrophysics Data System (ADS)

    Stranart, Jean-Claude E.

    Accurate characterisation of residual stress represents a major challenge to the engineering community. This is because it is difficult to validate the measurement and the accuracy is doubtful. It is with this in mind that the current research program concerning the characterisation of mechanically induced residual stresses was undertaken. Specifically, the cold expansion of fastener holes and the shot peening treatment of aerospace alloys, aluminium 7075 and titanium Ti-6Al-4V, are considered. The objective of this study is to characterise residual stresses resulting from cold working using three powerful techniques. These are: (i) theoretical using three dimensional non-linear finite element modelling, (ii) semi-destructive using a modified incremental hole drilling technique and (iii) nondestructive using a newly developed guided wave method supplemented by traditional C-scan measurements. The three dimensional finite element results of both simultaneous and sequential cold expansion of two fastener holes revealed the importance of the separation distance, the expansion level and the loading history upon the development and growth of the plastic zone and unloading residual stresses. It further showed that the commonly adopted two dimensional finite element models are inaccurate and incapable of predicting these residual stresses. Similarly, the dynamic elasto-plastic finite element studies of shot peening showed that the depth of the compressed layer, surface and sub-surface residual stresses are significantly influenced by the shot characteristics. Furthermore, the results reveal that the separation distance between two simultaneously impacting shots governs the plastic zone development and its growth. In the semi-destructive incremental hole drilling technique, the accuracy of the newly developed calibration coefficients and measurement techniques were verified with a known stress field and the method was used to measure peening residual stresses. Unlike

  8. Estimating seabed scattering mechanisms via Bayesian model selection.

    PubMed

    Steininger, Gavin; Dosso, Stan E; Holland, Charles W; Dettmer, Jan

    2014-10-01

    A quantitative inversion procedure is developed and applied to determine the dominant scattering mechanism (surface roughness and/or volume scattering) from seabed scattering-strength data. The classification system is based on trans-dimensional Bayesian inversion with the deviance information criterion used to select the dominant scattering mechanism. Scattering is modeled using first-order perturbation theory as due to one of three mechanisms: Interface scattering from a rough seafloor, volume scattering from a heterogeneous sediment layer, or mixed scattering combining both interface and volume scattering. The classification system is applied to six simulated test cases where it correctly identifies the true dominant scattering mechanism as having greater support from the data in five cases; the remaining case is indecisive. The approach is also applied to measured backscatter-strength data where volume scattering is determined as the dominant scattering mechanism. Comparison of inversion results with core data indicates the method yields both a reasonable volume heterogeneity size distribution and a good estimate of the sub-bottom depths at which scatterers occur.

  9. Strains, Mechanism, and Perspective: Salmonella-Based Cancer Therapy

    PubMed Central

    Wang, Cheng-Zhi; Kazmierczak, Robert A.; Eisenstark, Abraham

    2016-01-01

    Recently, investigation of bacterial-based tumor therapy has regained focus due to progress in molecular, cellular, and microbial biology. Many bacteria such as Salmonella, Listeria, Escherichia, and Clostridium have proved to have tumor targeting and in some cases even tumor-destroying phenotypes. Furthermore, bacterial clinical treatments for cancer have been improved by combination with other therapeutic methods such as chemotherapeutic drugs and radioactive agents. Synthetic biology techniques have also driven the development of new bacterial-based cancer therapies. However, basic questions about the mechanisms of bacterial-mediated tumor targeting and destruction are still being elucidated. In this review, we focus on three tumor-therapeutic Salmonella models, the most intensively studied bacterial genus in this field. One of these Salmonella models is our Salmonella enterica serovar Typhimurium LT2 derived strain CRC2631, engineered to minimize toxicity but maximize tumor-targeting and destruction effects. The other two are VNP20009 and A1-R. We compare the means by which these therapeutic candidate strain models were selected for study, their tumor targeting and tumor destruction phenotypes in vitro and in vivo, and what is currently known about the mechanisms by which they target and destroy tumors. PMID:27190519

  10. Distinct Element Modelling of Landslides in Mechanical Multilayers on Mars

    NASA Astrophysics Data System (ADS)

    Sims, D. W.; Smart, K. J.; Hooper, D. M.

    2008-12-01

    Mass wasting events such as landslides are an important component of the processes that have shaped the surface of Mars. Landslides are interpreted to have been active during much of the geologic history of Mars including the very recent past. The main scarp and displaced materials of landslides can tell us much about the mechanical nature of the surface and shallow subsurface of Mars. We use vertical two-dimensional distinct element models parallel with the slide direction to examine the effects of mechanical layering upon the morphology of slip surfaces and scarps that form as a result of slope failure on Mars. Bulk layer mechanical properties incorporated into the models and scaled to values likely be present on Mars include density, tensile strength, Young's modulus, Poisson's ratio, internal friction angle, cohesive strength, and unconfined compressive strength. Here we model horizontal layers with thickness range of 100 m to 500 m for a total thickness of 2500 m. Initial geometry is a 5 km long rectangle under conditions of Mars gravity where the top surface and one lateral boundary are free surfaces, and the horizontal base and opposing lateral boundary are rigid surfaces with friction coefficient of 0.5. Each layer represents one of five rock strengths, with strongest (strong basalt) to weakest (unconsolidated deposits) unconfined compressive strengths of 83, 44, 25, 8, and 2 MPa, respectively. Our models show that an initial slip surface forms some distance from the lateral free surface and subsequently migrates away from the free surface in discrete increments with concomitant decreasing slope of successive failure surfaces. Relative and absolute layer strength, thickness, and order control the morphology of the failure surfaces, the location and shape of the initial failure surface, and the kinematics of displaced material. In general, the size of coherent blocks and tendency towards sliding and spreading of displaced blocks increases with layer strength

  11. Impeller leakage flow modeling for mechanical vibration control

    NASA Technical Reports Server (NTRS)

    Palazzolo, Alan B.

    1996-01-01

    HPOTP and HPFTP vibration test results have exhibited transient and steady characteristics which may be due to impeller leakage path (ILP) related forces. For example, an axial shift in the rotor could suddenly change the ILP clearances and lengths yielding dynamic coefficient and subsequent vibration changes. ILP models are more complicated than conventional-single component-annular seal models due to their radial flow component (coriolis and centrifugal acceleration), complex geometry (axial/radial clearance coupling), internal boundary (transition) flow conditions between mechanical components along the ILP and longer length, requiring moment as well as force coefficients. Flow coupling between mechanical components results from mass and energy conservation applied at their interfaces. Typical components along the ILP include an inlet seal, curved shroud, and an exit seal, which may be a stepped labyrinth type. Von Pragenau (MSFC) has modeled labyrinth seals as a series of plain annular seals for leakage and dynamic coefficient prediction. These multi-tooth components increase the total number of 'flow coupled' components in the ILP. Childs developed an analysis for an ILP consisting of a single, constant clearance shroud with an exit seal represented by a lumped flow-loss coefficient. This same geometry was later extended to include compressible flow. The objective of the current work is to: supply ILP leakage-force impedance-dynamic coefficient modeling software to MSFC engineers, base on incompressible/compressible bulk flow theory; design the software to model a generic geometry ILP described by a series of components lying along an arbitrarily directed path; validate the software by comparison to available test data, CFD and bulk models; and develop a hybrid CFD-bulk flow model of an ILP to improve modeling accuracy within practical run time constraints.

  12. Modeling of coupled hydro-mechanical problem for porous media

    NASA Astrophysics Data System (ADS)

    Koudelka, T.; Krejci, T.; Broucek, M.

    2013-10-01

    The paper deals with numerical modelling of coupled hydro-mechanical problem for porous media. It is focused on coupled hydro-mechanical models for saturated - partially saturated soils. These models were implemented to the SIFEL software package and they were used for numerical simulation of a plate settlement experiment.

  13. Stochastical modeling for Viral Disease: Statistical Mechanics and Network Theory

    NASA Astrophysics Data System (ADS)

    Zhou, Hao; Deem, Michael

    2007-04-01

    Theoretical methods of statistical mechanics are developed and applied to study the immunological response against viral disease, such as dengue. We use this theory to show how the immune response to four different dengue serotypes may be sculpted. It is the ability of avian influenza, to change and to mix, that has given rise to the fear of a new human flu pandemic. Here we propose to utilize a scale free network based stochastic model to investigate the mitigation strategies and analyze the risk.

  14. Can mechanism inform species' distribution models?

    PubMed

    Buckley, Lauren B; Urban, Mark C; Angilletta, Michael J; Crozier, Lisa G; Rissler, Leslie J; Sears, Michael W

    2010-08-01

    Two major approaches address the need to predict species distributions in response to environmental changes. Correlative models estimate parameters phenomenologically by relating current distributions to environmental conditions. By contrast, mechanistic models incorporate explicit relationships between environmental conditions and organismal performance, estimated independently of current distributions. Mechanistic approaches include models that translate environmental conditions into biologically relevant metrics (e.g. potential duration of activity), models that capture environmental sensitivities of survivorship and fecundity, and models that use energetics to link environmental conditions and demography. We compared how two correlative and three mechanistic models predicted the ranges of two species: a skipper butterfly (Atalopedes campestris) and a fence lizard (Sceloporus undulatus). Correlative and mechanistic models performed similarly in predicting current distributions, but mechanistic models predicted larger range shifts in response to climate change. Although mechanistic models theoretically should provide more accurate distribution predictions, there is much potential for improving their flexibility and performance.

  15. Mechanical model of kinesin moving on microtubule

    NASA Astrophysics Data System (ADS)

    To, Kiwing; Chou, Ya-Chang; Hsiao, Yi-Feng; Chen, Kuan-Hua

    Kinesins are biomolecules that serve as intercellular motors for carrying cellular cargos along microtubules. Although the mechanism of converting the chemical energy of ATP to mechanical work is not fully understood, the motion of a kinesin on a microtubule has been measured and two different mechanisms, namely the ``hand-over-hand'' and ``inchworm'', has been proposed. The particular shape of kinesin and microtubules suggest a possible mechanism for force generation similar to Brownian ratchet. Using a bead chain connected to two heads that are attracted to a vibrated ratchet plate as a scaled up analog of the kinesinmicrotubule system, we manage to simulate both ``handoverhand'' and ``inchworm'' motion [Chou, et. al., Physica A443, 66 (2015)]. In addition, we find that chain, which play the role of the stalk in a kinesin molecule, can also generate force by interacting with the ratchet plate [Chen, et. al. Phys. Rev. E87, 012711 (2013)].

  16. Numerical simulation of two-way coupling mechanism in particle-laden turbulent flow based on one-dimensional turbulence model

    NASA Astrophysics Data System (ADS)

    Sun, Guangyuan; Lignell, David; Hewson, John; Gin, Craig

    2013-11-01

    We present three algorithms (type-I, type-C and type-IC) for Lagrangian particle transport within the context of the one-dimensional turbulence (ODT) approach. ODT is a stochastic model that captures the full range of length and time scales and provides statistical information on fine-scale turbulent-particle mixing and transport at low computational cost. Two of the particle transport algorithms are new as is an algorithm to provide two-way momentum and energy coupling between the particle and carrier phases. Using these methods we investigate particle-laden turbulent jet flow. In contrast to other previous particle implementation in ODT, the two new methods allow the particles to interact with multiple eddies simultaneously and evolve the particle phase continuously, and therefore are able to accurately capture turbulent mixing and fluctuation seen by inertial particles in ODT. Simulation results are compared with experimental data including the effect of two particle Stokes numbers (St = 3.6 and 10.8). Turbulence modification, particle number density PDFs and particle velocity evolution are presented.

  17. Simple micromechanical model of protein crystals for their mechanical characterizations

    NASA Astrophysics Data System (ADS)

    Yoon, G.; Eom, K.; Na, S.

    2010-06-01

    Proteins have been known to perform the excellent mechanical functions and exhibit the remarkable mechanical properties such as high fracture toughness in spider silk protein [1]. This indicates that the mechanical characterization of protein molecules and/or crystals is very essential to understand such remarkable mechanical function of protein molecules. In this study, for gaining insight into mechanical behavior of protein crystals, we developed the micromechanical model by using the empirical potential field prescribed to alpha carbon atoms of a protein crystal in a unit cell. We consider the simple protein crystals for their mechanical behavior under tensile loading to be compared with full atomic models

  18. Rule-based simulation models

    NASA Technical Reports Server (NTRS)

    Nieten, Joseph L.; Seraphine, Kathleen M.

    1991-01-01

    Procedural modeling systems, rule based modeling systems, and a method for converting a procedural model to a rule based model are described. Simulation models are used to represent real time engineering systems. A real time system can be represented by a set of equations or functions connected so that they perform in the same manner as the actual system. Most modeling system languages are based on FORTRAN or some other procedural language. Therefore, they must be enhanced with a reaction capability. Rule based systems are reactive by definition. Once the engineering system has been decomposed into a set of calculations using only basic algebraic unary operations, a knowledge network of calculations and functions can be constructed. The knowledge network required by a rule based system can be generated by a knowledge acquisition tool or a source level compiler. The compiler would take an existing model source file, a syntax template, and a symbol table and generate the knowledge network. Thus, existing procedural models can be translated and executed by a rule based system. Neural models can be provide the high capacity data manipulation required by the most complex real time models.

  19. The Two-Capacitor Problem Revisited: A Mechanical Harmonic Oscillator Model Approach

    ERIC Educational Resources Information Center

    Lee, Keeyung

    2009-01-01

    The well-known two-capacitor problem, in which exactly half the stored energy disappears when a charged capacitor is connected to an identical capacitor, is discussed based on the mechanical harmonic oscillator model approach. In the mechanical harmonic oscillator model, it is shown first that "exactly half" the work done by a constant applied…

  20. High performance liquid chromatography of substituted aromatics with the metal-organic framework MIL-100(Fe): Mechanism analysis and model-based prediction.

    PubMed

    Qin, Weiwei; Silvestre, Martin Eduardo; Li, Yongli; Franzreb, Matthias

    2016-02-05

    Metal-organic framework (MOF) MIL-100(Fe) with well-defined thickness was homogenously coated onto the outer surface of magnetic microparticles via a liquid-phase epitaxy method. The as-synthesized MIL-100(Fe) was used as stationary phase for high-performance liquid chromatography (HPLC) and separations of two groups of mixed aromatic hydrocarbons (toluene, styrene and p-xylene; acetanilide, 2-nirtoaniline and 1-naphthylamine) using methanol/water as mobile phase were performed to evaluate its performance. Increasing water content of the mobile phase composition can greatly improve the separations on the expense of a longer elution time. Stepwise elution significantly shortens the elution time of acetanilide, 2-nirtoaniline and 1-naphthylamine mixtures, while still achieving a baseline separation. Combining the experimental results and in-depth modeling using a recently developed chromatographic software (ChromX), adsorption equilibrium parameters, including the affinities and maximum capacities, for each analyte toward the MIL-100(Fe) are obtained. In addition, the pore diffusivity of aromatic hydrocarbons within MIL-100(Fe) was determined to be 5×10(-12)m(2)s(-1). While the affinities of MIL-100(Fe) toward the analyte molecules differs much, the maximum capacities of the analytes are in a narrow range with q*MOFmax,toluene=3.55molL(-1), q*MOFmax,styrene or p-xylene=3.53molL(-1), and q*MOFmax,anilines=3.12molL(-1) corresponding to approximately 842 toluene and 838 styrene or p-xylene, and 740 aniline molecules per MIL-100(Fe) unit cell, respectively.

  1. Mechanisms of protein assembly: lessons from minimalist models.

    PubMed

    Levy, Yaakov; Onuchic, José N

    2006-02-01

    Many cellular functions rely on interactions among proteins and between proteins and nucleic acids. The limited success of binding predictions may suggest that the physical and chemical principles of protein binding have to be revisited to correctly capture the essence of protein recognition. In this Account, we discuss the power of reduced models to study the physics of protein assembly. Since energetic frustration is sufficiently small, native topology-based models, which correspond to perfectly unfrustrated energy landscapes, have shown that binding mechanisms are robust and governed primarily by the protein's native topology. These models impressively capture many of the binding characteristics found in experiments and highlight the fundamental role of flexibility in binding. The essential role of solvent molecules and electrostatic interactions in binding is also discussed. Despite the success of the minimally frustrated models to describe the dynamics and mechanisms of binding, the actual degree of frustration has to be explored to quantify the capacity of a protein to bind specifically to other proteins. We have found that introducing mutations can significantly reduce specificity by introducing an additional binding mode. Deciphering and quantifying the key ingredients for biological self-assembly is invaluable to reading out genomic sequences and understanding cellular interaction networks.

  2. Mechanism-Based Modeling of Hydrogen Environment Assisted Cracking (HEAC) in High Strength Alloys for Marine Applications: Prediction of Monel K-500 HEAC for Select Environmental and Mechanical Conditions

    DTIC Science & Technology

    2012-10-15

    uncertain. Aged alloy X-750 (Ni- Cr -Fe-Al-Ti) shows a drop in effective hydrogen diffusivity of about a factor of nine from pure Ni, which is... alloy . This is consistent with previous results for a y’ strengthened Ni- Cr -Fe-AI-Ti alloy (X-750) where Ni3(Al,Ti) was found to be an intermediate...confidence associated with predictions of long - term component performance based on short term accelerated laboratory experimentation. CONCLUSIONS • The

  3. An agent-based modeling framework linking inflammation and cancer using evolutionary principles: description of a generative hierarchy for the hallmarks of cancer and developing a bridge between mechanism and epidemiological data.

