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Sample records for mechanics modeling based

  1. 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.

  2. 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.

  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. A dependency-based modelling mechanism for problem solving

    NASA Technical Reports Server (NTRS)

    London, P.

    1978-01-01

    The paper develops a technique of dependency net modeling which relies on an explicit representation of justifications for beliefs held by the problem solver. Using these justifications, the modeling mechanism is able to determine the relevant lines of inference to pursue during problem solving. Three particular problem-solving difficulties which may be handled by the dependency-based technique are discussed: (1) subgoal violation detection, (2) description binding, and (3) maintaining a consistent world model.

  5. Image-Based Predictive Modeling of Heart Mechanics.

    PubMed

    Wang, V Y; Nielsen, P M F; Nash, M P

    2015-01-01

    Personalized biophysical modeling of the heart is a useful approach for noninvasively analyzing and predicting in vivo cardiac mechanics. Three main developments support this style of analysis: state-of-the-art cardiac imaging technologies, modern computational infrastructure, and advanced mathematical modeling techniques. In vivo measurements of cardiac structure and function can be integrated using sophisticated computational methods to investigate mechanisms of myocardial function and dysfunction, and can aid in clinical diagnosis and developing personalized treatment. In this article, we review the state-of-the-art in cardiac imaging modalities, model-based interpretation of 3D images of cardiac structure and function, and recent advances in modeling that allow personalized predictions of heart mechanics. We discuss how using such image-based modeling frameworks can increase the understanding of the fundamental biophysics behind cardiac mechanics, and assist with diagnosis, surgical guidance, and treatment planning. Addressing the challenges in this field will require a coordinated effort from both the clinical-imaging and modeling communities. We also discuss future directions that can be taken to bridge the gap between basic science and clinical translation.

  6. Cascade process modeling with mechanism-based hierarchical neural networks.

    PubMed

    Cong, Qiumei; Yu, Wen; Chai, Tianyou

    2010-02-01

    Cascade process, such as wastewater treatment plant, includes many nonlinear sub-systems and many variables. When the number of sub-systems is big, the input-output relation in the first block and the last block cannot represent the whole process. In this paper we use two techniques to overcome the above problem. Firstly we propose a new neural model: hierarchical neural networks to identify the cascade process; then we use serial structural mechanism model based on the physical equations to connect with neural model. A stable learning algorithm and theoretical analysis are given. Finally, this method is used to model a wastewater treatment plant. Real operational data of wastewater treatment plant is applied to illustrate the modeling approach.

  7. 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).

  8. Time dependent mechanical modeling for polymers based on network theory

    NASA Astrophysics Data System (ADS)

    Billon, Noëlle

    2016-05-01

    Despite of a lot of attempts during recent years, complex mechanical behaviour of polymers remains incompletely modelled, making industrial design of structures under complex, cyclic and hard loadings not totally reliable. The non linear and dissipative viscoelastic, viscoplastic behaviour of those materials impose to take into account non linear and combined effects of mechanical and thermal phenomena. In this view, a visco-hyperelastic, viscoplastic model, based on network description of the material has recently been developed and designed in a complete thermodynamic frame in order to take into account those main thermo-mechanical couplings. Also, a way to account for coupled effects of strain-rate and temperature was suggested. First experimental validations conducted in the 1D limit on amorphous rubbery like PMMA in isothermal conditions led to pretty goods results. In this paper a more complete formalism is presented and validated in the case of a semi crystalline polymer, a PA66 and a PET (either amorphous or semi crystalline) are used. Protocol for identification of constitutive parameters is described. It is concluded that this new approach should be the route to accurately model thermo-mechanical behaviour of polymers using a reduced number of parameters of some physicl meaning.

  9. 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

  10. 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 ...

  11. 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.

  12. Mechanism-Based QSAR Modeling of Skin Sensitization.

    PubMed

    Dearden, J C; Hewitt, M; Roberts, D W; Enoch, S J; Rowe, P H; Przybylak, K R; Vaughan-Williams, G D; Smith, M L; Pillai, G G; Katritzky, A R

    2015-10-19

    Many chemicals can induce skin sensitization, and there is a pressing need for non-animal methods to give a quantitative indication of potency. Using two large published data sets of skin sensitizers, we have allocated each sensitizing chemical to one of 10 mechanistic categories and then developed good QSAR models for the seven categories that have a sufficient number of chemicals to allow modeling. Both internal and external validation checks showed that each model had good predictivity.

  13. 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.

  14. 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...

  15. A strain-based model for mechanical hemolysis based on a coarse-grained red blood cell model.

    PubMed

    Ezzeldin, Hussein M; de Tullio, Marco D; Vanella, Marcos; Solares, Santiago D; Balaras, Elias

    2015-06-01

    Mechanical hemolysis is a major concern in the design of cardiovascular devices, such as prosthetic heart valves and ventricular assist devices. The primary cause of mechanical hemolysis is the impact of the device on the local blood flow, which exposes blood elements to non-physiologic conditions. The majority of existing hemolysis models correlate red blood cell (RBC) damage to the imposed fluid shear stress and exposure time. Only recently more realistic, strain-based models have been proposed, where the RBC's response to the imposed hydrodynamic loading is accounted for. In the present work we extend strain-based models by introducing a high-fidelity representation of RBCs, which is based on existing coarse-grained particle dynamics approach. We report a series of numerical experiments in simple shear flows of increasing complexity, to illuminate the basic differences between existing models and establish their accuracy in comparison to the high-fidelity RBC approach. We also consider a practical configuration, where the flow through an artificial heart valve is computed. Our results shed light on the strengths and weaknesses of each approach and identify the key gaps that should be addressed in the development of new models.

  16. Model-based advice for mechanical ventilation: From research (INVENT) to product (Beacon Caresystem).

    PubMed

    Rees, Stephen E; Karbing, Dan S

    2015-01-01

    This paper describes the structure and functionality of a physiological model-based system for providing advice on the settings of mechanical ventilation. Use of the system is presented with examples of patients on support and control modes of mechanical ventilation.

  17. 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.

  18. Charge transport model in nanodielectric composites based on quantum tunneling mechanism and dual-level traps

    NASA Astrophysics Data System (ADS)

    Li, Guochang; Chen, George; Li, Shengtao

    2016-08-01

    Charge transport properties in nanodielectrics present different tendencies for different loading concentrations. The exact mechanisms that are responsible for charge transport in nanodielectrics are not detailed, especially for high loading concentration. A charge transport model in nanodielectrics has been proposed based on quantum tunneling mechanism and dual-level traps. In the model, the thermally assisted hopping (TAH) process for the shallow traps and the tunnelling process for the deep traps are considered. For different loading concentrations, the dominant charge transport mechanisms are different. The quantum tunneling mechanism plays a major role in determining the charge conduction in nanodielectrics with high loading concentrations. While for low loading concentrations, the thermal hopping mechanism will dominate the charge conduction process. The model can explain the observed conductivity property in nanodielectrics with different loading concentrations.

  19. 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.

  20. Prediction of anisotropic behavior of nano/micro composite based on damage mechanics with cell modeling.

    PubMed

    Lee, Dock-Jin; Kim, Young-Jin; Kim, Moon-Ki; Choi, Jae-Boong; Chang, Yoon-Suk; Liu, Wing Kam

    2011-01-01

    New advanced composite materials have recently been of great interest. Especially, many researchers have studied on nano/micro composites based on matrix filled with nano-particles, nano-tubes, nano-wires and so forth, which have outstanding characteristics on thermal, electrical, optical, chemical and mechanical properties. Therefore, the need of numerical approach for design and development of the advanced materials has been recognized. In this paper, finite element analysis based on multi-resolution continuum theory is carried out to predict the anisotropic behavior of nano/micro composites based on damage mechanics with a cell modeling. The cell modeling systematically evaluates constitutive relationships from microstructure of the composite material. Effects of plastic anisotropy on deformation behavior and damage evolution of nano/micro composite are investigated by using Hill's 48 yield function and also compared with those obtained from Gurson-Tvergaard-Needleman isotropic damage model based on von Mises yield function.

  1. The mechanical properties of a cell-based numerical model of epithelium.

    PubMed

    Merzouki, Aziza; Malaspinas, Orestis; Chopard, Bastien

    2016-05-25

    In this work we use a computational cell-based model to study the influence of the mechanical properties of cells on the mechanics of epithelial tissues. We analyze the effect of the model parameters on the elasticity and the mechanical response of tissues subjected to stress loading application. We compare our numerical results with experimental measurements of epithelial cell monolayer mechanics. Unlike previous studies, we have been able to estimate in physical units the parameter values that match the experimental results. A key observation is that the model parameters must vary with the tissue strain. In particular, it was found that, while the perimeter contractility and the area elasticity of cells remain constant at lower strains (<20%), they must increase to respond to larger strains (>20%). However, above a threshold of 50% extension, the cells stop counteracting the tissue strain and reduce both their perimeter contractility and area elasticity. PMID:27139927

  2. Application of Structure-Based Models of Mechanical and Thermal Properties on Plasma Sprayed Coatings

    NASA Astrophysics Data System (ADS)

    Vilémová, Monika; Matějíček, Jiří; Mušálek, Radek; Nohava, Jiří

    2012-06-01

    Mechanical and thermal properties of thermal sprayed coatings, especially ceramics, are strongly influenced by cracks and pores that are present in the coating microstructure. In the recent past, there have been efforts to find an analytical model describing the coating properties based on the microstructural characteristics. Various analytical models were developed and published in the literature. In this study, several major models were applied to ceramic and metal coatings to describe their elastic modulus and thermal conductivity. The sensitivity of the models to the variations in the microstructure and relevancy of their use in specific cases were examined. The results were compared with those obtained by FEM modeling and experimentally measured values.

  3. A Study of Mechanical Optimization Strategy for Cardiac Resynchronization Therapy Based on an Electromechanical Model

    PubMed Central

    Dou, Jianhong; Xia, Ling; Deng, Dongdong; Zang, Yunliang; Shou, Guofa; Bustos, Cesar; Tu, Weifeng; Liu, Feng; Crozier, Stuart

    2012-01-01

    An optimal electrode position and interventricular (VV) delay in cardiac resynchronization therapy (CRT) improves its success. However, the precise quantification of cardiac dyssynchrony and magnitude of resynchronization achieved by biventricular (BiV) pacing therapy with mechanical optimization strategies based on computational models remain scant. The maximum circumferential uniformity ratio estimate (CURE) was used here as mechanical optimization index, which was automatically computed for 6 different electrode positions based on a three-dimensional electromechanical canine model of heart failure (HF) caused by complete left bundle branch block (CLBBB). VV delay timing was adjusted accordingly. The heart excitation propagation was simulated with a monodomain model. The quantification of mechanical intra- and interventricular asynchrony was then investigated with eight-node isoparametric element method. The results showed that (i) the optimal pacing location from maximal CURE of 0.8516 was found at the left ventricle (LV) lateral wall near the equator site with a VV delay of 60 ms, in accordance with current clinical studies, (ii) compared with electrical optimization strategy of ERMS, the LV synchronous contraction and the hemodynamics improved more with mechanical optimization strategy. Therefore, measures of mechanical dyssynchrony improve the sensitivity and specificity of predicting responders more. The model was subject to validation in future clinical studies. PMID:23118802

  4. Mechanism-based mathematical modeling of combined gemcitabine and birinapant in pancreatic cancer cells

    PubMed Central

    Zhu, Xu; Straubinger, Robert M.; Jusko, William J.

    2015-01-01

    Combination chemotherapy is standard treatment for pancreatic cancer. However, current drugs lack efficacy for most patients and selection and evaluation of new combination regimens is empirical and time-consuming. The efficacy of gemcitabine, a standard-of-care agent, combined with birinapant, a pro-apoptotic antagonist of Inhibitor of Apoptosis Proteins (IAPs), was investigated in pancreatic cancer cells. PANC-1 cells were treated with vehicle, gemcitabine (6, 10, 20 nM), birinapant (50, 200, 500 nM), and combinations of the two drugs. Temporal changes in cell numbers, cell cycle distribution, and apoptosis were measured. A basic pharmacodynamic (PD) model based on cell numbers, and a mechanism-based PD model integrating all measurements, were developed. The basic PD model indicated that synergistic effects occurred in both cell proliferation and death processes. The mechanism-based model captured key features of drug action: temporary cell cycle arrest in S phase induced by gemcitabine alone, apoptosis induced by birinapant alone, and prolonged cell cycle arrest and enhanced apoptosis induced by the combination. A drug interaction term ψ was employed in the models to signify interactions of the combination when data were limited. When more experimental information was utilized, ψ values approaching 1 indicated that specific mechanisms of interactions were captured better. PD modeling identified the potential benefit of combining gemcitabine and birinapant, and characterized the key interaction pathways. An optimal treatment schedule of pretreatment with gemcitabine for 24-48 h was suggested based on model prediction and was verified experimentally. This approach provides a generalizable modeling platform for exploring combinations of cytostatic and cytotoxic agents in cancer cell cultures. PMID:26252969

  5. 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

  6. 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.

  7. 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.

  8. Dislocation Density-Based Constitutive Model for the Mechanical Behavior of Irradiated Cu

    SciTech Connect

    Arsenlis, A; Wirth, B D; Rhee, M

    2003-04-10

    Performance degradation of structural steels in nuclear environments results from the development of a high number density of nanometer scale defects. The defects observed in copper-based alloys are composed of vacancy clusters in the form of stacking fault tetrahedra and/or prismatic dislocation loops, which impede dislocation glide and are evidenced in macroscopic uniaxial stress-strain curves as increased yield strengths, decreased total strain to failure, decreased work hardening and the appearance of a distinct upper yield point above a critical defect concentration (neutron dose). In this paper, we describe the development of an internal state variable model for the mechanical behavior of materials subject to these environments. This model has been developed within an information-passing multiscale materials modeling framework, in which molecular dynamics simulations of dislocation--radiation defect interactions, inform the final coarse-grained continuum model. The plasticity model includes mechanisms for dislocation density growth and multiplication and for radiation defect density evolution with dislocation interaction. The general behavior of the constitutive (single material point) model shows that as the defect density increases, the initial yield point increases and the initial strain hardening decreases. The final coarse-grained model is implemented into a finite element framework and used to simulate the behavior of tensile specimens with varying levels of irradiation induced material damage. The simulation results compare favorably with the experimentally observed mechanical properties of irradiated materials in terms of their increased strength, decreased hardening, and decreased ductility with increasing irradiation dose.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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.

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

    PubMed

    Guarnera, Enrico; Berezovsky, Igor N

    2016-03-01

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

    PubMed

    Guarnera, Enrico; Berezovsky, Igor N

    2016-03-01

    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.

  16. 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

  17. 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

  18. 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

  19. 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.

  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

    Nelis, Lisa Castillo; Wootton, J Timothy

    2010-02-22

    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.

  3. 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

  4. Mechanism-based common reactivity pattern (COREPA) modelling of aryl hydrocarbon receptor binding affinity

    PubMed Central

    Petkov, P.I.; Rowlands, J.C.; Budinsky, R.; Zhao, B.; Denison, M.S.; Mekenyan, O.

    2011-01-01

    The aryl hydrocarbon receptor is a ligand-activated transcription factor responsive to both natural and synthetic environmental compounds, with the most potent agonist being 2,3,7,8-tetrachlotrodibenzo-p-dioxin. The aim of this work was to develop a categorical COmmon REactivity PAttern (COREPA)-based structure–activity relationship model for predicting aryl hydrocarbon receptor ligands within different binding ranges. The COREPA analysis suggested two different binding mechanisms called dioxin- and biphenyl-like, respectively. The dioxin-like model predicts a mechanism that requires a favourable interaction with a receptor nucleophilic site in the central part of the ligand and with electrophilic sites at both sides of the principal molecular axis, whereas the biphenyl-like model predicted a stacking-type interaction with the aryl hydrocarbon receptor allowing electron charge transfer from the receptor to the ligand. The current model was also adjusted to predict agonistic/antagonistic properties of chemicals. The mechanism of antagonistic properties was related to the possibility that these chemicals have a localized negative charge at the molecule's axis and ultimately bind with the receptor surface through the electron-donating properties of electron-rich groups. The categorization of chemicals as agonists/antagonists was found to correlate with their gene expression. The highest increase in gene expression was elicited by strong agonists, followed by weak agonists producing lower increases in gene expression, whereas all antagonists (and non-aryl hydrocarbon receptor binders) were found to have no effect on gene expression. However, this relationship was found to be quantitative for the chemicals populating the areas with extreme gene expression values only, leaving a wide fuzzy area where the quantitative relationship was unclear. The total concordance of the derived aryl hydrocarbon receptor binding categorical structure–activity relationship model was

  5. Mechanisms of self-organization and finite size effects in a minimal agent based model

    NASA Astrophysics Data System (ADS)

    Alfi, V.; Cristelli, M.; Pietronero, L.; Zaccaria, A.

    2009-03-01

    We present a detailed analysis of the self-organization phenomenon in which the stylized facts originate from finite size effects with respect to the number of agents considered and disappear in the limit of an infinite population. By introducing the possibility that agents can enter or leave the market depending on the behavior of the price, it is possible to show that the system self-organizes in a regime with a finite number of agents which corresponds to the stylized facts. The mechanism for entering or leaving the market is based on the idea that a too stable market is unappealing for traders, while the presence of price movements attracts agents to enter and speculate on the market. We show that this mechanism is also compatible with the idea that agents are scared by a noisy and risky market at shorter timescales. We also show that the mechanism for self-organization is robust with respect to variations of the exit/entry rules and that the attempt to trigger the system to self-organize in a region without stylized facts leads to an unrealistic dynamics. We study the self-organization in a specific agent based model but we believe that the basic ideas should be of general validity.

  6. Mechanical properties of methacrylate-based model dentin adhesives: effect of loading rate and moisture exposure.

    PubMed

    Singh, Viraj; Misra, Anil; Parthasarathy, Ranganathan; Ye, Qiang; Park, Jonggu; Spencer, Paulette

    2013-11-01

    The aim of this study is to investigate the mechanical behavior of model methacrylate-based dentin adhesives under conditions that simulate the wet oral environment. A series of monotonic and creep experiments were performed on rectangular beam samples of dentin adhesive in three-point bending configuration under different moisture conditions. The monotonic test results show a significant effect of loading rate on the failure strength and the linear limit (yield point) of the stress-strain response. In addition, these tests show that the failure strength is low, and the failure occurs at a smaller deformation when the test is performed under continuously changing moisture conditions. The creep test results show that under constant moisture conditions, the model dentin adhesives can have a viscoelastic response under certain low loading levels. However, when the moisture conditions vary under the same low loading levels, the dentin adhesives have an anomalous creep response accompanied by large secondary creep and high strain accumulation. PMID:23744598

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  8. 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.

  9. 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.

  10. Modelling and Simulation Based on Matlab/Simulink: A Press Mechanism

    NASA Astrophysics Data System (ADS)

    Halicioglu, R.; Dulger, L. C.; Bozdana, A. T.

    2014-03-01

    In this study, design and kinematic analysis of a crank-slider mechanism for a crank press is studied. The crank-slider mechanism is the commonly applied one as direct and indirect drive alternatives in practice. Since inexpensiveness, flexibility and controllability are getting more and more important in many industrial applications especially in automotive industry, a crank press with servo actuator (servo crank press) is taken as an application. Design and kinematic analysis of representative mechanism is presented with geometrical analysis for the inverse kinematic of the mechanism by using desired motion concept of slider. The mechanism is modelled in MATLAB/Simulink platform. The simulation results are presented herein.

  11. 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

  12. Microstructurally based mechanisms for modeling shrinkage of cement paste at multiple levels

    SciTech Connect

    Jennings, H.M.; Xi, Yunping

    1993-07-15

    Shrinkage of cement paste is controlled by a number of mechanisms that operate in various parts of the microstructure and at various length scales. A model for creep and shrinkage can be developed by combining several models that describe phenomena at each of several length scales, ranging from the nanometer to the meter. This model is described and preliminary results are discussed.

  13. Quantifying subpopulation synergy for antibiotic combinations via mechanism-based modeling and a sequential dosing design.

    PubMed

    Landersdorfer, Cornelia B; Ly, Neang S; Xu, Hongmei; Tsuji, Brian T; Bulitta, Jürgen B

    2013-05-01

    Quantitative modeling of combination therapy can describe the effects of each antibiotic against multiple bacterial populations. Our aim was to develop an efficient experimental and modeling strategy that evaluates different synergy mechanisms using a rapidly killing peptide antibiotic (nisin) combined with amikacin or linezolid as probe drugs. Serial viable counts over 48 h were obtained in time-kill experiments with all three antibiotics in monotherapy against a methicillin-resistant Staphylococcus aureus USA300 strain (inoculum, 10(8) CFU/ml). A sequential design (initial dosing of 8 or 32 mg/liter nisin, switched to amikacin or linezolid at 1.5 h) assessed the rate of killing by amikacin and linezolid against nisin-intermediate and nisin-resistant populations. Simultaneous combinations were additionally studied and all viable count profiles comodeled in S-ADAPT and NONMEM. A mechanism-based model with six populations (three for nisin times two for amikacin) yielded unbiased and precise (r = 0.99, slope = 1.00; S-ADAPT) individual fits. The second-order killing rate constants for nisin against the three populations were 5.67, 0.0664, and 0.00691 liter/(mg · h). For amikacin, the maximum killing rate constants were 10.1 h(-1) against its susceptible and 0.771 h(-1) against its less-susceptible populations, with 14.7 mg/liter amikacin causing half-maximal killing. After incorporating the effects of nisin and amikacin against each population, no additional synergy function was needed. Linezolid inhibited successful bacterial replication but did not efficiently kill populations less susceptible to nisin. Nisin plus amikacin achieved subpopulation synergy. The proposed sequential and simultaneous dosing design offers an efficient approach to quantitatively characterize antibiotic synergy over time and prospectively evaluate antibiotic combination dosing strategies. PMID:23478962

  14. A Comparative Data-Based Modeling Study on Respiratory CO2 Gas Exchange during Mechanical Ventilation

    PubMed Central

    Kim, Chang-Sei; Ansermino, J. Mark; Hahn, Jin-Oh

    2016-01-01

    The goal of this study is to derive a minimally complex but credible model of respiratory CO2 gas exchange that may be used in systematic design and pilot testing of closed-loop end-tidal CO2 controllers in mechanical ventilation. We first derived a candidate model that captures the essential mechanisms involved in the respiratory CO2 gas exchange process. Then, we simplified the candidate model to derive two lower-order candidate models. We compared these candidate models for predictive capability and reliability using experimental data collected from 25 pediatric subjects undergoing dynamically varying mechanical ventilation during surgical procedures. A two-compartment model equipped with transport delay to account for CO2 delivery between the lungs and the tissues showed modest but statistically significant improvement in predictive capability over the same model without transport delay. Aggregating the lungs and the tissues into a single compartment further degraded the predictive fidelity of the model. In addition, the model equipped with transport delay demonstrated superior reliability to the one without transport delay. Further, the respiratory parameters derived from the model equipped with transport delay, but not the one without transport delay, were physiologically plausible. The results suggest that gas transport between the lungs and the tissues must be taken into account to accurately reproduce the respiratory CO2 gas exchange process under conditions of wide-ranging and dynamically varying mechanical ventilation conditions. PMID:26870728

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. Unveiling the molecular mechanism of brassinosteroids: Insights from structure-based molecular modeling studies.

    PubMed

    Lei, Beilei; Liu, Jiyuan; Yao, Xiaojun

    2015-12-01

    Brassinosteroid (BR) phytohormones play indispensable roles in plant growth and development. Brassinolide (BL) and 24-epibrassinolide (24-epiBL) are the most active ones among the BRs reported thus far. Unfortunately, the extremely low natural content and intricate synthesis process limit their popularization in agricultural production. Earlier reports to discover alternative compounds have resulted in molecules with nearly same scaffold structure and without diversity in chemical space. In the present study, receptors structure based BRs regulation mechanism was analyzed. First, we examined the detailed binding interactions and their dynamic stability between BL and its receptor BRI1 and co-receptor BAK1. Then, the binding modes and binding free energies for 24-epiBL and a series of representative BRs binding with BRI1 and BRI1-BAK1 were carried out by molecular docking, energy minimization and MM-PBSA free energy calculation. The obtained binding structures and energetic results provided vital insights into the structural factors affecting the activity from both receptors and BRs aspects. Subsequently, the obtained knowledge will serve as valuable guidance to build pharmacophore models for rational screening of new scaffold alternative BRs.

  1. 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.

  2. 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

  3. Model-based analysis of the effect of different operating conditions on fouling mechanisms in a membrane bioreactor.

    PubMed

    Sabia, Gianpaolo; Ferraris, Marco; Spagni, Alessandro

    2016-01-01

    This study proposes a model-based evaluation of the effect of different operating conditions with and without pre-denitrification treatment and applying three different solids retention times on the fouling mechanisms involved in membrane bioreactors (MBRs). A total of 11 fouling models obtained from literature were used to fit the transmembrane pressure variations measured in a pilot-scale MBR treating real wastewater for more than 1 year. The results showed that all the models represent reasonable descriptions of the fouling processes in the MBR tested. The model-based analysis confirmed that membrane fouling started by pore blocking (complete blocking model) and by a reduction of the pore diameter (standard blocking) while cake filtration became the dominant fouling mechanism over long-term operation. However, the different fouling mechanisms occurred almost simultaneously making it rather difficult to identify each one. The membrane "history" (i.e. age, lifespan, etc.) seems the most important factor affecting the fouling mechanism more than the applied operating conditions. Nonlinear regression of the most complex models (combined models) evaluated in this study sometimes demonstrated unreliable parameter estimates suggesting that the four basic fouling models (complete, standard, intermediate blocking and cake filtration) contain enough details to represent a reasonable description of the main fouling processes occurring in MBRs.

  4. [Study of mechanical effects of the EVA glove on finger base with finite element modeling].

    PubMed

    Li, Zhuoyou; Ding, Li; Yue, Guodong

    2013-08-01

    The hand strength of astronauts, when they are outside the space capsule, is highly influenced by the residual pressure (the pressure difference between inside pressure and outside one of the suit) of extravehicular activity spacesuit glove and the pressure exerted by braided fabric. The hand strength decreases significantly on extravehicular activity, severely reducing the operation efficiency. To measure mechanical influence caused by spacesuit glove on muscle-tendon and joints, the present paper analyzes the movement anatomy and biomechanical characteristics of gripping, and then proposes a grip model. With phalangeal joint simplified as hinges, seven muscles as a finger grip energy unit, the Hill muscle model was used to compute the effects. We also used ANSYS in this study to establish a 3-D finite element model of an index finger which included both bones and muscles with glove, and then we verified the model. This model was applied to calculate the muscle stress in various situations of bare hands or hands wearing gloves in three different sizes. The results showed that in order to achieve normal grip strength with the influence caused by superfluous press, the finger's muscle stress should be increased to 5.4 times of that in normal situation, with most of the finger grip strength used to overcome the influence of superfluous pressure. When the gap between the finger surface and the glove is smaller, the mechanical influence which superfluous press made will decrease. The results would provide a theoretical basis for the design of the EVA Glove.

  5. Use of Agent-Based Modeling To Explore the Mechanisms of Intracellular Phosphorus Heterogeneity in Cultured Phytoplankton

    PubMed Central

    Fredrick, Neil D.; Berges, John A.; Twining, Benjamin S.; Nuñez-Milland, Daliangelis

    2013-01-01

    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. PMID:23666327

  6. Morphologic Interpretation of Rock Failure Mechanisms Under Uniaxial Compression Based on 3D Multiscale High-resolution Numerical Modeling

    NASA Astrophysics Data System (ADS)

    Li, Gen; Liang, Zheng-Zhao; Tang, Chun-An

    2015-11-01

    Multiscale continuous lab oratory observation of the progressive failure process has become a powerful means to reveal the complex failure mechanism of rock. Correspondingly, the representative volume element (RVE)-based models, which are capable of micro/meso- to macro-scale simulations, have been proposed, for instance, the rock failure process analysis (RFPA) program. Limited by the computational bottleneck due to the RVE size, multiscale high-resolution modeling of rock failure process can hardly be implemented, especially for three-dimensional (3D) problems. In this paper, the self-developed parallel RFPA3D code is employed to investigate the failure mechanisms and various fracture morphology of laboratory-scale rectangular prism rock specimens under unconfined uniaxial compression. The specimens consist of either heterogeneous rock with low strength or relatively homogeneous rock with high strength. The numerical simulations, such as the macroscopic fracture pattern and stress-strain responses, can reproduce the well-known phenomena of physical experiments. In particular, the 3D multiscale continuum modeling is carried out to gain new insight into the morphologic interpretation of brittle failure mechanisms, which is calibrated and validated by comparing the actual laboratory experiments and field evidence. The advantages of 3D multiscale high-resolution modeling are demonstrated by comparing the failure modes against 2D numerical predictions by other models. The parallel RVE-based modeling tool in this paper can provide an alternative way to investigate the complicated failure mechanisms of rock.

