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Sample records for elastic network modeling

  1. New generation of elastic network models.

    PubMed

    López-Blanco, José Ramón; Chacón, Pablo

    2016-04-01

    The intrinsic flexibility of proteins and nucleic acids can be grasped from remarkably simple mechanical models of particles connected by springs. In recent decades, Elastic Network Models (ENMs) combined with Normal Model Analysis widely confirmed their ability to predict biologically relevant motions of biomolecules and soon became a popular methodology to reveal large-scale dynamics in multiple structural biology scenarios. The simplicity, robustness, low computational cost, and relatively high accuracy are the reasons behind the success of ENMs. This review focuses on recent advances in the development and application of ENMs, paying particular attention to combinations with experimental data. Successful application scenarios include large macromolecular machines, structural refinement, docking, and evolutionary conservation. PMID:26716577

  2. Adaptive elastic networks as models of supercooled liquids

    NASA Astrophysics Data System (ADS)

    Yan, Le; Wyart, Matthieu

    2015-08-01

    The thermodynamics and dynamics of supercooled liquids correlate with their elasticity. In particular for covalent networks, the jump of specific heat is small and the liquid is strong near the threshold valence where the network acquires rigidity. By contrast, the jump of specific heat and the fragility are large away from this threshold valence. In a previous work [Proc. Natl. Acad. Sci. USA 110, 6307 (2013), 10.1073/pnas.1300534110], we could explain these behaviors by introducing a model of supercooled liquids in which local rearrangements interact via elasticity. However, in that model the disorder characterizing elasticity was frozen, whereas it is itself a dynamic variable in supercooled liquids. Here we study numerically and theoretically adaptive elastic network models where polydisperse springs can move on a lattice, thus allowing for the geometry of the elastic network to fluctuate and evolve with temperature. We show numerically that our previous results on the relationship between structure and thermodynamics hold in these models. We introduce an approximation where redundant constraints (highly coordinated regions where the frustration is large) are treated as an ideal gas, leading to analytical predictions that are accurate in the range of parameters relevant for real materials. Overall, these results lead to a description of supercooled liquids, in which the distance to the rigidity transition controls the number of directions in phase space that cost energy and the specific heat.

  3. Towards synthetic molecular motors: a model elastic-network study

    NASA Astrophysics Data System (ADS)

    Sarkar, Amartya; Flechsig, Holger; Mikhailov, Alexander S.

    2016-04-01

    Protein molecular motors play a fundamental role in biological cells and development of their synthetic counterparts is a major challenge. Here, we show how a model motor system with the operation mechanism resembling that of muscle myosin can be designed at the concept level, without addressing the implementation aspects. The model is constructed as an elastic network, similar to the coarse-grained descriptions used for real proteins. We show by numerical simulations that the designed synthetic motor can operate as a deterministic or Brownian ratchet and that there is a continuous transition between such two regimes. The motor operation under external load, approaching the stall condition, is also analysed.

  4. Coarse-graining of proteins based on elastic network models

    NASA Astrophysics Data System (ADS)

    Sinitskiy, Anton V.; Voth, Gregory A.

    2013-08-01

    To simulate molecular processes on biologically relevant length- and timescales, coarse-grained (CG) models of biomolecular systems with tens to even hundreds of residues per CG site are required. One possible way to build such models is explored in this article: an elastic network model (ENM) is employed to define the CG variables. Free energy surfaces are approximated by Taylor series, with the coefficients found by force-matching. CG potentials are shown to undergo renormalization due to roughness of the energy landscape and smoothing of it under coarse-graining. In the case study of hen egg-white lysozyme, the entropy factor is shown to be of critical importance for maintaining the native structure, and a relationship between the proposed ENM-mode-based CG models and traditional CG-bead-based models is discussed. The proposed approach uncovers the renormalizable character of CG models and offers new opportunities for automated and computationally efficient studies of complex free energy surfaces.

  5. Elastic Network Models are Robust to Variations in Formalism.

    PubMed

    Leioatts, Nicholas; Romo, Tod D; Grossfield, Alan

    2012-07-10

    Understanding the functions of biomolecules requires insight not only from structures, but from dynamics as well. Often, the most interesting processes occur on time scales too slow for exploration by conventional molecular dynamics (MD) simulations. For this reason, alternative computational methods such as elastic network models (ENMs) have become increasingly popular. These simple, coarse-grained models represent molecules as beads connected by harmonic springs; the system's motions are solved analytically by normal mode analysis. In the past few years, many different formalisms for performing ENM calculations have emerged, and several have been optimized using all-atom MD simulations. In contrast to other studies, we have compared the various formalisms in a systematic, quantitative way. In this study, we optimize many ENM functional forms using a uniform dataset containing only long (> 1 μs) all-atom MD simulations. Our results show that all models once optimized produce spring constants for immediate neighboring residues that are orders of magnitude stiffer than more distal contacts. In addition, the statistical significance of ENM performance varied with model resolution. We also show that fitting long trajectories does not improve ENM performance due to a problem inherent in all network models tested: they underestimate the relative importance of the most concerted motions. Finally, we characterize ENMs' resilience by tessellating the parameter space to show that broad ranges of parameters produce similar quality predictions. Taken together our data reveals that choice of spring function and parameters are not vital to performance of a network model and that simple parameters can by derived "by hand" when no data is available for fitting, thus illustrating the robustness of these models. PMID:22924033

  6. Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence

    PubMed Central

    Isami, Shuhei; Sakamoto, Naoaki; Nishimori, Hiraku; Awazu, Akinori

    2015-01-01

    Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately ∼150 bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences. PMID:26624614