    PubMed

    An, Gary; Kulkarni, Swati

    2015-02-01

    Inflammation plays a critical role in the development and progression of cancer, evident in multiple patient populations manifesting increased, non-resolving inflammation, such as inflammatory bowel disease, viral hepatitis and obesity. Given the complexity of both the inflammatory response and the process of oncogenesis, we utilize principles from the field of Translational Systems Biology to bridge the gap between basic mechanistic knowledge and clinical/epidemiologic data by integrating inflammation and oncogenesis within an agent-based model, the Inflammation and Cancer Agent-based Model (ICABM). The ICABM utilizes two previously published and clinically/epidemiologically validated mechanistic models to demonstrate the role of an increased inflammatory milieu on oncogenesis. Development of the ICABM required the creation of a generative hierarchy of the basic hallmarks of cancer to provide a foundation to ground the plethora of molecular and pathway components currently being studied. The ordering schema emphasizes the essential role of a fitness/selection frame shift to sub-organismal evolution as a basic property of cancer, where the generation of genetic instability as a negative effect for multicellular eukaryotic organisms represents the restoration of genetic plasticity used as an adaptive strategy by colonies of prokaryotic unicellular organisms. Simulations with the ICABM demonstrate that inflammation provides a functional environmental context that drives the shift to sub-organismal evolution, where increasingly inflammatory environments led to increasingly damaged genomes in microtumors (tumors below clinical detection size) and cancers. The flexibility of this platform readily facilitates tailoring the ICABM to specific cancers, their associated mechanisms and available epidemiological data. One clinical example of an epidemiological finding that could be investigated with this platform is the increased incidence of triple negative breast cancers in

  4. Tribo-chemical mechanisms of copper chemical mechanical planarization (CMP) - Fundamental investigations and integrated modeling

    NASA Astrophysics Data System (ADS)

    Tripathi, Shantanu

    In this work, copper Chemical Mechanical Planarization is identified primarily as a wear enhanced corrosion process (as opposed to the corrosion enhanced wear process assumed in existing modeling work), where intermittent abrasive action enhances the local oxidation rate, and is followed by time-dependant passivation of copper. Based on this mechanism, an integrated tribo-chemical model of material removal at the abrasive scale was developed based on oxidation of copper. This considers abrasive and pad properties, process parameters, and slurry chemistry. Three important components of this model -- the passivation kinetics of copper in CMP slurry chemicals; the mechanical properties of passive films on copper; and the interaction frequency of copper and abrasives -- are introduced. The first two components, in particular the passivation kinetics of copper, are extensively studied experimentally, while the third component is addressed theoretically. The passivation kinetics of copper (i.e. decrease in oxidation currents as passive films form on bare copper) were investigated by potential step chronoamperometry. Low cost microelectrodes were developed (first of its kind for studying copper CMP) to reduce many of the problems of traditional macroelectrodes, such as interference from capacitive charging, IR drops and low diffusion limited current. Electrochemical impedance spectroscopy (EIS) was used on copper microelectrodes in CMP slurry constituents to obtain equivalent circuit elements associated with different electrochemical phenomena (capacitive, kinetics, diffusion etc.) at different polarization potentials. The circuit elements were used to simulate chronoamperometry in a system where copper actively corrodes at anodic potentials; from the simulation and the experimental results, the current decay in this system was attributed entirely to capacitive charging. The circuit elements were also used to explain the chronoamperometry results in passivating and

  5. Inverse modeling of geochemical and mechanical compaction in sedimentary basins

    NASA Astrophysics Data System (ADS)

    Colombo, Ivo; Porta, Giovanni Michele; Guadagnini, Alberto

    2015-04-01

    We study key phenomena driving the feedback between sediment compaction processes and fluid flow in stratified sedimentary basins formed through lithification of sand and clay sediments after deposition. Processes we consider are mechanic compaction of the host rock and the geochemical compaction due to quartz cementation in sandstones. Key objectives of our study include (i) the quantification of the influence of the uncertainty of the model input parameters on the model output and (ii) the application of an inverse modeling technique to field scale data. Proper accounting of the feedback between sediment compaction processes and fluid flow in the subsurface is key to quantify a wide set of environmentally and industrially relevant phenomena. These include, e.g., compaction-driven brine and/or saltwater flow at deep locations and its influence on (a) tracer concentrations observed in shallow sediments, (b) build up of fluid overpressure, (c) hydrocarbon generation and migration, (d) subsidence due to groundwater and/or hydrocarbons withdrawal, and (e) formation of ore deposits. Main processes driving the diagenesis of sediments after deposition are mechanical compaction due to overburden and precipitation/dissolution associated with reactive transport. The natural evolution of sedimentary basins is characterized by geological time scales, thus preventing direct and exhaustive measurement of the system dynamical changes. The outputs of compaction models are plagued by uncertainty because of the incomplete knowledge of the models and parameters governing diagenesis. Development of robust methodologies for inverse modeling and parameter estimation under uncertainty is therefore crucial to the quantification of natural compaction phenomena. We employ a numerical methodology based on three building blocks: (i) space-time discretization of the compaction process; (ii) representation of target output variables through a Polynomial Chaos Expansion (PCE); and (iii) model

  6. Numerical modeling of compensation mechanisms for peripheral arterial stenoses.

    PubMed

    Drzisga, D; Köppl, T; Pohl, U; Helmig, R; Wohlmuth, B

    2016-03-01

    The goal of this paper is to develop a numerical model for physiological mechanisms that help to compensate reduced blood flow caused by a peripheral arterial stenosis. Thereby we restrict ourselves to the following compensation mechanisms: Metabolic regulation and arteriogenesis, i.e., growth of pre-existing collateral arteries. Our model is based on dimensionally reduced differential equations to simulate large time periods with low computational cost. As a test scenario, we consider a stenosis located in the right posterior tibial artery of a human. We study its impact on blood supply for different narrowing degrees by the help of numerical simulations. Moreover, the efficiency of the above compensation mechanisms is examined. Our results reveal that even a complete occlusion of this artery exhibiting a cross-section area of 0.442cm(2) can be compensated at rest, if metabolic regulation is combined with collateral arteries whose total cross-section area accounts for 8.14% of the occluded artery.

  7. Numerical Modelling and Damage Assessment of Rotary Wing Aircraft Cabin Door Using Continuum Damage Mechanics Model

    NASA Astrophysics Data System (ADS)

    Boyina, Gangadhara Rao T.; Rayavarapu, Vijaya Kumar; V. V., Subba Rao

    2017-02-01

    The prediction of ultimate strength remains the main challenge in the simulation of the mechanical response of composite structures. This paper examines continuum damage model to predict the strength and size effects for deformation and failure response of polymer composite laminates when subjected to complex state of stress. The paper also considers how the overall results of the exercise can be applied in design applications. The continuum damage model is described and the resulting prediction of size effects are compared against the standard benchmark solutions. The stress analysis for strength prediction of rotary wing aircraft cabin door is carried out. The goal of this study is to extend the proposed continuum damage model such that it can be accurately predict the failure around stress concentration regions. The finite element-based continuum damage mechanics model can be applied to the structures and components of arbitrary configurations where analytical solutions could not be developed.

  8. An Improved Model for Demonstrating the Mechanism of Breathing.

    ERIC Educational Resources Information Center

    Yip, Din-yan

    1998-01-01

    Points out that the standard bell-jar model used to illustrate breathing has some features that may lead to a misunderstanding of the mechanism of ventilation. Proposes modifications to the model. (DDR)

  9. "Piekara's Chair": Mechanical Model for Atomic Energy Levels.

    ERIC Educational Resources Information Center

    Golab-Meyer, Zofia

    1991-01-01

    Uses the teaching method of models or analogies, specifically the model called "Piekara's chair," to show how teaching classical mechanics can familiarize students with the notion of energy levels in atomic physics. (MDH)

  10. 16. YAZOO BACKWATER PUMPING STATION MODEL, YAZOO RIVER BASIN. MECHANICAL ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    16. YAZOO BACKWATER PUMPING STATION MODEL, YAZOO RIVER BASIN. MECHANICAL AND HYDRAULIC ENGINEERS EXAMINING MODEL PUMPS. - Waterways Experiment Station, Hydraulics Laboratory, Halls Ferry Road, 2 miles south of I-20, Vicksburg, Warren County, MS

  11. Differential Geometry Based Multiscale Models

    PubMed Central

    Wei, Guo-Wei

    2010-01-01

    Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atom-istic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier–Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson–Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson–Nernst–Planck equations that

  12. Differential geometry based multiscale models.

    PubMed

    Wei, Guo-Wei

    2010-08-01

    Large chemical and biological systems such as fuel cells, ion channels, molecular motors, and viruses are of great importance to the scientific community and public health. Typically, these complex systems in conjunction with their aquatic environment pose a fabulous challenge to theoretical description, simulation, and prediction. In this work, we propose a differential geometry based multiscale paradigm to model complex macromolecular systems, and to put macroscopic and microscopic descriptions on an equal footing. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum mechanical description of the aquatic environment with the microscopic discrete atomistic description of the macromolecule. Multiscale free energy functionals, or multiscale action functionals are constructed as a unified framework to derive the governing equations for the dynamics of different scales and different descriptions. Two types of aqueous macromolecular complexes, ones that are near equilibrium and others that are far from equilibrium, are considered in our formulations. We show that generalized Navier-Stokes equations for the fluid dynamics, generalized Poisson equations or generalized Poisson-Boltzmann equations for electrostatic interactions, and Newton's equation for the molecular dynamics can be derived by the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows. Comparison is given to classical descriptions of the fluid and electrostatic interactions without geometric flow based micro-macro interfaces. The detailed balance of forces is emphasized in the present work. We further extend the proposed multiscale paradigm to micro-macro analysis of electrohydrodynamics, electrophoresis, fuel cells, and ion channels. We derive generalized Poisson-Nernst-Planck equations that are

  13. Model to Estimate Threshold Mechanical Stability of Lower Lateral Cartilage

    PubMed Central

    Kim, James Hakjune; Hamamoto, Ashley; Kiyohara, Nicole; Wong, Brian J. F.

    2015-01-01

    IMPORTANCE In rhinoplasty, techniques used to alter the shape of the nasal tip often compromise the structural stability of the cartilage framework in the nose. Determining the minimum threshold level of cartilage stiffness required to maintain long-term structural stability is a critical aspect in performing these surgical maneuvers. OBJECTIVE To quantify the minimum threshold mechanical stability (elastic modulus) of lower lateral cartilage (LLC) according to expert opinion. METHODS Five anatomically correct LLC phantoms were made from urethane via a 3-dimensional computer modeling and injection molding process. All 5 had identical geometry but varied in stiffness along the intermediate crural region (0.63–30.6 MPa). DESIGN, SETTING, AND PARTICIPANTS A focus group of experienced rhinoplasty surgeons (n = 33) was surveyed at a regional professional meeting on October 25, 2013. Each survey participant was presented the 5 phantoms in a random order and asked to arrange the phantoms in order of increasing stiffness based on their sense of touch. Then, they were asked to select a single phantom out of the set that they believed to have the minimum acceptable mechanical stability for LLC to maintain proper form and function. MAIN OUTCOMES AND MEASURES A binary logistic regression was performed to calculate the probability of mechanical acceptability as a function of the elastic modulus of the LLC based on survey data. A Hosmer-Lemeshow test was performed to measure the goodness of fit between the logistic regression and survey data. The minimum threshold mechanical stability for LLC was taken at a 50% acceptability rating. RESULTS Phantom 4 was selected most frequently by the participants as having the minimum acceptable stiffness for LLC intermediate care. The minimum threshold mechanical stability for LLC was determined to be 3.65 MPa. The Hosmer-Lemeshow test revealed good fit between the logistic regression and survey data ( χ32=0.92 , P = .82). CONCLUSIONS AND

  14. Identification of the mechanism of action of a glucokinase activator from oral glucose tolerance test data in type 2 diabetic patients based on an integrated glucose-insulin model.

    PubMed

    Jauslin, Petra M; Karlsson, Mats O; Frey, Nicolas

    2012-12-01

    A mechanistic drug-disease model was developed on the basis of a previously published integrated glucose-insulin model by Jauslin et al. A glucokinase activator was used as a test compound to evaluate the model's ability to identify a drug's mechanism of action and estimate its effects on glucose and insulin profiles following oral glucose tolerance tests. A kinetic-pharmacodynamic approach was chosen to describe the drug's pharmacodynamic effects in a dose-response-time model. Four possible mechanisms of action of antidiabetic drugs were evaluated, and the corresponding affected model parameters were identified: insulin secretion, glucose production, insulin effect on glucose elimination, and insulin-independent glucose elimination. Inclusion of drug effects in the model at these sites of action was first tested one-by-one and then in combination. The results demonstrate the ability of this model to identify the dual mechanism of action of a glucokinase activator and describe and predict its effects: Estimating a stimulating drug effect on insulin secretion and an inhibiting effect on glucose output resulted in a significantly better model fit than any other combination of effect sites. The model may be used for dose finding in early clinical drug development and for gaining more insight into a drug candidate's mechanism of action.

  15. New Mechanical Model for the Transmutation Fuel Performance Code

    SciTech Connect

    Gregory K. Miller

    2008-04-01

    A new mechanical model has been developed for implementation into the TRU fuel performance code. The new model differs from the existing FRAPCON 3 model, which it is intended to replace, in that it will include structural deformations (elasticity, plasticity, and creep) of the fuel. Also, the plasticity algorithm is based on the “plastic strain–total strain” approach, which should allow for more rapid and assured convergence. The model treats three situations relative to interaction between the fuel and cladding: (1) an open gap between the fuel and cladding, such that there is no contact, (2) contact between the fuel and cladding where the contact pressure is below a threshold value, such that axial slippage occurs at the interface, and (3) contact between the fuel and cladding where the contact pressure is above a threshold value, such that axial slippage is prevented at the interface. The first stage of development of the model included only the fuel. In this stage, results obtained from the model were compared with those obtained from finite element analysis using ABAQUS on a problem involving elastic, plastic, and thermal strains. Results from the two analyses showed essentially exact agreement through both loading and unloading of the fuel. After the cladding and fuel/clad contact were added, the model demonstrated expected behavior through all potential phases of fuel/clad interaction, and convergence was achieved without difficulty in all plastic analysis performed. The code is currently in stand alone form. Prior to implementation into the TRU fuel performance code, creep strains will have to be added to the model. The model will also have to be verified against an ABAQUS analysis that involves contact between the fuel and cladding.

  16. Model based vibration monitoring

    SciTech Connect

    Esat, I.; Paya, B.; Badi, M.N.M.

    1996-11-01

    The principal source of vibratory excitation of gear system is the unsteady component of the relative angular motion of pair of meshing spur gears. This vibratory excitation is described by the transmission error. The transmission error present itself as a varying force at the contact point of the meshing gear teeth. The varying force is also influenced by the varying tooth stiffness due to change of orientation of teeth relative to each other, during the contact phase of each pair. Such a varying force produces both lateral and torsional excitation to the gear system. This paper presents analytical formulation of a simple two meshing spur gear system as a three mass system (18 DOF). The mathematical model also incorporates the analytical formulation of the tooth stiffness. The analytical results are compared with the experimental results. At this stage of analysis the procedure developed for handling the nonlinear influences of the tooth geometry is not fully implemented and the tooth stiffness taken as a constant value representing the average tooth stiffness. The comparison between the analytical and experimental results are encouraging as three main frequency obtained from FFT of the experimental results correlates very closely with the analytical results.

  17. Tractor Mechanic--Teacher's Guide. Competency Based Education Curriculum.

    ERIC Educational Resources Information Center

    McCann, Edward W.

    This teacher's guide is designed to accompany the Tractor Mechanic Competency Based Education (CBE) Curriculum (CE 022 480). The following information is included: a discussion of the uses of the Tractor Mechanic CBE curriculum; definitions of related terms; the table of contents for the Tractor Mechanic CBE curriculum; a list of competencies by…

  18. Pathway Model and Nonextensive Statistical Mechanics

    NASA Astrophysics Data System (ADS)

    Mathai, A. M.; Haubold, H. J.; Tsallis, C.

    2015-12-01

    The established technique of eliminating upper or lower parameters in a general hypergeometric series is profitably exploited to create pathways among confluent hypergeometric functions, binomial functions, Bessel functions, and exponential series. One such pathway, from the mathematical statistics point of view, results in distributions which naturally emerge within nonextensive statistical mechanics and Beck-Cohen superstatistics, as pursued in generalizations of Boltzmann-Gibbs statistics.

  19. Representing Model Inadequacy in Combustion Mechanisms of Laminar Flames

    NASA Astrophysics Data System (ADS)

    Morrison, Rebecca; Moser, Robert; Oliver, Todd

    2015-11-01

    An accurate description of the chemical processes involved in the oxidation of hydrocarbons may include hundreds of reactions and thirty or more chemical species. Kinetics models of these chemical mechanisms are often embedded in a fluid dynamics solver to represent combustion. Because the computational cost of such detailed mechanisms is so high, it is common practice to use drastically reduced mechanisms. But, this introduces modeling errors which may render the model inadequate. In this talk, we present a formulation of the model inadequacy in reduced models of combustion mechanisms. Our goal is to account for the discrepancy between the detailed model and its reduced version by incorporating an additive, linear, probabilistic inadequacy model. In effect, it is a random matrix, whose entries are characterized by probability distributions and which displays interesting properties due to conservation constraints. In particular, we investigate how the inclusion of the random matrix affects the prediction of flame speed in a one-dimensional hydrogen laminar flame.

  20. Modeling Guru: Knowledge Base for NASA Modelers

    NASA Astrophysics Data System (ADS)

    Seablom, M. S.; Wojcik, G. S.; van Aartsen, B. H.

    2009-05-01

    Modeling Guru is an on-line knowledge-sharing resource for anyone involved with or interested in NASA's scientific models or High End Computing (HEC) systems. Developed and maintained by the NASA's Software Integration and Visualization Office (SIVO) and the NASA Center for Computational Sciences (NCCS), Modeling Guru's combined forums and knowledge base for research and collaboration is becoming a repository for the accumulated expertise of NASA's scientific modeling and HEC communities. All NASA modelers and associates are encouraged to participate and provide knowledge about the models and systems so that other users may benefit from their experience. Modeling Guru is divided into a hierarchy of communities, each with its own set forums and knowledge base documents. Current modeling communities include those for space science, land and atmospheric dynamics, atmospheric chemistry, and oceanography. In addition, there are communities focused on NCCS systems, HEC tools and libraries, and programming and scripting languages. Anyone may view most of the content on Modeling Guru (available at http://modelingguru.nasa.gov/), but you must log in to post messages and subscribe to community postings. The site offers a full range of "Web 2.0" features, including discussion forums, "wiki" document generation, document uploading, RSS feeds, search tools, blogs, email notification, and "breadcrumb" links. A discussion (a.k.a. forum "thread") is used to post comments, solicit feedback, or ask questions. If marked as a question, SIVO will monitor the thread, and normally respond within a day. Discussions can include embedded images, tables, and formatting through the use of the Rich Text Editor. Also, the user can add "Tags" to their thread to facilitate later searches. The "knowledge base" is comprised of documents that are used to capture and share expertise with others. The default "wiki" document lets users edit within the browser so others can easily collaborate on the

  1. The Modeling of the Effects of Soiling, Its Mechanisms, and the Corresponding Abrasion

    SciTech Connect

    Simpson, Lin; Muller, Matthew; Deceglie, Michael; Miller, David; Moutinho, Helio

    2016-02-24

    Decreasing LCOE with predictive soiling loss models (using site data to predict annualized energy loss), quantification of different soiling mechanisms (using AFM-based characterization), and developing standards for PV module coatings.