  7. Model of the catalytic mechanism of human aldose reductase based on quantum chemical calculations.

    SciTech Connect

    Cachau, R. C.; Howard, E. H.; Barth, P. B.; Mitschler, A. M.; Chevrier, B. C.; Lamour, V.; Joachimiak, A.; Sanishvili, R.; Van Zandt, M.; Sibley, E.; Moras, D.; Podjarny, A.; UPR de Biologie Structurale; National Cancer Inst.; Univ. Louis Pasteur; Inst. for Diabetes Discovery, Inc.

    2000-01-01

    Aldose Reductase is an enzyme involved in diabetic complications, thoroughly studied for the purpose of inhibitor development. The structure of an enzyme-inhibitor complex solved at sub-atomic resolution has been used to develop a model for the catalytic mechanism. This model has been refined using a combination of Molecular Dynamics and Quantum calculations. It shows that the proton donation, the subject of previous controversies, is the combined effect of three residues: Lys 77, Tyr 48 and His 110. Lys 77 polarises the Tyr 48 OH group, which donates the proton to His 110, which becomes doubly protonated. His 110 then moves and donates the proton to the substrate. The key information from the sub-atomic resolution structure is the orientation of the ring and the single protonafion of the His 110 in the enzyme-inhibitor complex. This model is in full agreement with all available experimental data.

  8. 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.

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

    PubMed Central

    Anderson, Debra F.; Cheung, Cecilia Y.

    2014-01-01

    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. PMID:25186112

  10. 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.

  11. Development of antipsychotic medications with novel mechanisms of action based on computational modeling of hippocampal neuropathology.

    PubMed

    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

  12. 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.

  13. Alteration in refractive index profile during accommodation based on mechanical modelling

    PubMed Central

    Bahrami, Mehdi; Heidari, Ali; Pierscionek, Barbara K.

    2015-01-01

    The lens of the eye has a gradient refractive index (GRIN). Ocular accommodation, which alters the shape of the lens in response to visual demand, causes a redistribution of the internal structure of the lens leading to a change in the GRIN profile. The nature of this redistribution and the consequence of change in the GRIN profile are not understood. A modelling approach that considers how the GRIN profile may change with accommodation needs to take into account optical and mechanical parameters and be cognisant of individual variability in the shape and size of lenses. This study models the normalised axial GRIN profile during accommodation using reduced modelling and incorporating finite element analysis to connect inhomogenous mechanical characteristics of the lens to optical performance. The results show that simulated stretching changes the length of the plateau but does not alter the cortical gradient, which supports clinical findings. There is a very small change to the accommodated and non-accommodated profiles when normalised, yet this yields measurable changes in aberrations with around 11% and almost 13% difference in spherical aberration and astigmatism respectively. The results can be used in reconstruction of the refractive index and for investigating gradual changes with age. PMID:26819821

  14. Plasma etching of Hf-based high-k thin films. Part III. Modeling the reaction mechanisms

    SciTech Connect

    Martin, Ryan M.; Chang, Jane P.

    2009-03-15

    A generalized etch rate model was formulated to describe metal oxide etching in complex plasma chemistries, based on the understanding gained from detailed plasma characterization and experimental investigation into the metal oxide etching mechanisms. Using a surface site balance-based approach, the correct etch rate dependencies on neutral-to-ion flux ratio, ion energy, competing deposition and etching reaction pathways, and film properties were successfully incorporated into the model. The applicability of the model was assessed by fitting to experimental etch rate data in both Cl{sub 2} and BCl{sub 3} chemistries. Plasma gas phase analysis as well as etch and deposition rate measurements were used to calculate initial values and appropriate ranges for model parameter variation. Physically meaningful parameter values were extracted from the modeling fitting to the experimental data, thereby demonstrating the applicability of this model in assessing the plasma etching of other complex materials systems.

  15. 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

  16. 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.

  17. 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.

  18. An effective stress based numerical model for hydro-mechanical analysis in unsaturated porous media

    NASA Astrophysics Data System (ADS)

    Khalili, N.; Khabbaz, M. H.; Valliappan, S.

    A fully coupled flow-deformation model is presented for the behaviour of unsaturated porous media. The governing equations are derived based on the equations of equilibrium, effective stress concept, Darcy's law, Henry's law, and the conservation of fluid mass. Macroscopic coupling between the flow and deformation fields is established through the effective stress parameters. The microscopic link between the volumetric deformations of the two pore system (i.e. the pore-air and the pore-water) is established using Betti's reciprocal theorem. Both links are essential for a proper modelling of flow and deformation in unsaturated porous media. The discretised form of the governing equations is obtained using the finite element technique. As application of the model, experimental results from several laboratory tests reported in the literature are modelled numerically. Good agreement is obtained between the numerical and the experimental results in all cases.

  19. Tracking control of nonlinear lumped mechanical continuous-time systems: A model-based iterative learning approach

    NASA Astrophysics Data System (ADS)

    Smolders, K.; Volckaert, M.; Swevers, J.

    2008-11-01

    This paper presents a nonlinear model-based iterative learning control procedure to achieve accurate tracking control for nonlinear lumped mechanical continuous-time systems. The model structure used in this iterative learning control procedure is new and combines a linear state space model and a nonlinear feature space transformation. An intuitive two-step iterative algorithm to identify the model parameters is presented. It alternates between the estimation of the linear and the nonlinear model part. It is assumed that besides the input and output signals also the full state vector of the system is available for identification. A measurement and signal processing procedure to estimate these signals for lumped mechanical systems is presented. The iterative learning control procedure relies on the calculation of the input that generates a given model output, so-called offline model inversion. A new offline nonlinear model inversion method for continuous-time, nonlinear time-invariant, state space models based on Newton's method is presented and applied to the new model structure. This model inversion method is not restricted to minimum phase models. It requires only calculation of the first order derivatives of the state space model and is applicable to multivariable models. For periodic reference signals the method yields a compact implementation in the frequency domain. Moreover it is shown that a bandwidth can be specified up to which learning is allowed when using this inversion method in the iterative learning control procedure. Experimental results for a nonlinear single-input-single-output system corresponding to a quarter car on a hydraulic test rig are presented. It is shown that the new nonlinear approach outperforms the linear iterative learning control approach which is currently used in the automotive industry on durability test rigs.

  20. 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.

  1. 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.

  2. 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.

  3. Locating and navigation mechanism based on place-cell and grid-cell models.

    PubMed

    Yan, Chuankui; Wang, Rubin; Qu, Jingyi; Chen, Guanrong

    2016-08-01

    Extensive experiments on rats have shown that environmental cues play an important role in goal locating and navigation. Major studies about locating and navigation are carried out based only on place cells. Nevertheless, it is known that navigation may also rely on grid cells. Therefore, we model locating and navigation based on both, thus developing a novel grid-cell model, from which firing fields of grid cells can be obtained. We found a continuous-time dynamic system to describe learning and direction selection. In our simulation experiment, according to the results from physiology experiments, we successfully rebuild place fields of place cells and firing fields of grid cells. We analyzed the factors affecting the locating accuracy. Results show that the learning rate, firing threshold and cell number can influence the outcomes from various tasks. We used our system model to perform a goal navigation task and showed that paths that are changed for every run in one experiment converged to a stable one after several runs. PMID:27468322

  4. Locating and navigation mechanism based on place-cell and grid-cell models.

    PubMed

    Yan, Chuankui; Wang, Rubin; Qu, Jingyi; Chen, Guanrong

    2016-08-01

    Extensive experiments on rats have shown that environmental cues play an important role in goal locating and navigation. Major studies about locating and navigation are carried out based only on place cells. Nevertheless, it is known that navigation may also rely on grid cells. Therefore, we model locating and navigation based on both, thus developing a novel grid-cell model, from which firing fields of grid cells can be obtained. We found a continuous-time dynamic system to describe learning and direction selection. In our simulation experiment, according to the results from physiology experiments, we successfully rebuild place fields of place cells and firing fields of grid cells. We analyzed the factors affecting the locating accuracy. Results show that the learning rate, firing threshold and cell number can influence the outcomes from various tasks. We used our system model to perform a goal navigation task and showed that paths that are changed for every run in one experiment converged to a stable one after several runs.

  5. Mechanical model for ductility loss

    SciTech Connect

    Hu, W.L.

    1980-02-11

    A mechanical model was constructed to probe into the mechanism of ductility loss. Fracture criterion based on critical localized deformation was undertaken. Two microstructure variables were considered in the model. Namely, the strength ratio of grain boundary affected area to the matrix, ..cap omega.., and the linear fraction, x, of grain boundary affected area. A parametrical study was carried out. The study shows that the ductility is very sensitive to those microstructure parameters. The functional dependence of ductility to temperature as well as strain-rate, suggested by the model, is demonstrated to be consistent with the observation.

  6. 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.

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

    PubMed Central

    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. PMID:26198910

  8. 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

  9. 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. PMID:22527364

  10. Mechanism-Based Model of the Pharmacokinetics of Enfuvirtide, an HIV Fusion Inhibitor

    PubMed Central

    Mohanty, Utkala; Dixit, Narendra M.

    2008-01-01

    We present a model of the pharmacokinetics of enfuvirtide, a potent inhibitor of the fusion of human immunodeficiency virus type 1 (HIV-1) with target cells. We assume that subcutaneously administered enfuvirtide accumulates in the injection region, diffuses locally, and gets absorbed into blood, where it reversibly associates with lipidic cell membranes and is eventually eliminated. We develop mathematical descriptions of each of these processes and predict the time-evolution of the concentration of enfuvirtide in plasma, Cp. We find, interestingly, that diffusion of enfuvirtide in the subcutaneous region is decoupled from absorption, which enables deduction of analytical expressions for Cp following single dose administration and ordinary differential equations following multiple dose administration and renders our model amenable to data analysis. Model predictions provide excellent fits to observed plasma concentration-time profiles of enfuvirtide following the intravenous and subcutaneous administration of a single dose and without any adjustable parameters capture quantitatively concentration-time profiles following the administration of multiple doses. Our model thus presents a robust description of the pharmacokinetics of enfuvirtide and may be applied in conjunction with models of viral dynamics to assess responses of HIV-1 patients to alternative enfuvirtide-based therapies. Further, our model reveals that key pharmacokinetic characteristics of enfuvirtide, viz., steady state values of peak and trough concentrations and area under the concentration-time curve, vary nearly linearly with dosage over a broad range of dosages and for different dosing regimens, which enables a priori estimation of enfuvirtide exposure levels for different treatment protocols and may serve to establish guidelines for therapy optimization. PMID:18258267

  11. An information diffusion model based on retweeting mechanism for online social media

    NASA Astrophysics Data System (ADS)

    Xiong, Fei; Liu, Yun; Zhang, Zhen-jiang; Zhu, Jiang; Zhang, Ying

    2012-06-01

    To characterize information propagation on online microblogs, we propose a diffusion model (SCIR) which contains four possible states: Susceptible, contacted, infected and refractory. Agents that read the information but have not decided to spread it, stay in the contacted state. They may become infected or refractory, and both the infected and refractory state are stable. Results show during the evolution process, more contacted agents appear in scale-free networks than in regular lattices. The degree based density of infected agents increases with the degree monotonously, but larger average network degree doesn't always mean less relaxation time.

  12. 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.

  13. Mechanism-based pharmacokinetic-pharmacodynamic modeling of concentration-dependent hysteresis and biphasic electroencephalogram effects of alphaxalone in rats.

    PubMed

    Visser, S A G; Smulders, C J G M; Reijers, B P R; Van der Graaf, P H; Peletier, L A; Danhof, M

    2002-09-01

    The neuroactive steroid alphaxalone reveals a complex biphasic concentration-effect relationship using the 11.5 to 30 Hz frequency band of the electroencephalogram (EEG) as biomarker. The purpose of the present investigation was to develop a mechanism-based pharmacokinetic-pharmacodynamic model to describe this observation. The proposed model is based on receptor theory and aims to separate the drug-receptor interaction from the transduction of the initial stimulus into the observed biphasic response. Individual concentration-time courses of alphaxalone were obtained in combination with continuous recording of the EEG parameter. Alphaxalone was administered intravenously in various dosages. The pharmacokinetics were described by a two-compartment model, and parameter estimates for clearance, intercompartmental clearance, volume of distribution 1 and 2 were 158 +/- 29 ml. min(-1). kg(-1), 143 +/- 31 ml. min(-1). kg(-1), 122 +/- 20 ml. kg(-1) and 606 +/- 48 ml. kg(-1), respectively. Concentration-effect relationships exhibited a biphasic pattern and delay in onset of effect. The hysteresis was described on the basis of an effect-compartment model with C(max) as covariate. The pharmacodynamic model consisted of a receptor model, featuring a monophasic saturable receptor activation model in combination with a biphasic stimulus-response model. The in vivo affinity (K(PD)) was estimated at 432 +/- 26 ng. ml(-1). Unique parameter estimates were obtained that were independent of the dose and the duration of the infusion. In conclusion, we have shown that this mechanism-based approach, which separates drug- and system-related properties in vivo, was successfully applied for the characterization of the biphasic effect versus time patterns of alphaxalone. The model should be of use in the characterization of other biphasic responses.

  14. A Pulse-type Hardware Level Difference Detection Model Based on Sound Source Localization Mechanism in Barn Owl

    NASA Astrophysics Data System (ADS)

    Sakurai, Tsubasa; Sekine, Yoshifumi

    Auditory information processing is very important in the darkness where vision information is extremely limited. Barn owls have excellent hearing information processing function. Barn owls can detect a sound source in the high accuracy of less than two degrees in both of the vertical and horizontal directions. When they perform the sound source localization, the barn owls use the interaural time difference for localization in the horizontal plane, and the interaural level difference for localization in the vertical plane. We are constructing the two-dimensional sound source localization model using pulse-type hardware neuron models based on sound source localization mechanism of barn owl for the purpose of the engineering application. In this paper, we propose a pulse-type hardware model for level difference detection based on sound source localization mechanism of barn owl. Firstly, we discuss the response characteristics of the mathematical model for level difference detection. Next we discuss the response characteristics of the hardware mode. As a result, we show clearly that this proposal model can be used as a sound source localization model of vertical direction.

  15. Investigation of the best coseismic fault model of the 2006 Java tsunami earthquake based on mechanisms of postseismic deformation

    NASA Astrophysics Data System (ADS)

    Gunawan, Endra; Meilano, Irwan; Abidin, Hasanuddin Z.; Hanifa, Nuraini Rahma; Susilo

    2016-03-01

    We investigate three available coseismic fault models of the 2006 M7.8 Java tsunami earthquake, as reported by Fujii and Satake (2006), Bilek and Engdahl (2007), and Yagi and Fukahata (2011), in order to find the best coseismic model based on mechanisms of postseismic deformation associated with viscoelastic relaxation and afterslip. We construct a preliminary rheological model using vertical data, obtaining a final rheological model after we include horizontal and vertical components of afterslip in the further process. Our analysis indicates that the coseismic fault model of Fujii and Satake (2006) provides a better and more realistic result for a rheological model than the others. The best-fit rheological model calculated using the coseismic fault model of Fujii and Satake (2006) comprises a 60 ± 5 km elastic layer thickness with a viscosity of 2.0 ± 1.0 × 1017 Pa s in the asthenosphere. Also, we find that afterslip is dominant over the horizontal displacements, while viscoelastic relaxation is dominant over the vertical displacement. Additionally, in comparison to the coseismic displacement found through GPS data taken at BAKO station, our calculation indicates that Fujii and Satake (2006) modeled coseismic displacements with less GPS data misfit than the other examined models. Finally, we emphasize that our methodology for evaluating the best coseismic fault model can satisfactorily explain the postseismic deformation of the 2006 Java tsunami earthquake.

  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 phase-contrast microscopy-based method for modeling the mechanical behavior of mesenchymal stem cells.

    PubMed

    Saeed, Mayssam; Sharabani-Yosef, Orna; Weihs, Daphne; Gefen, Amit

    2016-10-01

    We present three-dimensional (3D) finite element (FE) models of single, mesenchymal stem cells (MSCs), generated from images obtained by optical phase-contrast microscopy and used to quantify the structural responses of the studied cells to externally applied mechanical loads. Mechanical loading has been shown to affect cell morphology and structure, phenotype, motility and other biological functions. Cells experience mechanical loads naturally, yet under prolonged or sizable loading, damage and cell death may occur, which motivates research regarding the structural behavior of loaded cells. For example, near the weight-bearing boney prominences of the buttocks of immobile persons, tissues may become highly loaded, eventually leading to massive cell death that manifests as pressure ulcers. Cell-specific computational models have previously been developed by our group, allowing simulations of cell deformations under compressive or stretching loads. These models were obtained by reconstructing specific cell structures from series of 2D fluorescence, confocal image-slices, requiring cell-specific fluorescent-staining protocols and costly (confocal) microscopy equipment. Alternative modeling approaches represent cells simply as half-spheres or half-ellipsoids (i.e. idealized geometries), which neglects the curvature details of the cell surfaces associated with changes in concentrations of strains and stresses. Thus, we introduce here for the first time an optical image-based FE modeling, where loads are simulated on reconstructed 3D geometrical cell models from a single 2D, phase-contrast image. Our novel modeling method eliminates the need for confocal imaging and fluorescent staining preparations (both expensive), and makes cell-specific FE modeling affordable and accessible to the biomechanics community. We demonstrate the utility of this cost-effective modeling method by performing simulations of compression of MSCs embedded in a gel. PMID:26856632

  18. A phase-contrast microscopy-based method for modeling the mechanical behavior of mesenchymal stem cells.

    PubMed

    Saeed, Mayssam; Sharabani-Yosef, Orna; Weihs, Daphne; Gefen, Amit

    2016-10-01

    We present three-dimensional (3D) finite element (FE) models of single, mesenchymal stem cells (MSCs), generated from images obtained by optical phase-contrast microscopy and used to quantify the structural responses of the studied cells to externally applied mechanical loads. Mechanical loading has been shown to affect cell morphology and structure, phenotype, motility and other biological functions. Cells experience mechanical loads naturally, yet under prolonged or sizable loading, damage and cell death may occur, which motivates research regarding the structural behavior of loaded cells. For example, near the weight-bearing boney prominences of the buttocks of immobile persons, tissues may become highly loaded, eventually leading to massive cell death that manifests as pressure ulcers. Cell-specific computational models have previously been developed by our group, allowing simulations of cell deformations under compressive or stretching loads. These models were obtained by reconstructing specific cell structures from series of 2D fluorescence, confocal image-slices, requiring cell-specific fluorescent-staining protocols and costly (confocal) microscopy equipment. Alternative modeling approaches represent cells simply as half-spheres or half-ellipsoids (i.e. idealized geometries), which neglects the curvature details of the cell surfaces associated with changes in concentrations of strains and stresses. Thus, we introduce here for the first time an optical image-based FE modeling, where loads are simulated on reconstructed 3D geometrical cell models from a single 2D, phase-contrast image. Our novel modeling method eliminates the need for confocal imaging and fluorescent staining preparations (both expensive), and makes cell-specific FE modeling affordable and accessible to the biomechanics community. We demonstrate the utility of this cost-effective modeling method by performing simulations of compression of MSCs embedded in a gel.

  19. 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.

  20. Rainfall-triggered shallow landslides at catchment scale: Threshold mechanics-based modeling for abruptness and localization

    NASA Astrophysics Data System (ADS)

    Ruette, J.; Lehmann, P.; Or, D.

    2013-10-01

    Rainfall-induced shallow landslides may occur abruptly without distinct precursors and could span a wide range of soil mass released during a triggering event. We present a rainfall-induced landslide-triggering model for steep catchments with surfaces represented as an assembly of hydrologically and mechanically interconnected soil columns. The abruptness of failure was captured by defining local strength thresholds for mechanical bonds linking soil and bedrock and adjacent columns, whereby a failure of a single bond may initiate a chain reaction of subsequent failures, culminating in local mass release (a landslide). The catchment-scale hydromechanical landslide-triggering model (CHLT) was applied to results from two event-based landslide inventories triggered by two rainfall events in 2002 and 2005 in two nearby catchments located in the Prealps in Switzerland. Rainfall radar data, surface elevation and vegetation maps, and a soil production model for soil depth distribution were used for hydromechanical modeling of failure patterns for the two rainfall events at spatial and temporal resolutions of 2.5 m and 0.02 h, respectively. The CHLT model enabled systematic evaluation of the effects of soil type, mechanical reinforcement (soil cohesion and lateral root strength), and initial soil water content on landslide characteristics. We compared various landslide metrics and spatial distribution of simulated landslides in subcatchments with observed inventory data. Model parameters were optimized for the short but intense rainfall event in 2002, and the calibrated model was then applied for the 2005 rainfall, yielding reasonable predictions of landslide events and volumes and statistically reproducing localized landslide patterns similar to inventory data. The model provides a means for identifying local hot spots and offers insights into the dynamics of locally resolved landslide hazards in mountainous regions.

  1. Based on Nucleotides Analysis of Tumor Cell Lines to Construct and Validate a Prediction Model of Mechanisms of Chemotherapeutics.

    PubMed

    Liu, Cuichai; Wang, Fang; Liu, Xi; Liu, Min; Liu, Zheng; Sun, Lixin

    2016-01-01

    Cancer is one of the diseases that seriously threaten to human life worldwide. Up to now, chemotherapy remains to be a critical means of cancer treatment, thus the development of chemotherapeutical drugs has become a top priority. An ion pair high performance liquid chromatography (ion pair RP-HPLC) was established for analyzing intracellular nucleotides of tumor cell lines. In this article, a partial least-squares discriminant analysis (PLS-DA) prediction model of mechanisms of chemotherapeutics was established based on four types of drugs with different mechanisms, including antimetabolic agents, antineoplastic agents that affect protein synthesis, agents directly acting on DNA, and RNA interference agents. Then four anti-tumor agents commonly used in clinical were used to validate the availability of the prediction model. Three natural compounds, including 16- dehydropregnenolone (16-DHP), apigenin (API) and diosgenin (DIO), were reported to display anti-tumor effect with unclear mechanisms. The three components were applied to this prediction model firstly. In conclusion, the recognition model was proved to be accurate and feasible to some degree and might become a promising auxiliary method in the process of chemotherapeutic drugs development. PMID:26234361

  2. Articular surface approximation in equivalent spatial parallel mechanism models of the human knee joint: an experiment-based assessment.

    PubMed

    Ottoboni, A; Parenti-Castelli, V; Sancisi, N; Belvedere, C; Leardini, A

    2010-01-01

    In-depth comprehension of human joint function requires complex mathematical models, which are particularly necessary in applications of prosthesis design and surgical planning. Kinematic models of the knee joint, based on one-degree-of-freedom equivalent mechanisms, have been proposed to replicate the passive relative motion between the femur and tibia, i.e., the joint motion in virtually unloaded conditions. In the mechanisms analysed in the present work, some fibres within the anterior and posterior cruciate and medial collateral ligaments were taken as isometric during passive motion, and articulating surfaces as rigid. The shapes of these surfaces were described with increasing anatomical accuracy, i.e. from planar to spherical and general geometry, which consequently led to models with increasing complexity. Quantitative comparison of the results obtained from three models, featuring an increasingly accurate approximation of the articulating surfaces, was performed by using experimental measurements of joint motion and anatomical structure geometries of four lower-limb specimens. Corresponding computer simulations of joint motion were obtained from the different models. The results revealed a good replication of the original experimental motion by all models, although the simulations also showed that a limit exists beyond which description of the knee passive motion does not benefit considerably from further approximation of the articular surfaces.

  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. Modeling mechanisms of cell secretion.

    PubMed

    Tsaneva-Atanasova, Krasimira; Osinga, Hinke M; Tabak, Joël; Pedersen, Morten Gram

    2010-12-01

    Secretion is a fundamental cellular process involving the regulated release of intracellular products from cells. Physiological functions such as neurotransmission, or the release of hormones and digestive enzymes, are all governed by cell secretion. Anomalies in the processes involved in secretion contribute to the development and progression of diseases such as diabetes and other hormonal disorders. To unravel the mechanisms that govern such diseases, it is essential to understand how hormones, growth factors and neurotransmitters are synthesized and processed, and how their signals are recognized, amplified and transmitted by intracellular signaling pathways in the target cells. Here, we discuss diverse aspects of the detailed mechanisms involved in secretion based on mathematical models. The models range from stochastic ones describing the trafficking of secretory vesicles to deterministic ones investigating the regulation of cellular processes that underlie hormonal secretion. In all cases, the models are closely related to experimental results and suggest theoretical predictions for the secretion mechanisms.

  5. Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics.

    PubMed

    Herberg, Maria; Glauche, Ingmar; Zerjatke, Thomas; Winzi, Maria; Buchholz, Frank; Roeder, Ingo

    2016-04-01

    Pluripotent mouse embryonic stem cells (mESCs) show heterogeneous expression levels of transcription factors (TFs) involved in pluripotency regulation, among them Nanog and Rex1. The expression of both TFs can change dynamically between states of high and low activity, correlating with the cells' capacity for self-renewal. Stochastic fluctuations as well as sustained oscillations in gene expression are possible mechanisms to explain this behaviour, but the lack of suitable data hampered their clear distinction. Here, we present a systems biology approach in which novel experimental data on TF heterogeneity is complemented by an agent-based model of mESC self-renewal. Because the model accounts for intracellular interactions, cell divisions and heredity structures, it allows for evaluating the consistency of the proposed mechanisms with data on population growth and on TF dynamics after cell sorting. Our model-based analysis revealed that a bistable, noise-driven network model fulfils the minimal requirements to consistently explain Nanog and Rex1 expression dynamics in heterogeneous and sorted mESC populations. Moreover, we studied the impact of TF-related proliferation capacities on the frequency of state transitions and demonstrate that cellular genealogies can provide insights into the heredity structures of mESCs.

  6. Modelling and simulations of the chemo-mechanical behaviour of leached cement-based materials: Interactions between damage and leaching

    SciTech Connect

    Stora, E.; Bary, B.; Deville, E.; Montarnal, P.

    2010-08-15

    The assessment of the durability of cement-based materials, which could be employed in underground structures for nuclear waste disposal, requires accounting for deterioration factors, such as chemical attacks and damage, and for the interactions between these phenomena. The objective of the present paper consists in investigating the long-term behaviour of cementitious materials by simulating their response to chemical and mechanical solicitations. In a companion paper (Stora et al., submitted to Cem. Concr. Res. 2008), the implementation of a multi-scale homogenization model into an integration platform has allowed for evaluating the evolution of the mineral composition, diffusive and elastic properties inside a concrete material subjected to leaching. To complete this previous work, an orthotropic micromechanical damage model is presently developed and incorporated in this numerical platform to estimate the mechanical and diffusive properties of damaged cement-based materials. Simulations of the chemo-mechanical behaviour of leached cementitious materials are performed with the tool thus obtained and compared with available experiments. The numerical results are insightful about the interactions between damage and chemical deteriorations.

  7. A mechanism-based model for the population pharmacokinetics of free and bound aflibercept in healthy subjects

    PubMed Central

    Thai, Hoai-Thu; Veyrat-Follet, Christine; Vivier, Nicole; Dubruc, Catherine; Sanderink, Gerard; Mentré, France; Comets, Emmanuelle

    2011-01-01

    AIM Aflibercept (VEGF-Trap), a novel anti-angiogenic agent that binds to VEGF, has been investigated for the treatment of cancer. The aim of this study was to develop a mechanism-based pharmacokinetic (PK) model for aflibercept to characterize its binding to VEGF and its PK properties in healthy subjects. METHODS Data from two phase I clinical studies with aflibercept administered as a single intravenous infusion were included in the analysis. Free and bound aflibercept concentration−time data were analysed using a nonlinear mixed-effects modelling approach with MONOLIX 3.1. RESULTS The best structural model involved two compartments for free aflibercept and one for bound aflibercept, with a Michaelis–Menten type binding of free aflibercept to VEGF from the peripheral compartment. The typical estimated clearances for free and bound aflibercept were 0.88 l day−1 and 0.14 l day−1, respectively. The central volume of distribution of free aflibercept was 4.94 l. The maximum binding capacity was 0.99 mg day−1 and the concentration of aflibercept corresponding to half of maximum binding capacity was 2.91 µg ml−1. Interindividual variability of model parameters was moderate, ranging from 13.6% (Vmax) to 49.8% (Q). CONCLUSION The present PK model for aflibercept adequately characterizes the underlying mechanism of disposition of aflibercept and its nonlinear binding to VEGF. PMID:21575034

  8. 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

  9. 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.

  10. 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…

  11. 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

  12. 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.

  13. 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

  14. Modelling of the interaction between chemical and mechanical behaviour of ion exchange resins incorporated into a cement-based matrix

    NASA Astrophysics Data System (ADS)

    Neji, M.; Bary, B.; Burlion, N.; Le Bescop, P.

    2013-07-01

    In this paper, we present a predictive model, based on experimental data, to determine the macroscopic mechanical behavior of a material made up of ion exchange resins solidified into a CEM III cement paste. Some observations have shown that in some cases, a significant macroscopic expansion of this composite material may be expected, due to internal pressures generated in the resin. To build the model, we made the choice to break down the problem in two scale's studies. The first deals with the mechanical behavior of the different heterogeneities of the composite, i.e. the resin and the cement paste. The second upscales the information from the heterogeneities to the Representative Elementary Volume (REV) of the composite. The heterogeneities effects are taken into account in the REV by applying a homogenization method derived from the Eshelby theory combined with an interaction coefficient drawn from the poroelasticity theory. At the first scale, from the second thermodynamic law, a formulation is developed to estimate the resin microscopic swelling. The model response is illustrated on a simple example showing the impact of the calculated internal pressure, on the macroscopic strain.