  2. Model-Based Safety Analysis

    NASA Technical Reports Server (NTRS)

    Joshi, Anjali; Heimdahl, Mats P. E.; Miller, Steven P.; Whalen, Mike W.

    2006-01-01

    System safety analysis techniques are well established and are used extensively during the design of safety-critical systems. Despite this, most of the techniques are highly subjective and dependent on the skill of the practitioner. Since these analyses are usually based on an informal system model, it is unlikely that they will be complete, consistent, and error free. In fact, the lack of precise models of the system architecture and its failure modes often forces the safety analysts to devote much of their effort to gathering architectural details about the system behavior from several sources and embedding this information in the safety artifacts such as the fault trees. This report describes Model-Based Safety Analysis, an approach in which the system and safety engineers share a common system model created using a model-based development process. By extending the system model with a fault model as well as relevant portions of the physical system to be controlled, automated support can be provided for much of the safety analysis. We believe that by using a common model for both system and safety engineering and automating parts of the safety analysis, we can both reduce the cost and improve the quality of the safety analysis. Here we present our vision of model-based safety analysis and discuss the advantages and challenges in making this approach practical.

  3. Experimental Septic Shock: Models and Mechanisms

    DTIC Science & Technology

    1976-06-14

    E . coli endotoxin or live E . coli organisms were evaluated during a 24-hour period or until death. Results suggest significant differences between the two shock models: large dosages of endotoxin on contrast to those used in the canine species were required to elicit lethality characteristics. Hypoglycemia and hypoinsulinemia were regularly observed in live E . coli organism induced shock; however, hyperglycemia was a consistent hallmark in the endotoxin infused model. Renal fibrin thrombi were presented only after E .

  4. A damage mechanics based general purpose interface/contact element

    NASA Astrophysics Data System (ADS)

    Yan, Chengyong

    Most of the microelectronics packaging structures consist of layered substrates connected with bonding materials, such as solder or epoxy. Predicting the thermomechanical behavior of these multilayered structures is a challenging task in electronic packaging engineering. In a layered structure the most complex part is always the interfaces between the strates. Simulating the thermo-mechanical behavior of such interfaces, is the main theme of this dissertation. The most commonly used solder material, Pb-Sn alloy, has a very low melting temperature 180sp°C, so that the material demonstrates a highly viscous behavior. And, creep usually dominates the failure mechanism. Hence, the theory of viscoplasticity is adapted to describe the constitutive behavior. In a multilayered assembly each layer has a different coefficient of thermal expansion. Under thermal cycling, due to heat dissipated from circuits, interfaces and interconnects experience low cycle fatigue. Presently, the state-of-the art damage mechanics model used for fatigue life predictions is based on Kachanov (1986) continuum damage model. This model uses plastic strain as a damage criterion. Since plastic strain is a stress path dependent value, the criterion does not yield unique damage values for the same state of stress. In this dissertation a new damage evolution equation based on the second law of thermodynamic is proposed. The new criterion is based on the entropy of the system and it yields unique damage values for all stress paths to the final state of stress. In the electronics industry, there is a strong desire to develop fatigue free interconnections. The proposed interface/contact element can also simulate the behavior of the fatigue free Z-direction thin film interconnections as well as traditional layered interconnects. The proposed interface element can simulate behavior of a bonded interface or unbonded sliding interface, also called contact element. The proposed element was verified against

  5. 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).

  6. Cement design based on cement mechanical response

    SciTech Connect

    Thiercelin, M.J.; Dargaud, B.; Baret, J.F.; Rodriquez, W.J.

    1998-12-01

    The disappearance of cement bond log response as a result of variations of downhole conditions has been observed in numerous wells. This observation has led to concern about the loss of proper zonal isolation. Stresses induced in the cement, through deformation of the cemented casing resulting from the variation of downhole conditions, are the cause of this damage. The authors present an analysis of the mechanical response of set cement in a cased wellbore to quantify this damage and determine the key controlling parameters. The results show that the thermo-elastic properties of the casing, cement, and formation play a significant role. The type of failure, either cement debonding or cement cracking, is a function of the nature of the downhole condition variations. This analysis allows one to propose appropriate cement mechanical properties to avoid cement failure and debonding. The authors show that the use of high compressive strength cement is not always the best solution and, in some cases, flexible cements are preferred.

  7. Modeling mercury porosimetry using statistical mechanics.

    PubMed

    Porcheron, F; Monson, P A; Thommes, M

    2004-07-20

    We consider mercury porosimetry from the perspective of the statistical thermodynamics of penetration of a nonwetting liquid into a porous material under an external pressure. We apply density functional theory to a lattice gas model of the system and use this to compute intrusion/extrusion curves. We focus on the specific example of a Vycor glass and show that essential features of mercury porosimetry experiments can be modeled in this way. The lattice model exhibits a symmetry that provides a direct relationship between intrusion/extrusion curves for a nonwetting fluid and adsorption/desorption isotherms for a wetting fluid. This relationship clarifies the status of methods that are used for transforming mercury intrusion/extrusion curves into gas adsorption/desorption isotherms. We also use Monte Carlo simulations to investigate the nature of the intrusion and extrusion processes.

  8. Reconstruction of Sedimentary Rock Based on MechanicalProperties

    SciTech Connect

    Jin, Guodong; Patzek, Tad W.; Silin, Dmitry B.

    2004-05-04

    We describe a general, physics-based approach to numericalreconstruction of the geometrical structure and mechanical properties ofnatural sedimentary rock in 3D. Our procedure consists of three mainsteps: sedimentation, compaction, and diagenesis, followed by theverification of rock mechanical properties. The dynamic geologicprocesses of grain sedimentation and compaction are simulated by solvinga dimensionless form of Newton's equations of motion for an ensemble ofgrains. The diagenetic rock transformation is modeled using a cementationalgorithm, which accounts for the effect of rock grain size on therelative rate of cement overgrowth. Our emphasis is on unconsolidatedsand and sandstone. The main input parameters are the grain sizedistribution, the final rock porosity, the type and amount of cement andclay minerals, and grain mechanical properties: the inter-grain frictioncoefficient, the cement strength, and the grain stiffness moduli. We usea simulated 2D Fontainebleau sandstone to obtain the grain mechanicalproperties. This Fontainebleau sandstone is also used to study theinitiation, growth, and coalescence of micro-cracks under increasingvertical stress. The box fractal dimension of the micro-crackdistribution, and its variation with the applied stress areestimated.

  9. Putting mechanisms into crop production models.

    PubMed

    Boote, Kenneth J; Jones, James W; White, Jeffrey W; Asseng, Senthold; Lizaso, Jon I

    2013-09-01

    Crop growth models dynamically simulate processes of C, N and water balance on daily or hourly time-steps to predict crop growth and development and at season-end, final yield. Their ability to integrate effects of genetics, environment and crop management have led to applications ranging from understanding gene function to predicting potential impacts of climate change. The history of crop models is reviewed briefly, and their level of mechanistic detail for assimilation and respiration, ranging from hourly leaf-to-canopy assimilation to daily radiation-use efficiency is discussed. Crop models have improved steadily over the past 30-40 years, but much work remains. Improvements are needed for the prediction of transpiration response to elevated CO₂ and high temperature effects on phenology and reproductive fertility, and simulation of root growth and nutrient uptake under stressful edaphic conditions. Mechanistic improvements are needed to better connect crop growth to genetics and to soil fertility, soil waterlogging and pest damage. Because crop models integrate multiple processes and consider impacts of environment and management, they have excellent potential for linking research from genomics and allied disciplines to crop responses at the field scale, thus providing a valuable tool for deciphering genotype by environment by management effects.

  10. Quantum mechanical models with strictly ergodic disorder

    NASA Astrophysics Data System (ADS)

    Mavi, Rajinder

    We study quantum Hamiltonians with potentials defined by strictly ergodic dynamical systems. Our interest here are models where physical properties are understood in some regimes of disorder and the extent to which they vary in alternate regimes of disorder. For Schrodinger operators we show properties known to hold in the case of analytic potentials on the torus hold even for rough potentials only required to be Holder continuous. Specifically in this case we show, assuming a positive Lyapunov exponent, dynamical localization properties hold; as well as continuity of the measure of the spectrum for all rotations. For the quantum Ising model we show for phase structure that occur in the random regime, there are similar conditions for existence under the assumption of strictly ergodic dynamics. That is, moment conditions for random disorder are paralleled by conditions on the sampling functions in deterministic disorder. We obtain conditions for existence of phase transitions given any strictly egodically defined disorder. In addition, a new multiscale analysis method is developed to show the existence of stretched exponential decay in the random cluster model generalization of the quantum Ising model where only slower decay was obainable by previous methods.

  11. Quark Model in the Quantum Mechanics Curriculum.

    ERIC Educational Resources Information Center

    Hussar, P. E.; And Others

    1980-01-01

    This article discusses in detail the totally symmetric three-quark karyonic wave functions. The two-body mesonic states are also discussed. A brief review of the experimental efforts to identify the quark model multiplets is given. (Author/SK)

  12. Statistical mechanical models of virus capsid assembly

    NASA Astrophysics Data System (ADS)

    Hicks, Stephen Daniel

    Viruses have become an increasingly popular subject of physics investigation, particularly in the last decade. Advances in imaging of virus capsids---the protective protein shells---in a wide variety of stages of assembly have encouraged physical assembly models at a similarly wide variety of scales, while the apparent simplicity of the capsid system---typically, many identical units assembling spontaneously into an icosahedrally symmetric (rather than amorphous) shell---makes the problem particularly interesting. We take a look at the existing physical assembly models in light of the question of how a particular assembly target can be consistently achieved in the presence of so many possible incorrect results. This review leads us to pose our own model of fully irreversible virus assembly, which we study in depth using a large ensemble of simulated assembled capsids, generated under a variety of capsid shell elastic parameters. While this irreversible model (predictably) did not yield consistently symmetric results, we do glean some insight into the effect of elasticity on growth, as well as an understanding of common failure modes. In particular, we found that (i) capsid size depends strongly on the spontaneous curvature and weakly on the ratio of bending to stretching elastic stiffnesses, (ii) the probability of successful capsid completion decays exponentially with capsid size, and (iii) the degree of localization of Gaussian curvature depends heavily on the ratio of elastic stiffnesses. We then go on to consider more thoroughly the nature of the ensemble of symmetric and almost-symmetric capsids---ultimately computing a phase diagram of minimum-energy capsids as a function of the two above-mentioned elastic parameters---and also look at a number of modifications we can make to our irreversible model, finally putting forth a rather different type of model potentially appropriate for understanding immature HIV assembly, and concluding with a fit of this new

  13. Visual-adaptation-mechanism based underwater object extraction

    NASA Astrophysics Data System (ADS)

    Chen, Zhe; Wang, Huibin; Xu, Lizhong; Shen, Jie

    2014-03-01

    Due to the major obstacles originating from the strong light absorption and scattering in a dynamic underwater environment, underwater optical information acquisition and processing suffer from effects such as limited range, non-uniform lighting, low contrast, and diminished colors, causing it to become the bottleneck for marine scientific research and projects. After studying and generalizing the underwater biological visual mechanism, we explore its advantages in light adaption which helps animals to precisely sense the underwater scene and recognize their prey or enemies. Then, aiming to transform the significant advantage of the visual adaptation mechanism into underwater computer vision tasks, a novel knowledge-based information weighting fusion model is established for underwater object extraction. With this bionic model, the dynamical adaptability is given to the underwater object extraction task, making them more robust to the variability of the optical properties in different environments. The capability of the proposed method to adapt to the underwater optical environments is shown, and its outperformance for the object extraction is demonstrated by comparison experiments.

  14. Studies on sulfate attack: Mechanisms, test methods, and modeling

    NASA Astrophysics Data System (ADS)

    Santhanam, Manu

    concentration of the solution were seen to change the rate and mechanism of the attack in both sodium and magnesium sulfate solutions. The test results from these experiments were used to generate models for prediction of physical properties such as expansion and mass change, which could be used either for service life predictions, or for designing more reliable laboratory tests. Lastly, mechanisms for the attack by sodium and magnesium sulfate were proposed, based on the observations in the various studies. These mechanisms were able to simplify the understanding of the sulfate attack phenomenon.

  15. Magnetic flux leakage modeling for mechanical damage in transmission pipelines

    SciTech Connect

    Ivanov, P.A.; Zhang, Z.; Yeoh, C.H.; Udpa, L.; Sun, Y.; Udpa, S.S.; Lord, W.

    1998-09-01

    This paper presents a two stage FE model for prediction of magnetic flux leakage, resulting from mechanical damage. In the first stage the stress distribution associated with mechanical damage is obtained from a structural model. In the second stage the stress distribution is incorporated into a magnetic FE model, by mapping stress levels to permeability. MFL signals are calculated and compared with experimental gouge MFL signatures.

  16. Combined quantum mechanical/molecular mechanics modeling for large organometallic and metallobiochemical systems

    NASA Astrophysics Data System (ADS)

    Leong, Max Kangchien

    A method of combined quantum mechanics/molecular mechanics has been developed to model larger organometallic and metallobiochemical systems where neither quantum mechanics nor molecular mechanics, applied separately, can solve the problem. An electronically transparent interface, which allows charge transfers between the quantum and classical fragments, is devised and realized by employing a special iterative procedure of double (intrafragment and interfragment) self-consistent calculations. The combined QM/MM scheme was successfully applied to model iron picket-fence porphyrin, vitamin B12, aquocobalamin, and vitamin B12 coenzyme molecules.

  17. Mechanical Model of Globular Transition in Polymers

    SciTech Connect

    Tricard, Simon; Shepherd, Robert F.; Stan, Claudiu A.; Snyder, Phillip W.; Cademartiri, Rebecca; Zhu, Danny; Aranson, Igor S.; Shakhnovich, Eugene I.; Whitesides, George M.

    2014-07-30

    In complex, multicomponent systems, polymers often undergo phase transitions between distinct conformations. This paper reports a millimeter-scale granular model of coil-to-globule transitions: one “polymer” chain—a cylinders-on-a-string “pearl necklace”—and many spheres, all shaken on a horizontal surface. It is possible to describe the behavior of this granular system by using formalisms generally used in statistical physics of polymers. Two sets of experiments allowed the observation of first- and second- order coil-to-globule transitions. The model shows that the competition between long- and short range interactions leads to a first-order transition. Well-designed granular system represents another kind of approach to the study of polymer phase transitions and might inspire future designs of polymer-like mesoscale systems.

  18. Fluid mechanics in stented arterial model

    NASA Astrophysics Data System (ADS)

    Bernad, S. I.; Totorean, A.; Bosioc, A.; Crainic, N.; Hudrea, C.; Bernad, E. S.

    2015-12-01

    Local hemodynamic factors are known affect the natural history of the restenosis critically after coronary stenting of atherosclerosis. Stent-induced flows disturbance magnitude dependent directly on the strut design. Strut shape, strut thickness and the distance between consecutive struts have been associated clinically with the with post-intervention clinical outcomes. Hemodynamically favorable designs according to computational modeling can reduced in-stent restenosis after coronary stenting intervention.

  19. A model of the mechanism of cooperativity and associativity of long-term potentiation in the hippocampus: a fundamental mechanism of associative memory and learning.

    PubMed

    Kitajima, T; Hara, K

    1991-01-01

    Long-Term Potentiation (LTP) has three properties: (1) input specificity, (2) cooperativity and (3) associativity. In a previous paper, we proposed an integrated model of the mechanisms of the induction and maintenance of LTP with input specificity. In this paper, a model of the mechanism of cooperative and associative LTP is described. According to computer simulations of the model, its mechanism is based on the spread of synaptic potentials.

  20. Mechanical modeling of the growth of salt structures

    SciTech Connect

    Alfaro, Ruben Alberto Mazariegos

    1993-05-01

    A 2D numerical model for studying the morphology and history of salt structures by way of computer simulations is presented. The model is based on conservation laws for physical systems, a fluid marker equation to keep track of the salt/sediments interface, and two constitutive laws for rocksalt. When buoyancy alone is considered, the fluid-assisted diffusion model predicts evolution of salt structures 2.5 times faster than the power-law creep model. Both rheological laws predict strain rates of the order of 4.0 x 10-15 s-1 for similar structural maturity level of salt structures. Equivalent stresses and viscosities predicted by the fluid-assisted diffusion law are 102 times smaller than those predicted by the power-law creep rheology. Use of East Texas Basin sedimentation rates and power-law creep rheology indicate that differential loading is an effective mechanism to induce perturbations that amplify and evolve to mature salt structures, similar to those observed under natural geological conditions.

  1. Model-based machine learning.

    PubMed

    Bishop, Christopher M

    2013-02-13

    Several decades of research in the field of machine learning have resulted in a multitude of different algorithms for solving a broad range of problems. To tackle a new application, a researcher typically tries to map their problem onto one of these existing methods, often influenced by their familiarity with specific algorithms and by the availability of corresponding software implementations. In this study, we describe an alternative methodology for applying machine learning, in which a bespoke solution is formulated for each new application. The solution is expressed through a compact modelling language, and the corresponding custom machine learning code is then generated automatically. This model-based approach offers several major advantages, including the opportunity to create highly tailored models for specific scenarios, as well as rapid prototyping and comparison of a range of alternative models. Furthermore, newcomers to the field of machine learning do not have to learn about the huge range of traditional methods, but instead can focus their attention on understanding a single modelling environment. In this study, we show how probabilistic graphical models, coupled with efficient inference algorithms, provide a very flexible foundation for model-based machine learning, and we outline a large-scale commercial application of this framework involving tens of millions of users. We also describe the concept of probabilistic programming as a powerful software environment for model-based machine learning, and we discuss a specific probabilistic programming language called Infer.NET, which has been widely used in practical applications.

  2. Model-based machine learning

    PubMed Central

    Bishop, Christopher M.

    2013-01-01

    Several decades of research in the field of machine learning have resulted in a multitude of different algorithms for solving a broad range of problems. To tackle a new application, a researcher typically tries to map their problem onto one of these existing methods, often influenced by their familiarity with specific algorithms and by the availability of corresponding software implementations. In this study, we describe an alternative methodology for applying machine learning, in which a bespoke solution is formulated for each new application. The solution is expressed through a compact modelling language, and the corresponding custom machine learning code is then generated automatically. This model-based approach offers several major advantages, including the opportunity to create highly tailored models for specific scenarios, as well as rapid prototyping and comparison of a range of alternative models. Furthermore, newcomers to the field of machine learning do not have to learn about the huge range of traditional methods, but instead can focus their attention on understanding a single modelling environment. In this study, we show how probabilistic graphical models, coupled with efficient inference algorithms, provide a very flexible foundation for model-based machine learning, and we outline a large-scale commercial application of this framework involving tens of millions of users. We also describe the concept of probabilistic programming as a powerful software environment for model-based machine learning, and we discuss a specific probabilistic programming language called Infer.NET, which has been widely used in practical applications. PMID:23277612

  3. Mathematical model of depolarization mechanism of conducted vasoreactivity

    NASA Astrophysics Data System (ADS)

    Neganova, Anastasiia Y.; Stiukhina, Elena S.; Postnov, Dmitry E.

    2015-03-01

    We address the problem of conducted vasodilation, the phenomenon which is also known as functional hyperemia. Specifically, we test the mechanism of nondecremental propagation of electric signals along endothelial cell layer recently hypothesized by Figueroa et al. By means of functional modeling we focus on possible nonlinear mechanisms that can underlie such regenerative pulse transmission (RPT). Since endothelial cells (EC) are generally known as electrically inexcitable, the possible role of ECs in RPT mechanisms is not evident. By means of mathematical modeling we check the dynamical self-consistency of Figueroa's hypothesis, as well as estimate the possible contribution of specific ionic currents to the suggested RPT mechanism.

  4. Epigenetics and psychoneuroimmunology: mechanisms and models.

    PubMed

    Mathews, Herbert L; Janusek, Linda Witek

    2011-01-01

    In this Introduction to the Named Series "Epigenetics, Brain, Behavior, and Immunity" an overview of epigenetics is provided with a consideration of the nature of epigenetic regulation including DNA methylation, histone modification and chromatin re-modeling. Illustrative examples of recent scientific developments are highlighted to demonstrate the influence of epigenetics in areas of research relevant to those who investigate phenomena within the scientific discipline of psychoneuroimmunology. These examples are presented in order to provide a perspective on how epigenetic analysis will add insight into the molecular processes that connect the brain with behavior, neuroendocrine responsivity and immune outcome.

  5. Mouse Mammary Cancer Models - Mechanisms and Markers

    DTIC Science & Technology

    2001-08-01

    Wipl knockout mouse model and have shown defects in cell cycle control in cells derived from Wipl null animals. We are crossing these mice to mammary...compartment of the testes (13,14). Mice lacking Wipl are viable, but males show a reduced longevity and frequent runting (14). Wipl null males also show...predominates and thus the other TG/p53 mouse . Wnt-1 TG mice contain several copies nontumor components should not obscure any strong of a germline Wnt-1

  6. Mechanically based generative laws of morphogenesis

    NASA Astrophysics Data System (ADS)

    Beloussov, Lev V.

    2008-03-01

    A deep (although at the first glance naïve) question which may be addressed to embryonic development is why during this process quite definite and accurately reproduced successions of precise and complicated shapes are taking place, or why, in several cases, the result of development is highly precise in spite of an extensive variability of intermediate stages. This problem can be attacked in two different ways. One of them, up to now just slightly employed, is to formulate robust macroscopic generative laws from which the observed successions of shapes could be derived. Another one, which dominates in modern embryology, regards the development as a succession of highly precise 'micropatterns', each of them arising due to the action of specific factors, having, as a rule, nothing in common with each other. We argue that the latter view contradicts a great bulk of firmly established data and gives no satisfactory answers to the main problems of development. Therefore we intend to follow the first way. By doing this, we regard developing embryos as self-organized systems transpierced by feedbacks among which we pay special attention to those linked with mechanical stresses (MS). We formulate a hypothesis of so-called MS hyper-restoration as a common basis for the developmentally important feedback loops. We present a number of examples confirming this hypothesis and use it for reconstructing prolonged chains of developmental events. Finally, we discuss the application of the same set of assumptions to the first steps of egg development and to the internal differentiation of embryonic cells.

  7. Mechanical krill models for studying coordinated swimming

    NASA Astrophysics Data System (ADS)

    Montague, Alice; Lai, Hong Kuan; Samaee, Milad; Santhanakrishnan, Arvind

    2016-11-01

    The global biomass of Homo sapiens is about a third of the biomass of Euphausia superba, commonly known as the Antarctic krill. Krill participate in organized social behavior. Propulsive jets generated by individual krill in a school have been suggested to be important in providing hydrodynamic sensory cues. The importance of body positions and body angles on the wakes generated is challenging to study in free swimming krill. Our solution to study the flow fields of multiple krill was to develop mechanical krill robots. We designed krillbots using mostly 3D printed parts that are actuated by stepper motors. The krillbot limb lengths, angles, inter-limb spacing and pleopod stroke frequency were dynamically scaled using published data on free-swimming krill kinematics. The vertical and horizontal spacing between krillbots, as well as the body angle, are adjustable. In this study, we conducted particle image velocimetry (PIV) measurements with two tethered krillbots in a flow tank with no background flow. One krillbot was placed above and behind the other. Both krillbots were at a zero-degree body angle. Wake-body interactions visualized from PIV data will be presented.

  8. Nuclear magnetic shielding constants of liquid water: Insights from hybrid quantum mechanics/molecular mechanics models

    NASA Astrophysics Data System (ADS)

    Kongsted, Jacob; Nielsen, Christian B.; Mikkelsen, Kurt V.; Christiansen, Ove; Ruud, Kenneth

    2007-01-01

    We present a gauge-origin independent method for the calculation of nuclear magnetic shielding tensors of molecules in a structured and polarizable environment. The method is based on a combination of density functional theory (DFT) or Hartree-Fock wave functions with molecular mechanics. The method is unique in the sense that it includes three important properties that need to be fulfilled in accurate calculations of nuclear magnetic shielding constants: (i) the model includes electron correlation effects, (ii) the model uses gauge-including atomic orbitals to give gauge-origin independent results, and (iii) the effect of the environment is treated self-consistently using a discrete reaction-field methodology. The authors present sample calculations of the isotropic nuclear magnetic shielding constants of liquid water based on a large number of solute-solvent configurations derived from molecular dynamics simulations employing potentials which treat solvent polarization either explicitly or implicitly. For both the O17 and H1 isotropic shielding constants the best predicted results compare fairly well with the experimental data, i.e., they reproduce the experimental solvent shifts to within 4ppm for the O17 shielding and 1ppm for the H1 shielding.

  9. Suction based mechanical characterization of superficial facial soft tissues.

    PubMed

    Weickenmeier, J; Jabareen, M; Mazza, E

    2015-12-16

    The present study is aimed at a combined experimental and numerical investigation of the mechanical response of superficial facial tissues. Suction based experiments provide the location, time, and history dependent behavior of skin and SMAS (superficial musculoaponeurotic system) by means of Cutometer and Aspiration measurements. The suction method is particularly suitable for in vivo, multi-axial testing of soft biological tissue including a high repeatability in subsequent tests. The campaign comprises three measurement sites in the face, i.e. jaw, parotid, and forehead, using two different loading profiles (instantaneous loading and a linearly increasing and decreasing loading curve), multiple loading magnitudes, and cyclic loading cases to quantify history dependent behavior. In an inverse finite element analysis based on anatomically detailed models an optimized set of material parameters for the implementation of an elastic-viscoplastic material model was determined, yielding an initial shear modulus of 2.32kPa for skin and 0.05kPa for SMAS, respectively. Apex displacements at maximum instantaneous and linear loading showed significant location specificity with variations of up to 18% with respect to the facial average response while observing variations in repeated measurements in the same location of less than 12%. In summary, the proposed parameter sets for skin and SMAS are shown to provide remarkable agreement between the experimentally observed and numerically predicted tissue response under all loading conditions considered in the present study, including cyclic tests.

  10. Aging mechanism in model Pickering emulsion

    NASA Astrophysics Data System (ADS)

    Fouilloux, Sarah; Malloggi, Florent; Daillant, Jean; Thill, Antoine

    We study the stability of a model Pickering emulsion system. A special counter-flow microfluidics set-up was used to prepare monodisperse Pickering emulsions, with oil droplets in water. The wettability of the monodisperse silica nanoparticles (NPs) could be tuned by surface grafting and the surface coverage of the droplets was controlled using the microfluidics setup. A surface coverage as low as 23$\\%$ is enough to stabilize the emulsions and we evidence a new regime of Pickering emulsion stability where the surface coverage of emulsion droplets of constant size increases in time, in coexistence with a large amount of dispersed phase. Our results demonstrate that the previously observed limited coalescence regime where surface coverage tends to control the average size of the final droplets must be put in a broader perspective.

  11. United polarizable multipole water model for molecular mechanics simulation

    PubMed Central

    Qi, Rui; Wang, Lee-Ping; Wang, Qiantao; Pande, Vijay S.; Ren, Pengyu

    2015-01-01

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water. PMID:26156485

  12. United polarizable multipole water model for molecular mechanics simulation

    SciTech Connect

    Qi, Rui; Wang, Qiantao; Ren, Pengyu; Wang, Lee-Ping; Pande, Vijay S.

    2015-07-07

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

  13. United polarizable multipole water model for molecular mechanics simulation

    NASA Astrophysics Data System (ADS)

    Qi, Rui; Wang, Lee-Ping; Wang, Qiantao; Pande, Vijay S.; Ren, Pengyu

    2015-07-01

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3-5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

  14. Sketch-based geologic modeling

    NASA Astrophysics Data System (ADS)

    Rood, M. P.; Jackson, M.; Hampson, G.; Brazil, E. V.; de Carvalho, F.; Coda, C.; Sousa, M. C.; Zhang, Z.; Geiger, S.

    2015-12-01

    Two-dimensional (2D) maps and cross-sections, and 3D conceptual models, are fundamental tools for understanding, communicating and modeling geology. Yet geologists lack dedicated and intuitive tools that allow rapid creation of such figures and models. Standard drawing packages produce only 2D figures that are not suitable for quantitative analysis. Geologic modeling packages can produce 3D models and are widely used in the groundwater and petroleum communities, but are often slow and non-intuitive to use, requiring the creation of a grid early in the modeling workflow and the use of geostatistical methods to populate the grid blocks with geologic information. We present an alternative approach to rapidly create figures and models using sketch-based interface and modelling (SBIM). We leverage methods widely adopted in other industries to prototype complex geometries and designs. The SBIM tool contains built-in geologic rules that constrain how sketched lines and surfaces interact. These rules are based on the logic of superposition and cross-cutting relationships that follow from rock-forming processes, including deposition, deformation, intrusion and modification by diagenesis or metamorphism. The approach allows rapid creation of multiple, geologically realistic, figures and models in 2D and 3D using a simple, intuitive interface. The user can sketch in plan- or cross-section view. Geologic rules are used to extrapolate sketched lines in real time to create 3D surfaces. Quantitative analysis can be carried our directly on the models. Alternatively, they can be output as simple figures or imported directly into other modeling tools. The software runs on a tablet PC and can be used in a variety of settings including the office, classroom and field. The speed and ease of use of SBIM enables multiple interpretations to be developed from limited data, uncertainty to be readily appraised, and figures and models to be rapidly updated to incorporate new data or concepts.

  15. A simple polymeric model describes cell nuclear mechanical response

    NASA Astrophysics Data System (ADS)

    Banigan, Edward; Stephens, Andrew; Marko, John

    The cell nucleus must continually resist inter- and intracellular mechanical forces, and proper mechanical response is essential to basic cell biological functions as diverse as migration, differentiation, and gene regulation. Experiments probing nuclear mechanics reveal that the nucleus stiffens under strain, leading to two characteristic regimes of force response. This behavior depends sensitively on the intermediate filament protein lamin A, which comprises the outer layer of the nucleus, and the properties of the chromatin interior. To understand these mechanics, we study a simulation model of a polymeric shell encapsulating a semiflexible polymer. This minimalistic model qualitatively captures the typical experimental nuclear force-extension relation and observed nuclear morphologies. Using a Flory-like theory, we explain the simulation results and mathematically estimate the force-extension relation. The model and experiments suggest that chromatin organization is a dominant contributor to nuclear mechanics, while the lamina protects cell nuclei from large deformations.

  16. A novel insight into membrane fouling mechanism regarding gel layer filtration: Flory-Huggins based filtration mechanism.

    PubMed

    Lei, Qian; Zhang, Meijia; Shen, Liguo; Li, Renjie; Liao, Bao-Qiang; Lin, Hongjun

    2016-09-15

    This study linked the chemical potential change to high specific filtration resistance (SFR) of gel layer, and then proposed a novel membrane fouling mechanism regarding gel layer filtration, namely, Flory-Huggins based filtration mechanism. A mathematical model for this mechanism was theoretically deduced. Agar was used as a model polymer for gel formation. Simulation of the mathematical model for agar gel showed that volume fraction of polymer and Flory-Huggins interaction parameter were the two key factors governing the gel SFR, whereas, pH and ionic strength were not related with the gel SFR. Filtration tests of gel layer showed that the total SFR value, effects of pH and ionic strength on the gel SFR well agreed with the perditions of model's simulation, indicating the real occurrence of this mechanism and the feasibility of the proposed model. This mechanism can satisfactorily explain the extremely high SFR of gel layer, and improve fundamental insights into membrane fouling regarding gel layer filtration.

  17. Links between fluid mechanics and quantum mechanics: a model for information in economics?

    PubMed

    Haven, Emmanuel

    2016-05-28

    This paper tallies the links between fluid mechanics and quantum mechanics, and attempts to show whether those links can aid in beginning to build a formal template which is usable in economics models where time is (a)symmetric and memory is absent or present. An objective of this paper is to contemplate whether those formalisms can allow us to model information in economics in a novel way.

  18. A hybrid agent-based approach for modeling microbiological systems.

    PubMed

    Guo, Zaiyi; Sloot, Peter M A; Tay, Joc Cing

    2008-11-21

    Models for systems biology commonly adopt Differential Equations or Agent-Based modeling approaches for simulating the processes as a whole. Models based on differential equations presuppose phenomenological intracellular behavioral mechanisms, while models based on Multi-Agent approach often use directly translated, and quantitatively less precise if-then logical rule constructs. We propose an extendible systems model based on a hybrid agent-based approach where biological cells are modeled as individuals (agents) while molecules are represented by quantities. This hybridization in entity representation entails a combined modeling strategy with agent-based behavioral rules and differential equations, thereby balancing the requirements of extendible model granularity with computational tractability. We demonstrate the efficacy of this approach with models of chemotaxis involving an assay of 10(3) cells and 1.2x10(6) molecules. The model produces cell migration patterns that are comparable to laboratory observations.

  19. Mirror neurons: functions, mechanisms and models.

    PubMed

    Oztop, Erhan; Kawato, Mitsuo; Arbib, Michael A

    2013-04-12

    Mirror neurons for manipulation fire both when the animal manipulates an object in a specific way and when it sees another animal (or the experimenter) perform an action that is more or less similar. Such neurons were originally found in macaque monkeys, in the ventral premotor cortex, area F5 and later also in the inferior parietal lobule. Recent neuroimaging data indicate that the adult human brain is endowed with a "mirror neuron system," putatively containing mirror neurons and other neurons, for matching the observation and execution of actions. Mirror neurons may serve action recognition in monkeys as well as humans, whereas their putative role in imitation and language may be realized in human but not in monkey. This article shows the important role of computational models in providing sufficient and causal explanations for the observed phenomena involving mirror systems and the learning processes which form them, and underlines the need for additional circuitry to lift up the monkey mirror neuron circuit to sustain the posited cognitive functions attributed to the human mirror neuron system.

  20. Multiscale physics-based modeling of friction

    NASA Astrophysics Data System (ADS)

    Eriten, Melih

    Frictional contacts between solids exist in nature and in a wide range of engineering applications. Friction causes energy loss, and it is the main source of wear and surface degradation which limits the lifetime of mechanical systems. Yet, friction is needed to walk, run, accelerate, slow down or stop moving systems. Whether desirable or not, friction is a very complex physical phenomenon. The behavior of systems with friction is nonlinear, and the physical mechanisms governing friction behavior span a wide range of spatial and temporal scales. A thorough study of friction should employ experimentalists and theoreticians in chemistry, materials science, tribology, mechanics, dynamics, and structural engineering. High spatial and temporal resolutions are required to capture and model essential physics of a frictional contact. However, such a detailed model is impractical in large-scale structural dynamics simulations; especially since frictional contacts can be numerous in a given application. Reduced-order models (ROMs) achieve broader applicability by compromising several aspects and accounting for the important physics. Hence, rather simple Coulomb friction is still the most ubiquitous model in the modeling and simulation literature. As an alternative, a reduced-order friction model built-up from micromechanics of surfaces is proposed in this work. Continuum-scale formulation of pre-sliding friction behavior is combined with material-strength-based friction coefficients to develop a physics-based friction model at asperity-scale. Then, the statistical summation technique is utilized to build a multiscale modeling framework. A novel joint fretting setup is designed for friction experiments in a practical setting, and the developed models are tested. Both asperity and rough surface friction models show good agreement with experimental data. The influences of materials, surface roughness and contact contamination on the friction are also studied. Finally, the

  1. Mathematical modelling of the cellular mechanics of plants.

    PubMed Central

    Bruce, David M

    2003-01-01

    The complex mechanical behaviour of plant tissues reflects the complexity of their structure and material properties. Modelling has been widely used in studies of how cell walls, single cells and tissue respond to loading, both externally applied loading and loads on the cell wall resulting from changes in the pressure within fluid-filled cells. This paper reviews what approaches have been taken to modelling and simulation of cell wall, cell and tissue mechanics, and to what extent models have been successful in predicting mechanical behaviour. Advances in understanding of cell wall ultrastructure and the control of cell growth present opportunities for modelling to clarify how growth-related mechanical properties arise from wall polymeric structure and biochemistry. PMID:14561334

  2. A Simplified Quantum Mechanical Model of Diatomic Molecules

    ERIC Educational Resources Information Center

    Nielsen, Lars Drud

    1978-01-01

    Introduces a simple one-dimensional model of a diatomic molecule that can explain all the essential features of a real two particle quantum mechanical system and gives quantitative results in fair agreement with those of a hydrogen molecule. (GA)

  3. Understanding the mechanism of base development of HSQ

    SciTech Connect

    Kim, Jihoon; Chao, Weilun; Griedel, Brian; Liang, Xiaogan; Lewis, Mark; Hilken, Dawn; Olynick, Deirdre

    2009-06-16

    We study the dissolution mechanism of HSQ (hydrogen silsesquioxane) in base solutions with the addition of chloride salts to elucidate the development mechanism. Reaction mechanisms are proposed based on the dissolution mechanism of quartz. Development kinetics points to two dose-dependent development mechanisms. Considering ion sizes, both hydrated and non-hydrated, and ion exchange, we propose that a combination of a surface dominated reaction at higher doses and a matrix dominated reaction at lower doses accounts for the high development contrast with a NaOH base/NaCl salt mixture. The interplay between the hydrated and non-hydrated ion size leads to higher contrast developers, such as tetramethyl ammonium hydroxide (TMAH) with NaCl.