  15. Microstructure Based Modeling of β Phase Influence on Mechanical Response of Cast AM Series Mg Alloys

    SciTech Connect

    Barker, Erin I.; Choi, Kyoo Sil; Sun, Xin; Deda, Erin; Allison, John; Li, Mei; Forsmark, Joy; Zindel, Jacob; Godlewski, Larry

    2014-09-30

    Magnesium alloys have become popular alternatives to aluminums and steels for the purpose of vehicle light-weighting. However, Mg alloys are hindered from wider application due to limited ductility as well as poor creep and corrosion performance. Understanding the impact of microstructural features on bulk response is key to improving Mg alloys for more widespread use and for moving towards truly predicting modeling capabilities. This study focuses on modeling the intrinsic features, particularly volume fraction and morphology of beta phase present, of cast Mg alloy microstructure and quantifying their impact on bulk performance. Computational results are compared to experimental measurements of cast plates of Mg alloy with varying aluminum content.

  16. 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

  17. 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.

  18. 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.

  19. Formation Mechanism and Characteristics Research of Ball Lightning Based on Vortex Model

    NASA Astrophysics Data System (ADS)

    Li, Zi-Cheng; Yang, Guo-Hua

    2011-05-01

    The strange characteristics of ball lightning are considered as a question hard to explain. In order to solve the problem, in this paper a complete model of plasma vortex is presented for the ball lightning. By ideal MHD equations, through imposing disturbance to plasma column, the possibility of sausage and kink instability of the lightning channel is analyzed from the perspective the minimum potential energy. The conclusion is that the kink instability (m = 1) is most prone to occur. And when instability occurs, because of the difference of the magnetic field in the twisted area, the magnetic pressure makes the trend further and therefore forming the plasma vortex that may eventually turn into ball lightning if the energy of the vortex is large enough. The existence of the vortex makes ball lightning have a short period of time stability. By the proposed model, the ball lightning features that are hard to understand in the past are explained. In this paper, the reason for bead lightning is also explained from the perspective of the sausage instability.

  20. An anisotropic micromechanical-based model for characterizing the magneto-mechanical behavior of NiMnGa alloys

    NASA Astrophysics Data System (ADS)

    Wang, Xingzhe; Li, Fang; Hu, Qiang

    2012-06-01

    As a typical ferromagnetic shape memory alloy (FSMA), NiMnGa alloy at room temperature is a heterogeneous material with martensitic variants and a high magnetic anisotropy property to produce a giant magnetic-induced strain and high frequency response. A theoretical model based on micromechanical and thermodynamic theory is proposed to describe the magneto-mechanical behavior of single-crystal FSMAs during the reorientation process of martensitic variants. It follows the well-established Eshelby equivalent inclusion method and the Mori-Tanaka scheme, and incorporates the influence of the material anisotropy and the variant inclusion morphology on the reorientation of the martensite variants. The modified micromechanical model is further applied to characterize the stress-strain behavior and magnetic-field-induced strain during the martensite variant rearrangement process in a single-crystal NiMnGa rod under applied magnetic field and/or mechanical loading. The simulation results show good agreement with the experimental data. The effects of the material anisotropy and inclusion morphology on the magnetoelastic constitutive behavior of FSMAs are discussed.

  1. 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).

  2. Mechanism-based crystal plasticity modeling of twin boundary migration in nanotwinned face-centered-cubic metals

    NASA Astrophysics Data System (ADS)

    Mirkhani, Hamidreza; Joshi, Shailendra P.

    2014-08-01

    Nanotwinned (nt) metals are an important subset of nanostructured materials because they exhibit impressive strength and ductility. Several recent investigations on nt face-centered-cubic (FCC) metals indicate that their macroscopic responses emerge from complex microscopic mechanisms that are dominated by dislocation-TB interactions. Under applied stimulus, nt microstructures evolve through migration of twin boundaries (TBs) that may have implications on the material strength and stability. This work focuses on modeling TB migration within finite element framework in an explicit manner and studying its effects on the micromechanics of twinned FCC metals under quasi-static loading conditions. The theoretical setting is developed using three-dimensional single crystal plasticity as a basis wherein the plastic slip on the {111}<1bar10> slip systems in an FCC crystal structure is modeled as visco-plastic behavior. Owing to their governing role, twins are modeled as discrete lamellas with full crystallographic anisotropy. To model TB migration, an additional visco-plastic slip-law for twinning partial systems ({111}<112bar>) based on the nucleation and motion of twin partial dislocations is introduced. This size-dependent constitutive law is presumed to prevail in the vicinity of the TB and naturally facilitates TB migration when combined with a twinning condition that is based on the accrual of the necessary shear strain. The constitutive development is implemented within a finite element framework through a User Material (UMAT) facility within ABAQUS/STANDARD®. Detailed micromechanics simulations on model microstructures involving single-grained and polycrystalline topologies are presented.

  3. Mechanical effects in cookoff modeling

    SciTech Connect

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

    1994-07-01

    Complete cookoff modeling of energetic material in confined geometries must couple thermal, chemical and mechanical effects. In the past, modeling has focused on the prediction of the onset of combustion behavior based only on thermal-chemistry effects with little or no regard to the mechanical behavior of the energetic material. In this paper, an analysis tool is outlined which couples thermal, chemical, and mechanical behavior for one-dimensional Geometries comprised of multi-materials. A reactive heat flow code, XCHEM, and a quasistatic mechanics code, SANTOS, have been completely coupled using, a reactive, elastic-plastic constitutive model describing pressurization of the energetic material. This new Thermally Reactive Elastic-plastic explosive code, TREX, was developed to assess the coupling, of mechanics with thermal chemistry making multidimensional cookoff analysis possible. In this study, TREX is applied to confined and unconfined systems. The confined systems simulate One-Dimensional Time to explosion (ODTX) experiments in both spherical and cylindrical configurations. The spherical ODTX system is a 1.27 cm diameter sphere of TATB confined by aluminum exposed to a constant external temperature. The cylindrical ODTX system is an aluminum tube filled with HMX, NC, and inert exposed to a constant temperature bath. Finally. an unconfined system consisting of a hollow steel cylinder filled with a propellant composed of Al, RMX, and NC, representative of a rocket motor, is considered. This model system is subjected to transient internal and external radiative/convective boundary conditions representative of 5 minutes exposure to a fire. The confined systems show significant pressure prior to ignition, and the unconfined system shows extrusion of the propellent suggesting that the energetic material becomes more shock sensitive.

  4. 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. PMID:27236420

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

    PubMed Central

    Kraft, Reuben H.; Mckee, Phillip Justin; Dagro, Amy M.; Grafton, Scott T.

    2012-01-01

    This article presents the integration of brain injury biomechanics and graph theoretical analysis of neuronal connections, or connectomics, to form a neurocomputational model that captures spatiotemporal characteristics of trauma. We relate localized mechanical brain damage predicted from biofidelic finite element simulations of the human head subjected to impact with degradation in the structural connectome for a single individual. The finite element model incorporates various length scales into the full head simulations by including anisotropic constitutive laws informed by diffusion tensor imaging. Coupling between the finite element analysis and network-based tools is established through experimentally-based cellular injury thresholds for white matter regions. Once edges are degraded, graph theoretical measures are computed on the “damaged” network. For a frontal impact, the simulations predict that the temporal and occipital regions undergo the most axonal strain and strain rate at short times (less than 24 hrs), which leads to cellular death initiation, which results in damage that shows dependence on angle of impact and underlying microstructure of brain tissue. The monotonic cellular death relationships predict a spatiotemporal change of structural damage. Interestingly, at 96 hrs post-impact, computations predict no network nodes were completely disconnected from the network, despite significant damage to network edges. At early times () network measures of global and local efficiency were degraded little; however, as time increased to 96 hrs the network properties were significantly reduced. In the future, this computational framework could help inform functional networks from physics-based structural brain biomechanics to obtain not only a biomechanics-based understanding of injury, but also neurophysiological insight. PMID:22915997

  6. 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

  7. 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.

  8. 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…

  9. 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.

    2016-05-01

    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.

  10. A knowledge- and model-based system for automated weaning from mechanical ventilation: technical description and first clinical application.

    PubMed

    Schädler, Dirk; Mersmann, Stefan; Frerichs, Inéz; Elke, Gunnar; Semmel-Griebeler, Thomas; Noll, Oliver; Pulletz, Sven; Zick, Günther; David, Matthias; Heinrichs, Wolfgang; Scholz, Jens; Weiler, Norbert

    2014-10-01

    To describe the principles and the first clinical application of a novel prototype automated weaning system called Evita Weaning System (EWS). EWS allows an automated control of all ventilator settings in pressure controlled and pressure support mode with the aim of decreasing the respiratory load of mechanical ventilation. Respiratory load takes inspired fraction of oxygen, positive end-expiratory pressure, pressure amplitude and spontaneous breathing activity into account. Spontaneous breathing activity is assessed by the number of controlled breaths needed to maintain a predefined respiratory rate. EWS was implemented as a knowledge- and model-based system that autonomously and remotely controlled a mechanical ventilator (Evita 4, Dräger Medical, Lübeck, Germany). In a selected case study (n = 19 patients), ventilator settings chosen by the responsible physician were compared with the settings 10 min after the start of EWS and at the end of the study session. Neither unsafe ventilator settings nor failure of the system occurred. All patients were successfully transferred from controlled ventilation to assisted spontaneous breathing in a mean time of 37 ± 17 min (± SD). Early settings applied by the EWS did not significantly differ from the initial settings, except for the fraction of oxygen in inspired gas. During the later course, EWS significantly modified most of the ventilator settings and reduced the imposed respiratory load. A novel prototype automated weaning system was successfully developed. The first clinical application of EWS revealed that its operation was stable, safe ventilator settings were defined and the respiratory load of mechanical ventilation was decreased.

  11. Origami based mechanical metamaterials.

    PubMed

    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

  12. 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

  13. A Collector Plate Mechanism-Based Classical Intergranular Precipitation Model for Al Alloys Sensitized at Different Temperatures

    NASA Astrophysics Data System (ADS)

    Yi, Gaosong; Derrick, Alexander T.; Zhu, Yakun; Free, Michael L.

    2015-11-01

    The sensitization behavior of Al 5xxx alloys is mainly caused by the formation of Mg-rich precipitates at grain boundaries. In this study, a classical nucleation-growth-coarsening theory for the description of intergranular precipitation is formulated, which adopts a collector plate mechanism, an equivalent average Mg concentration at the grain boundary, and new coarsening mechanisms. Three coarsening mechanisms, the modified Lifshitz-Slyozov-Wagner, the Kirchner mechanism, and a combination of these two mechanisms, are compared. Modeling results reveal that the Kirchner mechanism will breakdown when continuity ( √ {Nπ R2 } ) is close to 1. According to the new model, the coarsening still accounts for a small fraction (only 10 pct) in the final growth rate after aging at 343 K (70 °C) for 40 months, which is confirmed by the precipitate size distribution data. Thickness and continuity results predicted by the new model agree well with the experimental results obtained from scanning transmission electron microscopy images of Al 5083 H131 alloys aged at 343 K (70 °C) for different times. In addition, the new model is also applied to a high-temperature [453 K (180 °C)] situation, where coarsening of precipitates is observed.

  14. Global modelling of secondary organic aerosol from α-pinene oxidation using a parameterization based on a detailed chemical mechanism

    NASA Astrophysics Data System (ADS)

    Ceulemans, Karl; Müller, Jean-Francois; Compernolle, Steven; Stavrakou, Jenny

    2010-05-01

    Monoterpenes are oxidized in the atmosphere by ozone and the hydroxyl and nitrate radicals. The condensable products resulting from these reactions contribute to Secondary Organic Aerosol (SOA). We have developed a detailed α-pinene chemical mechanism BOREAM (Capouet et al. 2008), in which the primary gas phase chemistry is based on quantum-chemical results, structure activity relationships and experimental data. The secondary chemistry of the most important products is treated explicitly, while further chemistry is reduced by the aid of generic species classes. The partitioning between gas phase and SOA is modeled using Pankow's partitioning approach (Pankow 1994), with vapor pressures (Capouet and Müller 2006) and activity coefficients (Compernolle et al. 2009) obtained from group contribution methods. We will discuss the performance of BOREAM through comparison of model predictions for SOA formation with experimental SOA yields for a large number (>150) of photo-oxidation and dark ozonolysis experiments (Ceulemans et al. 2009). Although the BOREAM SOA yields are significantly higher than in several previous box modeling studies, a reasonable agreement is found in comparison with most laboratory measurements. For use in a global model, the detailed BOREAM chemistry is replaced by a parameterized scheme based on the two-product approach (Odum et al. 1996) with parameters obtained through regressions of full model simulations. The reduced scheme accounts for the dependence of SOA yield on the oxidant (ozone, OH or NO3) and the NOx regime. For example, the reaction of alpha-pinene with OH generates a peroxy radical which, upon reaction with either NO or HO2 leads to the formation of two condensable products. The branching ratios and partitioning coefficients are temperature dependent. We inserted the obtained parameterized scheme in the global model IMAGES, where it is used to represent the SOA formation due to the monoterpenes. For aromatics, isoprene and

  15. Quantum mechanical modeling of self-assembly and photoinduced electron transfer in PNA-based artificial living organisms.

    PubMed

    Tamulis, A; Tamulis, V; Graja, A

    2006-04-01

    In order to support the creation of both artificial living organisms in the USA LANL "Protocell Assembly" project and programmable nano-biorobots in the EU "Programmable Artificial Cell Evolution" project, we used quantum mechanical (QM), density functional theory (DFT), the semiempirical PM3 method, and molecular mechanics (MM) software to investigate various complex photosynthetic systems based on peptide nucleic acid (PNA) in a water environment. Quantum mechanical DFT PBEPBE simulations, including electron correlations, confirm that water molecules that surround all the photosynthetic complex of the LANL protoorganism are main constructing factors and stabilize this system consisting of: PNA fragment attached by covalent bond sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule, lipid precursor molecule and fragment of lipid molecules mono layer. The absorption spectrum shift to the red wavelengths in the complex artificial protocell photosynthetic center might be used as the measure of the complexity of this system. The electron pi-pi* transitions in the first and third excited states are from HOMO and HOMO-1 located on the conjugated water molecules and sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the LUMO of the lipid precursor molecule as calculated using the time dependent (TD) PBEPBE/6-31G model. Electron charge tunneling in the first and third excited states should induce metabolic photodissociation of the lipid precursor molecule because of localization of the transferred electron cloud on the head (waste) of the lipid precursor molecule. TD electron correlation PBEPBE/6-31G calculations show that in the different energies of excitation, the charge transfer tunneling is from sensitizer to lipid precursor and cytosine molecules. One should note that in a water solvent, the electron charge transfer pi-pi* transition in the fifth and sixth excited state is from the HOMO and HOMO-1 located on the sensitizer 1,4-bis

  16. 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.

  17. 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.

  18. The Thermal-Mechanical Evolution of the Middle Hsuehshan Range in Taiwan Based on Zircon Thermochronology and Numerical Modeling

    NASA Astrophysics Data System (ADS)

    Shyu, Chase J.; Tan, Eh; Kirstein, Linda A.; Stuart, Finlay M.; Chen, Yue-Gau

    2016-04-01

    The Hsuehshan Range is the second largest mountain belt in Taiwan. Despite extensive previous research, past thermo-mechanical studies of orogenesis in Taiwan have failed to adequately explain the origin of the Hseuhshan Range. In this study we present new zircon fission track and (U-Th)/He ages from the mid Hsuehshan Range (mid-HR). The data is used to provide thermochronological constraints on thermal-mechanical models. These models incorporate a cooling-rate-dependent closure temperature, rather than assuming that this is constant. With imposed constant uplift rate the thermochronological data are best explained if exhumation of the mid-HR started around 5.6 Ma with a rate of 2.0 km/Myr. We further simulate the formation of mid-HR with thermal-mechanical models. The model results suggest that the low strength of lithologies that comprise the Hsuehshan Range has led to homogeneous deformation of the mountain range and that the eastern part of mid-HR was an active deformation zone during the initial stages of orogenesis.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. Wear mechanism based on adhesion

    NASA Technical Reports Server (NTRS)

    Yamamoto, T.; Buckley, D. H.

    1982-01-01

    Various concepts concerning wear mechanisms and deformation behavior observed in the sliding wear track are surveyed. The mechanisms for wear fragment formation is discussed on the basis of adhesion. The wear process under unlubricated sliding conditions is explained in relation to the concept of adhesion at the interface during the sliding process. The mechanism for tearing away the surface layer from the contact area and forming the sliding track contour is explained by assuming the simplified process of material removal based on the adhesion theory.

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

    PubMed

    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

  7. 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

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

    PubMed

    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.

  9. Patient-specific Modeling of Cardiovascular Mechanics

    PubMed Central

    Taylor, C.A.; Figueroa, C.A.

    2015-01-01

    Advances in numerical methods and three-dimensional imaging techniques have enabled the quantification of cardiovascular mechanics in subject-specific anatomic and physiologic models. Patient-specific models are being used to guide cell culture and animal experiments and test hypotheses related to the role of biomechanical factors in vascular diseases. Furthermore, biomechanical models based on noninvasive medical imaging could provide invaluable data on the in vivo service environment where cardiovascular devices are employed and the effect of the devices on physiologic function. Finally, the patient-specific modeling has enabled an entirely new application of cardiovascular mechanics, namely predicting outcomes of alternate therapeutic interventions for individual patients. We will review methods to create anatomic and physiologic models, obtain properties, assign boundary conditions, and solve the equations governing blood flow and vessel wall dynamics. Applications of patient-specific models of cardiovascular mechanics will be presented followed by a discussion of the challenges and opportunities that lie ahead. PMID:19400706

  10. Surface sealing as a modulating mechanism of water content variability: Physically based modeling and field observations at the hillslope scale

    NASA Astrophysics Data System (ADS)

    Sela, S.; Svoray, T.; Assouline, S.

    2011-12-01

    Understanding the mechanisms underlying temporal and spatial water content variability at the hillslope and catchment scales remains a current challenge in hydrology. Currently, only few models are validated against flux measurements within the catchment scale, thus offering reliable information regarding internal catchment processes. In arid and semi-arid areas, these include the formation of surface seal that directly affects infiltration and evaporation fluxes but is often disregarded. At the LTER Lehavim site, in the center of Israel (31020' N, 34045' E), a typical hillslope (0.115 Km2) was chosen offering different aspects and a classic geomorphologic banding. Annual rainfall is 290 mm, the soils are brown lithosols and arid brown loess, prone to soil sealing. The vegetation is characterized by scattered dwarf shrubs (dominant species Sarcopoterium spinosum). An extensive spatial database of soil hydraulic and topographical parameters was measured in the field and interpolated to continuous maps using geostatistical techniques. Hydraulic properties of the seal layer at the soil surface were modeled following Mualem and Assouline (1989). This spatio-temporal database was used to characterize 8240 cells (3X3 m2) serving as an input to a numeric model solving the flow equations to predict soil water content at all temporal scales. Predictions were verified (R2=0.89) by sampling root zone gravimetric water content at 82 random locations within the hillsope, during ten consecutive field campaigns in the 2010-11 rainy season (for a total of 2450 samples). Accounting for surface sealing was found to improve water content predictions. Furthermore, extensive synthetic modeling found the sealed layer to be a highly efficient mechanism reducing temporal water content variability, compared to an unsealed domain (a reduction of 54% in variability at the 0-50 soil depth). It was found that reduced evaporation in the sealed domain compensates for the loss in infiltrated

  11. Mechanical integrity of a carbon nanotube/copper-based through-silicon via for 3D integrated circuits: a multi-scale modeling approach

    NASA Astrophysics Data System (ADS)

    Awad, Ibrahim; Ladani, Leila

    2015-12-01

    Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions.

  12. Mechanical integrity of a carbon nanotube/copper-based through-silicon via for 3D integrated circuits: a multi-scale modeling approach.

    PubMed

    Awad, Ibrahim; Ladani, Leila

    2015-12-01

    Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions.

  13. Mechanical integrity of a carbon nanotube/copper-based through-silicon via for 3D integrated circuits: a multi-scale modeling approach.

    PubMed

    Awad, Ibrahim; Ladani, Leila

    2015-12-01

    Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions. PMID:26559788

  14. 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.

  15. 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.

  16. Development of a new physics-based internal coordinate mechanics force field (ICMFF) and its application to protein loop modeling

    PubMed Central

    Arnautova, Yelena A.; Abagyan, Ruben A.

    2010-01-01

    We report the development of ICMFF, new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε=2) instead of vacuum; (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions; and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the Cα atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the Biased Probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for 4 residues loops, 0.84/0.46 Å for 8 residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable to those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. PMID:21069716

  17. Synergy between scientific advancement and technological innovation, illustrated by a mechanism-based model characterizing sodium-glucose cotransporter-2 inhibition.

    PubMed

    Zhang, Liping; Ng, Chee M; List, James F; Pfister, Marc

    2010-09-01

    Advances in experimental medicine and technological innovation during the past century have brought tremendous progress in modern medicine and generated an ever-increasing amount of data from bench and bedside. The desire to extend scientific knowledge motivates effective data integration. Technological innovation makes this possible, which in turn accelerates the advancement in science. This mutually beneficial interaction is illustrated by the development of an expanded mechanism-based model for understanding a novel mechanism, sodium-glucose cotransporter-2 SGLT2 inhibition for potential treatment of type 2 diabetes mellitus.

  18. 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.

  19. 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. PMID:26509578

  20. Architecture-based multiscale computational modeling of plant cell wall mechanics to examine the hydrogen-bonding hypothesis of cell wall network structure model

    SciTech Connect

    Yi, Hojae; Puri, Virendra M.

    2012-11-01

    A primary plant cell wall network was computationally modeled using the finite element approach to study the hypothesis of hemicellulose (HC) tethering with the cellulose microfibrils (CMFs) as one of the major load-bearing mechanisms of the growing cell wall. A computational primary cell wall network fragment (10 × 10 μm) comprising typical compositions and properties of CMFs and HC was modeled with well-aligned CMFs. The tethering of HC to CMFs is modeled in accordance with the strength of the hydrogen bonding by implementing a specific load-bearing connection (i.e. the joint element). The introduction of the CMF-HC interaction to the computational cell wall network model is a key to the quantitative examination of the mechanical consequences of cell wall structure models, including the tethering HC model. When the cell wall network models with and without joint elements were compared, the hydrogen bond exhibited a significant contribution to the overall stiffness of the cell wall network fragment. When the cell wall network model was stretched 1% in the transverse direction, the tethering of CMF-HC via hydrogen bonds was not strong enough to maintain its integrity. When the cell wall network model was stretched 1% in the longitudinal direction, the tethering provided comparable strength to maintain its integrity. This substantial anisotropy suggests that the HC tethering with hydrogen bonds alone does not manifest sufficient energy to maintain the integrity of the cell wall during its growth (i.e. other mechanisms are present to ensure the cell wall shape).

  1. 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. PMID:26944689

  2. 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.

  3. 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.

  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. PMID:26275487

  5. 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.

  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. Modelling enzyme reaction mechanisms, specificity and catalysis.

    PubMed

    Mulholland, Adrian J

    2005-10-15

    Modern modelling methods can now give uniquely detailed understanding of enzyme-catalyzed reactions, including the analysis of mechanisms and the identification of determinants of specificity and catalytic efficiency. A new field of computational enzymology has emerged that has the potential to contribute significantly to structure-based design and to develop predictive models of drug metabolism and, for example, of the effects of genetic polymorphisms. This review outlines important techniques in this area, including quantum-chemical model studies and combined quantum-mechanics and molecular-mechanics (QM/MM) methods. Some recent applications to enzymes of pharmacological interest are also covered, showing the types of problems that can be tackled and the insight they can give.

  8. Mechanism Study of Pulsus Paradoxus Using Mechanical Models

    PubMed Central

    Yuan, Li-jun; Wang, Zhen; Wang, Kun; Ren, Hua-ri; Yang, Yong; Duan, Yun-you

    2013-01-01

    Pulsus paradoxus is an exaggeration of the normal inspiratory decrease in systolic blood pressure. Despite a century of attempts to explain this sign consensus is still lacking. To solve the controversy and reveal the exact mechanism, we reexamined the characteristic anatomic arrangement of the circulation system in the chest and designed these mechanical models based on related hydromechanic principles. Model 1 was designed to observe the primary influence of respiratory intrathoracic pressure change (RIPC) on systemic and pulmonary venous return systems (SVR and PVR) respectively. Model 2, as an equivalent mechanical model of septal swing, was to study the secondary influence of RIPC on the motion of the interventriclar septum (IVS), which might be the direct cause for pulsus paradoxus. Model 1 demonstrated that the simulated RIPC had different influence on the simulated SVR and PVR. It increased the volume of the simulated right ventricle (SRV) when the internal pressure was kept constant (8.16 cmH2O), while it had the opposite effect on PVR. Model 2 revealed the three major factors determining the respiratory displacement of IVS in normal and different pathophysiological conditions: the magnitude of RIPC, the pressure difference between the two ventricles and the intrapericardial pressure. Our models demonstrate that the different anatomical arrangement of the two venous return systems leads to a different effect of RIPC on right and left ventricles, and thus a pressure gradient across IVS that tends to shift IVS left- and rightwards. When the leftward displacement of IVS reaches a considerable amplitude in some pathologic condition such as cardiac tamponade, the pulsus paradoxus occurs. PMID:23469010

  9. 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

  10. 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.

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

    PubMed Central

    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

    2015-01-01

    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. PMID:26133240

  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. PMID:24824318

  13. 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.

  14. 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,...

  15. PC-based pseudo-model following discrete integral variable structure control of positions in slider-crank mechanisms

    NASA Astrophysics Data System (ADS)

    Chuang, Chin-Wen

    2007-04-01

    This paper proposes a pseudo-model following (PMF) discrete integral variable structure control (DIVSC) scheme to control the position of a slider crank coupled with a pseudo-model (PM) synchronous motor. Applying the Grey modeling method, the reference model and plant are on-line converted to pseudo-reference model and accumulated model, respectively. The advantage is that the least data and memory are used in this modeling procedure. The DIVSC is introduced to guide the model following motion. The integral controller is used to reduce the steady-state error. The switching controller is used to finish the sliding motion. The two existing condition of the discrete sliding mode are introduced in this paper, too. Finally, the position control of the slider crank is used to show the performance of the proposed control scheme. The simulation and experimental results show the robustness and the practicability.

  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

    2016-02-01

    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. 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

    2016-02-01

    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

  18. Markov-Chain Monte Carlo Simulation of Inverse-Halftoning for Error Diffusion based on Statistical Mechanics of the Q-Ising Model

    NASA Astrophysics Data System (ADS)

    Saika, Yohei

    2008-02-01

    On the basis of statistical mechanics of the Q-Ising model we formulate the problem of inverse-halftoning for the halftone image which is obtained by the error diffusion method using the Floyd-Steinburg and two weight kernels. Then using the Markov-Chain Monte Carlo simulation both for a set of the snapshots of the Q-Ising model and a gray-level standard image, we estimate the performance of our method based on the mean square error and the edge structures observed both in the halftone image and reconstructed images, such as the edge length and the gradient of the gray-level. We clarify that our method reconstructs the gray-level image from the halftone image by suppressing the gradient of the gray-level on the edges embedded in the halftone image and by removing a part of the edges if we appropriately set parameters of our model.

  19. 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.

  20. Physiologically Based Pharmacokinetic Modeling for Substitutability Analysis of Venlafaxine Hydrochloride Extended-Release Formulations Using Different Release Mechanisms: Osmotic Pump Versus Openable Matrix.

    PubMed

    Lin, Ho-Pi; Sun, Dajun; Zhang, Xinyuan; Wen, Hong

    2016-10-01

    A Food and Drug Administration-approved generic oral product of venlafaxine hydrochloride (HCl) extended-release (ER) tablets has used a release mechanism based on an openable matrix, which is different from the push-pull osmotic pump system of its reference-listed drug. In an extreme case, a delay in the bursting of the openable matrix may be considered a product failure mode that alters the intended profile of systemic exposure. A physiologically based pharmacokinetic absorption model was established and verified to simulate the pharmacokinetic profiles after a single-dose oral administration of ER venlafaxine HCl tablets based on an osmotic pump or openable matrix design. This model adequately predicted the observed human mean pharmacokinetic metrics with <20% difference between the predicted and observed data. Based on the modeling and simulation results, Cmax and AUCt of the venlafaxine openable matrix tablets were entirely within the bioequivalence acceptance limits (i.e., 80%-125%) when the lag time varied from 0 to 4 h and using drug-release profiles under most dissolution conditions. The results indicated that a bioinequivalence risk is minimal for a delayed onset of drug release from the approved generic venlafaxine HCl ER tablets with an openable matrix design, supporting its substitutability to the reference product. PMID:27449228

  1. Effective Diffusion Coefficient and Controlling Process of P Diffusion in Si Based on the Pair Diffusion Models of Vacancy and Interstitial Mechanisms

    NASA Astrophysics Data System (ADS)

    Yoshida, Masayuki; Morooka, Masami; Takahashi, Manabu; Tomokage, Hajime

    2000-05-01

    Based on the pair diffusion models of vacancy and interstitial (V and I) mechanisms, the V and I components of effective P diffusion coefficient, DP^+,Veff and DP^+,Ieff, and the controlling process of P diffusion in Si are obtained. Assuming that the I mechanism is dominant, not only the I- concentration, CI^-, but also its gradient, d CI^-/d λ , is effective on DP^+,Ieff at high CP^+. DP^+,Ieff is large at d CI^-/d λ <0 and small at d CI^-/d λ >0. P+ and I- are generated by the dissociation of P-I pair. When excess I- thus generated is removed, d CI^-/d λ <0 is obtained. d CI^-/d λ <0 is also obtained by the decrease in quasi self-interstitial formation energy. Several diffusion models simulate the P diffusion profile well under an inert atmosphere. Applying the controlling process to them, the reason why they simulate the P profile well is investigated. Because all of them simulate the P profile well, it is difficult to conclude which model is correct. It is suggested that it is possible to conclude which model is correct from the P profile under oxidation at CP^+s >1× 1020 cm-3 (s: surface).