  4. Mechanical vasoconstriction for a cerebral myogenic autoregulatory model.

    PubMed

    Stan, E; McNames, J; Kohles, S S; Biber, C; Biberic, N; Leech, N; Mangan, R W; McKinney, T J; Surdu, M; Goldstein, B

    2004-01-01

    This work presents the design of a mechanical vasoconstriction mechanism with application for cerebral autoregulation. The relationship between the applied voltage of a DC motor and the tension within a pressurized vessel wall was utilized for constricting an arteriole segment within an intracranial vascular model. Using current proportional to the string tension, options for closed loop feedback control are considered.

  5. Generation Mechanism of Alternans in Luo-Rudy Model

    NASA Astrophysics Data System (ADS)

    Kitajima, Hiroyuki; Ioka, Eri; Yazawa, Toru

    Electrical alternans is the alternating amplitude from beat to beat in the action potential of the cardiac cell. It has been associated with ventricular arrhythmias in many clinical studies; however, its dynamical mechanisms remain unknown. The reason is that we do not have realistic network models of the heart system. Recently, Yazawa clarified the network structure of the heart and the central nerve system in the crustacean heart. In this study, we construct a simple model of the heart system based on Yazawa’s experimental data. Using this model, we clarify that two parameters (the conductance of sodium ions and free concentration of potassium ions in the extracellular compartment) play the key roles of generating alternans. In particular, we clarify that the inactivation gate of the time-independent potassium channel is the most important parameter. Moreover, interaction between the membrane potential and potassium ionic currents is significant for generating alternate rhythms. This result indicates that if the muscle cell has problems such as channelopathies, there is great risk of generating alternans.

  6. Non-Fourier based thermal-mechanical tissue damage prediction for thermal ablation.

    PubMed

    Li, Xin; Zhong, Yongmin; Smith, Julian; Gu, Chengfan

    2017-01-02

    Prediction of tissue damage under thermal loads plays important role for thermal ablation planning. A new methodology is presented in this paper by combing non-Fourier bio-heat transfer, constitutive elastic mechanics as well as non-rigid motion of dynamics to predict and analyze thermal distribution, thermal-induced mechanical deformation and thermal-mechanical damage of soft tissues under thermal loads. Simulations and comparison analysis demonstrate that the proposed methodology based on the non-Fourier bio-heat transfer can account for the thermal-induced mechanical behaviors of soft tissues and predict tissue thermal damage more accurately than classical Fourier bio-heat transfer based model.

  7. Benefits of detailed models of muscle activation and mechanics

    NASA Technical Reports Server (NTRS)

    Lehman, S. L.; Stark, L.

    1981-01-01

    Recent biophysical and physiological studies identified some of the detailed mechanisms involved in excitation-contraction coupling, muscle contraction, and deactivation. Mathematical models incorporating these mechanisms allow independent estimates of key parameters, direct interplay between basic muscle research and the study of motor control, and realistic model behaviors, some of which are not accessible to previous, simpler, models. The existence of previously unmodeled behaviors has important implications for strategies of motor control and identification of neural signals. New developments in the analysis of differential equations make the more detailed models feasible for simulation in realistic experimental situations.

  8. Mechanisms of Synaptic Alterations in a Neuroinflammation Model of Autism

    DTIC Science & Technology

    2014-10-01

    1 Award Number: W81XWH-13-1-0440 TITLE: Mechanisms of Synaptic Alterations in a Neuroinflammation Model of Autism PRINCIPAL INVESTIGATOR: Anna...29Sep2014 4. TITLE AND SUBTITLE Mechanisms of Synaptic Alterations in a Neuroinflammation Model of Autism 5a. CONTRACT NUMBER W81XWH-13-1-0440 5b...Here we investigated how Maternal Immune Activation (MIA), a risk factor for autism spectrum disorders (ASD) affects the development of synapses

  9. Tractor Mechanic--Student Material. Competency Based Education Curriculum.

    ERIC Educational Resources Information Center

    McCann, Edward W.

    Developed to assist vocational agricultural mechanics students in learning to be tractor mechanics, this curriculum guide contains all the student competency sheets which comprise this competency-based curriculum. These competency sheets are categorized under sixteen instructional units. The first two units cover employment opportunities and…

  10. An Action-Based Fine-Grained Access Control Mechanism for Structured Documents and Its Application

    PubMed Central

    Su, Mang; Li, Fenghua; Tang, Zhi; Yu, Yinyan; Zhou, Bo

    2014-01-01

    This paper presents an action-based fine-grained access control mechanism for structured documents. Firstly, we define a describing model for structured documents and analyze the application scenarios. The describing model could support the permission management on chapters, pages, sections, words, and pictures of structured documents. Secondly, based on the action-based access control (ABAC) model, we propose a fine-grained control protocol for structured documents by introducing temporal state and environmental state. The protocol covering different stages from document creation, to permission specification and usage control are given by using the Z-notation. Finally, we give the implementation of our mechanism and make the comparisons between the existing methods and our mechanism. The result shows that our mechanism could provide the better solution of fine-grained access control for structured documents in complicated networks. Moreover, it is more flexible and practical. PMID:25136651

  11. Carbon-based nano-electro-mechanical systems

    NASA Astrophysics Data System (ADS)

    Kaul, A. B.; Khan, A. R.; Megerian, K. G.; Epp, L.; LeDuc, H. G.; Bagge, L.; Jennings, A. T.; Jang, D.; Greer, J. R.

    2010-04-01

    We provide an overview of our work where carbon-based nanostructures have been applied to twodimensional (2D) planar and three-dimensional (3D) vertically-oriented nano-electro-mechanical (NEM) switches. In the first configuration, laterally oriented single-walled nanotubes (SWNTs) synthesized using thermal chemical vapor deposition (CVD) were implemented for forming bridge-type 2D NEMS switches, where switching voltages were on the order of a few volts. In the second configuration, vertically oriented carbon nanofibers (CNFs) synthesized using plasma-enhanced (PE) CVD have been explored for their potential application in 3D NEMS. We have performed nanomechanical measurements on such vertically oriented tubes using nanoindentation to determine the mechanical properties of the CNFs. Electrostatic switching was demonstrated in the CNFs synthesized on refractory metallic nitride substrates, where a nanoprobe was used as the actuating electrode inside a scanning-electron-microscope. The switching voltages were determined to be in the tens of volts range and van der Waals interactions at these length scales appeared significant, suggesting such structures are promising for nonvolatile memory applications. A finite element model was also developed to determine a theoretical pull-in voltage which was compared to experimental results.

  12. Graphene mechanics: I. Efficient first principles based Morse potential.

    PubMed

    Costescu, Bogdan I; Baldus, Ilona B; Gräter, Frauke

    2014-06-28

    We present a computationally efficient pairwise potential for use in molecular dynamics simulations of large graphene or carbon nanotube systems, in particular, for those under mechanical deformation, and also for mixed systems including biomolecules. Based on the Morse potential, it is only slightly more complex and computationally expensive than a harmonic bond potential, allowing such large or mixed simulations to reach experimentally relevant time scales. By fitting to data obtained from quantum mechanics (QM) calculations to represent bond breaking in graphene patches, we obtain a dissociation energy of 805 kJ mol(-1) which reflects the steepness of the QM potential up to the inflection point. A distinctive feature of our potential is its truncation at the inflection point, allowing a realistic treatment of ruptured C-C bonds without relying on a bond order model. The results obtained from equilibrium MD simulations using our potential compare favorably with results obtained from experiments and from similar simulations with more complex and computationally expensive potentials.

  13. Carbon-Based Nano-Electro-Mechanical-Systems

    NASA Technical Reports Server (NTRS)

    Kaul, A. B.; Khan, A. R.; Megerian, K. G.; Epp, L.; LeDuc, G.; Bagge, L.; Jennings, A. T.; Jang, D.; Greer, J. R.

    2011-01-01

    We provide an overview of our work where carbon-based nanostructures have been applied to two-dimensional (2D) planar and three-dimensional (3D) vertically-oriented nano-electro-mechanical (NEM) switches. In the first configuration, laterally oriented single-walled nanotubes (SWNTs) synthesized using thermal chemical vapor deposition (CVD) were implemented for forming bridge-type 2D NEMS switches, where switching voltages were on the order of a few volts. In the second configuration, vertically oriented carbon nanofibers (CNFs) synthesized using plasma-enhanced (PE) CVD have been explored for their potential application in 3D NEMS. We have performed nanomechanical measurements on such vertically oriented tubes using nanoindentation to determine the mechanical properties of the CNFs. Electrostatic switching was demonstrated in the CNFs synthesized on refractory metallic nitride substrates, where a nanoprobe was used as the actuating electrode inside a scanning-electron-microscope. The switching voltages were determined to be in the tens of volts range and van der Waals interactions at these length scales appeared significant, suggesting such structures are promising for nonvolatile memory applications. A finite element model was also developed to determine a theoretical pull-in voltage which was compared to experimental results.

  14. Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

    PubMed

    Ferrer, Silvia; Ruiz-Pernía, Javier; Martí, Sergio; Moliner, Vicent; Tuñón, Iñaki; Bertrán, Juan; Andrés, Juan

    2011-01-01

    The development of characterization techniques, advanced synthesis methods, as well as molecular modeling has transformed the study of systems in a well-established research field. The current research challenges in biocatalysis and biotransformation evolve around enzyme discovery, design, and optimization. How can we find or create enzymes that catalyze important synthetic reactions, even reactions that may not exist in nature? What is the source of enzyme catalytic power? To answer these and other related questions, the standard strategies have evolved from trial-and-error methodologies based on chemical knowledge, accumulated experience, and common sense into a clearly multidisciplinary science that allows one to reach the molecular design of tailor-made enzyme catalysts. This is even more so when one refers to enzyme catalysts, for which the detailed structure and composition are known and can be manipulated to introduce well-defined residues which can be implicated in the chemical rearrangements taking place in the active site. The methods and techniques of theoretical and computational chemistry are becoming more and more important in both understanding the fundamental biological roles of enzymes and facilitating their utilization in biotechnology. Improvement of the catalytic function of enzymes is important from scientific and industrial viewpoints, and to put this fact in the actual perspective as well as the potentialities, we recommend the very recent report of Sanderson [Sanderson, K. (2011). Chemistry: enzyme expertise. Nature 471, 397.]. Great fundamental advances have been made toward the ab initio design of enzyme catalysts based on molecular modeling. This has been based on the molecular mechanistic knowledge of the reactions to be catalyzed, together with the development of advanced synthesis and characterization techniques. The corresponding molecular mechanism can be studied by means of powerful quantum chemical calculations. The catalytic

  15. Evaluating Arctic warming mechanisms in CMIP5 models

    NASA Astrophysics Data System (ADS)

    Franzke, Christian L. E.; Lee, Sukyoung; Feldstein, Steven B.

    2016-07-01

    Arctic warming is one of the most striking signals of global warming. The Arctic is one of the fastest warming regions on Earth and constitutes, thus, a good test bed to evaluate the ability of climate models to reproduce the physics and dynamics involved in Arctic warming. Different physical and dynamical mechanisms have been proposed to explain Arctic amplification. These mechanisms include the surface albedo feedback and poleward sensible and latent heat transport processes. During the winter season when Arctic amplification is most pronounced, the first mechanism relies on an enhancement in upward surface heat flux, while the second mechanism does not. In these mechanisms, it has been proposed that downward infrared radiation (IR) plays a role to a varying degree. Here, we show that the current generation of CMIP5 climate models all reproduce Arctic warming and there are high pattern correlations—typically greater than 0.9—between the surface air temperature (SAT) trend and the downward IR trend. However, we find that there are two groups of CMIP5 models: one with small pattern correlations between the Arctic SAT trend and the surface vertical heat flux trend (Group 1), and the other with large correlations (Group 2) between the same two variables. The Group 1 models exhibit higher pattern correlations between Arctic SAT and 500 hPa geopotential height trends, than do the Group 2 models. These findings suggest that Arctic warming in Group 1 models is more closely related to changes in the large-scale atmospheric circulation, whereas in Group 2, the albedo feedback effect plays a more important role. Interestingly, while Group 1 models have a warm or weak bias in their Arctic SAT, Group 2 models show large cold biases. This stark difference in model bias leads us to hypothesize that for a given model, the dominant Arctic warming mechanism and trend may be dependent on the bias of the model mean state.

  16. Inferring brain-computational mechanisms with models of activity measurements

    PubMed Central

    Diedrichsen, Jörn

    2016-01-01

    High-resolution functional imaging is providing increasingly rich measurements of brain activity in animals and humans. A major challenge is to leverage such data to gain insight into the brain's computational mechanisms. The first step is to define candidate brain-computational models (BCMs) that can perform the behavioural task in question. We would then like to infer which of the candidate BCMs best accounts for measured brain-activity data. Here we describe a method that complements each BCM by a measurement model (MM), which simulates the way the brain-activity measurements reflect neuronal activity (e.g. local averaging in functional magnetic resonance imaging (fMRI) voxels or sparse sampling in array recordings). The resulting generative model (BCM-MM) produces simulated measurements. To avoid having to fit the MM to predict each individual measurement channel of the brain-activity data, we compare the measured and predicted data at the level of summary statistics. We describe a novel particular implementation of this approach, called probabilistic representational similarity analysis (pRSA) with MMs, which uses representational dissimilarity matrices (RDMs) as the summary statistics. We validate this method by simulations of fMRI measurements (locally averaging voxels) based on a deep convolutional neural network for visual object recognition. Results indicate that the way the measurements sample the activity patterns strongly affects the apparent representational dissimilarities. However, modelling of the measurement process can account for these effects, and different BCMs remain distinguishable even under substantial noise. The pRSA method enables us to perform Bayesian inference on the set of BCMs and to recognize the data-generating model in each case. This article is part of the themed issue ‘Interpreting BOLD: a dialogue between cognitive and cellular neuroscience’. PMID:27574316

  17. A Computer-based Course in Classical Mechanics.

    ERIC Educational Resources Information Center

    Kane, D.; Sherwood, B.

    1980-01-01

    Describes and illustrates the tutorial and homework exercise lessons, student routing, course organization, administration, and evaluation of a PLATO computer-based course in classical mechanics. An appendix lists 41 lessons developed for the course. (CMV)

  18. Thermal fluid-solid interaction model and experimental validation for hydrostatic mechanical face seals

    NASA Astrophysics Data System (ADS)

    Huang, Weifeng; Liao, Chuanjun; Liu, Xiangfeng; Suo, Shuangfu; Liu, Ying; Wang, Yuming

    2014-09-01

    Hydrostatic mechanical face seals for reactor coolant pumps are very important for the safety and reliability of pressurized-water reactor power plants. More accurate models on the operating mechanism of the seals are needed to help improve their performance. The thermal fluid-solid interaction (TFSI) mechanism of the hydrostatic seal is investigated in this study. Numerical models of the flow field and seal assembly are developed. Based on the mechanism for the continuity condition of the physical quantities at the fluid-solid interface, an on-line numerical TFSI model for the hydrostatic mechanical seal is proposed using an iterative coupling method. Dynamic mesh technology is adopted to adapt to the changing boundary shape. Experiments were performed on a test rig using a full-size test seal to obtain the leakage rate as a function of the differential pressure. The effectiveness and accuracy of the TFSI model were verified by comparing the simulation results and experimental data. Using the TFSI model, the behavior of the seal is presented, including mechanical and thermal deformation, and the temperature field. The influences of the rotating speed and differential pressure of the sealing device on the temperature field, which occur widely in the actual use of the seal, are studied. This research proposes an on-line and assembly-based TFSI model for hydrostatic mechanical face seals, and the model is validated by full-sized experiments.

  19. Vibration Stabilization of a Mechanical Model of a X-Band Linear Collider Final Focus Magnet

    SciTech Connect

    Frisch, Josef; Chang, Allison; Decker, Valentin; Doyle, Eric; Eriksson, Leif; Hendrickson, Linda; Himel, Thomas; Markiewicz, Thomas; Partridge, Richard; Seryi, Andrei; /SLAC

    2006-09-28

    The small beam sizes at the interaction point of a X-band linear collider require mechanical stabilization of the final focus magnets at the nanometer level. While passive systems provide adequate performance at many potential sites, active mechanical stabilization is useful if the natural or cultural ground vibration is higher than expected. A mechanical model of a room temperature linear collider final focus magnet has been constructed and actively stabilized with an accelerometer based system.

  20. Statistical mechanics of the Huxley-Simmons model

    NASA Astrophysics Data System (ADS)

    Caruel, M.; Truskinovsky, L.

    2016-06-01

    The chemomechanical model of Huxley and Simmons (HS) [A. F. Huxley and R. M. Simmons, Nature 233, 533 (1971), 10.1038/233533a0] provides a paradigmatic description of mechanically induced collective conformational changes relevant in a variety of biological contexts, from muscles power stroke and hair cell gating to integrin binding and hairpin unzipping. We develop a statistical mechanical perspective on the HS model by exploiting a formal analogy with a paramagnetic Ising model. We first study the equilibrium HS model with a finite number of elements and compute explicitly its mechanical and thermal properties. To model kinetics, we derive a master equation and solve it for several loading protocols. The developed formalism is applicable to a broad range of allosteric systems with mean-field interactions.

  1. Mechanical Slosh Models for Rocket-Propelled Spacecraft

    NASA Technical Reports Server (NTRS)

    Jang, Jiann-Woei; Alaniz, Abram; Yang, Lee; Powers. Joseph; Hall, Charles

    2013-01-01

    Several analytical mechanical slosh models for a cylindrical tank with flat bottom are reviewed. Even though spacecrafts use cylinder shaped tanks, most of those tanks usually have elliptical domes. To extend the application of the analytical models for a cylindrical tank with elliptical domes, the modified slosh parameter models are proposed in this report by mapping an elliptical dome cylindrical tank to a flat top/bottom cylindrical tank while maintaining the equivalent liquid volume. For the low Bond number case, the low-g slosh models were also studied. Those low-g models can be used for Bond number > 10. The current low-g slosh models were also modified to extend their applications for the case that liquid height is smaller than the tank radius. All modified slosh models are implemented in MATLAB m-functions and are collected in the developed MST (Mechanical Slosh Toolbox).

  2. A novel insight into membrane fouling mechanism regarding gel layer filtration: Flory-Huggins based filtration mechanism

    NASA Astrophysics Data System (ADS)

    Lei, Qian; Zhang, Meijia; Shen, Liguo; Li, Renjie; Liao, Bao-Qiang; Lin, Hongjun

    2016-09-01

    This study linked the chemical potential change to high specific filtration resistance (SFR) of gel layer, and then proposed a novel membrane fouling mechanism regarding gel layer filtration, namely, Flory-Huggins based filtration mechanism. A mathematical model for this mechanism was theoretically deduced. Agar was used as a model polymer for gel formation. Simulation of the mathematical model for agar gel showed that volume fraction of polymer and Flory-Huggins interaction parameter were the two key factors governing the gel SFR, whereas, pH and ionic strength were not related with the gel SFR. Filtration tests of gel layer showed that the total SFR value, effects of pH and ionic strength on the gel SFR well agreed with the perditions of model’s simulation, indicating the real occurrence of this mechanism and the feasibility of the proposed model. This mechanism can satisfactorily explain the extremely high SFR of gel layer, and improve fundamental insights into membrane fouling regarding gel layer filtration.

  3. A novel insight into membrane fouling mechanism regarding gel layer filtration: Flory-Huggins based filtration mechanism

    PubMed Central

    Lei, Qian; Zhang, Meijia; Shen, Liguo; Li, Renjie; Liao, Bao-Qiang; Lin, Hongjun

    2016-01-01

    This study linked the chemical potential change to high specific filtration resistance (SFR) of gel layer, and then proposed a novel membrane fouling mechanism regarding gel layer filtration, namely, Flory-Huggins based filtration mechanism. A mathematical model for this mechanism was theoretically deduced. Agar was used as a model polymer for gel formation. Simulation of the mathematical model for agar gel showed that volume fraction of polymer and Flory-Huggins interaction parameter were the two key factors governing the gel SFR, whereas, pH and ionic strength were not related with the gel SFR. Filtration tests of gel layer showed that the total SFR value, effects of pH and ionic strength on the gel SFR well agreed with the perditions of model’s simulation, indicating the real occurrence of this mechanism and the feasibility of the proposed model. This mechanism can satisfactorily explain the extremely high SFR of gel layer, and improve fundamental insights into membrane fouling regarding gel layer filtration. PMID:27627851

  4. Drosophila models reveal novel insights into mechanisms underlying neurodegeneration

    PubMed Central

    Mohan, Ryan D; Workman, Jerry L; Abmayr, Susan M

    2014-01-01

    The SAGA chromatin modifying complex functions as a transcriptional coactivator for a large number of genes, and SAGA dysfunction has been linked to carcinogenesis and neurodegenerative disease. The protein complex is comprised of approximately 20 subunits, arranged in a modular fashion, and includes 2 enzymatic subunits: the Gcn5 acetyltransferase and the Non-stop deubiquitinase. As we learn more about SAGA, it becomes evident that this complex functions through sophisticated mechanisms that support very precise regulation of gene expression. Here we describe recent findings in which a Drosophila loss-of-function model revealed novel mechanisms for regulation of SAGA-mediated histone H2B deubiquitination. This model also yielded novel and surprising insights into mechanisms that underlie progressive neurodegenerative disease. Lastly, we comment on the utility of Drosophila as a model for neurodegenerative disease through which crucial and conserved mechanisms may be revealed. PMID:25483136

  5. Modeling the Digging Process of Tree Root System by the Mechanism with Hydropulse Drive

    NASA Astrophysics Data System (ADS)

    Drapalyuk, Michael V.; Popikov, Petr I.; Yudin, Roman V.; Fomin, Anatoly A.; Chernukhin, Roman V.

    2016-08-01

    A mathematical model of the mechanism for digging large-sized seedlings or removing stumps on the undergrowth is developed, which is based on the idea of the root system and surrounding soil, as a combination of plurality of spherical elements, interacting with each other, and the knife mechanism, as a set of elementary surfaces that interact with elements of the stump and soil. The effect of blade vibration on the stump removal efficiency with the help of the model is studied.

  6. Transfer function modeling of damping mechanisms in distributed parameter models

    NASA Technical Reports Server (NTRS)

    Slater, J. C.; Inman, D. J.

    1994-01-01

    This work formulates a method for the modeling of material damping characteristics in distributed parameter models which may be easily applied to models such as rod, plate, and beam equations. The general linear boundary value vibration equation is modified to incorporate hysteresis effects represented by complex stiffness using the transfer function approach proposed by Golla and Hughes. The governing characteristic equations are decoupled through separation of variables yielding solutions similar to those of undamped classical theory, allowing solution of the steady state as well as transient response. Example problems and solutions are provided demonstrating the similarity of the solutions to those of the classical theories and transient responses of nonviscous systems.

  7. A Simple Mechanical Model for the Isotropic Harmonic Oscillator

    ERIC Educational Resources Information Center

    Nita, Gelu M.

    2010-01-01

    A constrained elastic pendulum is proposed as a simple mechanical model for the isotropic harmonic oscillator. The conceptual and mathematical simplicity of this model recommends it as an effective pedagogical tool in teaching basic physics concepts at advanced high school and introductory undergraduate course levels. (Contains 2 figures.)

  8. An improved anti-leech mechanism based on session identifier

    NASA Astrophysics Data System (ADS)

    Zhang, Jianbiao; Zhu, Tong; Zhang, Han; Lin, Li

    2011-12-01

    With the rapid development of information technology and extensive requirement of network resource sharing, plenty of resource hotlinking phenomenons appear on the internet. The hotlinking problem not only harms the interests of legal websites but also leads to a great affection to fair internet environment. The anti-leech technique based on session identifier is highly secure, but the transmission of session identifier in plaintext form causes some security flaws. In this paper, a proxy hotlinking technique based on session identifier is introduced firstly to illustrate these security flaws; next, this paper proposes an improved anti-leech mechanism based on session identifier, the mechanism takes the random factor as the core and detects hotlinking request using a map table that contains random factor, user's information and time stamp; at last the paper analyzes the security of mechanism in theory. The result reveals that the improved mechanism has the merits of simple realization, high security and great flexibility.

  9. An improved anti-leech mechanism based on session identifier

    NASA Astrophysics Data System (ADS)

    Zhang, Jianbiao; Zhu, Tong; Zhang, Han; Lin, Li

    2012-01-01

    With the rapid development of information technology and extensive requirement of network resource sharing, plenty of resource hotlinking phenomenons appear on the internet. The hotlinking problem not only harms the interests of legal websites but also leads to a great affection to fair internet environment. The anti-leech technique based on session identifier is highly secure, but the transmission of session identifier in plaintext form causes some security flaws. In this paper, a proxy hotlinking technique based on session identifier is introduced firstly to illustrate these security flaws; next, this paper proposes an improved anti-leech mechanism based on session identifier, the mechanism takes the random factor as the core and detects hotlinking request using a map table that contains random factor, user's information and time stamp; at last the paper analyzes the security of mechanism in theory. The result reveals that the improved mechanism has the merits of simple realization, high security and great flexibility.

  10. Wetting mechanisms of gel-based controlled-release fertilizers.

    PubMed

    Shavit, U; Reiss, M; Shaviv, A

    2003-02-14

    The release mechanism of gel-based controlled release fertilizers (CRFs) involves water penetration into dry mixtures of fertilizers and gel forming polymers. Water penetration provides an upper limit to the whole release process. Where wetting prediction is often based on models that describe the flow of the liquid phase, vapor motion may become significant when a sharp wetting front exists. In this study we examine the role of vapor and fluid flows in the wetting process of CRFs consisting of urea or KNO(3) mixed with polyacrylamide (PAM). Vapor adsorption isotherms were obtained for typical fertilizer-PAM mixtures. Wetting and release experiments were conducted by dividing the CRFs into regions alternately filled with a pure fertilizer and mixtures of PAM and fertilizer. The experiments were designed in such a way that when the wetting front reaches a mixtures interface, its motion depends on the gradient imposed by the difference in osmotic potential (OP). The coupled equations of vapor and liquid flow in initially dry conditions were solved numerically to demonstrate the conceptual understanding gained by the experiments. The results show that wetting front motion is affected by transport and adsorption of vapor. It was also shown that the release rate is different when wetting is governed by vapor flow or by liquid flow. The release pattern from a multi-regions device was consistent with the wetting pattern, demonstrating the possibility to tailor the release according to periods of peak demand.

  11. The von Neumann model of measurement in quantum mechanics

    SciTech Connect

    Mello, Pier A.

    2014-01-08

    We describe how to obtain information on a quantum-mechanical system by coupling it to a probe and detecting some property of the latter, using a model introduced by von Neumann, which describes the interaction of the system proper with the probe in a dynamical way. We first discuss single measurements, where the system proper is coupled to one probe with arbitrary coupling strength. The goal is to obtain information on the system detecting the probe position. We find the reduced density operator of the system, and show how Lüders rule emerges as the limiting case of strong coupling. The von Neumann model is then generalized to two probes that interact successively with the system proper. Now we find information on the system by detecting the position-position and momentum-position correlations of the two probes. The so-called 'Wigner's formula' emerges in the strong-coupling limit, while 'Kirkwood's quasi-probability distribution' is found as the weak-coupling limit of the above formalism. We show that successive measurements can be used to develop a state-reconstruction scheme. Finally, we find a generalized transform of the state and the observables based on the notion of successive measurements.

  12. Statistical mechanics models for motion and force planning

    NASA Technical Reports Server (NTRS)

    Rodriguez, G.

    1990-01-01

    The models of statistical mechanics provide an alternative to the methods of classical mechanics more traditionally used in robotics. They have a potential to: improve analysis of object collisions; handle kinematic and dynamic contact interactions within the same frmework; and reduce the need for perfect deterministic world model information. The statistical mechanics models characterize the state of the system as a probability density function (p.d.f.) whose time evolution is governed by a partial differential equation subject to boundary and initial conditions. The boundary conditions when rigid objects collide reflect the conservation of momentum. The models are being developed to embedd in remote semi-autonomous systems with a need to reason and interact with a multiobject environment.

  13. Carbon nanotube mechanics: Continuum model development from molecular mechanics virtual experiments

    NASA Astrophysics Data System (ADS)

    Sears, Aaron T.

    the van der Waals forces, and find through-the-thickness elastic moduli (Young's modulus in the radial direction, Er, and Poisson's ratio nu rtheta) of the SWNT. We have found four out of the five elastic constants of a SWNT taken to be transversely isotropic about a radial line. MWNTs were studied using the same testing procedures as those used SWNTs. Based on the results from those simulations a continuum model is proposed for a MWNT whose response to mechanical deformations is the same as that of the MWNT. The continuum structure is comprised of concentric cylindrical tubes interconnected by truss elements. Young's modulus, Poisson's ratio, the thickness of each concentric tube, and the stiffness of the truss elements are given. The proposed continuum model is validated by studying its bending and buckling deformations and comparing these results to those from MM simulations. The major contributions to the field on nanotubes and the scientific literature is a simple and robust continuum model for nanotubes. This model can be used to study both SWNTs and MWNTs in either global or local responses by applying different analytic techniques. This model was developed using a consistent engineering methodology that mimicked traditional engineering testing, assumptions and constraints.

  14. Enhanced mathematical modeling of the displacement amplification ratio for piezoelectric compliant mechanisms

    NASA Astrophysics Data System (ADS)

    Ling, Mingxiang; Cao, Junyi; Zeng, Minghua; Lin, Jing; Inman, Daniel J.

    2016-07-01

    Piezo-actuated, flexure hinge-based compliant mechanisms have been frequently used in precision engineering in the last few decades. There have been a considerable number of publications on modeling the displacement amplification behavior of rhombus-type and bridge-type compliant mechanisms. However, due to an unclear geometric approximation and mechanical assumption between these two flexures, it is very difficult to obtain an exact description of the kinematic performance using previous analytical models, especially when the designed angle of the compliant mechanisms is small. Therefore, enhanced theoretical models of the displacement amplification ratio for rhombus-type and bridge-type compliant mechanisms are proposed to improve the prediction accuracy based on the distinct force analysis between these two flexures. The energy conservation law and the elastic beam theory are employed for modeling with consideration of the translational and rotational stiffness. Theoretical and finite elemental results show that the prediction errors of the displacement amplification ratio will be enlarged if the bridge-type flexure is simplified as a rhombic structure to perform mechanical modeling. More importantly, the proposed models exhibit better performance than the previous models, which is further verified by experiments.

  15. Constitutive Modeling of the Mechanical Properties of Optical Fibers

    NASA Technical Reports Server (NTRS)

    Moeti, L.; Moghazy, S.; Veazie, D.; Cuddihy, E.

    1998-01-01

    Micromechanical modeling of the composite mechanical properties of optical fibers was conducted. Good agreement was obtained between the values of Young's modulus obtained by micromechanics modeling and those determined experimentally for a single mode optical fiber where the wave guide and the jacket are physically coupled. The modeling was also attempted on a polarization-maintaining optical fiber (PANDA) where the wave guide and the jacket are physically decoupled, and found not to applicable since the modeling required perfect bonding at the interface. The modeling utilized constituent physical properties such as the Young's modulus, Poisson's ratio, and shear modulus to establish bounds on the macroscopic behavior of the fiber.

  16. Coupled thermal/chemical/mechanical modeling of insensitive explosives in thermal environments

    SciTech Connect

    Nichols, A.L. III

    1996-05-01

    The ability to predict the response of a weapon system that contains insensitive explosives to elevated temperatures is important in understanding its safety characteristics. To model such a system at elevated temperatures in a finite element computer code requires a variety of capabilities. These modeling capabilities include thermal diffusion and convection to transport the heat to the explosives in the weapon system, temperature based chemical reaction modeling of the decomposition of the explosive materials, and mechanical modeling of both the metal casing and the unreacted and decomposed explosive. The Chemical TOPAZ code has been developed to model coupled thermal/chemical problems where we do not need to model the mass motion. We have also developed the LYNX2D code, based on PALM2D and Chemical TOPAZ, which is an implicit, two-dimensional coupled thermal/chemical/mechanical finite element model computer code. Some representative examples are shown. {copyright} {ital 1996 American Institute of Physics.}

  17. A finite element musculoskeletal model of the shoulder mechanism.

    PubMed

    van der Helm, F C

    1994-05-01

    The finite element method described in this study provides an easy method to simulate the kinetics of multibody mechanisms. It is used in order to develop a musculoskeletal model of the shoulder mechanism. Each relevant morphological structure has been represented by an appropriate element. For the shoulder mechanism two special-purpose elements have been developed: a SURFACE element representing the scapulothoracic gliding plane and a CURVED-TRUSS element to represent muscles which are wrapped around bony contours. The model contains four bones, three joints, three extracapsular ligaments, the scapulothoracic gliding plane and 20 muscles and muscle parts. In the model, input variables are the positions of the shoulder girdle and humerus and the external load on the humerus. Output variables are muscles forces subject to an optimization procedure in which the mechanical stability of the glenohumeral joint is one of the constraints. Four different optimization criteria are compared. For 12 muscles, surface EMG is used to verify the model. Since the optimum muscle length and force-length relationship are unknown, and since maximal EMG amplitude is length dependent, verification is only possible in a qualitative sense. Nevertheless, it is concluded that a detailed model of the shoulder mechanism has been developed which provides good insight into the function of morphological structures.

  18. Model-based tomographic reconstruction

    DOEpatents

    Chambers, David H; Lehman, Sean K; Goodman, Dennis M

    2012-06-26

    A model-based approach to estimating wall positions for a building is developed and tested using simulated data. It borrows two techniques from geophysical inversion problems, layer stripping and stacking, and combines them with a model-based estimation algorithm that minimizes the mean-square error between the predicted signal and the data. The technique is designed to process multiple looks from an ultra wideband radar array. The processed signal is time-gated and each section processed to detect the presence of a wall and estimate its position, thickness, and material parameters. The floor plan of a building is determined by moving the array around the outside of the building. In this paper we describe how the stacking and layer stripping algorithms are combined and show the results from a simple numerical example of three parallel walls.

  19. Correlation Based Geomagnetic Field Modeling

    NASA Astrophysics Data System (ADS)

    Holschneider, M.; Mauerberger, S.; Lesur, V.; Baerenzung, J.

    2015-12-01

    We present a new method for determining geomagnetic field models. It is based on the construction of an a priori correlation structure derived from our knowledge about characteristic length scales and sources of the geomagnetic field. The magnetic field measurements are then seen as correlated random variables too and the inversion process amounts to compute the a posteriori correlation structure using Bayes theorem. We show how this technique allows the statistical separation of the various field contributions and the assessment of their uncertainties.

  20. Toward a rule-based biome model

    SciTech Connect

    Neilson, R.P.; King, G.A.; Koerper, G.

    1991-01-01

    Current projections of the response of the biosphere to global climatic change indicate as much as 50% to 90% spatial displacement of extratropical biomes. The mechanism of spatial shift could be dominated by either (1) competitive displacement of northern biomes by southern biomes, or (2) drought-induced dieback of areas susceptible to change. The current suite of global biosphere models cannot distinguish between these two processes, thus determining the need for a mechanistically based biome model. The model is in an early stage of development and will require several enhancements, including explicit simulation of potential evapotranspiration, extension to boreal and tropical biomes, a shift from steady-state to transient dynamics, and validation on other continents.