  2. 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...

  3. 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

  4. 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.

  5. 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'…

  6. A Simplified model of mutually inhibitory sleep-active and wake-active neuronal populations employing a noise-based switching mechanism.

    PubMed

    Patel, Mainak

    2016-04-01

    Infant rats switch randomly between the sleeping and waking states; during early infancy (up to postnatal day 8), sleep and wake bouts are random, brief (with means on the order of several seconds) and exponentially distributed, with the length of a particular bout independent of the length of prior bouts. As the rat ages during this early period, mean sleep and wake bout lengths gradually increase, though sleep and wake bouts remain exponentially distributed. Additionally, sleep and wake bouts are regulated independently of each other - alterations in the development of sleep (wake) bouts has no impact on the regulation wake (sleep) bouts. Sleep and wake bout behavior is associated with the activity of mutually inhibitory sleep-active and wake-active brainstem populations. In this work, I employ a simplified biophysical model of two mutually inhibitory populations consisting of ten integrate-and-fire neurons each and a noise-based switching mechanism. I show that such a noise-based switching mechanism naturally accounts for the experimentally observed features of sleep-wake switching during early infancy - random alternating activity bouts occur as a consequence of noise (provided inhibition is strong relative to excitation), bout durations are exponential (due to a lack of memory within the system), and cross-population inhibition or intrapopulation excitatory coupling provide mechanisms for changing and independently regulated sleep and wake bout means. PMID:26802484

  7. A Simplified model of mutually inhibitory sleep-active and wake-active neuronal populations employing a noise-based switching mechanism.

    PubMed

    Patel, Mainak

    2016-04-01

    Infant rats switch randomly between the sleeping and waking states; during early infancy (up to postnatal day 8), sleep and wake bouts are random, brief (with means on the order of several seconds) and exponentially distributed, with the length of a particular bout independent of the length of prior bouts. As the rat ages during this early period, mean sleep and wake bout lengths gradually increase, though sleep and wake bouts remain exponentially distributed. Additionally, sleep and wake bouts are regulated independently of each other - alterations in the development of sleep (wake) bouts has no impact on the regulation wake (sleep) bouts. Sleep and wake bout behavior is associated with the activity of mutually inhibitory sleep-active and wake-active brainstem populations. In this work, I employ a simplified biophysical model of two mutually inhibitory populations consisting of ten integrate-and-fire neurons each and a noise-based switching mechanism. I show that such a noise-based switching mechanism naturally accounts for the experimentally observed features of sleep-wake switching during early infancy - random alternating activity bouts occur as a consequence of noise (provided inhibition is strong relative to excitation), bout durations are exponential (due to a lack of memory within the system), and cross-population inhibition or intrapopulation excitatory coupling provide mechanisms for changing and independently regulated sleep and wake bout means.

  8. Modeling the binding mechanism of Alzheimer's Aβ1-42 to nicotinic acetylcholine receptors based on similarity with snake α-neurotoxins.

    PubMed

    Maatuk, Noa; Samson, Abraham O

    2013-01-01

    For over a decade, it has been known that amyloid β (Aβ) peptides of Alzheimer's disease bind to the nicotinic α7 acetylcholine receptor (AChR) with picomolar affinity, and that snake α-neurotoxins competitively inhibit this binding. Here we propose a model of the binding mechanism of Aβ peptides to α7-AChR at atomic level. The binding mechanism is based on sequence and structure similarities of Aβ residues with functional residues of snake α-neurotoxins (ATX) in complex with AChR. The binding mechanism involves residue (Aβ)K28 (similar to (ATX)R32) which forms cation/π interactions in the acetylcholine binding site, and residues (Aβ)G29-(Aβ)I32 [GAII] (similar to (ATX)G33-(ATX)I36 [GTII]) which form an intermolecular β-sheet with residues (α7)F189-(α7)E191 of AChR. Through these interactions, we propose that the AChR serves as a chaperone for Aβ conformational changes from α- to β-hairpin. The interactions which block channel opening provide fundamental insight into Aβ neurotoxicity and cognition impairment, that could contribute to pathogenic processes in Alzheimer's disease, thus paving the way for structure based therapies.

  9. 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

  10. 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 Central

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

    2013-01-01

    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. PMID:24384778

  11. 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...

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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. PMID:27017268

  17. 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.

  18. Application of the Johnson-Kendall-Roberts model in AFM-based mechanical measurements on cells and gel.

    PubMed

    Efremov, Yu M; Bagrov, D V; Kirpichnikov, M P; Shaitan, K V

    2015-10-01

    The force-distance curves (FCs) obtained by the atomic force microscope (AFM) with colloid probes contain information about both the viscoelastic properties and adhesion of a sample. Here, we processed both the approach and retraction parts of FCs obtained on polyacrylamide gels (in water or PBS) and Vero cells (in a culture medium). The Johnson-Kendall-Roberts model was applied to the retraction curves to account for the adhesion. The effects of loading rate, holding time and indentation depth on adhesion force and Young's modulus, calculated from approach and retraction curves, were studied. It was shown that both bulk and local interfacial viscoelasticity can affect the observed approach-retraction hysteresis and measured parameters. The addition of 1% bovine serum albumin (BSA) decreased adhesion of the probe to the PAA gel surface, so interfacial viscoelasticity effects were diminished. On the contrary, the adhesiveness of Vero cells increased after BSA addition, indicating the complex nature of the cell-probe interaction.

  19. Thermal, chemical, and mechanical cookoff modeling

    SciTech Connect

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

    1994-08-01

    A Thermally Reactive, Elastic-plastic eXplosive code, TREX, has been developed to analyze coupled thermal, chemical and mechanical effects associated with cookoff simulation of confined or unconfined energetic materials. In confined systems, pressure buildup precedes thermal runaway, and unconfined energetic material expands to relieve high stress. The model was developed based on nucleation, decomposition chemistry, and elastic/plastic mechanical behavior of a material with a distribution of internal defects represented as clusters of spherical inclusions. A local force balance, with mass continuity constraints, forms the basis of the model requiring input of temperature and reacted gas fraction. This constitutive material model has been incorporated into a quasistatic mechanics code SANTOS as a material module which predicts stress history associated with a given strain history. The thermal-chemical solver XCHEM has been coupled to SANTOS to provide temperature and reacted gas fraction. Predicted spatial history variables include temperature, chemical species, solid/gas pressure, solid/gas density, local yield stress, and gas volume fraction. One-Dimensional Time to explosion (ODTX) experiments for TATB and PBX 9404 (HMX and NC) are simulated using global multistep kinetic mechanisms and the reactive elastic-plastic constitutive model. Pressure explosions, rather than thermal runaway, result in modeling slow cookoff experiments of confined conventional energetic materials such as TATB. For PBX 9404, pressure explosions also occur at fast cookoff conditions because of low temperature reactions of nitrocellulose resulting in substantial pressurization. A demonstrative calculation is also presented for reactive heat flow in a hollow, propellant-filled, stainless steel cylinder, representing a rocket motor. This example simulation show

  20. 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.

  1. 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.

  2. 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

  3. Cellobiose as a model system to reveal cellulose dissolution mechanism in acetate-based ionic liquids: Density functional theory study substantiated by NMR spectra.

    PubMed

    Cao, Bobo; Du, Jiuyao; Du, Dongmei; Sun, Haitao; Zhu, Xiao; Fu, Hui

    2016-09-20

    Cellulose dissolution mechanism in acetate-based ionic liquids was systematically studied in Nuclear Magnetic Resonance (NMR) spectra and Density Functional Theory (DFT) methods by using cellobiose and 1-butyl-3-methylimidazolium acetate (BmimAc) as a model system. The solubility of cellulose in ionic liquid increased with temperature increase in the range of 90-140°C. NMR spectra suggested OAc(-) preferred to form stronger hydrogen bonds with hydrogen of hydroxyl in cellulose. Electrostatic potential method was employed to predict the most possible reaction sites and locate the most stable configuration. Atoms in molecules (AIM) theory was used to study the features of bonds at bond critical points and the variations of bond types. Simultaneously, noncovalent interactions were characterized and visualized by employing reduced density gradient analysis combined with Visual Molecular Dynamics (VMD) program. Natural bond orbital (NBO) theory was applied to study the noncovalent nature and characterize the orbital interactions between cellobiose and Bmim[OAc]. PMID:27261759

  4. Cellobiose as a model system to reveal cellulose dissolution mechanism in acetate-based ionic liquids: Density functional theory study substantiated by NMR spectra.

    PubMed

    Cao, Bobo; Du, Jiuyao; Du, Dongmei; Sun, Haitao; Zhu, Xiao; Fu, Hui

    2016-09-20

    Cellulose dissolution mechanism in acetate-based ionic liquids was systematically studied in Nuclear Magnetic Resonance (NMR) spectra and Density Functional Theory (DFT) methods by using cellobiose and 1-butyl-3-methylimidazolium acetate (BmimAc) as a model system. The solubility of cellulose in ionic liquid increased with temperature increase in the range of 90-140°C. NMR spectra suggested OAc(-) preferred to form stronger hydrogen bonds with hydrogen of hydroxyl in cellulose. Electrostatic potential method was employed to predict the most possible reaction sites and locate the most stable configuration. Atoms in molecules (AIM) theory was used to study the features of bonds at bond critical points and the variations of bond types. Simultaneously, noncovalent interactions were characterized and visualized by employing reduced density gradient analysis combined with Visual Molecular Dynamics (VMD) program. Natural bond orbital (NBO) theory was applied to study the noncovalent nature and characterize the orbital interactions between cellobiose and Bmim[OAc].

  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. Characterisation of mixing in the proximal duodenum of the rat during longitudinal contractions and comparison with a fluid mechanical model based on spatiotemporal motility data.

    PubMed

    de Loubens, Clément; Lentle, Roger G; Hulls, Corrin; Janssen, Patrick W M; Love, Richard J; Chambers, J Paul

    2014-01-01

    The understanding of mixing and mass transfers of nutrients and drugs in the small intestine is of prime importance in creating formulations that manipulate absorption and digestibility. We characterised mixing using a dye tracer methodology during spontaneous longitudinal contractions, i.e. pendular activity, in 10 cm segments of living proximal duodenum of the rat maintained ex-vivo. The residence time distribution (RTD) of the tracer was equivalent to that generated by a small number (8) of continuous stirred tank reactors in series. Fluid mechanical modelling, that was based on real sequences of longitudinal contractions, predicted that dispersion should occur mainly in the periphery of the lumen. Comparison with the experimental RTD showed that centriluminal dispersion was accurately simulated whilst peripheral dispersion was underestimated. The results therefore highlighted the potential importance of micro-phenomena such as microfolding of the intestinal mucosa in peripheral mixing. We conclude that macro-scale modeling of intestinal flow is useful in simulating centriluminal mixing, whereas multi-scales strategies must be developed to accurately model mixing and mass transfers at the periphery of the lumen. PMID:24747714

  8. Characterisation of Mixing in the Proximal Duodenum of the Rat during Longitudinal Contractions and Comparison with a Fluid Mechanical Model Based on Spatiotemporal Motility Data

    PubMed Central

    de Loubens, Clément; Lentle, Roger G.; Hulls, Corrin; Janssen, Patrick W. M.; Love, Richard J.; Chambers, J. Paul

    2014-01-01

    The understanding of mixing and mass transfers of nutrients and drugs in the small intestine is of prime importance in creating formulations that manipulate absorption and digestibility. We characterised mixing using a dye tracer methodology during spontaneous longitudinal contractions, i.e. pendular activity, in 10 cm segments of living proximal duodenum of the rat maintained ex-vivo. The residence time distribution (RTD) of the tracer was equivalent to that generated by a small number (8) of continuous stirred tank reactors in series. Fluid mechanical modelling, that was based on real sequences of longitudinal contractions, predicted that dispersion should occur mainly in the periphery of the lumen. Comparison with the experimental RTD showed that centriluminal dispersion was accurately simulated whilst peripheral dispersion was underestimated. The results therefore highlighted the potential importance of micro-phenomena such as microfolding of the intestinal mucosa in peripheral mixing. We conclude that macro-scale modeling of intestinal flow is useful in simulating centriluminal mixing, whereas multi-scales strategies must be developed to accurately model mixing and mass transfers at the periphery of the lumen. PMID:24747714

  9. Methods for modeling contact dynamics of capture mechanisms

    NASA Technical Reports Server (NTRS)

    Williams, Philip J.; Tobbe, Patrick A.; Glaese, John

    1991-01-01

    In this paper, an analytical approach for studying the contact dynamics of space-based vehicles during docking/berthing maneuvers is presented. Methods for modeling physical contact between docking/berthing mechanisms, examples of how these models have been used to evaluate the dynamic behavior of automated capture mechanisms, and experimental verification of predicted results are shown.

  10. Mechanisms and Geochemical Models of Core Formation

    NASA Astrophysics Data System (ADS)

    David Rubie; Seth Andrew Jacobson

    2016-03-01

    The formation of the Earth's core is a consequence of planetary accretion and processes in the Earth's interior. The mechanical process of planetary differentiation is likely to occur in large, if not global, magma oceans created by the collisions of planetary embryos. Metal-silicate segregation in magma oceans occurs rapidly and efficiently unlike grain scale percolation according to laboratory experiments and calculations. Geochemical models of the core formation process as planetary accretion proceeds are becoming increasingly realistic. Single stage and continuous core formation models have evolved into multi-stage models that are couple to the output of dynamical models of the giant impact phase of planet formation. The models that are most successful in matching the chemical composition of the Earth's mantle, based on experimentally-derived element partition coefficients, show that the temperature and pressure of metal-silicate equilibration must increase as a function of time and mass accreted and so must the oxygen fugacity of the equilibrating material. The latter can occur if silicon partitions into the core and through the late delivery of oxidized material. Coupled dynamical accretion and multi-stage core formation models predict the evolving mantle and core compositions of all the terrestrial planets simultaneously and also place strong constraints on the bulk compositions and oxidation states of primitive bodies in the protoplanetary disk.

  11. Modelling a Simple Mechanical System.

    ERIC Educational Resources Information Center

    Morland, Tim

    1999-01-01

    Provides an example of the modeling power of Mathematics, demonstrated in a piece of A-Level student coursework which was undertaken as part of the MEI Structured Mathematics scheme. A system of two masses and two springs oscillating in one dimension is found to be accurately modeled by a system of linear differential equations. (Author/ASK)

  12. Mechanism-based QSAR Models for the Toxicity of Quorum Sensing Inhibitors to Gram-negative and Gram-positive Bacteria.

    PubMed

    Wang, Dali; Lin, Zhifen; Huo, Zhengyang; Wang, Ting; Yao, Zhifeng; Cong, Yongping

    2016-07-01

    Quorum sensing inhibitors (QSIs) are a promising alternative to the antibiotics and unlikely to induce drug resistance. However, toxicity studies on the QSIs remain limited; therefore in this paper we investigated the acute (15 min) and chronic (24 h) toxicity of some potential QSIs on both gram-negative (V. fischeri) and gram-positive bacteria (B. subtilis). It was found that the toxicity of the QSIs differed with the toxicity test periods. QSAR models were developed for both the acute and chronic toxicity, using the interaction energies between QSIs and the relevant proteins, and the frontier orbital energies. Based on the QSAR models, it was suggested that QSIs primarily bind with the luciferase at 15 min, but LuxR at 24 h in V. fischeri; whereas in B. subtilis, the QSIs mainly bind with LuxS. Our study provided an insight into the toxicity mechanism for QSIs during different exposure periods. PMID:27084097

  13. Simulation Model Based on Non-Newtonian Fluid Mechanics Applied to the Evaluation of the Embolic Effect of Emulsions of Iodized Oil and Anticancer Drug

    SciTech Connect

    Demachi, Hiroshi; Matsui, Osamu; Abo, Hitoshi; Tatsu, Hiroki

    2000-07-15

    Purpose: To verify the difference in embolic effect between oil-in-water (O-W) and water-in-oil (W-O) emulsions composed of iodized oil and an anticancer drug, epirubicin, using a simulation model based on non-Newtonian fluid mechanics.Methods: Flow curves of pure iodized oil and two types of O-W and W-O emulsions immediately and 1 hr after preparation were examined with a viscometer. Using the yield stress data obtained, we simulated the stagnation of each fluid with steady flow in a rigid tube.Results: The W-O emulsions were observed to stagnate in the thin tube at a low pressure gradient. However, the embolic effect of the W-O emulsions decreased 1 hr after preparation. The O-W emulsions were stable and did not stagnate under the conditions in which the W-O emulsions stagnated.Conclusion: The simulation model showed that the embolic effect of the W-O emulsions was superior to that of the O-W emulsions.

  14. Study of laser-plasma interaction using a physics-based model for understanding the physical mechanism of double-pulse effect in nanosecond laser ablation

    SciTech Connect

    Wu Benxin; Zhou Yun; Forsman, Andrew

    2009-12-21

    This paper studies the double-pulse effect in high-intensity ({>=}{approx}GW/cm{sup 2}) nanosecond (ns) laser ablation, which refers to the significant material removal rate enhancement for ablation by two ns laser pulses (often separated by a delay time of {approx}10 to 100 ns). The early-stage interaction of the second laser pulse with the plasma plume created by the first pulse is very important for understanding the physical mechanism of the double pulse effect. However, the plasma properties in the early stage (during a laser pulse or within 20 to 30 ns after the completion of the pulse) are very difficult to measure experimentally. In this letter, a physics-based predictive model is used as the investigation tool, which was previously verified based on experiments on plasma properties in the late stage, which are relatively easy to measure. The study shows that the second laser pulse does not directly strike the target condensed phase. Instead, it mainly interacts with the plasma plume created by the first laser pulse, heats and accelerates the ablated material in the plume lingering above the target surface.

  15. 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.

  16. 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. PMID:27199835

  17. 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

  18. Multi-layer composite mechanical modeling for the inhomogeneous biofilm mechanical behavior.

    PubMed

    Wang, Xiaoling; Han, Jingshi; Li, Kui; Wang, Guoqing; Hao, Mudong

    2016-08-01

    Experiments showed that bacterial biofilms are heterogeneous, for example, the density, the diffusion coefficient, and mechanical properties of the biofilm are different along the biofilm thickness. In this paper, we establish a multi-layer composite model to describe the biofilm mechanical inhomogeneity based on unified multiple-component cellular automaton (UMCCA) model. By using our model, we develop finite element simulation procedure for biofilm tension experiment. The failure limit and biofilm extension displacement obtained from our model agree well with experimental measurements. This method provides an alternative theory to study the mechanical inhomogeneity in biological materials. PMID:27122202

  19. Viscoelastic mechanical behavior of soft microcantilever-based force sensors

    NASA Astrophysics Data System (ADS)

    Lin, I.-Kuan; Liao, Yen-Ming; Liu, Yan; Ou, Kuang-Shun; Chen, Kuo-Shen; Zhang, Xin

    2008-12-01

    Polydimethylsiloxane (PDMS) microcantilevers have been used as force sensors for studying cellular mechanics by converting their displacements to cellular mechanical forces. However, PDMS is an inherently viscoelastic material and its elastic modulus changes with loading rates and elapsed time. Therefore, the traditional approach to calculating cellular mechanical forces based on elastic mechanics can result in errors. This letter reports a more in-depth method for viscoelastic characterization, modeling, and analysis associated with the bending behavior of the PDMS microcantilevers. A viscoelastic force conversion model was developed and validated by proof-of-principle bending tests.

  20. Computational Models for Mechanics of Morphogenesis

    PubMed Central

    Wyczalkowski, Matthew A.; Chen, Zi; Filas, Benjamen A.; Varner, Victor D.; Taber, Larry A.

    2012-01-01

    In the developing embryo, tissues differentiate, deform, and move in an orchestrated manner to generate various biological shapes driven by the complex interplay between genetic, epigenetic, and environmental factors. Mechanics plays a key role in regulating and controlling morphogenesis, and quantitative models help us understand how various mechanical forces combine to shape the embryo. Models allow for the quantitative, unbiased testing of physical mechanisms, and when used appropriately, can motivate new experimental directions. This knowledge benefits biomedical researchers who aim to prevent and treat congenital malformations, as well as engineers working to create replacement tissues in the laboratory. In this review, we first give an overview of fundamental mechanical theories for morphogenesis, and then focus on models for specific processes, including pattern formation, gastrulation, neurulation, organogenesis, and wound healing. The role of mechanical feedback in development is also discussed. Finally, some perspectives are given on the emerging challenges in morphomechanics and mechanobiology. PMID:22692887

  1. Mechanical bidomain model of cardiac tissue

    NASA Astrophysics Data System (ADS)

    Puwal, Steffan; Roth, Bradley J.

    2010-10-01

    Intracellular and extracellular spaces are separately considered in an electrical bidomain model of tissue. We propose a mechanical bidomain model separately considering the intracellular and extracellular spaces, coupled through a linear restoring force proportional to the displacement difference of the two spaces. We consider a mechanically passive model of heart fibers (no tension) with an action potential, and an electrically passive model (no action potential) in tissue with an ischemic boundary. We find the pressure and displacement fields arising from our consideration of a bidomain instead of a monodomain and note interesting characteristics evident only with a bidomain approach.

  2. Mathematical models of regulatory mechanisms of sleep-wake rhythms.

    PubMed

    Nakao, M; Karashima, A; Katayama, N

    2007-05-01

    Studies of regulatory mechanisms of sleep-wake rhythms have benefited greatly from mathematical modeling. There are two major frameworks of modeling: one integrates homeostatic and circadian regulations and the other consists of multiple interacting oscillators. In this article, model constructions based on these respective frameworks and their characteristics are reviewed. The two-process model and the multioscillator model are explained in detail. An appropriate mathematical abstraction is also shown to provide a viewpoint unifying the model structures, which might seem to be distinct. Recently acquired knowledge of neural regulatory mechanisms of sleep-wake rhythm has prompted modeling at the neural network level. Such a detailed model is also reviewed, and could be used to explore a possible neural mechanism underlying a pathological state of sleep-wake rhythm. PMID:17364138

  3. 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

  4. Finite element modeling of retinal prosthesis mechanics

    NASA Astrophysics Data System (ADS)

    Basinger, B. C.; Rowley, A. P.; Chen, K.; Humayun, M. S.; Weiland, J. D.

    2009-10-01

    Epiretinal prostheses used to treat degenerative retina diseases apply stimulus via an electrode array fixed to the ganglion cell side of the retina. Mechanical pressure applied by these arrays to the retina, both during initial insertion and throughout chronic use, could cause sufficient retinal damage to reduce the device's effectiveness. In order to understand and minimize potential mechanical damage, we have used finite element analysis to model mechanical interactions between an electrode array and the retina in both acute and chronic loading configurations. Modeling indicates that an acute tacking force distributes stress primarily underneath the tack site and heel edge of the array, while more moderate chronic stresses are distributed more evenly underneath the array. Retinal damage in a canine model chronically implanted with a similar array occurred in correlating locations, and model predictions correlate well with benchtop eyewall compression tests. This model provides retinal prosthesis researchers with a tool to optimize the mechanical electrode array design, but the techniques used here represent a unique effort to combine a modifiable device and soft biological tissues in the same model and those techniques could be extended to other devices that come into mechanical contact with soft neural tissues.

  5. 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

  6. 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.

  7. A method for modeling contact dynamics for automated capture mechanisms

    NASA Technical Reports Server (NTRS)

    Williams, Philip J.

    1991-01-01

    Logicon Control Dynamics develops contact dynamics models for space-based docking and berthing vehicles. The models compute contact forces for the physical contact between mating capture mechanism surfaces. Realistic simulation requires proportionality constants, for calculating contact forces, to approximate surface stiffness of contacting bodies. Proportionality for rigid metallic bodies becomes quite large. Small penetrations of surface boundaries can produce large contact forces.

  8. Control mechanisms for a nonlinear model of international relations

    SciTech Connect

    Pentek, A.; Kadtke, J.; Lenhart, S.; Protopopescu, V.

    1997-07-15

    Some issues of control in complex dynamical systems are considered. The authors discuss two control mechanisms, namely: a short range, reactive control based on the chaos control idea and a long-term strategic control based on an optimal control algorithm. They apply these control ideas to simple examples in a discrete nonlinear model of a multi-nation arms race.

  9. 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.

  10. 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

  11. 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

  12. Mechanical model of the recovery from stumbling.

    PubMed

    Cordero, A Forner; Koopman, H J F M; van der Helm, F C T

    2004-10-01

    Several strategies have been described as a reaction to a stumble during gait. The elevating strategy, which tries to proceed with the perturbed step, was executed as a response to a perturbation during early swing. The lowering strategy, bringing the perturbed leg to the ground and overtaking the obstacle with the contralateral limb, was executed more frequently when the perturbation appeared at mid or late swing. The goal of this paper is to analyze which mechanical factors determine the most advantageous strategy. In order to determine these factors, a mechanical model of the recovery was developed and used to analyze a series of perturbation experiments. It was assumed that the goal of the recovery reaction was to control the trunk as an inverted pendulum during the double-stance phase. In order to be able to control the trunk angle, one foot should be up front and one foot should be behind the hips; otherwise it would be impossible to generate the required trunk torques. The trunk dynamics were expressed in terms of the ground reaction forces and their application point. A larger step (elevation strategy) gives the opportunity to dissolve the perturbation in one step. A small step (lowering strategy) necessarily results in a second quick step, after which the perturbation energy can be dissipated in the second double-stance phase. If a recovery step is too slow, it becomes impossible to counteract the forward flexion of the trunk. It is suggested that a measure of the ability to recover from a stumble could be based on the ability to perform quick steps. PMID:15378375

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Alberta's Performance-Based Funding Mechanism.

    ERIC Educational Resources Information Center

    Barnetson, Bob

    This paper provides an overview of the performance indicator-based accountability and funding mechanism implemented in the higher education system of Alberta, Canada. The paper defines the terms accountability and regulation, examines the use of performance indicators to demonstrate accountability, and explains how performance indicator-based…

  19. Modelling approaches for evaluating multiscale tendon mechanics.

    PubMed

    Fang, Fei; Lake, Spencer P

    2016-02-01

    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.

  20. 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.

  1. Reliability mechanisms in distributed data base systems

    SciTech Connect

    Son, S.H.

    1986-01-01

    Distributed database systems operate in computer networking environments where component failures are inevitable during normal operation. Failures not only threaten normal operation of the system, but they may destroy the correctness of the data base by direct damage to the storage subsystem. In order to cope with these failures, distributed data base systems must provide reliability mechanisms that maintain the system consistency. There are two major parts in this dissertation. In the first part, mechanisms are presented for recovery management in distributed data base system. The recovery management of a distributed data bases system consists of two parts: the preparation for the recovery by saving necessary information during normal operation of the data base system, and the coordination of the actual recovery in order to avoid the possible inconsistency after the recovery. The preparation for the recovery is done through the checkpointing and logging. A new scheme is proposed for reconstruction of the data base in distributed environments. In the second part, a token-based resiliency control scheme for replicated distributed data base systems. The proposed control scheme increases the reliability as well as the degree of concurrency while maintaining the consistency of the system.