  1. Constitutive Models Based on Compressible Plastic Flows

    NASA Technical Reports Server (NTRS)

    Rajendran, A. M.

    1983-01-01

    The need for describing materials under time or cycle dependent loading conditions has been emphasized in recent years by several investigators. In response to the need, various constitutive models describing the nonlinear behavior of materials under creep, fatigue, or other complex loading conditions were developed. The developed models for describing the fully dense (non-porous) materials were mostly based on uncoupled plasticity theory. The improved characterization of materials provides a better understanding of the structual response under complex loading conditions. The pesent studies demonstrate that the rate or time dependency of the response of a porous aggregate can be incorporated into the nonlinear constitutive behavior of a porous solid by appropriately modeling the incompressible matrix behavior. It is also sown that the yield function which wads determined by a continuum mechanics approach must be verified by appropriate experiments on void containing sintered materials in order to obtain meaningful numbers for the constants that appear in the yield function.

  2. STATISTICAL MECHANICS MODELING OF MESOSCALE DEFORMATION IN METALS

    SciTech Connect

    Anter El-Azab

    2013-04-08

    The research under this project focused on a theoretical and computational modeling of dislocation dynamics of mesoscale deformation of metal single crystals. Specifically, the work aimed to implement a continuum statistical theory of dislocations to understand strain hardening and cell structure formation under monotonic loading. These aspects of crystal deformation are manifestations of the evolution of the underlying dislocation system under mechanical loading. The project had three research tasks: 1) Investigating the statistical characteristics of dislocation systems in deformed crystals. 2) Formulating kinetic equations of dislocations and coupling these kinetics equations and crystal mechanics. 3) Computational solution of coupled crystal mechanics and dislocation kinetics. Comparison of dislocation dynamics predictions with experimental results in the area of statistical properties of dislocations and their field was also a part of the proposed effort. In the first research task, the dislocation dynamics simulation method was used to investigate the spatial, orientation, velocity, and temporal statistics of dynamical dislocation systems, and on the use of the results from this investigation to complete the kinetic description of dislocations. The second task focused on completing the formulation of a kinetic theory of dislocations that respects the discrete nature of crystallographic slip and the physics of dislocation motion and dislocation interaction in the crystal. Part of this effort also targeted the theoretical basis for establishing the connection between discrete and continuum representation of dislocations and the analysis of discrete dislocation simulation results within the continuum framework. This part of the research enables the enrichment of the kinetic description with information representing the discrete dislocation systems behavior. The third task focused on the development of physics-inspired numerical methods of solution of the coupled

  3. Modeling and testing of docking and berthing mechanisms

    NASA Astrophysics Data System (ADS)

    Hall, Drew P.; Slone, B. Mark; Tobbe, Patrick A.

    2006-05-01

    The Contact Dynamics Simulation Laboratory (CDSL) of the Marshall Space Flight Center provides for refined hardware-in-the-loop real-time simulation of docking and berthing mechanisms and associated control systems. This facility is employed to verify the performance of docking/berthing mechanisms during Earth-orbit operations, determine the capture envelope of docking/berthing devices, measure contact loads at vehicle interfaces, and evaluate visual cues for man-in-the-loop operations. The CDSL has developed test verified analytical models of such systems as the International Space Station (ISS) Common Berthing Mechanism (CBM) and the Hubble Space Telescope (HST) Three Point Docking Mechanism. This paper will describe the modeling and test techniques employed at the CDSL and present results from recent programs.

  4. Modeling and Testing of Docking and Berthing Mechanisms

    NASA Technical Reports Server (NTRS)

    Hall, D. P.; Slone, M. M.; Tobbe, P. A.

    2006-01-01

    The Contact Dynamics Simulation Laboratory (CDSL) of the Marshall Space Flight Center provides for refined hardware-in-the-loop real-time simulation of docking and berthing mechanisms and associated control systems. This facility is employed to verify the performance of docking/berthing mechanisms during Earth-orbit operations, determine the capture envelope of dockingherthing devices, measure contact loads at vehicle interfaces, and evaluate visual cues for man-in-the-loop operations. The CDSL has developed test verified analytical models of such systems as the ISS Common Berthing Mechanism and HST Three Point Docking Mechanism. This paper will describe the modeling and test techniques employed at the CDSL and present results from recent programs.

  5. Shape memory-based actuators and release mechanisms therefrom

    NASA Technical Reports Server (NTRS)

    Vaidyanathan, Rajan (Inventor); Snyder, Daniel W. (Inventor); Schoenwald, David K. (Inventor); Lam, Nhin S. (Inventor); Watson, Daniel S. (Inventor); Krishnan, Vinu B. (Inventor); Noebe, Ronald D. (Inventor)

    2012-01-01

    SM-based actuators (110) and release mechanisms (100) therefrom and systems (500) including one or more release mechanisms (100). The actuators (110) comprise a SM member (118) and a deformable member (140) mechanically coupled to the SM member (118) which deforms upon a shape change of the SM member triggered by a phase transition of the SM member. A retaining element (160) is mechanically coupled to the deformable member (140), wherein the retaining element (160) moves upon the shape change. Release mechanism (100) include an actuator, a rotatable mechanism (120) including at least one restraining feature (178) for restraining rotational movement of the retaining element (160) before the shape change, and at least one spring (315) that provides at least one locked spring-loaded position when the retaining element is in the restraining feature and at least one released position that is reached when the retaining element is in a position beyond the restraining feature (178). The rotatable mechanism (120) includes at least one load-bearing protrusion (310). A hitch (400) is for mechanically coupling to the load, wherein the hitch is supported on the load bearing protrusion (310) when the rotatable mechanism is in the locked spring-loaded position.

  6. PECASE - First Principles Modeling of Mechanics and Chemistry of Materials

    DTIC Science & Technology

    2013-01-18

    deformation kinetics of a component, but also the tuning of its physical and chemical properties by stress. Reaching ultrastrength enables ‘‘elastic strain...strength phenomena not only have to do with the shape stability and deformation kinetics of a component, but also the tuning of its physical and...processes that initiate and sustain plastic flow and fracture, and the mechanics and physics of both displacive and diffusive mechanisms are being modeled

  7. Anisotropic Damage Mechanics Modeling in Metal Matrix Composites

    DTIC Science & Technology

    1993-05-15

    conducted on a titanium aluminide SiC-reinforced metal matrix composite. Center-cracked plates with laminate layups of (0/90) and (±45). were tested...Kattan, P. I., "Finite Strain Plasticity and Damage in Constitutive Modeling of Metals with Spin Tensors," Applied Mechanics Reviews, Vol. 45, No. 3...34Contractors Meeting on Mechanics of Materials," Dayton, Ohio, October 1991. Voyiadjis, G. Z., and Kattan, P. I., "Finite Strain Plasticity and Damage in

  8. $\\cN$-FOLD SUPERSYMMETRY IN QUANTUM MECHANICAL MATRIX MODELS

    NASA Astrophysics Data System (ADS)

    Tanaka, Toshiaki

    2012-03-01

    We formulate Ņ-fold supersymmetry in quantum mechanical matrix models. As an example, we construct general two-by-two Hermitian matrix two-fold supersymmetric quantum mechanical systems. We find that there are two inequivalent such systems, both of which are characterized by two arbitrary scalar functions, and one of which does not reduce to the scalar system. The obtained systems are all weakly quasi-solvable.

  9. Modeling of Band-to-Band Tunneling Mechanisms

    NASA Astrophysics Data System (ADS)

    Wolfgang, Bergner; Roland, Kircher

    1990-12-01

    Measurements and simulations are presented, which allow a better understanding of leakage mechanisms in reverse biased gated diodes. The model for the device simulation describes two mechanisms. In the high field regime the leakage current is identified as direct band-to-band tunneling. In the low field regime it is described as surface-state enhanced tunneling, which combines thermal activation of an electron to a surface-state with tunneling.

  10. Modeling the Interactions Between Multiple Crack Closure Mechanisms at Threshold

    NASA Technical Reports Server (NTRS)

    Newman, John A.; Riddell, William T.; Piascik, Robert S.

    2003-01-01

    A fatigue crack closure model is developed that includes interactions between the three closure mechanisms most likely to occur at threshold; plasticity, roughness, and oxide. This model, herein referred to as the CROP model (for Closure, Roughness, Oxide, and Plasticity), also includes the effects of out-of plane cracking and multi-axial loading. These features make the CROP closure model uniquely suited for, but not limited to, threshold applications. Rough cracks are idealized here as two-dimensional sawtooths, whose geometry induces mixed-mode crack- tip stresses. Continuum mechanics and crack-tip dislocation concepts are combined to relate crack face displacements to crack-tip loads. Geometric criteria are used to determine closure loads from crack-face displacements. Finite element results, used to verify model predictions, provide critical information about the locations where crack closure occurs.

  11. Neural mechanisms of the cognitive model of depression.

    PubMed

    Disner, Seth G; Beevers, Christopher G; Haigh, Emily A P; Beck, Aaron T

    2011-07-06

    In the 40 years since Aaron Beck first proposed his cognitive model of depression, the elements of this model--biased attention, biased processing, biased thoughts and rumination, biased memory, and dysfunctional attitudes and schemas--have been consistently linked with the onset and maintenance of depression. Although numerous studies have examined the neural mechanisms that underlie the cognitive aspects of depression, their findings have not been integrated with Beck's cognitive model. In this Review, we identify the functional and structural neurobiological architecture of Beck's cognitive model of depression. Although the mechanisms underlying each element of the model differ, in general the negative cognitive biases in depression are facilitated by increased influence from subcortical emotion processing regions combined with attenuated top-down cognitive control.

  12. Geomorphological-thermo-mechanical modeling: Application to orogenic wedge dynamics

    NASA Astrophysics Data System (ADS)

    Ueda, K.; Willett, S. D.; Gerya, T.; Ruh, J.

    2015-09-01

    Coupled geomorphological-thermo-mechanical modeling is presented in a new implementation that combines two established thermo-mechanical and landscape evolution models. A finite-difference marker-in-cell technique is used to solve for the thermo-mechanical problem including complex visco-plastic rheologies in high resolution. Each timestep is synchronously solved with a fluvial landscape evolution model that includes numerical solution of fluvial incision and analytical hillslope processes for both diffusive and slope-limited processes on an adaptive grid. The implementation is successful in modeling large deformation at different scales. We demonstrate high degrees of coupling through processes such as exhumation of rocks with different erodibilities. Sensitivity of the coupled system evolution to surface parameters, and mechanical parameters, is explored for the established case of development of compressive wedges. The evolution of wedge models proves to be primarily sensitive to erodibility and the degree of river network integration. Relief follows deformation in propagating forward with wedge growth. We apply the method to a large-scale model of continental collision, in which a close relationship between deep tectonics, fluvial network evolution, and uplift and erosion can be demonstrated.

  13. Immune mechanisms of Concanavalin A model of autoimmune hepatitis

    PubMed Central

    Wang, Hai-Xia; Liu, Man; Weng, Shun-Yan; Li, Jing-Jing; Xie, Chao; He, Hong-Lin; Guan, Wen; Yuan, Yun-Sheng; Gao, Jin

    2012-01-01

    As a chronic inflammatory disease of the liver, the pa-thogenic mechanisms of autoimmune hepatitis (AIH) have not yet been elucidated, with prognosis and diagnosis remaining unsatisfied. Currently the only viable treatments of AIH are immunosuppressant application and liver transplantation. It is considered that lack of good animal AIH models is the main reason for the shortage of a simple and efficient cure. The Concanavalin A (Con A) model is a typical and well established model for investigating T-cell and macrophage dependent liver injury in mice, which closely mimics the pathogenesis mechanisms and pathological changes of patients, and is regarded as the best experimental model for AIH research so far. In this paper we elucidated the pathogenic mechanisms of AIH and the evolution of relative animal models. We go on to further focus on Con A-induced liver injury from the point of immunological mechanisms and the change of cytokine levels. Finally, we manifested the clinical significance of the AIH animal models and the challenges they would meet during their future development. PMID:22253517

  14. SAFOD Brittle Microstructure and Mechanics Knowledge Base (BM2KB)

    NASA Astrophysics Data System (ADS)

    Babaie, Hassan A.; Broda Cindi, M.; Hadizadeh, Jafar; Kumar, Anuj

    2013-07-01

    Scientific drilling near Parkfield, California has established the San Andreas Fault Observatory at Depth (SAFOD), which provides the solid earth community with short range geophysical and fault zone material data. The BM2KB ontology was developed in order to formalize the knowledge about brittle microstructures in the fault rocks sampled from the SAFOD cores. A knowledge base, instantiated from this domain ontology, stores and presents the observed microstructural and analytical data with respect to implications for brittle deformation and mechanics of faulting. These data can be searched on the knowledge base‧s Web interface by selecting a set of terms (classes, properties) from different drop-down lists that are dynamically populated from the ontology. In addition to this general search, a query can also be conducted to view data contributed by a specific investigator. A search by sample is done using the EarthScope SAFOD Core Viewer that allows a user to locate samples on high resolution images of core sections belonging to different runs and holes. The class hierarchy of the BM2KB ontology was initially designed using the Unified Modeling Language (UML), which was used as a visual guide to develop the ontology in OWL applying the Protégé ontology editor. Various Semantic Web technologies such as the RDF, RDFS, and OWL ontology languages, SPARQL query language, and Pellet reasoning engine, were used to develop the ontology. An interactive Web application interface was developed through Jena, a java based framework, with AJAX technology, jsp pages, and java servlets, and deployed via an Apache tomcat server. The interface allows the registered user to submit data related to their research on a sample of the SAFOD core. The submitted data, after initial review by the knowledge base administrator, are added to the extensible knowledge base and become available in subsequent queries to all types of users. The interface facilitates inference capabilities in the

  15. Mechanical behavior in living cells consistent with the tensegrity model

    NASA Technical Reports Server (NTRS)

    Wang, N.; Naruse, K.; Stamenovic, D.; Fredberg, J. J.; Mijailovich, S. M.; Tolic-Norrelykke, I. M.; Polte, T.; Mannix, R.; Ingber, D. E.

    2001-01-01

    Alternative models of cell mechanics depict the living cell as a simple mechanical continuum, porous filament gel, tensed cortical membrane, or tensegrity network that maintains a stabilizing prestress through incorporation of discrete structural elements that bear compression. Real-time microscopic analysis of cells containing GFP-labeled microtubules and associated mitochondria revealed that living cells behave like discrete structures composed of an interconnected network of actin microfilaments and microtubules when mechanical stresses are applied to cell surface integrin receptors. Quantitation of cell tractional forces and cellular prestress by using traction force microscopy confirmed that microtubules bear compression and are responsible for a significant portion of the cytoskeletal prestress that determines cell shape stability under conditions in which myosin light chain phosphorylation and intracellular calcium remained unchanged. Quantitative measurements of both static and dynamic mechanical behaviors in cells also were consistent with specific a priori predictions of the tensegrity model. These findings suggest that tensegrity represents a unified model of cell mechanics that may help to explain how mechanical behaviors emerge through collective interactions among different cytoskeletal filaments and extracellular adhesions in living cells.

  16. Optimal Tuning for Disturbance Suppression Mechanism for Model Predictive Control

    NASA Astrophysics Data System (ADS)

    Tange, Yoshio; Nakazawa, Chikashi

    Disturbance suppression is one of most required performances in process control. We recently proposed a new disturbance suppression mechanism applicable for model predictive control in order to enhance disturbance suppression performance for ramp-like disturbances. The proposed method utilized the prediction error of controlled values and generates a disturbance compensation signal by a constant gain feedback. In this paper, we propose an improved version of the disturbance suppression mechanism by applying a low-pass filter and parameter tuning methods by which we can make the mechanism more tolerant to various disturbances such as ramp, step, and other supposable ones. We also show numerical simulation results with an oil distillation tower plant.

  17. Density functional theory and quantum mechanics/molecular mechanics study of cysteine protease inhibition by nitrile-based inhibitors.

    NASA Astrophysics Data System (ADS)

    De Visser, Sam; Quesne, Matthew; Ward, Richard

    2013-12-01

    Cysteine protease enzymes are important for human physiology and catalyze key protein degradation pathways. These enzymes react via a nucleophilic reaction mechanism that involves a cysteine residue and the proton of a proximal histidine. Particularly efficient inhibitors of these enzymes are nitrile-based, however, the details of the catalytic reaction mechanism currently are poorly understood. To gain further insight into the inhibition of these molecules, we have performed a combined density functional theory and quantum mechanics/molecular mechanics study on the reaction of a nitrile-based inhibitor with the enzyme active site amino acids. We show here that small perturbations to the inhibitor structure can have dramatic effects on the catalysis and inhibition processes. Thus, we investigated a range of inhibitor templates and show that specific structural changes reduce the inhibitory efficiency by several orders of magnitude. Moreover, as the reaction takes place on a polar surface, we find strong differences between the DFT and QM/MM calculated energetics. In particular, the DFT model led to dramatic distortions from the starting structure and the convergence to a structure that would not fit the enzyme active site. In the subsequent QM/MM study we investigated the use of mechanical versus electronic embedding on the kinetics, thermodynamics and geometries along the reaction mechanism. We find minor effects on the kinetics of the reaction but large geometric and thermodynamics differences as a result of inclusion of electronic embedding corrections. The work here highlights the importance of model choice in the investigation of this biochemical reaction mechanism.

  18. Mechanical, Mathematical, and Computer Modeling in Penetration Mechanics - IV (Hybrid Models for Nanostructured Ceramics - II)

    DTIC Science & Technology

    2006-11-30

    model of penetration of long elastically deformable projectiles into semi- infinite targets 3 Introduction 3 1. Basic model equations of penetration...of non- deformable projectiles into semi-infinite target 4 1.1. Geometrical scheme of penetration model of non- deformable projectile 4 1.2. Velocity...c. 20 1.3. Pulverized region (a < r < b). 22 2. Example 25 III. Investigation of deformation process at high-speed loadings of ceramic materials

  19. Revisiting the mechanism of neutral hydrolysis of esters: water autoionization mechanisms with acid or base initiation pathways.