  2. Biaxial mechanical modeling of the small intestine.

    PubMed

    Bellini, Chiara; Glass, Paul; Sitti, Metin; Di Martino, Elena S

    2011-11-01

    Capsule endoscopes are pill-size devices provided with a camera that capture images of the small intestine from inside the body after being ingested by a patient. The interaction between intestinal tissue and capsule endoscopes needs to be investigated to optimize capsule design while preventing tissue damage. To that purpose, a constitutive model that can reliably predict the mechanical response of the intestinal tissue under complex mechanical loading is required. This paper describes the development and numerical validation of a phenomenological constitutive model for the porcine duodenum, jejunum and ileum. Parameters characterizing the mechanical behavior of the material were estimated from planar biaxial test data, where intestinal tissue specimens were simultaneously loaded along the circumferential and longitudinal directions. Specimen-specific Fung constitutive models were able to accurately predict the planar stress-strain behavior of the tested samples under a wide range of loading conditions. To increase model generality, average anisotropic constitutive relationships were also generated for each tissue region by fitting average stress-strain curves to the Fung potential. Due to the observed variability in the direction of maximum stiffness, the average Fung models were less anisotropic than the specimen-specific models. Hence, average isotropic models in the Neo-Hookean and Mooney-Rivlin forms were attempted, but they could not adequately describe the degree of nonlinearity in the tissue. Values of the R2 for the nonlinear regressions were 0.17, 0.44 and 0.93 for the average Neo-Hookean, Mooney-Rivlin and Fung models, respectively. Average models were successfully implemented into FORTRAN routines and used to simulate capsule deployment with a finite element method analysis. PMID:22098873

  3. A fast quantum mechanics based contour extraction algorithm

    NASA Astrophysics Data System (ADS)

    Lan, Tian; Sun, Yangguang; Ding, Mingyue

    2009-02-01

    A fast algorithm was proposed to decrease the computational cost of the contour extraction approach based on quantum mechanics. The contour extraction approach based on quantum mechanics is a novel method proposed recently by us, which will be presented on the same conference by another paper of us titled "a statistical approach to contour extraction based on quantum mechanics". In our approach, contour extraction was modeled as the locus of a moving particle described by quantum mechanics, which is obtained by the most probable locus of the particle simulated in a large number of iterations. In quantum mechanics, the probability that a particle appears at a point is equivalent to the square amplitude of the wave function. Furthermore, the expression of the wave function can be derived from digital images, making the probability of the locus of a particle available. We employed the Markov Chain Monte Carlo (MCMC) method to estimate the square amplitude of the wave function. Finally, our fast quantum mechanics based contour extraction algorithm (referred as our fast algorithm hereafter) was evaluated by a number of different images including synthetic and medical images. It was demonstrated that our fast algorithm can achieve significant improvements in accuracy and robustness compared with the well-known state-of-the-art contour extraction techniques and dramatic reduction of time complexity compared to the statistical approach to contour extraction based on quantum mechanics.

  4. Modelling of volatility in monetary transmission mechanism

    SciTech Connect

    Dobešová, Anna; Klepáč, Václav; Kolman, Pavel; Bednářová, Petra

    2015-03-10

    The aim of this paper is to compare different approaches to modeling of volatility in monetary transmission mechanism. For this purpose we built time-varying parameter VAR (TVP-VAR) model with stochastic volatility and VAR-DCC-GARCH model with conditional variance. The data from three European countries are included in the analysis: the Czech Republic, Germany and Slovakia. Results show that VAR-DCC-GARCH system captures higher volatility of observed variables but main trends and detected breaks are generally identical in both approaches.

  5. A new mechanism for regional atmospheric chemistry modeling

    NASA Astrophysics Data System (ADS)

    Stockwell, William R.; Kirchner, Frank; Kuhn, Michael; Seefeld, Stephan

    1997-11-01

    A new gas-phase chemical mechanism for the modeling of regional atmospheric chemistry, the "Regional Atmospheric Chemistry Mechanism" (RACM) is presented. The mechanism is intended to be valid for remote to polluted conditions and from the Earth's surface through the upper troposphere. The RACM mechanism is based upon the earlier Regional Acid Deposition Model, version 2 (RADM2) mechanism [Stockwell et al., 1990] and the more detailed Euro-RADM mechanism [Stockwell and Kley, 1994]. The RACM mechanism includes rate constants and product yields from the most recent laboratory measurements, and it has been tested against environmental chamber data. A new condensed reaction mechanism is included for biogenic compounds: isoprene, α-pinene, and d-limonene. The branching ratios for alkane decay were reevaluated, and in the revised mechanism the aldehyde to ketone ratios were significantly reduced. The relatively large amounts of nitrates resulting from the reactions of unbranched alkenes with NO3 are now included, and the production of HO from the ozonolysis of alkenes has a much greater yield. The aromatic chemistry has been revised through the use of new laboratory data. The yield of cresol production from aromatics was reduced, while the reactions of HO, NO3, and O3 with unsaturated dicarbonyl species and unsaturated peroxynitrate are now included in the RACM mechanism. The peroxyacetyl nitrate chemistry and the organic peroxy radical-peroxy radical reactions were revised, and organic peroxy radical +NO3 reactions were added.

  6. 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

  7. Systematic comparison of model polymer nanocomposite mechanics.

    PubMed

    Xiao, Senbo; Peter, Christine; Kremer, Kurt

    2016-01-01

    Polymer nanocomposites render a range of outstanding materials from natural products such as silk, sea shells and bones, to synthesized nanoclay or carbon nanotube reinforced polymer systems. In contrast to the fast expanding interest in this type of material, the fundamental mechanisms of their mixing, phase behavior and reinforcement, especially for higher nanoparticle content as relevant for bio-inorganic composites, are still not fully understood. Although polymer nanocomposites exhibit diverse morphologies, qualitatively their mechanical properties are believed to be governed by a few parameters, namely their internal polymer network topology, nanoparticle volume fraction, particle surface properties and so on. Relating material mechanics to such elementary parameters is the purpose of this work. By taking a coarse-grained molecular modeling approach, we study an range of different polymer nanocomposites. We vary polymer nanoparticle connectivity, surface geometry and volume fraction to systematically study rheological/mechanical properties. Our models cover different materials, and reproduce key characteristics of real nanocomposites, such as phase separation, mechanical reinforcement. The results shed light on establishing elementary structure, property and function relationship of polymer nanocomposites. PMID:27623170

  8. A contact mechanics based model for partially-closed randomly distributed surface microcracks and their effect on acoustic nonlinearity in Rayleigh surface waves

    NASA Astrophysics Data System (ADS)

    Oberhardt, Tobias; Kim, Jin-Yeon; Qu, Jianmin; Jacobs, Laurence J.

    2016-02-01

    This research investigates the modeling of randomly distributed surface-breaking microcracks and the dependency of higher harmonic generation in Rayleigh surface waves on microcrack density. The microcrack model is based on micromechanical considerations of rough surface contact. An effective stress-strain relationship is derived to describe the nonlinear behavior of a single microcrack and implemented into a finite-element model via a hyperelastic constitutive law. Finite-element simulations of nonlinear wave propagation in a solid with distributed surface microcracks are performed for a range of microcrack densities. The evolution of fundamental and second harmonic amplitudes along the propagation distance is studied and the acoustic nonlinearity parameter is calculated. The results show that the nonlinearity parameter increases with crack density. While, for small crack densities (dilute concentration of microcracks) a proportionality between crack density and acoustic nonlinearity is observed, this is not valid for higher crack densities, as the microcracks start to interact.

  9. Quantum mechanical Hamiltonian models of discrete processes

    SciTech Connect

    Benioff, P.

    1981-03-01

    Here the results of other work on quantum mechanical Hamiltonian models of Turing machines are extended to include any discrete process T on a countably infinite set A. The models are constructed here by use of scattering phase shifts from successive scatterers to turn on successive step interactions. Also a locality requirement is imposed. The construction is done by first associating with each process T a model quantum system M with associated Hilbert space H/sub M/ and step operator U/sub T/. Since U/sub T/ is not unitary in general, M, H/sub M/, and U/sub T/ are extended into a (continuous time) Hamiltonian model on a larger space which satisfies the locality requirement. The construction is compared with the minimal unitary dilation of U/sub T/. It is seen that the model constructed here is larger than the minimal one. However, the minimal one does not satisfy the locality requirement.

  10. The heat dissipation model and desensitizing mechanism of the HMX/additive interfaces: a theoretical investigation based on linear response theory

    NASA Astrophysics Data System (ADS)

    Long, Yao; Chen, Jun

    2013-07-01

    Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) is a high-energy explosive with high sensitivity. The heat dissipation of the HMX/additive interface is a key issue in understanding the hot spot formation and desensitizing mechanism of mixture explosive. In this work, we derive new formulae to calculate the heat dissipation rate for a set of HMX/additive interfaces, and build a physical model to describe the energy dissipation time and distance in mixture explosive. Four kinds of additives are considered: 1,3,5-triamino-2,4,6-trinitrobenzene, graphite, paraffin and fluoropolymers. At low strength loading, we prove that the heat dissipation rate is proportional to the square of frequency, and suggest a way to decrease the sensitivity of the explosive. At medium strength loading, the viscosity coefficient and friction coefficient of interface are calculated. The desensitizing abilities of additives to HMX are discussed systematically.

  11. 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.

  12. cyp51A-based mechanism of azole resistance in Aspergillus fumigatus: Illustration by a new 3D Structural Model of Aspergillus fumigatus CYP51A protein.

    PubMed

    Liu, Musang; Zheng, Nan; Li, Dongmei; Zheng, Hailin; Zhang, Lili; Ge, Hu; Liu, Weida

    2016-05-01

    Mutations of CYP51A protein (Cytochrome P450 14-α Sterol demethylase) play a central role in the azole resistance of Aspergillus fumigatus The available structural models of CYP51A protein ofA. fumigatus are built based on that of Homo sapiens and that of Mycobacterium tuberculosis, of which the amino acid homology is only 38% and 29% compared with CYP51A protein ofA. fumigatus, respectively. In the present study, we constructed a new 3D structural model ofA. fumigatus CYP51A protein based on a recently resolved crystal structure of the homologous protein in the fungus S. cerevisiae, which shares 50% amino acid homology with A. fumigatus CYP51A protein. Three azole molecules, itraconazole, voriconazole, and posaconazole, were docked to the wild-type and the mutant A. fumigatus CYP51A protein models, respectively, to illustrate the impact of cyp51A mutations to azole-resistance. We found the mutations that occurred at L98, M220, and Y431 positions would decrease the binding affinity of azoles to the CYP51A protein and therefore would reduce their inhibitory effects. Additionally, the mutations of L98 and G432 would reduce the stability of the protein, which might lead to conformational change of its binding pocket and eventually the resistance to azoles.

  13. 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…

  14. Material modeling of biofilm mechanical properties.

    PubMed

    Laspidou, C S; Spyrou, L A; Aravas, N; Rittmann, B E

    2014-05-01

    A biofilm material model and a procedure for numerical integration are developed in this article. They enable calculation of a composite Young's modulus that varies in the biofilm and evolves with deformation. The biofilm-material model makes it possible to introduce a modeling example, produced by the Unified Multi-Component Cellular Automaton model, into the general-purpose finite-element code ABAQUS. Compressive, tensile, and shear loads are imposed, and the way the biofilm mechanical properties evolve is assessed. Results show that the local values of Young's modulus increase under compressive loading, since compression results in the voids "closing," thus making the material stiffer. For the opposite reason, biofilm stiffness decreases when tensile loads are imposed. Furthermore, the biofilm is more compliant in shear than in compression or tension due to the how the elastic shear modulus relates to Young's modulus. PMID:24560820

  15. Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism

    PubMed Central

    Campennì, Marco

    2016-01-01

    Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-based models of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by agents adopting symmetry-based reciprocity showed differentiated “social relationships” and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to stand competition from alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry-based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions. PMID:26998412

  16. Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism.

    PubMed

    Campennì, Marco; Schino, Gabriele

    2016-01-01

    Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-based models of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by agents adopting symmetry-based reciprocity showed differentiated "social relationships" and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to stand competition from alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry-based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions.

  17. Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism.

    PubMed

    Campennì, Marco; Schino, Gabriele

    2016-01-01

    Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-based models of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by agents adopting symmetry-based reciprocity showed differentiated "social relationships" and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to stand competition from alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry-based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions. PMID:26998412

  18. A fuzzy logic controller based approach to model the switching mechanism of the mammalian central carbon metabolic pathway in normal and cancer cells.

    PubMed

    Dasgupta, Abhijit; Paul, Debjyoti; De, Rajat K

    2016-07-19

    Dynamics of large nonlinear complex systems, like metabolic networks, depend on several parameters. A metabolic pathway may switch to another pathway in accordance with the current state of parameters in both normal and cancer cells. Here, most of the parameter values are unknown to us. A fuzzy logic controller (FLC) has been developed here for the purpose of modeling metabolic networks by approximating the reasons for the behaviour of a system and applying expert knowledge to track switching between metabolic pathways. The simulation results can track the switching between glycolysis and gluconeogenesis, as well as glycolysis and pentose phosphate pathways (PPP) in normal cells. Unlike normal cells, pyruvate kinase (M2 isoform) (PKM2) switches alternatively between its two oligomeric forms, i.e. an active tetramer and a relatively low activity dimer, in cancer cells. Besides, there is a coordination among PKM2 switching and enzymes catalyzing PPP. These phenomena help cancer cells to maintain their high energy demand and macromolecular synthesis. However, the reduction of initial adenosine triphosphate (ATP) to a very low concentration, decreasing initial glucose uptake, destroying coordination between glycolysis and PPP, and replacement of PKM2 by its relatively inactive oligomeric form (dimer) or inhibition of the translation of PKM2 may destabilize the mutated control mechanism of the mammalian central carbon metabolic (CCM) pathway in cancer cells. The performance of the model is compared appropriately with some existing ones. PMID:27225801

  19. A fuzzy logic controller based approach to model the switching mechanism of the mammalian central carbon metabolic pathway in normal and cancer cells.

    PubMed

    Dasgupta, Abhijit; Paul, Debjyoti; De, Rajat K

    2016-07-19

    Dynamics of large nonlinear complex systems, like metabolic networks, depend on several parameters. A metabolic pathway may switch to another pathway in accordance with the current state of parameters in both normal and cancer cells. Here, most of the parameter values are unknown to us. A fuzzy logic controller (FLC) has been developed here for the purpose of modeling metabolic networks by approximating the reasons for the behaviour of a system and applying expert knowledge to track switching between metabolic pathways. The simulation results can track the switching between glycolysis and gluconeogenesis, as well as glycolysis and pentose phosphate pathways (PPP) in normal cells. Unlike normal cells, pyruvate kinase (M2 isoform) (PKM2) switches alternatively between its two oligomeric forms, i.e. an active tetramer and a relatively low activity dimer, in cancer cells. Besides, there is a coordination among PKM2 switching and enzymes catalyzing PPP. These phenomena help cancer cells to maintain their high energy demand and macromolecular synthesis. However, the reduction of initial adenosine triphosphate (ATP) to a very low concentration, decreasing initial glucose uptake, destroying coordination between glycolysis and PPP, and replacement of PKM2 by its relatively inactive oligomeric form (dimer) or inhibition of the translation of PKM2 may destabilize the mutated control mechanism of the mammalian central carbon metabolic (CCM) pathway in cancer cells. The performance of the model is compared appropriately with some existing ones.

  20. Mechanical analyses on the digital behaviour of the Tokay gecko (Gekko gecko) based on a multi-level directional adhesion model

    PubMed Central

    Wu, Xuan; Wang, Xiaojie; Mei, Tao; Sun, Shaoming

    2015-01-01

    This paper proposes a multi-level hierarchical model for the Tokay gecko (Gekko gecko) adhesive system and analyses the digital behaviour of the G. gecko under macro/meso-level scale. The model describes the structures of G. gecko's adhesive system from the nano-level spatulae to the sub-millimetre-level lamella. The G. gecko's seta is modelled using inextensible fibril based on Euler's elastica theorem. Considering the side contact of the spatular pads of the seta on the flat and rigid substrate, the directional adhesion behaviour of the seta has been investigated. The lamella-induced attachment and detachment have been modelled to simulate the active digital hyperextension (DH) and the digital gripping (DG) phenomena. The results suggest that a tiny angular displacement within 0.25° of the lamellar proximal end is necessary in which a fast transition from attachment to detachment or vice versa is induced. The active DH helps release the torque to induce setal non-sliding detachment, while the DG helps apply torque to make the setal adhesion stable. The lamella plays a key role in saving energy during detachment to adapt to its habitat and provides another adhesive function which differs from the friction-dependent setal adhesion system controlled by the dynamic of G. gecko's body. PMID:26345081

  1. 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

  2. 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.

  3. Development of a mechanism and an accurate and simple mathematical model for the description of drug release: Application to a relevant example of acetazolamide-controlled release from a bio-inspired elastin-based hydrogel.

    PubMed

    Fernández-Colino, A; Bermudez, J M; Arias, F J; Quinteros, D; Gonzo, E

    2016-04-01

    Transversality between mathematical modeling, pharmacology, and materials science is essential in order to achieve controlled-release systems with advanced properties. In this regard, the area of biomaterials provides a platform for the development of depots that are able to achieve controlled release of a drug, whereas pharmacology strives to find new therapeutic molecules and mathematical models have a connecting function, providing a rational understanding by modeling the parameters that influence the release observed. Herein we present a mechanism which, based on reasonable assumptions, explains the experimental data obtained very well. In addition, we have developed a simple and accurate “lumped” kinetics model to correctly fit the experimentally observed drug-release behavior. This lumped model allows us to have simple analytic solutions for the mass and rate of drug release as a function of time without limitations of time or mass of drug released, which represents an important step-forward in the area of in vitro drug delivery when compared to the current state of the art in mathematical modeling. As an example, we applied the mechanism and model to the release data for acetazolamide from a recombinant polymer. Both materials were selected because of a need to develop a suitable ophthalmic formulation for the treatment of glaucoma. The in vitro release model proposed herein provides a valuable predictive tool for ensuring product performance and batch-to-batch reproducibility, thus paving the way for the development of further pharmaceutical devices.

  4. Development of a mechanism and an accurate and simple mathematical model for the description of drug release: Application to a relevant example of acetazolamide-controlled release from a bio-inspired elastin-based hydrogel.

    PubMed

    Fernández-Colino, A; Bermudez, J M; Arias, F J; Quinteros, D; Gonzo, E

    2016-04-01

    Transversality between mathematical modeling, pharmacology, and materials science is essential in order to achieve controlled-release systems with advanced properties. In this regard, the area of biomaterials provides a platform for the development of depots that are able to achieve controlled release of a drug, whereas pharmacology strives to find new therapeutic molecules and mathematical models have a connecting function, providing a rational understanding by modeling the parameters that influence the release observed. Herein we present a mechanism which, based on reasonable assumptions, explains the experimental data obtained very well. In addition, we have developed a simple and accurate “lumped” kinetics model to correctly fit the experimentally observed drug-release behavior. This lumped model allows us to have simple analytic solutions for the mass and rate of drug release as a function of time without limitations of time or mass of drug released, which represents an important step-forward in the area of in vitro drug delivery when compared to the current state of the art in mathematical modeling. As an example, we applied the mechanism and model to the release data for acetazolamide from a recombinant polymer. Both materials were selected because of a need to develop a suitable ophthalmic formulation for the treatment of glaucoma. The in vitro release model proposed herein provides a valuable predictive tool for ensuring product performance and batch-to-batch reproducibility, thus paving the way for the development of further pharmaceutical devices. PMID:26838852

  5. Effect of alcohol aggregation on the retention factors of chiral solutes with an amylose-based sorbent: modeling and implications for the adsorption mechanism.

    PubMed

    Tsui, Hung-Wei; Franses, Elias I; Wang, Nien-Hwa Linda

    2014-02-01

    Various displacement models in the literature have been widely used for understanding the adsorption mechanisms of solutes in various chromatography systems. The models were used for describing the often-observed linear plots of the logarithms of the retention factor versus the logarithms of the polar modifier concentration CI(0). The slopes of such a plot was inferred to be equal to the number of the displaced modifier molecules upon adsorption of one solute molecule, and were generally found to be greater than 1. In this study, the retention factors of four structurally related chiral solutes, ethyl lactate (EL), methyl mandelate (MM), benzoin (B), and pantolactone (PL), were measured for the amylose tris[(S)-α-methylbenzylcarbamate] sorbent, or AS, as a function of the concentration of isopropanol (IPA) in n-hexane. With increasing IPA concentration CI(0), the slopes increase from less than 1, at a concentration range from 0.13 to 1.3M, to slightly more than 1 at higher concentrations. Such slopes cannot be explained by the conventional retention models. It was found previously for monovalent solutes that such slopes can only be explained when the aggregation of the mobile phase modifier, isopropyl alcohol, was accounted for. A new retention model is presented here, accounting for alcohol aggregation, multivalent solute adsorption, multivalent solute-alcohol complexation, alcohol adsorption, and solute intra hydrogen-bonding, which occur in these four solutes. The slope is found to be controlled by three key dimensionless groups, the fraction of the sorbent binding sites covered by IPA, the fraction of the solute molecules in complex form, and the fraction of the IPA molecules in aggregate form. The limiting slope at a very high IPA concentration is equal to the value of (x+y)/n, where x is the number of the solute-sorbent binding sites and y is the number of the alcohol molecules in the solute-alcohol complex, and n is the alcohol aggregation number. The model

  6. 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.

  7. 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.

  8. A Retinal Mechanism Inspired Color Constancy Model.

    PubMed

    Zhang, Xian-Shi; Gao, Shao-Bing; Li, Ruo-Xuan; Du, Xin-Yu; Li, Chao-Yi; Li, Yong-Jie

    2016-03-01

    In this paper, we propose a novel model for the computational color constancy, inspired by the amazing ability of the human vision system (HVS) to perceive the color of objects largely constant as the light source color changes. The proposed model imitates the color processing mechanisms in the specific level of the retina, the first stage of the HVS, from the adaptation emerging in the layers of cone photoreceptors and horizontal cells (HCs) to the color-opponent mechanism and disinhibition effect of the non-classical receptive field in the layer of retinal ganglion cells (RGCs). In particular, HC modulation provides a global color correction with cone-specific lateral gain control, and the following RGCs refine the processing with iterative adaptation until all the three opponent channels reach their stable states (i.e., obtain stable outputs). Instead of explicitly estimating the scene illuminant(s), such as most existing algorithms, our model directly removes the effect of scene illuminant. Evaluations on four commonly used color constancy data sets show that the proposed model produces competitive results in comparison with the state-of-the-art methods for the scenes under either single or multiple illuminants. The results indicate that single opponency, especially the disinhibitory effect emerging in the receptive field's subunit-structured surround of RGCs, plays an important role in removing scene illuminant(s) by inherently distinguishing the spatial structures of surfaces from extensive illuminant(s). PMID:26766375

  9. 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

  10. 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.

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

    SciTech Connect

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

    1981-12-01

    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.

  12. 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.

  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. Rock mechanics models evaluation report. [Contains glossary

    SciTech Connect

    Not Available

    1987-08-01

    This report documents the evaluation of the thermal and thermomechanical models and codes for repository subsurface design and for design constraint analysis. The evaluation was based on a survey of the thermal and thermomechanical codes and models that are applicable to subsurface design, followed by a Kepner-Tregoe (KT) structured decision analysis of the codes and models. The primary recommendations of the analysis are that the DOT code be used for two-dimensional thermal analysis and that the STEALTH and HEATING 5/6 codes be used for three-dimensional and complicated two-dimensional thermal analysis. STEALTH and SPECTROM 32 are recommended for thermomechanical analyses. The other evaluated codes should be considered for use in certain applications. A separate review of salt creep models indicate that the commonly used exponential time law model is appropriate for use in repository design studies. 38 refs., 1 fig., 7 tabs.

  15. 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.

  16. CONDENSED MATTER: STRUCTURE, THERMAL AND MECHANICAL PROPERTIES: Degraded model of radiation-induced acceptor defects for GaN-based high electron mobility transistors (HEMTs)

    NASA Astrophysics Data System (ADS)

    Fan, Long; Hao, Yue; Zhao, Yuan-Fu; Zhang, Jin-Cheng; Gao, Zhi-Yuan; Li, Pei-Xian

    2009-07-01

    Using depletion approximation theory and introducing acceptor defects which can characterize radiation induced deep-level defects in AlGaN/GaN heterostructures, we set up a radiation damage model of AlGaN/GaN high electron mobility transistor (HEMT) to separately simulate the effects of several main radiation damage mechanisms and the complete radiation damage effect simultaneously considering the degradation in mobility. Our calculated results, consistent with the experimental results, indicate that thin AlGaN barrier layer, high Al content and high doping concentration are favourable for restraining the shifts of threshold voltage in the AlGaN/GaN HEMT; when the acceptor concentration induced is less than 1014cm-3, the shifts in threshold voltage are not obvious; only when the acceptor concentration induced is higher than 1016cm-3, will the shifts of threshold voltage remarkably increase; the increase of threshold voltage, resulting from radiation induced acceptor, mainly contributes to the degradation in drain saturation current of the current-voltage (I-V) characteristic, but has no effect on the transconductance in the saturation area.

  17. 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.

  18. 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

  19. 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).

  20. Mechanisms and models of somatic cell reprogramming

    PubMed Central

    Buganim, Yosef; Faddah, Dina A.; Jaenisch, Rudolf

    2014-01-01

    Conversion of somatic cells to pluripotency by defined factors is a long and complex process that yields embryonic stem cell-like cells that vary in their developmental potential. To improve the quality of resulting induced pluripotent stem cells (iPSCs), which is important for potential therapeutic applications, and to address fundamental questions about control of cell identity, molecular mechanisms of the reprogramming process must be understood. Here we discuss recent discoveries regarding the role of reprogramming factors in remodeling the genome, including new insights into the function of c-Myc, and describe the different phases, markers and emerging models of reprogramming. PMID:23681063

  1. 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.

  2. 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.

  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.

    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.

  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

    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.

  5. 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.

  6. Neuroprotective effects of quercetin in a mouse model of brain ischemic/reperfusion injury via anti-apoptotic mechanisms based on the Akt pathway.

    PubMed

    Lei, Xiaoming; Chao, Hailian; Zhang, Zhenni; Lv, Jianrui; Li, Siyuan; Wei, Haidong; Xue, Rongliang; Li, Fang; Li, Zongfang

    2015-09-01

    The present study provided experimental evidence for the neuroprotective effects of quercetin using a rat model of global brain ischemic/reperfusion (I/R) injury. Pre‑treatment with quercetin (5 or 10 mg/kg orally (p.o.); once daily) induced a dose‑dependent reduction in I/R‑induced hippocampal neuron cell loss, with 10 mg/kg/day being the lowest dose that achieved maximal neuroprotection. Administration of 10 mg/kg quercetin over at least 3 days prior to I/R was required to improve the survival rate of I/R rats. Fluorescence‑assisted cell sorting, hematoxylin and eosin staining and terminal deoxynucleotidyl transferase dUTP nick end labeling indicated neuronal cell loss in the CA1 hippocampus. Rats that had undergone transient global cerebral ischemia for 15 min followed by 1 h of reperfusion exhibited a significant increase in reactive oxygen species (ROS) production in the hippocampus. The I/R‑induced ROS overproduction in the hippocampus at 1, 12 and 24 h following I/R was significantly decreased by quercetin pre‑treatment. Western blot analysis revealed that the neuroprotective effects of quercetin (5 and 10 mg/kg/day, p.o.) were associated with an upregulation of the I/R‑induced suppression of B‑cell lymphoma‑2 (Bcl‑2), Bcl extra large and survivin expression as well as phosphorylation of Bcl‑2‑associated death promoter. Furthermore, the neuroprotective effects of quercetin (5, 10 mg/kg/day) in the brain were associated with an upregulation of Akt signaling. These findings suggested that the inhibition of I/R‑induced brain injury by quercetin likely involves a transcriptional mechanism to enhance anti‑apoptotic signaling.

  7. 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.

  8. 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.

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

    PubMed

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

    2016-01-01

    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. PMID:27598148

  10. A mechanical model of retinal detachment

    NASA Astrophysics Data System (ADS)

    Chou, Tom; Siegel, Michael

    2012-08-01

    We present a model of the mechanical and fluid forces associated with exudative retinal detachments where the retinal photoreceptor cells separate, typically from the underlying retinal pigment epithelium (RPE). By computing the total fluid volume flow arising from transretinal, vascular and RPE pump currents, we determine the conditions under which the subretinal fluid pressure exceeds the maximum yield stress holding the retina and RPE together, giving rise to an irreversible, extended retinal delamination. We also investigate localized, blister-like retinal detachments by balancing mechanical tension in the retina with both the retina-RPE adhesion energy and the hydraulic pressure jump across the retina. For detachments induced by traction forces, we find a critical radius beyond which the blister is unstable to growth. Growth of a detached blister can also be driven by inflamed lesions in which the tissue has a higher choroidal hydraulic conductivity, has insufficient RPE pump activity, or has defective adhesion bonds. We determine the parameter regimes in which the blister either becomes unstable to growth, remains stable and finite-sized, or shrinks, allowing possible healing. The corresponding stable blister radius and shape are calculated. Our analysis provides a quantitative description of the physical mechanisms involved in exudative retinal detachments and can help guide the development of retinal reattachment protocols or preventative procedures.

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

    PubMed Central

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

    2016-01-01

    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. PMID:27598148

  12. 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.

  13. 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.

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

    PubMed

    Hooft, Gerard 't

    2015-08-01

    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.

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

    PubMed

    Hooft, Gerard 't

    2015-08-01

    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. PMID:26124246

  16. A neuromusculoskeletal model exploring peripheral mechanism of tremor.

    PubMed

    Zhang, Dingguo; Ang, Wei Tech; Poignet, Philippe

    2008-01-01

    This paper studies the peripheral mechanism contributing to the tremor of human body. It is known that the reflex loops in peripheral nervous system have significant influences on the tremor. A neuromusculoskeletal model with several reflex loops is developed to explore the origin of tremor. The muscle model is developed based on a Hill-type muscle model. The feedback loops include the spindle organ, Golgi tendon organ and Renshaw cell. Their effects are investigated quantitatively in detail. Some results are in accordance with the previous research. Meanwhile, some new findings are proposed according to the simulation study.

  17. A unified creep-plasticity model suitable for thermo-mechanical loading

    NASA Technical Reports Server (NTRS)

    Slavik, D.; Sehitoglu, H.

    1988-01-01

    An experimentally based unified creep-plasticity constitutive model was implemented for 1070 steel. Accurate rate and temperature effects were obtained for isothermal and thermo-mechanical loading by incorporating deformation mechanisms into the constitutive equations in a simple way.

  18. Physical vs. Mathematical Models in Rock Mechanics

    NASA Astrophysics Data System (ADS)

    Morozov, I. B.; Deng, W.

    2013-12-01

    One of the less noted challenges in understanding the mechanical behavior of rocks at both in situ and lab conditions is the character of theoretical approaches being used. Currently, the emphasis is made on spatial averaging theories (homogenization and numerical models of microstructure), empirical models for temporal behavior (material memory, compliance functions and complex moduli), and mathematical transforms (Laplace and Fourier) used to infer the Q-factors and 'relaxation mechanisms'. In geophysical applications, we have to rely on such approaches for very broad spatial and temporal scales which are not available in experiments. However, the above models often make insufficient use of physics and utilize, for example, the simplified 'correspondence principle' instead of the laws of viscosity and friction. As a result, the commonly-used time- and frequency dependent (visco)elastic moduli represent apparent properties related to the measurement procedures and not necessarily to material properties. Predictions made from such models may therefore be inaccurate or incorrect when extrapolated beyond the lab scales. To overcome the above challenge, we need to utilize the methods of micro- and macroscopic mechanics and thermodynamics known in theoretical physics. This description is rigorous and accurate, uses only partial differential equations, and allows straightforward numerical implementations. One important observation from the physical approach is that the analysis should always be done for the specific geometry and parameters of the experiment. Here, we illustrate these methods on axial deformations of a cylindrical rock sample in the lab. A uniform, isotropic elastic rock with a thermoelastic effect is considered in four types of experiments: 1) axial extension with free transverse boundary, 2) pure axial extension with constrained transverse boundary, 3) pure bulk expansion, and 4) axial loading harmonically varying with time. In each of these cases, an

  19. 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.

  20. 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.

  1. Arctic Sea Ice Reemergence Mechanisms in a Model Hierarchy

    NASA Astrophysics Data System (ADS)

    Bushuk, M.; Giannakis, D.

    2015-12-01

    Lagged correlation analysis of Arctic sea ice area anomalies reveals that melt season sea ice anomalies tend to recur the following growth season, and growth season anomalies tend to recur the following melt season. In this work, the regional and temporal characteristics of this phenomenon, termed sea-ice reemergence, are investigated in a hierarchy of climate models. Coupled nonlinear Laplacian spectral analysis (NLSA), a multivariate data analysis technique, is used to study the covariability of Arctic sea-ice concentration (SIC), sea-surface temperature (SST), sea-level pressure (SLP), and sea-ice thickness (SIT). Two mechanisms related to melt season to growth season reemergence are identified: (1) An SST-SIC mechanism, related to local imprinting and persistence of SST anomalies in the seasonal ice zones, and (2) an SLP-SIC mechanism, related to winter-to-winter regime persistence of large-scale SLP teleconnection patterns. An SIT-SIC growth season to melt season reemergence mechanism is also identified, related to winter persistence of SIT anomalies in the central Arctic. The representation of these mechanisms is investigated using the model hierarchy to determine the relative roles of the ocean, atmosphere, and sea ice itself in producing reemergence. It is found that the SST-based and SIT-based mechanisms can exist as stand-alone processes, whereas the SLP mechanism cannot. Dynamical feedback from the ocean to the atmosphere is found to be essential in creating large-scale organized patterns of SIC-SLP covariability. A set of reemergence metrics is introduced, by which one can judge the amplitude and phase of reemergence events and associated mechanisms.

  2. Macrocomposite mechanical design, modeling, and behavior of physical models of bioinspired fish armor

    NASA Astrophysics Data System (ADS)

    Browning, Ashley; Ortiz, Christine; Boyce, Mary C.

    2012-02-01

    The macrocomposite design of flexible biological exoskeletons, consisting of overlapping mineralized armor units embedded in a compliant tissue, is a key determinant of their mechanical function (e.g penetration resistance and biomechanical flexibility). Here, we investigate the role of macrocomposite structure, composition, geometric orientation, and spatial distribution in a flexible model natural armor system present in the majority of teleost fish species. Physical multi-material composite models are fabricated using a combination of 3-D printing and molding methods. Mechanical experiments using digital image correlation enable measurement of both the macroscopic response and underlying deformation mechanisms during various loading scenarios. Finite element-based mechanical models yield detailed insights into the roles and the tradeoffs of the composite structure providing constraint, shear, and bending mechanisms to impart protection and flexibility.

  3. 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.

  4. 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.

  5. 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

  6. Mechanisms for integration of information models across related domains

    NASA Astrophysics Data System (ADS)

    Atkinson, Rob

    2010-05-01

    It is well recognised that there are opportunities and challenges in cross-disciplinary data integration. A significant barrier, however, is creating a conceptual model of the combined domains and the area of integration. For example, a groundwater domain application may require information from several related domains: geology, hydrology, water policy, etc. Each domain may have its own data holdings and conceptual models, but these will share various common concepts (eg. The concept of an aquifer). These areas of semantic overlap present significant challenges, firstly to choose a single representation (model) of a concept that appears in multiple disparate models,, then to harmonise these other models with the single representation. In addition, models may exist at different levels of abstraction depending on how closely aligned they are with a particular implementation. This makes it hard for modellers in one domain to introduce elements from another domain without either introducing a specific style of implementation, or conversely dealing with a set of abstract patterns that are hard to integrate with existing implementations. Models are easier to integrate if they are broken down into small units, with common concepts implemented using common models from well-known, and predictably managed shared libraries. This vision however requires development of a set of mechanisms (tools and procedures) for implementing and exploiting libraries of model components. These mechanisms need to handle publication, discovery, subscription, versioning and implementation of models in different forms. In this presentation a coherent suite of such mechanisms is proposed, using a scenario based on re-use of geosciences models. This approach forms the basis of a comprehensive strategy to empower domain modellers to create more interoperable systems. The strategy address a range of concerns and practice, and includes methodologies, an accessible toolkit, improvements to available

  7. 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.

  8. Model Based Testing for Agent Systems

    NASA Astrophysics Data System (ADS)

    Zhang, Zhiyong; Thangarajah, John; Padgham, Lin

    Although agent technology is gaining world wide popularity, a hindrance to its uptake is the lack of proper testing mechanisms for agent based systems. While many traditional software testing methods can be generalized to agent systems, there are many aspects that are different and which require an understanding of the underlying agent paradigm. In this paper we present certain aspects of a testing framework that we have developed for agent based systems. The testing framework is a model based approach using the design models of the Prometheus agent development methodology. In this paper we focus on model based unit testing and identify the appropriate units, present mechanisms for generating suitable test cases and for determining the order in which the units are to be tested, present a brief overview of the unit testing process and an example. Although we use the design artefacts from Prometheus the approach is suitable for any plan and event based agent system.

  9. Tensegrity finite element models of mechanical tests of individual cells.

    PubMed

    Bursa, Jiri; Lebis, Radek; Holata, Jakub

    2012-01-01

    A three-dimensional finite element model of a vascular smooth muscle cell is based on models published recently; it comprehends elements representing cell membrane, cytoplasm and nucleus, and a complex tensegrity structure representing the cytoskeleton. In contrast to previous models of eucaryotic cells, this tensegrity structure consists of several parts. Its external and internal parts number 30 struts, 60 cables each, and their nodes are interconnected by 30 radial members; these parts represent cortical, nuclear and deep cytoskeletons, respectively. This arrangement enables us to simulate load transmission from the extracellular space to the nucleus or centrosome via membrane receptors (focal adhesions); the ability of the model was tested by simulation of some mechanical tests with isolated vascular smooth muscle cells. Although material properties of components defined on the basis of the mechanical tests are ambiguous, modelling of different types of tests has shown the ability of the model to simulate substantial global features of cell behaviour, e.g. "action at a distance effect" or the global load-deformation response of the cell under various types of loading. Based on computational simulations, the authors offer a hypothesis explaining the scatter of experimental results of indentation tests. PMID:22508025

  10. 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

  11. 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.

  12. Theory of fracture mechanics based upon plasticity

    NASA Technical Reports Server (NTRS)

    Lee, J. D.

    1976-01-01

    A theory of fracture mechanics is formulated on the foundation of continuum mechanics. Fracture surface is introduced as an unknown quantity and is incorporated into boundary and initial conditions. Surface energy is included in the global form of energy conservation law and the dissipative mechanism is formulated into constitutive equations which indicate the thermodynamic irreversibility and the irreversibility of fracture process as well.

  13. 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.

  14. 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.

  15. 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.

  16. A transcriptomics-based kinetic model for ethylene biosynthesis in tomato (Solanum lycopersicum) fruit: development, validation and exploration of novel regulatory mechanisms.

    PubMed

    Van de Poel, Bram; Bulens, Inge; Hertog, Maarten L A T M; Nicolai, Bart M; Geeraerd, Annemie H

    2014-05-01

    The gaseous plant hormone ethylene is involved in many physiological processes including climacteric fruit ripening, in which it is a key determinant of fruit quality. A detailed model that describes ethylene biochemistry dynamics is missing. Often, kinetic modeling is used to describe metabolic networks or signaling cascades, mostly ignoring the link with transcriptomic data. We have constructed an elegant kinetic model that describes the transfer of genetic information into abundance and metabolic activity of proteins for the entire ethylene biosynthesis pathway during fruit development and ripening of tomato (Solanum lycopersicum). Our model was calibrated against a vast amount of transcriptomic, proteomic and metabolic data and showed good descriptive qualities. Subsequently it was validated successfully against several ripening mutants previously described in the literature. The model was used as a predictive tool to evaluate novel and existing hypotheses regarding the regulation of ethylene biosynthesis. This bottom-up kinetic network model was used to indicate that a side-branch of the ethylene pathway, the formation of the dead-end product 1-(malonylamino)-1-aminocyclopropane-1-carboxylic acid (MACC), might have a strong effect on eventual ethylene production. Furthermore, our in silico analyses indicated potential (post-) translational regulation of the ethylene-forming enzyme ACC oxidase.

  17. Oral biofilm models for mechanical plaque removal

    PubMed Central

    Verkaik, Martinus J.; Busscher, Henk J.; Rustema-Abbing, Minie; Slomp, Anje M.; Abbas, Frank

    2009-01-01

    In vitro plaque removal studies require biofilm models that resemble in vivo dental plaque. Here, we compare contact and non-contact removal of single and dual-species biofilms as well as of biofilms grown from human whole saliva in vitro using different biofilm models. Bacteria were adhered to a salivary pellicle for 2 h or grown after adhesion for 16 h, after which, their removal was evaluated. In a contact mode, no differences were observed between the manual, rotating, or sonic brushing; and removal was on average 39%, 84%, and 95% for Streptococcus mutans, Streptococcus oralis, and Actinomyces naeslundii, respectively, and 90% and 54% for the dual- and multi-species biofilms, respectively. However, in a non-contact mode, rotating and sonic brushes still removed considerable numbers of bacteria (24–40%), while the manual brush as a control (5–11%) did not. Single A. naeslundii and dual-species (A. naeslundii and S. oralis) biofilms were more difficult to remove after 16 h growth than after 2 h adhesion (on average, 62% and 93% for 16- and 2-h-old biofilms, respectively), while in contrast, biofilms grown from whole saliva were easier to remove (97% after 16 h and 54% after 2 h of growth). Considering the strong adhesion of dual-species biofilms and their easier more reproducible growth compared with biofilms grown from whole saliva, dual-species biofilms of A. naeslundii and S. oralis are suggested to be preferred for use in mechanical plaque removal studies in vitro. PMID:19565279

  18. Solvable model of mechanical unfolding of biopolymers

    NASA Astrophysics Data System (ADS)

    Jacobs, Donald; Livesay, Dennis; Vorov, Oleg

    2010-03-01

    We present exact analytical results for a hairpin to coil transition induced through mechanical pulling of dsDNA or peptides (beta-hairpin) within a distance constraint model [1], taking into account geometry of conformations. Starting from ab initio considerations, the configuration partition function is calculated exactly. Among other thermodynamic response functions, an expression for the end-to-end extension as a function of the applied force at a given temperature is derived. Our theoretical results agree well with data from single-molecule stretching experiments [2]. The employed method is general, and promises to remain a tractable computational approach when applied to larger, more complicated macromolecules. This work is supported by NIH R01 GM073082.[4pt] [1] O.K. Vorov, D.R. Livesay and D.J. Jacobs, ENTROPY, v.10 (3) 285-308 (2008).[0pt] [2] O.K. Vorov, D.R. Livesay and D.J. Jacobs, to be subm. to Phys. Rev. Lett., in preparation.

  19. 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.

  20. Mechanism of base-catalyzed Schiff base deprotonation in halorhodopsin

    SciTech Connect

    Lanyi, J.K.

    1986-10-21

    It has been shown earlier that the deprotonation of the Schiff base of illuminated halorhodopsin proceeds with a much lower pK/sub a/ than that of the unilluminated pigment and the reversible protonation change is catalyzed by azide and cyanate. The authors have studied the kinetics of the proton-transfer events with flash spectroscopy and compared a variety of anionic bases with different pK/sub a/ with regard to the apparent binding constants and the catalytic activities. The results suggest a general base catalysis mechanism in which the anionic bases bind with apparently low affinity to halorhodopsin, although with some degree of size- and/or shape-dependent specificity. The locus of the catalysis is accessible from the cytoplasmic side of the membrane and is not at site I, where various anions bind and shift the pK/sub a/ of the deprotonation. Neither is it at site II, where a few specific anions (like chloride) bind to the all-trans pigment. It may be concluded that while the all-trans pigment loses its Schiff base proton very rapidly at its pK/sub a/, there is a kinetic barrier to this deprotonation in the 13-cis photointermediate that can be partially overcome by the reversible protonation of an extrinsic anionic base, which shuttles protons between the interior of the protein and the aqueous medium. The need for an extrinsic proton acceptor for efficient deprotonation of the Schiff base of halorhodopsin is one of the main differences between this pigment and the analogous retinal protein, bacteriorhodopsin.

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

    NASA Astrophysics Data System (ADS)

    Meng, Qinghua; Wang, Zhenqing

    2016-05-01

    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.

  2. 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.

  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. 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.

  5. Quantitative phenomenological model of the BOLD contrast mechanism

    NASA Astrophysics Data System (ADS)

    Dickson, John D.; Ash, Tom W. J.; Williams, Guy B.; Sukstanskii, Alexander L.; Ansorge, Richard E.; Yablonskiy, Dmitriy A.

    2011-09-01

    Different theoretical models of the BOLD contrast mechanism are used for many applications including BOLD quantification (qBOLD) and vessel size imaging, both in health and disease. Each model simplifies the system under consideration, making approximations about the structure of the blood vessel network and diffusion of water molecules through inhomogeneities in the magnetic field created by deoxyhemoglobin-containing blood vessels. In this study, Monte-Carlo methods are used to simulate the BOLD MR signal generated by diffusing water molecules in the presence of long, cylindrical blood vessels. Using these simulations we introduce a new, phenomenological model that is far more accurate over a range of blood oxygenation levels and blood vessel radii than existing models. This model could be used to extract physiological parameters of the blood vessel network from experimental data in BOLD-based experiments. We use our model to establish ranges of validity for the existing analytical models of Yablonskiy and Haacke, Kiselev and Posse, Sukstanskii and Yablonskiy (extended to the case of arbitrary time in the spin echo sequence) and Bauer et al. (extended to the case of randomly oriented cylinders). Although these models are shown to be accurate in the limits of diffusion under which they were derived, none of them is accurate for the whole physiological range of blood vessels radii and blood oxygenation levels. We also show the extent of systematic errors that are introduced due to the approximations of these models when used for BOLD signal quantification.

  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. 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

  8. The Mechanics of Metastasis: Insights from a Computational Model

    PubMed Central

    Brodland, G. Wayne; Veldhuis, Jim H.

    2012-01-01

    Although it may seem obvious that mechanical forces are required to drive metastatic cell movements, understanding of the mechanical aspects of metastasis has lagged far behind genetic and biochemical knowledge. The goal of this study is to learn about the mechanics of metastasis using a cell-based finite element model that proved useful for advancing knowledge about the forces that drive embryonic cell and tissue movements. Metastasis, the predominant cause of cancer-related deaths, involves a series of mechanical events in which one or more cells dissociate from a primary tumour, migrate through normal tissue, traverse in and out of a multi-layer circulatory system vessel and resettle. The present work focuses on the dissemination steps, from dissociation to circulation. The model shows that certain surface tension relationships must be satisfied for cancerous cells to dissociate from a primary tumour and that these equations are analogous to those that govern dissociation of embryonic cells. For a dissociated cell to then migrate by invadopodium extension and contraction and exhibit the shapes seen in experiments, the invadopodium must generate a contraction equal to approximately twice that produced by the interfacial tension associated with surrounding cells. Intravasation through the wall of a vessel is governed by relationships akin to those in the previous two steps, while release from the vessel wall is governed by equations that involve surface and interfacial tensions. The model raises a number of potential research questions. It also identifies how specific mechanical properties and the sub-cellular structural components that give rise to them might be changed so as to thwart particular metastatic steps and thereby block the spread of cancer. PMID:23028513

  9. A micro-mechanical analysis of thermo-elastic properties and local residual stresses in ductile iron based on a new anisotropic model for the graphite nodules

    NASA Astrophysics Data System (ADS)

    Andriollo, Tito; Thorborg, Jesper; Tiedje, Niels; Hattel, Jesper

    2016-06-01

    In this paper, the thermo-elastic behavior of the graphite nodules contained in ductile iron is derived on the basis of recent transmission electron microscopy investigations of their real internal structure. The proposed model is initially validated by performing a finite element homogenization analysis to verify its consistency with the room-temperature elastic properties of ductile iron measured at the macro scale. Subsequently, it is used to investigate the formation of local residual stresses around the graphite particles by simulating the manufacturing process of a typical ferritic ductile iron grade, and the results are compared with preliminary measurements using synchrotron x-rays. Finally, the obtained accurate description of the stress & strain field at the micro scale is used to shed light on common failure modes reported for the nodules and on some peculiar properties observed in ductile iron at both micro and macro scale.

  10. SFT based cosmological models

    NASA Astrophysics Data System (ADS)

    Koshelev, Alexey S.

    2010-11-01

    We consider the appearance of multiple scalar fields in SFT inspired non-local models with a single scalar field at late times. In this regime all the scalar fields are free. This system minimally coupled to gravity is mainly analyzed in this note. We build one exact solution to the equations of motion. We consider an exactly solvable model which obeys a simple exact solution in the cosmological context for the Friedmann equations and that reproduces the behavior expected from SFT in the asymptotic regime.

  11. Cardiac mechanical parameter calibration based on the unscented transform.

    PubMed

    Marchesseau, Stéphanie; Delingette, Hervé; Sermesant, Maxime; Rhode, Kawal; Duckett, Simon G; Rinaldi, C Aldo; Razavi, Reza; Ayache, Nicholas

    2012-01-01

    Patient-specific cardiac modelling can help in understanding pathophysiology and predict therapy planning. However it requires to personalize the model geometry, kinematics, electrophysiology and mechanics. Calibration aims at providing global values (space invariant) of parameters before performing the personalization stage which involves solving an inverse problem to find regional values. We propose an automatic calibration method of the mechanical parameters of the Bestel-Clément-Sorine (BCS) electromechanical model of the heart based on the Unscented Transform algorithm. A sensitivity analysis is performed that reveals which observations on the volume and pressure evolution are significant to characterize the global behaviour of the myocardium. We show that the calibration method gives satisfying results by optimizing up to 7 parameters of the BCS model in only one iteration. This method was evaluated on 7 volunteers and 2 heart failure patients, with a mean relative error from the real data of 11%. This calibration enabled furthermore a preliminary study of the specific parameters to the studied pathologies. PMID:23286030

  12. Modeling of mechanical stimulation of hair cells in otolithic organs

    NASA Astrophysics Data System (ADS)

    Kondrachuk, A. V.

    2006-01-01

    Experimental investigations of the function of hair cell bundles (HCB) are based on artificial mechanical stimulation of the HCB by probes and fluid-jets. The purpose of the present work is to estimate the parameters of these stimulations and to analyze their correspondence to natural stimulation of the HCB in otoliths. This analysis is based on results of the previous modeling of transformations of mechanical input in the following series: acceleration of the otolithic membrane (OM), displacement of the OM gel layer, deflection of hair cell bundle, deformation of the ciliary tip-links, and formation of a temporal pattern of polarization [Kondrachuk, A.V. Models of the dynamics of the otolithic membrane and the hair cell bundle mechanics. J. Vest. Res. 11, 29 38, 2001; Kondrachuk, A.V. Models of otolithic membrane-hair cell bundle interaction. Hear. Res. 166, 96 112, 2002]. It is suggested that during natural stimulation, the contacts between the HCBs and the surrounding substance are spatially distributed over the body of the HCBs. The comparison of experimental and modeling data indicates that probe stimulation cannot imitate the effects of spatially distributed contacts. Stimulation of the HCB by fluid jet mimics the fluid-like gel interaction with the HCB, but application of the fluid jet is restricted by the low viscosity of the solution. The parameters of fluid jet stimulation indicate that inertial force, rather than viscous force, is responsible for the HCB deflection in these experiments. This could be verified by direct measurements of the parameters of fluid-jet stimulation. The present results show that the scarce and contradictory data about the nature and parameters of the substance that surrounds the surface of the HCBs of the otolithic organs is a great obstacle to understanding the function of the HCB.

  13. 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.

  14. The cognitive life of mechanical molecular models.

    PubMed

    Charbonneau, Mathieu

    2013-12-01

    The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment and extend the modeler's cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models' materiality contributing to the solving of the molecule's structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations.

  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. Shear mechanical properties of the spleen: experiment and analytical modelling.

    PubMed

    Nicolle, S; Noguer, L; Palierne, J-F

    2012-05-01

    This paper aims at providing the first shear mechanical properties of spleen tissue. Rheometric tests on porcine splenic tissues were performed in the linear and nonlinear regime, revealing a weak frequency dependence of the dynamic moduli in linear regime and a distinct strain-hardening effect in nonlinear regime. These behaviours are typical of soft tissues such as kidney and liver, with however a less pronounced strain-hardening for the spleen. An analytical model based on power laws is then proposed to describe the general shear viscoelastic behaviour of the spleen. PMID:22498291

  17. 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.

  18. 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

    2016-02-01

    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.

  19. 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

    2016-02-01

    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. PMID:26787165

  20. Thermal-mechanical-noise-based CMUT characterization and sensing.

    PubMed

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

    2012-06-01

    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. Because 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 when a direct connection to CMUT array element terminals is not available. Because these measurements can be performed in air at the wafer level, the approach is 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 to 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 methods 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

  1. 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.

  2. 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…

  3. 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

  4. 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

  5. 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

  6. 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; Subba Rao, V. V.

    2016-08-01

    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.

  7. Market-based control mechanisms for patient safety.

    PubMed

    Coiera, E; Braithwaite, J

    2009-04-01

    A new model is proposed for enhancing patient safety using market-based control (MBC), inspired by successful approaches to environmental governance. Emissions trading, enshrined in the Kyoto protocol, set a carbon price and created a carbon market--is it possible to set a patient safety price and let the marketplace find ways of reducing clinically adverse events? To "cap and trade," a regulator would need to establish system-wide and organisation-specific targets, based on the cost of adverse events, create a safety market for trading safety credits and then police the market. Organisations are given a clear policy signal to reduce adverse event rates, are told by how much, but are free to find mechanisms best suited to their local needs. The market would inevitably generate novel ways of creating safety credits, and accountability becomes hard to evade when adverse events are explicitly measured and accounted for in an organisation's bottom line.

  8. "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)

  9. 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.

  10. 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…

  11. Solitons in Skyrme - Faddeev spinor model and quantum mechanics

    NASA Astrophysics Data System (ADS)

    Rybakov, Y.

    2016-07-01

    We discuss the possibility of unification of Skyrme and Faddeev approaches for the description of baryons and leptons respectively as topological solitons within the scope of 16-spinor model. The motivation for such a unification is based on a special 8- semispinor identity invented by the Italian geometrician F. Brioschi. This remarkable identity permits one to realize baryon or lepton states through the effect of spontaneous symmetry breaking emerging due to special structure of the Higgs potential in the model. At large distances from the particle - soliton small excitation of the vacuum satisfies Klein - Gordon equation with some mass that permits one to establish the correspondence with quantum mechanics in special stochastic representation of the wave function for extended particles - solitons. Finally, we illustrate the peculiar properties of stochastic representation by the famous T. Young's experiment with n slits in soliton realization.

  12. 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

  13. Inflammation: maladies, models, mechanisms and molecules.

    PubMed

    Stewart, A G; Beart, P M

    2016-02-01

    The continued focus of attention on the diversity of mechanisms underpinning inflammation has improved our understanding of the potential to target specific pathways in the inflammatory network to achieve meaningful therapeutic gains. In this themed issue of the British Journal of Pharmacology our scope was deliberately broad, ranging across both acute and chronic disease in various organs. Pro- and anti-inflammatory mechanisms receive attention as does the phenotype of macrophages. Whilst the manifestations of neuro-inflammation are less obvious than those in peripheral tissues, central innate and adaptive immunity in brain and the M1/M2 phenotypes of microglia are topics of special interest. The contributions to the inflammatory milieu of cytokines, chemokines and associated signalling cascades are considered. Overall, the coverage herein advances the basic science underpinning our understanding of inflammation and emphasizes its importance in different pathologies.

  14. 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.

  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 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.

  17. 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).

  18. Constraint Based Modeling Going Multicellular

    PubMed Central

    Martins Conde, Patricia do Rosario; Sauter, Thomas; Pfau, Thomas

    2016-01-01

    Constraint based modeling has seen applications in many microorganisms. For example, there are now established methods to determine potential genetic modifications and external interventions to increase the efficiency of microbial strains in chemical production pipelines. In addition, multiple models of multicellular organisms have been created including plants and humans. While initially the focus here was on modeling individual cell types of the multicellular organism, this focus recently started to switch. Models of microbial communities, as well as multi-tissue models of higher organisms have been constructed. These models thereby can include different parts of a plant, like root, stem, or different tissue types in the same organ. Such models can elucidate details of the interplay between symbiotic organisms, as well as the concerted efforts of multiple tissues and can be applied to analyse the effects of drugs or mutations on a more systemic level. In this review we give an overview of the recent development of multi-tissue models using constraint based techniques and the methods employed when investigating these models. We further highlight advances in combining constraint based models with dynamic and regulatory information and give an overview of these types of hybrid or multi-level approaches. PMID:26904548

  19. Constraint Based Modeling Going Multicellular.

    PubMed

    Martins Conde, Patricia do Rosario; Sauter, Thomas; Pfau, Thomas

    2016-01-01

    Constraint based modeling has seen applications in many microorganisms. For example, there are now established methods to determine potential genetic modifications and external interventions to increase the efficiency of microbial strains in chemical production pipelines. In addition, multiple models of multicellular organisms have been created including plants and humans. While initially the focus here was on modeling individual cell types of the multicellular organism, this focus recently started to switch. Models of microbial communities, as well as multi-tissue models of higher organisms have been constructed. These models thereby can include different parts of a plant, like root, stem, or different tissue types in the same organ. Such models can elucidate details of the interplay between symbiotic organisms, as well as the concerted efforts of multiple tissues and can be applied to analyse the effects of drugs or mutations on a more systemic level. In this review we give an overview of the recent development of multi-tissue models using constraint based techniques and the methods employed when investigating these models. We further highlight advances in combining constraint based models with dynamic and regulatory information and give an overview of these types of hybrid or multi-level approaches.

  20. Constraint Based Modeling Going Multicellular.

    PubMed

    Martins Conde, Patricia do Rosario; Sauter, Thomas; Pfau, Thomas

    2016-01-01

    Constraint based modeling has seen applications in many microorganisms. For example, there are now established methods to determine potential genetic modifications and external interventions to increase the efficiency of microbial strains in chemical production pipelines. In addition, multiple models of multicellular organisms have been created including plants and humans. While initially the focus here was on modeling individual cell types of the multicellular organism, this focus recently started to switch. Models of microbial communities, as well as multi-tissue models of higher organisms have been constructed. These models thereby can include different parts of a plant, like root, stem, or different tissue types in the same organ. Such models can elucidate details of the interplay between symbiotic organisms, as well as the concerted efforts of multiple tissues and can be applied to analyse the effects of drugs or mutations on a more systemic level. In this review we give an overview of the recent development of multi-tissue models using constraint based techniques and the methods employed when investigating these models. We further highlight advances in combining constraint based models with dynamic and regulatory information and give an overview of these types of hybrid or multi-level approaches. PMID:26904548

  1. Insight into model mechanisms through automatic parameter fitting: a new methodological framework for model development

    PubMed Central

    2014-01-01

    Background Striking a balance between the degree of model complexity and parameter identifiability, while still producing biologically feasible simulations using modelling is a major challenge in computational biology. While these two elements of model development are closely coupled, parameter fitting from measured data and analysis of model mechanisms have traditionally been performed separately and sequentially. This process produces potential mismatches between model and data complexities that can compromise the ability of computational frameworks to reveal mechanistic insights or predict new behaviour. In this study we address this issue by presenting a generic framework for combined model parameterisation, comparison of model alternatives and analysis of model mechanisms. Results The presented methodology is based on a combination of multivariate metamodelling (statistical approximation of the input–output relationships of deterministic models) and a systematic zooming into biologically feasible regions of the parameter space by iterative generation of new experimental designs and look-up of simulations in the proximity of the measured data. The parameter fitting pipeline includes an implicit sensitivity analysis and analysis of parameter identifiability, making it suitable for testing hypotheses for model reduction. Using this approach, under-constrained model parameters, as well as the coupling between parameters within the model are identified. The methodology is demonstrated by refitting the parameters of a published model of cardiac cellular mechanics using a combination of measured data and synthetic data from an alternative model of the same system. Using this approach, reduced models with simplified expressions for the tropomyosin/crossbridge kinetics were found by identification of model components that can be omitted without affecting the fit to the parameterising data. Our analysis revealed that model parameters could be constrained to a standard

  2. 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.