    PubMed

    da Silva, Poliana Lima; Guimarães, Luciana; Pliego, Josefredo R

    2013-05-30

    The mechanism of neutral hydrolysis of ester has long been explored by theoretical studies. However, reliable theoretical calculations show that the usual bifunctional catalysis mechanism reported by different authors cannot explain the experimental kinetics. An important advance was recently reported by Gunaydin and Houk, suggesting that ions are involved in the mechanism and the process initiates by water autoionization followed by protonation of the ester (W(AI)A mechanism). However, this mechanism does not explain the hydrolysis of activated esters. In this work, we have used ab initio calculations, continuum solvation models, and intrinsic reaction coordinate method to support the W(AI)A mechanism for normal ester. In the case of activated esters, the process can also be viewed as water autoionization with formation of hydroxide ion aided by a second water molecule acting as a general base (W(AI)B mechanism). This is the mechanism that was proposed by Jencks and Carriuolo 50 years ago. Our analysis point out that the usual method for exploring mechanisms, searching for saddle points, may not work for problems like the present one, since there are no saddle points on the reaction pathway. Rather, the formation of a pair of ions from a neutral species may have an asymptotic barrier. The approach used in this paper allows the calculation of the free energy profile and enable us to explain the mechanism and kinetics of the neutral hydrolysis of normal (methyl acetate) and activated (methyl trifluoroacetate) esters. In addition, the present study suggests that formation of a pair of ions should always be considered in reactions in aqueous solution.

  20. A three-dimensional computational model of collagen network mechanics.

    PubMed

    Lee, Byoungkoo; Zhou, Xin; Riching, Kristin; Eliceiri, Kevin W; Keely, Patricia J; Guelcher, Scott A; Weaver, Alissa M; Jiang, Yi

    2014-01-01

    Extracellular matrix (ECM) strongly influences cellular behaviors, including cell proliferation, adhesion, and particularly migration. In cancer, the rigidity of the stromal collagen environment is thought to control tumor aggressiveness, and collagen alignment has been linked to tumor cell invasion. While the mechanical properties of collagen at both the single fiber scale and the bulk gel scale are quite well studied, how the fiber network responds to local stress or deformation, both structurally and mechanically, is poorly understood. This intermediate scale knowledge is important to understanding cell-ECM interactions and is the focus of this study. We have developed a three-dimensional elastic collagen fiber network model (bead-and-spring model) and studied fiber network behaviors for various biophysical conditions: collagen density, crosslinker strength, crosslinker density, and fiber orientation (random vs. prealigned). We found the best-fit crosslinker parameter values using shear simulation tests in a small strain region. Using this calibrated collagen model, we simulated both shear and tensile tests in a large linear strain region for different network geometry conditions. The results suggest that network geometry is a key determinant of the mechanical properties of the fiber network. We further demonstrated how the fiber network structure and mechanics evolves with a local formation, mimicking the effect of pulling by a pseudopod during cell migration. Our computational fiber network model is a step toward a full biomechanical model of cellular behaviors in various ECM conditions.

  1. 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

  2. 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.

  3. Crowdsourcing Based 3d Modeling

    NASA Astrophysics Data System (ADS)

    Somogyi, A.; Barsi, A.; Molnar, B.; Lovas, T.

    2016-06-01

    Web-based photo albums that support organizing and viewing the users' images are widely used. These services provide a convenient solution for storing, editing and sharing images. In many cases, the users attach geotags to the images in order to enable using them e.g. in location based applications on social networks. Our paper discusses a procedure that collects open access images from a site frequently visited by tourists. Geotagged pictures showing the image of a sight or tourist attraction are selected and processed in photogrammetric processing software that produces the 3D model of the captured object. For the particular investigation we selected three attractions in Budapest. To assess the geometrical accuracy, we used laser scanner and DSLR as well as smart phone photography to derive reference values to enable verifying the spatial model obtained from the web-album images. The investigation shows how detailed and accurate models could be derived applying photogrammetric processing software, simply by using images of the community, without visiting the site.

  4. Organism-level models: When mechanisms and statistics fail us

    NASA Astrophysics Data System (ADS)

    Phillips, M. H.; Meyer, J.; Smith, W. P.; Rockhill, J. K.

    2014-03-01

    Purpose: To describe the unique characteristics of models that represent the entire course of radiation therapy at the organism level and to highlight the uses to which such models can be put. Methods: At the level of an organism, traditional model-building runs into severe difficulties. We do not have sufficient knowledge to devise a complete biochemistry-based model. Statistical model-building fails due to the vast number of variables and the inability to control many of them in any meaningful way. Finally, building surrogate models, such as animal-based models, can result in excluding some of the most critical variables. Bayesian probabilistic models (Bayesian networks) provide a useful alternative that have the advantages of being mathematically rigorous, incorporating the knowledge that we do have, and being practical. Results: Bayesian networks representing radiation therapy pathways for prostate cancer and head & neck cancer were used to highlight the important aspects of such models and some techniques of model-building. A more specific model representing the treatment of occult lymph nodes in head & neck cancer were provided as an example of how such a model can inform clinical decisions. A model of the possible role of PET imaging in brain cancer was used to illustrate the means by which clinical trials can be modelled in order to come up with a trial design that will have meaningful outcomes. Conclusions: Probabilistic models are currently the most useful approach to representing the entire therapy outcome process.

  5. Stent-based mechanical thrombectomy in acute basilar artery occlusion.

    PubMed

    Cohen, José E; Leker, Ronen R; Moscovici, Samuel; Attia, Moshe; Itshayek, Eyal

    2011-12-01

    Stent-based mechanical thrombectomy was recently proposed as an effective alternative to other mechanical techniques to achieve recanalization of large-vessel embolic occlusions in the anterior circulation. To our knowledge, there are no reports of the use of this technique in acute basilar artery occlusion (ABAO). We present a patient with complete endovascular recanalization of ABAO using a stent-based thrombectomy technique. Advantages and limitations of this technique in the management of ABAO are discussed. The stent-thrombectomy technique is promising, and will need further evaluation in posterior circulation stroke.

  6. Computational modeling of nanoparticle charging mechanism in a hydrocarbon flame

    NASA Astrophysics Data System (ADS)

    Shah, Parth; Saveliev, Alexei

    2014-10-01

    A model that describes the charging mechanism of a 20 nm nanoparticle introduced in a methane-air counterflow laminar diffusion flame was developed and analyzed. The detailed kinetic model considers the production of ions and electrons in a methane-air flame due to chemi-ionization, thermal ionization and charging due to diffusion. The chemi-ionization model considers a one-step reaction that produces ions and electrons in a flame in addition to the detailed neutral reaction mechanism. The model is analyzed to study the effects of temperature, total nanoparticle concentration and chemi-ionization on charge formation in nanoparticles as well as on ions and electrons. The results show that thermal ionization is more dominant at high temperatures whereas diffusion charging is important at low temperatures. High concentration of nanoparticles influences the gas-phase ion and electron concentration to a very significant level whereas low concentration has a negligible effect on the same.

  7. Transport Processes from Mechanics: Minimal and Simplest Models

    NASA Astrophysics Data System (ADS)

    Bunimovich, Leonid A.; Grigo, Alexander

    2017-02-01

    We review the current state of a fundamental problem of rigorous derivation of transport processes in classical statistical mechanics from classical mechanics. Such derivations for diffusion and momentum transport (viscosities) were obtained for minimal models of these processes involving one and two particles respectively. However, a minimal model which demonstrates heat conductivity contains three particles. Its rigorous analysis is currently out of reach for existing mathematical techniques. The gas of localized balls is widely accepted as a basis for a simplest model for derivation of Fourier's law. We suggest a modification of the localized balls gas and argue that this gas of localized activated balls is a good candidate to rigorously prove Fourier's law. In particular, hyperbolicity is derived for a reduced version of this model.

  8. Transport Processes from Mechanics: Minimal and Simplest Models

    NASA Astrophysics Data System (ADS)

    Bunimovich, Leonid A.; Grigo, Alexander

    2016-12-01

    We review the current state of a fundamental problem of rigorous derivation of transport processes in classical statistical mechanics from classical mechanics. Such derivations for diffusion and momentum transport (viscosities) were obtained for minimal models of these processes involving one and two particles respectively. However, a minimal model which demonstrates heat conductivity contains three particles. Its rigorous analysis is currently out of reach for existing mathematical techniques. The gas of localized balls is widely accepted as a basis for a simplest model for derivation of Fourier's law. We suggest a modification of the localized balls gas and argue that this gas of localized activated balls is a good candidate to rigorously prove Fourier's law. In particular, hyperbolicity is derived for a reduced version of this model.

  9. Vertex models: from cell mechanics to tissue morphogenesis.

    PubMed

    Alt, Silvanus; Ganguly, Poulami; Salbreux, Guillaume

    2017-05-19

    Tissue morphogenesis requires the collective, coordinated motion and deformation of a large number of cells. Vertex model simulations for tissue mechanics have been developed to bridge the scales between force generation at the cellular level and tissue deformation and flows. We review here various formulations of vertex models that have been proposed for describing tissues in two and three dimensions. We discuss a generic formulation using a virtual work differential, and we review applications of vertex models to biological morphogenetic processes. We also highlight recent efforts to obtain continuum theories of tissue mechanics, which are effective, coarse-grained descriptions of vertex models.This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'.

  10. Vertex models: from cell mechanics to tissue morphogenesis

    PubMed Central

    Alt, Silvanus; Ganguly, Poulami

    2017-01-01

    Tissue morphogenesis requires the collective, coordinated motion and deformation of a large number of cells. Vertex model simulations for tissue mechanics have been developed to bridge the scales between force generation at the cellular level and tissue deformation and flows. We review here various formulations of vertex models that have been proposed for describing tissues in two and three dimensions. We discuss a generic formulation using a virtual work differential, and we review applications of vertex models to biological morphogenetic processes. We also highlight recent efforts to obtain continuum theories of tissue mechanics, which are effective, coarse-grained descriptions of vertex models. This article is part of the themed issue ‘Systems morphodynamics: understanding the development of tissue hardware’. PMID:28348254

  11. Mechanics, Mechanobiology, and Modeling of Human Abdominal Aorta and Aneurysms

    PubMed Central

    Humphrey, J.D.; Holzapfel, G.A.

    2011-01-01

    Biomechanical factors play fundamental roles in the natural history of abdominal aortic aneurysms (AAAs) and their responses to treatment. Advances during the past two decades have increased our understanding of the mechanics and biology of the human abdominal aorta and AAAs, yet there remains a pressing need for considerable new data and resulting patient-specific computational models that can better describe the current status of a lesion and better predict the evolution of lesion geometry, composition, and material properties and thereby improve interventional planning. In this paper, we briefly review data on the structure and function of the human abdominal aorta and aneurysmal wall, past models of the mechanics, and recent growth and remodeling models. We conclude by identifying open problems that we hope will motivate studies to improve our computational modeling and thus general understanding of AAAs. PMID:22189249

  12. A neural model of mechanisms of empathy deficits in narcissism.

    PubMed

    Jankowiak-Siuda, Kamila; Zajkowski, Wojciech

    2013-11-05

    From a multidimensional perspective, empathy is a process that includes affective sharing and imagining and understanding the emotions of others. The primary brain structures involved in mediating the components of empathy are the anterior insula (AI), the anterior cingulate cortex (ACC), and specific regions of the medial prefrontal cortex (MPFC). The AI and ACC are the main nodes in the salience network (SN), which selects and coordinates the information flow from the intero- and exteroreceptors. AI might play a role as a crucial hub - a dynamic switch between 2 separate networks of cognitive processing: the central executive network (CEN), which is concerned with effective task execution, and the default mode network (DMN), which is involved with self-reflective processes. Given various classifications, a deficit in empathy may be considered a central dysfunctional trait in narcissism. A recent fMRI study suggests that deficit in empathy is due to a dysfunction in the right AI. Based on the acquired data, we propose a theoretical model of imbalanced SN functioning in narcissism in which the dysfunctional AI hub is responsible for constant DMN activation, which, in turn, centers one's attention on the self. This might hinder the ability to affectively share and understand the emotions of others. This review paper on neural mechanisms of empathy deficits in narcissism aims to inspire and direct future research in this area.

  13. A neural model of mechanisms of empathy deficits in narcissism

    PubMed Central

    Jankowiak-Siuda, Kamila; Zajkowski, Wojciech

    2013-01-01

    From a multidimensional perspective, empathy is a process that includes affective sharing and imagining and understanding the emotions of others. The primary brain structures involved in mediating the components of empathy are the anterior insula (AI), the anterior cingulate cortex (ACC), and specific regions of the medial prefrontal cortex (MPFC). The AI and ACC are the main nodes in the salience network (SN), which selects and coordinates the information flow from the intero- and exteroreceptors. AI might play a role as a crucial hub – a dynamic switch between 2 separate networks of cognitive processing: the central executive network (CEN), which is concerned with effective task execution, and the default mode network (DMN), which is involved with self-reflective processes. Given various classifications, a deficit in empathy may be considered a central dysfunctional trait in narcissism. A recent fMRI study suggests that deficit in empathy is due to a dysfunction in the right AI. Based on the acquired data, we propose a theoretical model of imbalanced SN functioning in narcissism in which the dysfunctional AI hub is responsible for constant DMN activation, which, in turn, centers one’s attention on the self. This might hinder the ability to affectively share and understand the emotions of others. This review paper on neural mechanisms of empathy deficits in narcissism aims to inspire and direct future research in this area. PMID:24189465

  14. Model-based Utility Functions

    NASA Astrophysics Data System (ADS)

    Hibbard, Bill

    2012-05-01

    Orseau and Ring, as well as Dewey, have recently described problems, including self-delusion, with the behavior of agents using various definitions of utility functions. An agent's utility function is defined in terms of the agent's history of interactions with its environment. This paper argues, via two examples, that the behavior problems can be avoided by formulating the utility function in two steps: 1) inferring a model of the environment from interactions, and 2) computing utility as a function of the environment model. Basing a utility function on a model that the agent must learn implies that the utility function must initially be expressed in terms of specifications to be matched to structures in the learned model. These specifications constitute prior assumptions about the environment so this approach will not work with arbitrary environments. But the approach should work for agents designed by humans to act in the physical world. The paper also addresses the issue of self-modifying agents and shows that if provided with the possibility to modify their utility functions agents will not choose to do so, under some usual assumptions.

  15. Modeling the Mechanical Performance of Die Casting Dies

    SciTech Connect

    R. Allen Miller

    2004-02-27

    The following report covers work performed at Ohio State on modeling the mechanical performance of dies. The focus of the project was development and particularly verification of finite element techniques used to model and predict displacements and stresses in die casting dies. The work entails a major case study performed with and industrial partner on a production die and laboratory experiments performed at Ohio State.

  16. Base plate mechanics of the barnacle Balanus amphitrite (=Amphibalanus amphitrite).

    PubMed

    Ramsay, David B; Dickinson, Gary H; Orihuela, Beatriz; Rittschof, Daniel; Wahl, Kathryn J

    2008-01-01

    The mechanical properties of barnacle base plates were measured using a punch test apparatus, with the purpose of examining the effect that the base plate flexural rigidity may have on adhesion mechanics. Base plate compliance was measured for 43 Balanus amphitrite (=Amphibalanus amphitrite) barnacles. Compliance measurements were used to determine flexural rigidity (assuming a fixed-edge circular plate approximation) and composite modulus of the base plates. The barnacles were categorized by age and cement type (hard or gummy) for statistical analyses. Barnacles that were 'hard' (> or =70% of the base plate thin, rigid cement) and 'gummy' (>30% of the base plate covered in compliant, tacky cement) showed statistically different composite moduli but did not show a difference in base plate flexural rigidity. The average flexural rigidity for all barnacles was 0.0020 Nm (SEM +/- 0.0003). Flexural rigidity and composite modulus did not differ significantly between 3-month and 14-month-old barnacles. The relatively low flexural rigidity measured for barnacles suggests that a rigid punch approximation is not sufficient to account for the contributions to adhesion mechanics due to flexing of real barnacles during release.

  17. Creep deformation mechanism mapping in nickel base disk superalloys

    DOE PAGES

    Smith, Timothy M.; Unocic, Raymond R.; Deutchman, Hallee; ...

    2016-05-10

    We investigated the creep deformation mechanisms at intermediate temperature in ME3, a modern Ni-based disk superalloy, using diffraction contrast imaging. Both conventional transmission electron microscopy (TEM) and scanning TEM were utilised. Distinctly different deformation mechanisms become operative during creep at temperatures between 677-815 °C and at stresses ranging from 274 to 724 MPa. Both polycrystalline and single-crystal creep tests were conducted. The single-crystal tests provide new insight into grain orientation effects on creep response and deformation mechanisms. Creep at lower temperatures (≤760 °C) resulted in the thermally activated shearing modes such as microtwinning, stacking fault ribbons and isolated superlattice extrinsicmore » stacking faults. In contrast, these faulting modes occurred much less frequently during creep at 815 °C under lower applied stresses. Instead, the principal deformation mode was dislocation climb bypass. In addition to the difference in creep behaviour and creep deformation mechanisms as a function of stress and temperature, it was also observed that microstructural evolution occurs during creep at 760 °C and above, where the secondary coarsened and the tertiary precipitates dissolved. Based on this work, a creep deformation mechanism map is proposed, emphasising the influence of stress and temperature on the underlying creep mechanisms.« less

  18. Creep deformation mechanism mapping in nickel base disk superalloys

    SciTech Connect

    Smith, Timothy M.; Unocic, Raymond R.; Deutchman, Hallee; Mills, Michael J.

    2016-05-10

    We investigated the creep deformation mechanisms at intermediate temperature in ME3, a modern Ni-based disk superalloy, using diffraction contrast imaging. Both conventional transmission electron microscopy (TEM) and scanning TEM were utilised. Distinctly different deformation mechanisms become operative during creep at temperatures between 677-815 °C and at stresses ranging from 274 to 724 MPa. Both polycrystalline and single-crystal creep tests were conducted. The single-crystal tests provide new insight into grain orientation effects on creep response and deformation mechanisms. Creep at lower temperatures (≤760 °C) resulted in the thermally activated shearing modes such as microtwinning, stacking fault ribbons and isolated superlattice extrinsic stacking faults. In contrast, these faulting modes occurred much less frequently during creep at 815 °C under lower applied stresses. Instead, the principal deformation mode was dislocation climb bypass. In addition to the difference in creep behaviour and creep deformation mechanisms as a function of stress and temperature, it was also observed that microstructural evolution occurs during creep at 760 °C and above, where the secondary coarsened and the tertiary precipitates dissolved. Based on this work, a creep deformation mechanism map is proposed, emphasising the influence of stress and temperature on the underlying creep mechanisms.

  19. Some new extensio