  3. Mesh convergence differences based on failure mechanisms

    SciTech Connect

    Pilat, K.R.; Revelli, V.D.

    1994-04-01

    Material properties affect the deformation and failure modes in structural parts. When performing finite element analyses to compare response for different materials, different levels of mesh discretization may be necessary for each analyses because the failure mode changes, even through the part geometry and loading remain the same. Take, for example, strain localization, a material dependent phenomenon. When localization occurs, the mesh needs to be much finer to capture the steep strain gradients in the region of localization than in a case where localization does not occur. Although this requirement is almost intuitive once stated, it is often not used in practice because the effects are less pronounced when failure is not present, and also because failure modes are difficult to anticipate. The lack of availability of constitutive models for failure prediction is also a contributing factor. This paper describes a recent study regarding the effect of mesh refinement on failure prediction in a part modeled with two different materials.

  4. Electro-mechanical analogies for modeling the structural impedance response

    NASA Astrophysics Data System (ADS)

    Zagrai, Andrei

    2007-04-01

    Electro-mechanical (E/M) impedance is a powerful structural identification and health monitoring (SHM) technique that allows for inferring high-frequency structural dynamic characteristics directly by interrogating a network of embedded piezoelectric active sensors. In recent years, there has been a considerable interest in expanding range of applications of the electromechanical impedance technique, its synergistic integration into complementary SHM methodologies, and miniaturizing the associated impedance measurement circuitry. The present work is aimed at developing an E/M impedance modeling approach that explores analogies between electrical and mechanical systems and permits representation of the mechanical system elements in terms of equivalent electrical circuits. The advantage of such a representation is that analytical modeling is substantially simplified by considering a network of electrical elements, mechanical quantities are incorporated directly into the electrical model of a measurement unit, and modern circuit design, simulation and analysis software tools can be employed to improve the method performance. The electro-mechanical model of a piezoelectric impedance sensor is discussed and development of the electrical circuit representation of the sensor-structure interaction is presented. The proposed electrical and existing mechanical models are compared showing a good agreement. Applicability of the developed modeling approach is discussed and examples of numerical calculations are provided. It is suggested that describing a sensor-structure electro-mechanical system in terms of electro-mechanical analogies could simplify analytical modeling and improve instrumentation design.

  5. 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.

  6. Computational aspects in mechanical modeling of the articular cartilage tissue.

    PubMed

    Mohammadi, Hadi; Mequanint, Kibret; Herzog, Walter

    2013-04-01

    This review focuses on the modeling of articular cartilage (at the tissue level), chondrocyte mechanobiology (at the cell level) and a combination of both in a multiscale computation scheme. The primary objective is to evaluate the advantages and disadvantages of conventional models implemented to study the mechanics of the articular cartilage tissue and chondrocytes. From monophasic material models as the simplest form to more complicated multiscale theories, these approaches have been frequently used to model articular cartilage and have contributed significantly to modeling joint mechanics, addressing and resolving numerous issues regarding cartilage mechanics and function. It should be noted that attentiveness is important when using different modeling approaches, as the choice of the model limits the applications available. In this review, we discuss the conventional models applicable to some of the mechanical aspects of articular cartilage such as lubrication, swelling pressure and chondrocyte mechanics and address some of the issues associated with the current modeling approaches. We then suggest future pathways for a more realistic modeling strategy as applied for the simulation of the mechanics of the cartilage tissue using multiscale and parallelized finite element method.

  7. 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)

  8. 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

  9. Dynamic modeling and identification of a slider-crank mechanism

    NASA Astrophysics Data System (ADS)

    Ha, Jih-Lian; Fung, Rong-Fong; Chen, Kun-Yung; Hsien, Shao-Chien

    2006-02-01

    In this paper, Hamilton's principle, Lagrange multiplier, geometric constraints and partitioning method are employed to derive the dynamic equations of a slider-crank mechanism driven by a servomotor. The formulation is expressed by only one independent variable and considers the effects of mass, external force and motor electric inputs. Comparing the dynamic responses between the experimental results and numerical simulations, the dynamic modeling gives a wonderful interpretation of a slider-crank mechanism. The parameters of many industrial machines are difficult to obtain if these machines cannot be taken apart. In this paper, a new identification method based on the real-coded genetic algorithm (RGA) is presented to identify the parameters of a slider-crank mechanism. The method promotes the calculation efficiency very much, and is calculated by the real-code without the operations of encoding and decoding. The results of numerical simulations and the experiments prove that the identification method is feasible. Finally, the experimental results by the RGA and the recursive least squares (RLS) are also compared.

  10. Modeling the mechanisms of biological GTP hydrolysis.

    PubMed

    Carvalho, Alexandra T P; Szeler, Klaudia; Vavitsas, Konstantinos; Åqvist, Johan; Kamerlin, Shina C L

    2015-09-15

    Enzymes that hydrolyze GTP are currently in the spotlight, due to their molecular switch mechanism that controls many cellular processes. One of the best-known classes of these enzymes are small GTPases such as members of the Ras superfamily, which catalyze the hydrolysis of the γ-phosphate bond in GTP. In addition, the availability of an increasing number of crystal structures of translational GTPases such as EF-Tu and EF-G have made it possible to probe the molecular details of GTP hydrolysis on the ribosome. However, despite a wealth of biochemical, structural and computational data, the way in which GTP hydrolysis is activated and regulated is still a controversial topic and well-designed simulations can play an important role in resolving and rationalizing the experimental data. In this review, we discuss the contributions of computational biology to our understanding of GTP hydrolysis on the ribosome and in small GTPases.

  11. 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.

  12. Quantum mechanical model in gravity theory

    NASA Astrophysics Data System (ADS)

    Losyakov, V. V.

    2016-05-01

    We consider a model of a real massive scalar field defined as homogeneous on a d-dimensional sphere such that the sphere radius, time scale, and scalar field are related by the equations of the general theory of relativity. We quantize this system with three degrees of freedom, define the observables, and find dynamical mean values of observables in the regime where the scalar field mass is much less than the Planck mass.

  13. Modeling glutamatergic synapses: insights into mechanisms regulating synaptic efficacy.

    PubMed

    Bouteiller, Jean-Marie C; Baudry, Michel; Allam, Sushmita L; Greget, Renaud J; Bischoff, Serge; Berger, Theodore W

    2008-06-01

    The hippocampal formation is critically involved for the long-term storage of various forms of information, and it is widely believed that the phenomenon of long-term potentiation (LTP) of synaptic transmission is a molecular/cellular mechanism participating in memory formation. Although several high level models of hippocampal function have been developed, they do not incorporate detailed molecular information of the type necessary to understand the contribution of individual molecular events to the mechanisms underlying LTP and learning and memory. We are therefore developing new technological tools based on mathematical modeling and computer simulation of the molecular processes taking place in realistic biological networks to reach such an understanding. This article briefly summarizes the approach we are using and illustrates it by presenting data regarding the effects of changing the number of AMPA receptors on various features of glutamatergic transmission, including NMDA receptor-mediated responses and paired-pulse facilitation. We conclude by discussing the significance of these results and providing some ideas for future directions with this approach.

  14. 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. PMID:23277612

  15. 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.

  16. 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.

  17. Mechanical modeling of the growth of salt structures

    SciTech Connect

    Alfaro, R.A.M.

    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 {times} 10{sup {minus}15}s{sup {minus}1} for similar structural maturity level of salt structures. Equivalent stresses and viscosities predicted by the fluid-assisted diffusion law are 10{sup 2} 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.

  18. 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. PMID:2049412

  19. 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.

  20. RASopathies: unraveling mechanisms with animal models

    PubMed Central

    Jindal, Granton A.; Goyal, Yogesh; Burdine, Rebecca D.; Rauen, Katherine A.; Shvartsman, Stanislav Y.

    2015-01-01

    ABSTRACT RASopathies are developmental disorders caused by germline mutations in the Ras-MAPK pathway, and are characterized by a broad spectrum of functional and morphological abnormalities. The high incidence of these disorders (∼1/1000 births) motivates the development of systematic approaches for their efficient diagnosis and potential treatment. Recent advances in genome sequencing have greatly facilitated the genotyping and discovery of mutations in affected individuals, but establishing the causal relationships between molecules and disease phenotypes is non-trivial and presents both technical and conceptual challenges. Here, we discuss how these challenges could be addressed using genetically modified model organisms that have been instrumental in delineating the Ras-MAPK pathway and its roles during development. Focusing on studies in mice, zebrafish and Drosophila, we provide an up-to-date review of animal models of RASopathies at the molecular and functional level. We also discuss how increasingly sophisticated techniques of genetic engineering can be used to rigorously connect changes in specific components of the Ras-MAPK pathway with observed functional and morphological phenotypes. Establishing these connections is essential for advancing our understanding of RASopathies and for devising rational strategies for their management and treatment. PMID:26203125

  1. Mechanisms and models of REM sleep control.

    PubMed

    McCarley, R W

    2004-07-01

    The first sections of this paper survey the history and recent developments relevant to the major neurotransmitters and neuromodulators involved in REM sleep control. The last portion of this paper proposes a structural model of cellular interaction that produces the REM sleep cycle, and constitutes a further revision of the reciprocal interaction model This paper proposes seven criteria to define a causal role in REM sleep control for putative neuro-transmitters/modulators. The principal criteria are measurements during behavioral state changes of the extracellular concentrations of the putative substances, and electrophysiological recording of their neuronal source. A cautionary note is that, while pharmacological manipulations are suggestive, they alone do not provide definitive causal evidence. The extensive body of in vivo and in vitro evidence supporting cholinergic promotion of REM sleep via LDT/PPT neuronal activity is surveyed. An interesting question raised by some studies is whether cholinergic influences in rat are less puissant than in cat. At least some of the apparent lesser REM-inducing effect of carbachol in the rat may be due to incomplete control of circadian influences; almost all experiments have been run only in the daytime, inactive period, when REM sleep is more prominent, rather than in the REM-sparse nighttime inactive period. Monoaminergic inhibition of cholinergic neurons, once thought to be the most shaky proposal of the reciprocal interaction model, now enjoys considerable support from both in vivo and in vitro data. However, the observed time course of monoaminergic neurons, their "turning off" discharge activity as REM sleep is approached and entered would seem to be difficult to produce from feedback inhibition, as originally postulated by the reciprocal interaction model. New data suggest the possibility that GABAergic inhibition of Locus Coeruleus and Dorsal Raphe monoaminergic neurons may account for the "REM-off" neurons turning

  2. 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. PMID:26584965

  3. Exploring host-guest complexation mechanisms by a molecular dynamics/quantum mechanics/continuum solvent model approach

    NASA Astrophysics Data System (ADS)

    Ye, Renlong; Nie, Xuemei; Zhou, Yumei; Wong, Chung F.; Gong, Xuedong; Jiang, Wei; Tang, Weihua; Wang, Yan A.; Heine, Thomas; Zhou, Baojing

    2016-03-01

    We introduce a molecular dynamics/quantum mechanics/continuum solvent model (MD/QM/CSM) approach to investigate binding mechanisms of host-guest systems. The representative conformations of host, guest, and their complex generated from MD simulations at the molecular-mechanics level are used for binding free energy calculations based on a QM/CSM model. We use this approach to explore the binding mechanisms of β-cyclodextrin (β-CD) and 2, 6-di-methyl-β-CD (DM-β-CD) with various guest molecules. Our results suggest that solvent effects play a more important role in determining the relative binding affinities of DM-β-CD than those of β-CD mainly because the former is more flexible than the latter.

  4. Taming the zoo of supersymmetric quantum mechanical models

    NASA Astrophysics Data System (ADS)

    Smilga, A. V.

    2013-05-01

    We show that in many cases nontrivial and complicated supersymmetric quantum mechanical (SQM) models can be obtained from the simple model describing free dynamics in flat complex space by two operations: (i) Hamiltonian reduction and (ii) similarity transformation of the complex supercharges. We conjecture that it is true for any SQM model.

  5. GENERIC THERMO-MECHANICAL MODEL FOR JOINTED ROCK MASSES

    SciTech Connect

    Vorobiev, O

    2007-03-08

    A new nonlinear thermo-mechanical model for heavily jointed rock masses is presented. The model uses correlation functions between the porosity and the basic rock properties such as elastic moduli, tensile and compressive strength. The model assumes that the media is isotropic and is characterized by two variable parameters: insipient porosity and in-situ-to-intact modulus ratio.

  6. Mechanical model of the nucleosome and chromatin.

    PubMed

    Bishop, Thomas C; Zhmudsky, Oleksandr O

    2002-04-01

    A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. Experimentally determined elastic constants of linear DNA and a simple fold geometry are assumed in order to derive elastic constants for extended and condensed chromatin. The model predicts the Young s modulus of extended and condensed chromatin to within an order of magnitude of experimentally determined values. Thus we demonstrate that the elastic properties of DNA are a primary determinant of the elastic properties of the higher order folded states. The derived elastic constants are used to predict the speed of propagation of small amplitude waves that excite an extension(sound), twist, bend or shear motion in each folded state. Taken together the results demonstrate that folding creates a hierarchy of time, length and energy scales.

  7. 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.

  8. 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.

  9. 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.

  10. United polarizable multipole water model for molecular mechanics simulation.

    PubMed

    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.

  11. 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.

  12. 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

    2016-01-01

    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.

  13. 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

    2016-01-01

    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

  14. 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.

  15. 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.

  16. Observations and Modeling of the Component Mechanisms in Deflagration

    NASA Astrophysics Data System (ADS)

    Smilowitz, Laura; Henson, Bryan; Oschwald, David; Novak, Alan; Holmes, Matthew

    2013-06-01

    We have used dynamic x-ray and proton radiography to observe the behavior of a series of HMX based energetic materials formulations undergoing thermal explosions. The result of these observations is a mechanism for deflagration based on both gas phase convective burning and solid phase conductive burning. The velocities for both the convective and conductive burns are tied together by the single combustion pressure driving both in a single experiment. The convective rate is directly measured as the burn front in the radiographs. The pressure associated with that rate is inferred from independently measured burn rate verses pressure data. This same pressure is then assumed to drive the conductive burning which begins as the convective burn front lights the material surface. Using a single, independently validated particle size distribution for damaged HMX, the combination of pressure driven convective lighting and conductive consumption is then calculated and compared to the measured transmission data sets. This same model with different initial pressurizations is used to successfully model deflagration in PBX9501, PBXN-9, and LX-07. In addition, a correlation between initial pressurization, convective/conductive velocity, and final ``reaction violence'' is observed. This leads us to the use of convective velocity as a metric for final energy release rate and therefore overall reaction violence.

  17. Modeling the circadian clock: from molecular mechanism to physiological disorders.

    PubMed

    Leloup, Jean-Christophe; Goldbeter, Albert

    2008-06-01

    Based on genetic and biochemical advances on the molecular mechanism of circadian rhythms, a computational model for the mammalian circadian clock is used to examine the dynamical bases of circadian-clock-related physiological disorders in humans. Entrainment by the light-dark cycle with a phase advance or a phase delay is associated with the Familial advanced sleep phase syndrome (FASPS) or the Delayed sleep phase syndrome (DSPS), respectively. Lack of entrainment corresponding to the occurrence of quasiperiodic oscillations with or without phase jump can be associated with the non-24 h sleep-wake syndrome. In the close vicinity of the entrainment domain, the model uncovers the possibility of infradian oscillations of very long period. Perturbation in the form of chronic jet lag, as used in mice, prevents entrainment of the circadian clock and results in chaotic or quasiperiodic oscillations. It is important to clarify the conditions for entrainment and for its failure because dysfunctions of the circadian clock may lead to physiological disorders, which pertain not only to the sleep-wake cycle but also to mood and cancer. PMID:18478538

  18. 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.

  19. 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

  20. 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…

  1. 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.

  2. Host defense mechanism-based rational design of live vaccine.

    PubMed

    Jang, Yo Han; Byun, Young Ho; Lee, Kwang-Hee; Park, Eun-Sook; Lee, Yun Ha; Lee, Yoon-Jae; Lee, Jinhee; Kim, Kyun-Hwan; Seong, Baik Lin

    2013-01-01

    Live attenuated vaccine (LAV), mimicking natural infection, provides an excellent protection against microbial infection. The development of LAV, however, still remains highly empirical and the rational design of clinically useful LAV is scarcely available. Apoptosis and caspase activation are general host antiviral responses in virus-infected cells. Utilizing these tightly regulated host defense mechanisms, we present a novel apoptosis-triggered attenuation of viral virulence as a rational design of live attenuated vaccine with desired levels of safety, efficacy, and productivity. Mutant influenza viruses carrying caspase recognition motifs in viral NP and the interferon-antagonist NS1 proteins were highly attenuated both in vitro and in vivo by caspase-mediated cleavage of those proteins in infected cells. Both viral replication and interferon-resistance were substantially reduced, resulting in a marked attenuation of virulence of the virus. Despite pronounced attenuation, the viruses demonstrated high growth phenotype in embryonated eggs at lower temperature, ensuring its productivity. A single dose vaccination with the mutant virus elicited high levels of systemic and mucosal antibody responses and provided complete protection against both homologous and heterologous lethal challenges in mouse model. While providing a practical means to generate seasonal or pandemic influenza live vaccines, the sensitization of viral proteins to pathogen-triggered apoptotic signals presents a potentially universal, mechanism-based rational design of live vaccines against many viral infections.

  3. 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.

  4. Applied mechanics modeling of granulated ceramic powder compaction

    SciTech Connect

    Mahoney, F.M.; Readey, M.J.

    1995-08-01

    In ceramic manufacturing processes such as dry-pressing, correlations between applied compacting pressure and resultant powder compact density are essential for defining reliable process conditions for ceramic components. Pressure-density diagrams have been developed as a tool for both process control and for understanding the compaction behavior of different powders. These types of diagrams, however, pertain only to the averag@ properties of a powder compact and do not address a significant issue in powder compaction processes: the formation of density gradients within the compact. Continuum-based mechanics models of varying complexity have addressed the influence of frictional forces acting at the powder-die wall interface which dissipate the applied pressure throughout the compact. Resulting pressure distribution models are then typically coupled with empirical functions relating pressure and density to obtain a green density distribution in the compact. All of these models predict similar trends; however, none predict the distribution with sufficient accuracy to be considered as a design tool for industrial applications.

  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. 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)

  7. 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

  8. Minireview: Animal Models and Mechanisms of Ovarian Cancer Development

    PubMed Central

    Mullany, Lisa K.

    2012-01-01

    Ovarian cancer in women is a complex and deadly disease, where the molecular events that initiate and control tumor formation remain poorly defined. Therefore, mouse models provide one approach for determining the mechanisms by which specific oncogenic factors cause ovarian surface epithelial cell and granulosa cell transformation. This minireview summarizes the phenotypes of current mouse models that have been generated and some of the underlying mechanisms they have provided. PMID:22396450

  9. Semi-deterministic chemo-mechanical model of boundary lubrication.

    PubMed

    Andersson, Joel; Larsson, Roland; Almqvist, Andreas; Grahn, Mattias; Minami, Ichiro

    2012-01-01

    A model for tribofilm growth is developed. The model is used in combination with numerical contact mechanics tools to enable evaluation of the combined effects of chemistry and contact mechanics. The model is tuned with experimental data and is thereafter applied to rough surfaces. The growth of the tribofilm is evaluated for 3 different contact cases and short-term tribofilm growth behaviour is analyzed. The results show how tribofilms grow in patches. The model is expected to be used as a tool for analysis of the interaction between rough surfaces.

  10. 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.

  11. An action-based fine-grained access control mechanism for structured documents and its application.

    PubMed

    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.

  12. 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

  13. Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction

    PubMed Central

    CAO, Song; CHEN, Shi-Jie

    2016-01-01

    In spite of the success of computational methods for predicting RNA secondary structure, the problem of predicting RNA tertiary structure folding remains. Low-resolution structural models show promise as they allow for rigorous statistical mechanical computation for the conformational entropies, free energies, and the coarse-grained structures of tertiary folds. Molecular dynamics refinement of coarse-grained structures leads to all-atom 3D structures. Modeling based on statistical mechanics principles also has the unique advantage of predicting the full free energy landscape, including local minima and the global free energy minimum. The energy landscapes combined with the 3D structures form the basis for quantitative predictions of RNA functions. In this chapter, we present an overview of statistical mechanical models for RNA folding and then focus on a recently developed RNA statistical mechanical model -- the Vfold model. The main emphasis is placed on the physics underpinning the models, the computational strategies, and the connections to RNA biology. PMID:27293312

  14. 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.

  15. 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

  16. Inferring brain-computational mechanisms with models of activity measurements.

    PubMed

    Kriegeskorte, Nikolaus; Diedrichsen, Jörn

    2016-10-01

    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'.

  17. Inferring brain-computational mechanisms with models of activity measurements.

    PubMed

    Kriegeskorte, Nikolaus; Diedrichsen, Jörn

    2016-10-01

    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

  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. 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.

  20. 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.

  1. 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

  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. Mechanisms and models of effective thermal conductivities of nanofluids.

    SciTech Connect

    Yu, W.; France, D. M.; Singh, D.; Timofeeva, E. V.; Smith, D. S.; Routbort, J. L.; Univ. of Illinois

    2010-08-01

    The physical mechanisms and mathematical models of the effective thermal conductivities of nanofluids have long been of interest to the nanofluid research community because the effective thermal conductivities of nanofluids cannot generally be fully explained and predicted by classical effective medium theories. This review article summarizes considerable progress made on this topic. Specifically, the physical mechanisms and mathematical models of the effective thermal conductivities of nanofluids are reviewed, the potential contributions of those physical mechanisms are evaluated, and the comparisons of the theoretical predictions and experimental data are presented along with opportunities for future research.

  4. Material removal mechanism of copper chemical mechanical polishing in a periodate-based slurry

    NASA Astrophysics Data System (ADS)

    Cheng, Jie; Wang, Tongqing; He, Yongyong; Lu, Xinchun

    2015-05-01

    The material removal mechanism of copper in a periodate-based slurry during barrier layer chemical mechanical polishing (CMP) has not been intensively investigated. This paper presents a study of the copper surface film chemistry and mechanics in a periodate-based slurry. On this basis, the controlling factor of the copper CMP material removal mechanism is proposed. The results show that the chemical and electrochemical reaction products on the copper surface are complex and vary considerably as a function of the solution pH. Under acidic conditions (pH 4) the copper surface underwent strong chemical dissolution while the corrosion was mild and uniform under alkaline conditions (pH 11). The corrosion effect was the lowest in near neutral solutions because the surface was covered with non-uniform Cu(IO3)2·H2O/Cu-periodate/copper oxides films, which had better passivation effect. The surface film thickness and mechanical removal properties were studied by AES and AFM nano-scratch tests. Based on the combined surface film analysis and CMP experiment results, it can be concluded that the controlling factor during copper CMP in a periodate-based slurry is the chemical-enhanced mechanical removal of the surface films. The periodate-based slurry should be modified by the addition of corrosion inhibitors and complexing agents to achieve a good copper surface quality with moderate chemical dissolution.

  5. 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).

  6. Haptics-based dynamic implicit solid modeling.

    PubMed

    Hua, Jing; Qin, Hong

    2004-01-01

    This paper systematically presents a novel, interactive solid modeling framework, Haptics-based Dynamic Implicit Solid Modeling, which is founded upon volumetric implicit functions and powerful physics-based modeling. In particular, we augment our modeling framework with a haptic mechanism in order to take advantage of additional realism associated with a 3D haptic interface. Our dynamic implicit solids are semi-algebraic sets of volumetric implicit functions and are governed by the principles of dynamics, hence responding to sculpting forces in a natural and predictable manner. In order to directly manipulate existing volumetric data sets as well as point clouds, we develop a hierarchical fitting algorithm to reconstruct and represent discrete data sets using our continuous implicit functions, which permit users to further design and edit those existing 3D models in real-time using a large variety of haptic and geometric toolkits, and visualize their interactive deformation at arbitrary resolution. The additional geometric and physical constraints afford more sophisticated control of the dynamic implicit solids. The versatility of our dynamic implicit modeling enables the user to easily modify both the geometry and the topology of modeled objects, while the inherent physical properties can offer an intuitive haptic interface for direct manipulation with force feedback.

  7. 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.

  8. 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.

  9. Market-based control mechanisms for patient safety

    PubMed Central

    Coiera, E; Braithwaite, J

    2009-01-01

    A new model is proposed for enhancing patient safety using market-based control (MBC), inspired by successful approaches to environmental governance. Emissions trading, enshrined in the Kyoto protocol, set a carbon price and created a carbon market—is it possible to set a patient safety price and let the marketplace find ways of reducing clinically adverse events? To “cap and trade,” a regulator would need to establish system-wide and organisation-specific targets, based on the cost of adverse events, create a safety market for trading safety credits and then police the market. Organisations are given a clear policy signal to reduce adverse event rates, are told by how much, but are free to find mechanisms best suited to their local needs. The market would inevitably generate novel ways of creating safety credits, and accountability becomes hard to evade when adverse events are explicitly measured and accounted for in an organisation’s bottom line. PMID:19342522

  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. PMID:12586505

  11. 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.

  12. 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.)

  13. 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.

  14. 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.

  15. 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.

  16. DFT study on the oxygen transfer mechanism in nitroethenediamine based H2-receptor antagonists using the bis-dithiolene complex as the model catalyst for N-oxide reductase enzyme.

    PubMed

    Dhaked, Devendra K; Bharatam, Prasad V

    2015-01-01

    Nitroethenediamine is an important functional unit, which is present in H2-receptor antagonists. These drugs show low bioavailability due to the bacterial degradation caused by the N-oxide reductase type of enzymes present in the human colon. Quantum chemical studies have been carried out to elucidate the mechanism of metabolic degradation of nitroethenediamine in the active site of N-oxide reductase. Three different pathways have been explored for the N-oxide bond cleavage by the model system, Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)2](-), (where mdt=1,2-dimethyl-ethene-1,2-dithiolate) using B3LYP/6-311+G(d,p) and M06/6-311+G(d,p) Density Functional Theory methods. The oxygen atom transfer from the nitrogen atom of nitroethenediamine to the Mo(IV) complex, involves simultaneous weakening of the N-oxide bond and the formation of Mo-O bond through a least motion path. During this transfer, Mo center is converted from a square pyramidal geometry to a distorted octahedral geometry, to facilitate the process of oxygen atom transfer. The energy barrier for the oxygen atom transfer from the imine tautomer has been estimated to be 25.9kcal/mol however, the overall reaction has been found to be endothermic. On the other hand, oxygen transfer reaction from the nitronic acid tautomer requires 30.5kcal/mol energy leading to a highly exothermic metabolite (M-1) directly hence, this path can be considered thermodynamically favorable for this metabolite. The alternative path involving the oxygen atom transfer from the enamine tautomer requires comparatively a higher energy barrier (32.6kcal/mol) and leads to a slightly endothermic metabolite. This study established the structural and energetic details associated with the Mo(IV) bis-dithiolene complex that catalyzes the degradation of nitroethenediamine based drug molecules.

  17. 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.

  18. Energy based hybrid turbulence modeling

    NASA Astrophysics Data System (ADS)

    Haering, Sigfried; Moser, Robert

    2015-11-01

    Traditional hybrid approaches exhibit deficiencies when used for fluctuating smooth-wall separation and reattachment necessitating ad-hoc delaying functions and model tuning making them no longer useful as a predictive tool. Additionally, complex geometries and flows often require high cell aspect-ratios and large grid gradients as a compromise between resolution and cost. Such transitions and inconsistencies in resolution detrimentally effect the fidelity of the simulation. We present the continued development of a new hybrid RANS/LES modeling approach specifically developed to address these challenges. In general, modeled turbulence is returned to resolved scales by reduced or negative model viscosity until a balance between theoretical and actual modeled turbulent kinetic energy is attained provided the available resolution. Anisotropy in the grid and resolved field are directly integrated into this balance. A viscosity-based correction is proposed to account for resolution inhomogeneities. Both the hybrid framework and resolution gradient corrections are energy conserving through an exchange of resolved and modeled turbulence.

  19. 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.

  20. 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.

  1. 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.

  2. Inference on biological mechanisms using an integrated phenotype prediction model.

    PubMed

    Enomoto, Yumi; Ushijima, Masaru; Miyata, Satoshi; Matsuura, Masaaki; Ohtaki, Megu

    2008-03-01

    We propose a methodology for constructing an integrated phenotype prediction model that accounts for multiple pathways regulating a targeted phenotype. The method uses multiple prediction models, each expressing a particular pattern of gene-to-gene interrelationship, such as epistasis. We also propose a methodology using Gene Ontology annotations to infer a biological mechanism from the integrated phenotype prediction model. To construct the integrated models, we employed multiple logistic regression models using a two-step learning approach to examine a number of patterns of gene-to-gene interrelationships. We first selected individual prediction models with acceptable goodness of fit, and then combined the models. The resulting integrated model predicts phenotype as a logical sum of predicted results from the individual models. We used published microarray data on neuroblastoma from Ohira et al (2005) for illustration, constructing an integrated model to predict prognosis and infer the biological mechanisms controlling prognosis. Although the resulting integrated model comprised a small number of genes compared to a previously reported analysis of these data, the model demonstrated excellent performance, with an error rate of 0.12 in a validation analysis. Gene Ontology analysis suggested that prognosis of patients with neuroblastoma may be influenced by biological processes such as cell growth, G-protein signaling, phosphoinositide-mediated signaling, alcohol metabolism, glycolysis, neurophysiological processes, and catecholamine catabolism. PMID:18578362

  3. 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.}

  4. 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

  5. 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.

  6. Using computational models to discover and understand mechanisms.

    PubMed

    Bechtel, William

    2016-04-01

    Areas of biology such as cell and molecular biology have been dominated by research directed at constructing mechanistic explanations that identify parts and operations that when organized appropriately are responsible for the various phenomena they investigate. Increasingly the mechanisms hypothesized involve non-sequential organization of non-linear operations and so exceed the ability of researchers to mentally rehearse their behavior. Accordingly, scientists rely on tools of computational modeling and dynamical systems theory in advancing dynamic mechanistic explanations. Using circadian rhythm research as an exemplar, this paper explores the variety of roles computational modeling is playing. They serve not just to determine whether the mechanism will produce the desired behavior, but in the discovery process of hypothesizing mechanisms and in understanding why proposed mechanisms behave as they do.

  7. Coupling multi-physics models to cardiac mechanics.

    PubMed

    Nordsletten, D A; Niederer, S A; Nash, M P; Hunter, P J; Smith, N P

    2011-01-01

    We outline and review the mathematical framework for representing mechanical deformation and contraction of the cardiac ventricles, and how this behaviour integrates with other processes crucial for understanding and modelling heart function. Building on general conservation principles of space, mass and momentum, we introduce an arbitrary Eulerian-Lagrangian framework governing the behaviour of both fluid and solid components. Exploiting the natural alignment of cardiac mechanical properties with the tissue microstructure, finite deformation measures and myocardial constitutive relations are referred to embedded structural axes. Coupling approaches for solving this large deformation mechanics framework with three dimensional fluid flow, coronary hemodynamics and electrical activation are described. We also discuss the potential of cardiac mechanics modelling for clinical applications.

  8. 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

  9. $\\cN$-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.

  10. 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.

  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. 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.

  13. 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.

  14. Theoretical Modeling of Mechanical-Electrical Coupling of Carbon Nanotubes

    SciTech Connect

    Lu, Jun-Qiang; Jiang, Hanqiang

    2008-01-01

    Carbon nanotubes have been studied extensively due to their unique properties, ranging from electrical, mechanical, optical, to thermal properties. The coupling between the electrical and mechanical properties of carbon nanotubes has emerged as a new field, which raises both interesting fundamental problems and huge application potentials. In this article, we will review our recently work on the theoretical modeling on mechanical-electrical coupling of carbon nanotubes subject to various loading conditions, including tension/compression, torsion, and squashing. Some related work by other groups will be also mentioned.

  15. 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.

  16. An electro-mechanical multiscale model of uterine pregnancy contraction.

    PubMed

    Yochum, Maxime; Laforêt, Jérémy; Marque, Catherine

    2016-10-01

    Detecting preterm labor as early as possible is important because tocolytic drugs are much more likely to delay preterm delivery if administered early. Having good information on the real risk of premature labor also leads to fewer women who do not need aggressive treatment for premature labor threat. Currently, one of the most promising ways to diagnose preterm labor threat is the analysis of the electrohysterogram (EHG). Its characteristics have been related to preterm labor risk but they have not proven to be sufficiently accurate to use in clinical routine. One of the reasons for this is that the physiology of the pregnant uterus is insufficiently understood. Models already exist in literature that simulate either the electrical or the mechanical component of the uterine smooth muscle. Few include both components in a co-simulation of electrical and mechanical aspects. A model that can represent realistically both the electrical and the mechanical behavior of the uterine muscle could be useful for better understanding the EHG and therefore for preterm labor detection. Processing the EHG considers only the electrical component of the uterus but the electrical activity does not seem to explain by itself the synchronization of the uterine muscle that occurs during labor and not at other times. Recent studies have demonstrated that the mechanical behavior of the uterine muscle seems to play an important role in uterus synchronization during labor. The aim of the proposed study is to link three different models of the uterine smooth muscle behavior by using co-simulation. The models go from the electrical activity generated at the cellular level to the mechanical force generated by the muscle and from there to the deformation of the tissue. The results show the feasibility of combining these three models to model a whole uterus contraction on 3D realistic uterus model.

  17. An electro-mechanical multiscale model of uterine pregnancy contraction.

    PubMed

    Yochum, Maxime; Laforêt, Jérémy; Marque, Catherine

    2016-10-01

    Detecting preterm labor as early as possible is important because tocolytic drugs are much more likely to delay preterm delivery if administered early. Having good information on the real risk of premature labor also leads to fewer women who do not need aggressive treatment for premature labor threat. Currently, one of the most promising ways to diagnose preterm labor threat is the analysis of the electrohysterogram (EHG). Its characteristics have been related to preterm labor risk but they have not proven to be sufficiently accurate to use in clinical routine. One of the reasons for this is that the physiology of the pregnant uterus is insufficiently understood. Models already exist in literature that simulate either the electrical or the mechanical component of the uterine smooth muscle. Few include both components in a co-simulation of electrical and mechanical aspects. A model that can represent realistically both the electrical and the mechanical behavior of the uterine muscle could be useful for better understanding the EHG and therefore for preterm labor detection. Processing the EHG considers only the electrical component of the uterus but the electrical activity does not seem to explain by itself the synchronization of the uterine muscle that occurs during labor and not at other times. Recent studies have demonstrated that the mechanical behavior of the uterine muscle seems to play an important role in uterus synchronization during labor. The aim of the proposed study is to link three different models of the uterine smooth muscle behavior by using co-simulation. The models go from the electrical activity generated at the cellular level to the mechanical force generated by the muscle and from there to the deformation of the tissue. The results show the feasibility of combining these three models to model a whole uterus contraction on 3D realistic uterus model. PMID:27567400

  18. A Three-Dimensional Computational Model of Collagen Network Mechanics

    PubMed Central

    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. PMID:25386649

  19. UHPLC/Q-TOF MS-based plasma metabolic profiling analysis of the bleeding mechanism in a rat model of yeast and ethanol-induced blood heat and hemorrhage syndrome.

    PubMed

    Shang, Jing; Liu, Jia; He, Mu; Shang, Erxin; Zhang, Li; Shan, Mingqiu; Yao, Weifeng; Yu, Bing; Yao, Yingzhi; Ding, Anwei

    2014-04-01

    Blood heat and hemorrhage (BHH) syndrome is the most common bleeding disease in clinic. In this study, a rat model with BHH syndrome was built for the first time. Biochemical study showed the intrinsic coagulation pathways and the platelet aggregation rate in the rat model were inhibited, while extrinsic pathway of coagulation cascade was activated. An UHPLC/Q-TOF MS combined with orthogonal partial least squares-discriminant analysis (OPLS-DA) was employed to construct plasma metabolic profiling of the rat model with BHH syndrome. Twenty-four unique metabolites were identified, which were involved in glycerophospholipid metabolism, arachidonic acid metabolism, fatty acid metabolism, amino acid metabolism and cholic acid metabolism. In the end, we concluded that bleeding mechanism of the rat with BHH syndrome may be associated with augmenting blood viscosity, inhibiting platelet aggregation and intrinsic coagulation pathways.

  20. Designing Competency-Based Materials for the Automotive Mechanics Curriculum

    ERIC Educational Resources Information Center

    Richardson, Roger L.

    1977-01-01

    Describes the Career Education Center's (Florida State University) development of the "Automotive Mechanics Catalog" (a job inventory noting performance objectives for specific occupational programs), using the Vocational-Technical Education Consortium of States (V-TECS) model. Also describes the development of curriculum materials using the…

  1. 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.

  2. The activation mechanism of Fe-based olefin metathesis catalysts

    NASA Astrophysics Data System (ADS)

    Poater, Albert; Pump, Eva; Vummaleti, Sai Vikrama Chaitanya; Cavallo, Luigi

    2014-08-01

    Density functional theory calculations have been used to describe the first turnover for olefin metathesis reaction of a homogenous Fe-based catalyst bearing a N-heterocyclic carbene ligand with methoxyethene as a substrate. Equal to conventional Ru-based catalysts, the activation of its Fe congener occurs through a dissociative mechanism, however with a more exothermic reaction energy profile. Predicted upper energy barriers were calculated to be on average ∼2 kcal/mol more beneficial for Fe catalyzed metathesis. Overall, this present computational study emphasises on advantages of Fe-based metathesis and gives a potential recipe for the design of an efficient Fe-based olefin metathesis catalysts.

  3. 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.

  4. Creep deformation mechanism mapping in nickel base disk superalloys

    DOE PAGESBeta

    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 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

  5. 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

  6. A quantitative geometric mechanics lens model: insights into the mechanisms of accommodation and presbyopia.

    PubMed

    Reilly, Matthew A

    2014-10-01

    This study expands on a geometric model of ocular accommodation (Reilly and Ravi, Vision Res. 50:330-336; 2010) by relaxing assumptions regarding lens symmetry about the equator. A method for predicting stretching force was derived. Two models were then developed: Model 1 held the equatorial geometry constant at all stages of accommodation, while Model 2 allowed localized deformation at the equator. Both models were compared to recent data for axial thickness, anterior and posterior radii of curvature, surface area, cross-sectional area, volume, and stretching force for the 29-year-old lens. Age-related changes in accommodation were also simulated. Model 1 gave predictions which agreed with the Helmholtz theory of accommodation, while Model 2's predictions agreed with the Schachar mechanism of accommodation. Trends predicted by Model 1 agreed with all available experimental data, while Model 2 disagreed with recent surface area measurements. Further analysis indicated that Model 1 was fundamentally more efficient in that it required less force per diopter change in optical power than Model 2. Model 1 more accurately predicted age-related changes in accommodation amplitude. This implies that the zero-force (fully accommodated) state geometry changes with age due to a shifting balance in residual stresses between the lens and capsule.

  7. 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.

  8. A mechanical model for guided motion of mammalian cells

    NASA Astrophysics Data System (ADS)

    Bitter, P.; Beck, K. L.; Lenz, P.

    2015-12-01

    We introduce a generic, purely mechanical model for environment-sensitive motion of mammalian cells that is applicable to chemotaxis, haptotaxis, and durotaxis as modes of motility. It is able to theoretically explain all relevant experimental observations, in particular, the high efficiency of motion, the behavior on inhomogeneous substrates, and the fixation of the lagging pole during motion. Furthermore, our model predicts that efficiency of motion in following a gradient depends on cell geometry (with more elongated cells being more efficient).

  9. Experience on a cryogenic linear mechanism based on superconducting levitation

    NASA Astrophysics Data System (ADS)

    Serrano-Tellez, Javier; Romera-Juarez, Fernando; González-de-María, David; Lamensans, Mikel; Argelaguet-Vilaseca, Heribert; Pérez-Díaz, José-Luis; Sánchez-Casarrubios, Juan; Díez-Jiménez, Efrén.; Valiente-Blanco, Ignacio

    2012-09-01

    The instrumentation of many space missions requires operation in cryogenic temperatures. In all the cases, the use of mechanisms in this environment is a matter of concern, especially when long lifetime is required. With the aim of removing lifetime concerns and to benefit from the cryogenic environment, a cryogenic contactless linear mechanism has been developed. It is based on the levitation of a permanent magnet over superconductor disks. The mechanism has been designed, built, and tested to assess the performances of such technology. The levitation system solves the mechanical contact problems due to cold-welding effects, material degradation by fatigue, wearing, backlash, lubrication...etc, at cryogenic temperatures. In fact, the lower is the temperature the better the superconductor levitation systems work. The mechanism provides a wide stroke (18mm) and high resolution motion (1μm), where position is controlled by changing the magnetic field of its environment using electric-magnets. During the motion, the moving part of the mechanism levitates supported by the magnetic interaction with the high temperature type II superconductors after reaching the superconductor state down to 90K. This paper describes the results of the complete levitation system development, including extensive cryogenic testing to measure optically the motion range, resolution, run-outs and rotations in order to characterize the levitation mechanism and to verify its performance in a cryogenic environment.

  10. A mathematical model of cortical bone remodeling at cellular level under mechanical stimulus

    NASA Astrophysics Data System (ADS)

    Qin, Qing-Hua; Wang, Ya-Nan

    2012-12-01

    A bone cell population dynamics model for cortical bone remodeling under mechanical stimulus is developed in this paper. The external experiments extracted from the literature which have not been used in the creation of the model are used to test the validity of the model. Not only can the model compare reasonably well with these experimental results such as the increase percentage of final values of bone mineral content (BMC) and bone fracture energy (BFE) among different loading schemes (which proves the validity of the model), but also predict the realtime development pattern of BMC and BFE, as well as the dynamics of osteoblasts (OBA), osteoclasts (OCA), nitric oxide (NO) and prostaglandin E2 (PGE2) for each loading scheme, which can hardly be monitored through experiment. In conclusion, the model is the first of its kind that is able to provide an insight into the quantitative mechanism of bone remodeling at cellular level by which bone cells are activated by mechanical stimulus in order to start resorption/formation of bone mass. More importantly, this model has laid a solid foundation based on which future work such as systemic control theory analysis of bone remodeling under mechanical stimulus can be investigated. The to-be identified control mechanism will help to develop effective drugs and combined nonpharmacological therapies to combat bone loss pathologies. Also this deeper understanding of how mechanical forces quantitatively interact with skeletal tissue is essential for the generation of bone tissue for tissue replacement purposes in tissue engineering.

  11. Mechanism-Based Design of Green Oxidation Catalysts

    SciTech Connect

    Rybak-Akimova, Elena

    2015-03-16

    situation. Growing families of synthetic iron complexes that resemble active sites of metalloenzymes produce metal-based intermediates (rather than hydroxyl radicals) in reactions with oxygen donors. These complexes are very promising for selective oxygen and peroxide activation. In order to understand the mechanisms of metal-based small molecule activation, kinetically competent metal-oxygen intermediates must be identified. One of the grand challenges identified by the Department of Energy workshop "Catalysis for Energy" is understanding mechanisms and dynamics of catalyzed reactions. The research summarized herein focuses on detailed characterization of the formation and reactivity of various iron-peroxo- and iron-oxo intermediates that are involved in catalysis. Rates of rapid reactions were studied at low temperatures by a specialized technique termed cryogenic stopped-flow spectrophotometry. These measurements identified reaction conditions which favor the formation of catalytically competent oxidants. Chemical structures of reactive complexes was determined, and new, efficient catalysts for hydrocarbon oxidation were synthesized. Importantly, these catalysts are selective, they promote oxidation of hydrocarbons at a specific site. The catalysts are also efficient and robust, hundreds of cycles of substrate oxidation occur within minutes at room temperature. Furthermore, they enable utilization of environmentally friendly oxidants, such as hydrogen peroxide, which produces water as the only byproduct. Mechanistic insights uncovered the role of various acid-containing additives in catalytic oxidations. Proton delivery to the active catalytic sites facilitated oxidations, similarly to the catalytic pathways in metal-containing enzymes. Under certain conditions, two metals in one complex can act in concert, modeling the reactivity of a bacterial enzyme which converts methane into methanol. In related studies, a family of nickel complexes that react with carbon dioxide at

  12. Optimum selection of mechanism type for heavy manipulators based on particle swarm optimization method

    NASA Astrophysics Data System (ADS)

    Zhao, Yong; Chen, Genliang; Wang, Hao; Lin, Zhongqin

    2013-07-01

    The mechanism type plays a decisive role in the mechanical performance of robotic manipulators. Feasible mechanism types can be obtained by applying appropriate type synthesis theory, but there is still a lack of effective and efficient methods for the optimum selection among different types of mechanism candidates. This paper presents a new strategy for the purpose of optimum mechanism type selection based on the modified particle swarm optimization method. The concept of sub-swarm is introduced to represent the different mechanisms generated by the type synthesis, and a competitive mechanism is employed between the sub-swarms to reassign their population size according to the relative performances of the mechanism candidates to implement the optimization. Combining with a modular modeling approach for fast calculation of the performance index of the potential candidates, the proposed method is applied to determine the optimum mechanism type among the potential candidates for the desired manipulator. The effectiveness and efficiency of the proposed method is demonstrated through a case study on the optimum selection of mechanism type of a heavy manipulator where six feasible candidates are considered with force capability as the specific performance index. The optimization result shows that the fitness of the optimum mechanism type for the considered heavy manipulator can be up to 0.578 5. This research provides the instruction in optimum selection of mechanism types for robotic manipulators.

  13. Neural Network Models and Mechanisms of Strategy Development.

    ERIC Educational Resources Information Center

    Bray, Norman W.; Reilly, Kevin D.; Villa, Mark F.; Grupe, Lisa A.

    1997-01-01

    Reviews research on external memory strategies, provides a rationale for using neural network models, and discusses their application to intellectual and developmental differences in the external memory strategies of typical and atypical children, including those with mental retardation. Examines mechanisms of intellectual differences and…

  14. Quantum Mechanics of the Einstein-Hopf Model.

    ERIC Educational Resources Information Center

    Milonni, P. W.

    1981-01-01

    The Einstein-Hopf model for the thermodynamic equilibrium between the electromagnetic field and dipole oscillators is considered within the framework of quantum mechanics. Both the wave and particle aspects of the Einstein fluctuation formula are interpreted in terms of the fundamental absorption and emission processes. (Author/SK)

  15. Finite element modelling of cornea mechanics: a review.

    PubMed

    Nejad, Talisa Mohammad; Foster, Craig; Gongal, Dipika

    2014-01-01

    The cornea is a transparent tissue in front of the eye that refracts light and facilitates vision. A slight change in the geometry of the cornea remarkably affects the optical power. Because of this sensitivity, biomechanical study of the cornea can reveal much about its performance and function. In vivo and in vitro studies have been conducted to investigate the mechanics of the cornea and determine its characteristics. Numerical techniques such as the finite element method (FEM) have been extensively implemented as effective and noninvasive methods for analyzing corneal mechanics and possible disorders. This article reviews the use of FEM for assessing the mechanical behavior of the cornea. Different applications of FEM in corneal disease studies, surgical predictions, impact simulations, and clinical applications have been reviewed. Some suggestions for the future of this type of modeling in the area of corneal mechanics are also discussed. PMID:25076377

  16. The scanning mechanism for ROSETTA/MIDAS: from an engineering model to the flight model

    NASA Astrophysics Data System (ADS)

    Le Letty, R.; Barillot, F.; Lhermet, N.; Claeyssen, F.; Yorck, M.; Gavira Izquierdo, J.; Arends, H.

    2001-09-01

    The MIDAS (Micro Imaging Dust Analysis System) instrument jointly developed by IWF Graz (AT) and the Solar Space Division of ESA/ESTEC (NL) will flow on ROSETTA and will analyse the dust of the 46P/Wirtanen comet using an Atomic Force Microscope (AFM). A piezoelectric XYZ stage, used to scan the sample in 3 axis, is part of the instrument and has been fully designed and qualified under the ESA/ESTEC contract no13090/98/NL/MV. Two qualification models (EQM/QM) and two flight models (FM/FSM) have been integrated and fully tested within 18 months. The basic principle of the stage has been described in a previous paper. The XY stage includes a latch mechanism based on two Shape Memory actuators. This paper focuses on the lessons learned during the qualification campaign, especially on the testing activities and on the latch mechanism. The XYZ stage has followed a full qualification campaign including Thermal Vacuum cycles, Random Vibrations tests and lifetime tests. The latch mechanism has been designed and tested with the following features: easiness of locking and refurbishment operations, compatibility with the parallel two degrees of freedom mechanism, low shock device. It has been tested more than 20 times, including 4 tests in the worst case conditions (eg the most demanding power case at -20°C) and 2 times after a vibration test. The results and the parameters influencing the reproducibility are discussed. The functional performances have been assessed using a dedicated test bench. Comments are made on the measurements techniques used to get results independent from the drift effect displayed by the piezo components. The calibration work (static and gain of the position sensors) have played an important role during the testing activities. Several parameters (temperature, piezo drift effect and external forces acting on the stage and coming from the coarse approach mechanism) affects the static position. Because of the limited stroke range of reading of the

  17. Some new extensions to multi-mechanism models for plastic and viscoplastic material behavior under small strains

    NASA Astrophysics Data System (ADS)

    Wolff, Michael; Bökenheide, Simone; Böhm, Michael

    2016-05-01

    Multi-mechanism models (MM models) have become an important tool for modeling complex material behavior. In particular, two-mechanism models are used. They are applied to model ratcheting in metal plasticity as well as steel behavior during phase transformations. We consider a small-deformation setting. The characteristic trait of multi-mechanism models is the additive decomposition of the inelastic (e.g., plastic or viscoplastic) strain into several parts. These parts are sometimes called mechanisms. In comparison with rheological models, the mechanisms can interact with each other. This leads to new properties and allows to describe important observable effects. Up to now, each mechanism has one kinematic internal variable. As a new feature, we develop multi-mechanism models (in series) with several kinematic variables for each mechanism as well as with several isotropic variables for each flow criterion. We describe this complex situation by three structural matrices which express the mutual relations between mechanisms, flow criteria, kinematic, and isotropic variables. The well-known Chaboche model with a unique inelastic strain and several kinematic variables represents a special case of these general multi-mechanism models. In this work, we also present a matrix-based approach for these new complex MM models. The presented models can form the basis for developing numerical algorithms for simulation and parameter identification.

  18. Modeling the mechanical properties of liver fibrosis in rats.

    PubMed

    Zhu, Ying; Chen, Xin; Zhang, Xinyu; Chen, Siping; Shen, Yuanyuan; Song, Liang

    2016-06-14

    The progression of liver fibrosis changes the biomechanical properties of liver tissue. This study characterized and compared different liver fibrosis stages in rats in terms of viscoelasticity. Three viscoelastic models, the Voigt, Maxwell, and Zener models, were applied to experimental data from rheometer tests and then the elasticity and viscosity were estimated for each fibrosis stage. The study found that both elasticity and viscosity are correlated with the various stages of liver fibrosis. The study revealed that the Zener model is the optimal model for describing the mechanical properties of each fibrosis stage, but there is no significant difference between the Zener and Voigt models in their performance on liver fibrosis staging. Therefore the Voigt model can still be effectively used for liver fibrosis grading. PMID:27017300

  19. Innovating Method of Existing Mechanical Product Based on TRIZ Theory

    NASA Astrophysics Data System (ADS)

    Zhao, Cunyou; Shi, Dongyan; Wu, Han

    Main way of product development is adaptive design and variant design based on existing product. In this paper, conceptual design frame and its flow model of innovating products is put forward through combining the methods of conceptual design and TRIZ theory. Process system model of innovating design that includes requirement analysis, total function analysis and decomposing, engineering problem analysis, finding solution of engineering problem and primarily design is constructed and this establishes the base for innovating design of existing product.

  20. A physically-based abrasive wear model for composite materials

    SciTech Connect

    Lee, Gun Y.; Dharan, C.K.H.; Ritchie, Robert O.

    2001-05-01

    A simple physically-based model for the abrasive wear of composite materials is presented based on the mechanics and mechanisms associated with sliding wear in soft (ductile) matrix composites containing hard (brittle) reinforcement particles. The model is based on the assumption that any portion of the reinforcement that is removed as wear debris cannot contribute to the wear resistance of the matrix material. The size of this non-contributing portion of the reinforcement is estimated by modeling the three primary wear mechanisms, specifically plowing, interfacial cracking and particle removal. Critical variables describing the role of the reinforcement, such as its relative size and the nature of the matrix/reinforcement interface, are characterized by a single contribution coefficient, C. Predictions are compared with the results of experimental two-body (pin-on drum) abrasive wear tests performed on a model aluminum particulate-reinforced epoxy matrix composite material.

  1. Insights into the Thiamine Diphosphate Enzyme Activation Mechanism: Computational Model for Transketolase Using a Quantum Mechanical/Molecular Mechanical Method.

    PubMed

    Nauton, Lionel; Hélaine, Virgil; Théry, Vincent; Hecquet, Laurence

    2016-04-12

    We propose the first computational model for transketolase (TK), a thiamine diphosphate (ThDP)-dependent enzyme, using a quantum mechanical/molecular mechanical method on the basis of crystallographic TK structures from yeast and Escherichia coli, together with experimental kinetic data reported in the literature with wild-type and mutant TK. This model allowed us to define a new route for ThDP activation in the enzyme environment. We evidenced a strong interaction between ThDP and Glu418B of the TK active site, itself stabilized by Glu162A. The crucial point highlighted here is that deprotonation of ThDP C2 is not performed by ThDP N4' as reported in the literature, but by His481B, involving a HOH688A molecule bridge. Thus, ThDP N4' is converted from an amino form to an iminium form, ensuring the stabilization of the C2 carbanion or carbene. Finally, ThDP activation proceeds via an intermolecular process and not by an intramolecular one as reported in the literature. More generally, this proposed ThDP activation mechanism can be applied to some other ThDP-dependent enzymes and used to define the entire TK mechanism with donor and acceptor substrates more accurately.

  2. An instructional design process based on expert knowledge for teaching students how mechanisms are explained.

    PubMed

    Trujillo, Caleb M; Anderson, Trevor R; Pelaez, Nancy J

    2016-06-01

    In biology and physiology courses, students face many difficulties when learning to explain mechanisms, a topic that is demanding due to the immense complexity and abstract nature of molecular and cellular mechanisms. To overcome these difficulties, we asked the following question: how does an instructor transform their understanding of biological mechanisms and other difficult-to-learn topics so that students can comprehend them? To address this question, we first reviewed a model of the components used by biologists to explain molecular and cellular mechanisms: the MACH model, with the components of methods (M), analogies (A), context (C), and how (H). Next, instructional materials were developed and the teaching activities were piloted with a physical MACH model. Students who used the MACH model to guide their explanations of mechanisms exhibited both improvements and some new difficulties. Third, a series of design-based research cycles was applied to bring the activities with an improved physical MACH model into biology and biochemistry courses. Finally, a useful rubric was developed to address prevalent student difficulties. Here, we present, for physiology and biology instructors, the knowledge and resources for explaining molecular and cellular mechanisms in undergraduate courses with an instructional design process aimed at realizing pedagogical content knowledge for teaching. Our four-stage process could be adapted to advance instruction with a range of models in the life sciences.

  3. Modelling of shear lag effect for piezo-elstodynamic structure for electro-mechanical imedance technique

    NASA Astrophysics Data System (ADS)

    Moharana, Sumedha; Bhalla, Suresh

    2015-03-01

    The impedance based structural health monitoring (SHM) techniques have utilized the electro-mechanical coupling property of piezoelectric materials (piezo-impedance transducers), due to their self-sensing nature (ability to act both as actuators and sensors), and its diminutive in shape and size, cost effectiveness and ease of installation. The adhesive bond acts as an elastic medium which facilitates the transfer of stresses and strains developed due to piezo displacement and also couples the impedance of PZT patch with that of the host structure. The sensitivity of the electro-mechanical impedance (EMI) technique can be enhanced by understanding shear mechanism phenomena of the adhesive layer. This paper reviews the existing shear lag models and discuss the recent advances in impedance based coupled piezo-structural model duly considering the shear lag effect with all responsible piezo-mechanical parameters.

  4. Mechanical modeling of porous oxide fuel pellet A Test Problem

    SciTech Connect

    Nukala, Phani K; Barai, Pallab; Simunovic, Srdjan; Ott, Larry J

    2009-10-01

    A poro-elasto-plastic material model has been developed to capture the response of oxide fuels inside the nuclear reactors under operating conditions. Behavior of the oxide fuel and variation in void volume fraction under mechanical loading as predicted by the developed model has been reported in this article. The significant effect of void volume fraction on the overall stress distribution of the fuel pellet has also been described. An important oxide fuel issue that can have significant impact on the fuel performance is the mechanical response of oxide fuel pellet and clad system. Specifically, modeling the thermo-mechanical response of the fuel pellet in terms of its thermal expansion, mechanical deformation, swelling due to void formation and evolution, and the eventual contact of the fuel with the clad is of significant interest in understanding the fuel-clad mechanical interaction (FCMI). These phenomena are nonline