  7. Robust elastic network model: A general modeling for precise understanding of protein dynamics.

    PubMed

    Kim, Min Hyeok; Lee, Byung Ho; Kim, Moon Ki

    2015-06-01

    In the study of protein dynamics relevant to functions, normal mode analysis based on elastic network models (ENMs) has become popular. These models are usually validated by comparing the calculated atomic fluctuation for a single protein in a vacuum to experimental temperature factors in the crystal packing state. Without reflecting the crystal packing effect, in addition, their arbitrary assignment of spring constants leads to inaccurate simulation results, yielding a low correlation of the B-factor. To overcome this limitation, we propose a robust elastic network model (RENM) that not only considers the crystalline effect by using symmetric constraint information but also uses lumped masses and specific spring constants based on the type of amino acids and chemical interactions, respectively. Simulation results with more than 500 protein structures verify qualitatively and quantitatively that one can obtain the better correlation of the B-factor by RENM without additional computational burden. Moreover, an optimal spring constant in physical units (dyne/cm) is quantitatively determined as a function of the temperature at 100 and 290K, which enables us to predict the atomic fluctuations and vibrational density of states (VDOS) without a fitting process. The additional investigation of 80 high-resolution crystal structures with anisotropic displacement parameters (ADPs) indicates that RENM could give a full description of vibrational characteristics of individual residues in proteins. PMID:25891099

  8. Efficient perturbation analysis of elastic network models - Application to acetylcholinesterase of T. californica

    NASA Astrophysics Data System (ADS)

    Hamacher, K.

    2010-09-01

    Elastic network models in their different flavors have become useful models for the dynamics and functions of biomolecular systems such as proteins and their complexes. Perturbation to the interactions occur due to randomized and fixated changes (in molecular evolution) or designed modifications of the protein structures (in bioengineering). These perturbations are modifications in the topology and the strength of the interactions modeled by the elastic network models. We discuss how a naive approach to compute properties for a large number of perturbed structures and interactions by repeated diagonalization can be replaced with an identity found in linear algebra. We argue about the computational complexity and discuss the advantages of the protocol. We apply the proposed algorithm to the acetylcholinesterase, a well-known enzyme in neurobiology, and show how one can gain insight into the "breathing dynamics" of a structural funnel necessary for the function of the protein. The computational speed-up was a 60-fold increase in this example.

  9. Application of Elastic Network Models to Proteins in the Crystalline State

    PubMed Central

    Riccardi, Demian; Cui, Qiang; Phillips, George N.

    2009-01-01

    Abstract Normal mode analysis using elastic network models has grown popular for probing the low-frequency collective dynamics of proteins and other biomolecular assemblies. In most previous studies, these models were validated by comparing calculated atomic fluctuations for isolated proteins with experimental temperature factors determined in the crystalline state, although there were also hints that including crystal contacts in the calculations has an impact on the comparison. In this study, a set of 83 ultra-high resolution crystal structures with experimentally determined anisotropic displacement parameters is used to evaluate several Cα-based elastic network models that either ignore or treat the crystal environment in different ways; the latter include using periodic boundary conditions defined with respect to the asymmetric unit or the primitive unit cell as well as using the Born-von Kármán boundary condition that accounts for lattice vibrations. For all elastic network models, treating the crystal environment leads to better agreement with experimental anisotropic displacement parameters with the Born-von Kármán boundary condition giving the best agreement. Atomic correlations over the entire protein are clearly affected by the presence of the crystal contacts and fairly sensitive to the way that the crystal environment is treated. These observations highlight the importance of properly treating the protein system in an environment consistent with experiment when either evaluating approximate protein models or using approximate dynamic models in structural refinement application types. Finally, investigation of the scaling behaviors of the cumulative density of states and the heat capacity indicates that there are still gaps between simplified elastic models and all-atom models for proteins. PMID:19167297

  10. An improved scheduled traffic model utilizing bandwidth splitting in elastic optical networks

    NASA Astrophysics Data System (ADS)

    Vyas, Upama; Prakash, Shashi

    2016-07-01

    The surge of traffic in today's networks gave birth to elastic optical networking paradigm. In this paper, first we propose to use the scheduled traffic model (STM) in elastic optical networks (EONs) to ensure guaranteed availability of resources to demands which enter into the network with a predetermined start and end times. In optical networks, such demands are referred to as scheduled lightpath demands (SLDs). To increase the amount of bandwidth accepted in network, next we introduce a time aware routing and spectrum assignment (TA-RSA) approach. We observed that provisioning of bulky SLDs has become more challenging in EONs due to enforcement of RSA constraints. To address this challenge, we improve the proposed STM and designed three heuristics for its implementation in EONs. In this work, we collectively refer to these heuristics as bandwidth segmented RSA (BSRSA). The improved STM (iSTM) allows splitting of SLDs in bandwidth dimension by utilizing the knowledge of attributes viz. demand holding time, overlapping in time and bandwidth requested by SLDs. Our numerical results show that BSRSA consistently outperformed over TA-RSA under all distinctive experimental cases that we considered and achieved fairness in serving heterogeneous bandwidth SLDs. The impact of splitting on the number and capacity of transponders at nodes is also gauged. It is observed that ingenious splitting of demands increases the number of resources (on links and nodes) used, and their utilization, leading to an increase in bandwidth accepted in the network.

  11. A multiscale modelling of bone ultrastructure elastic proprieties using finite elements simulation and neural network method.

    PubMed

    Barkaoui, Abdelwahed; Tlili, Brahim; Vercher-Martínez, Ana; Hambli, Ridha

    2016-10-01

    Bone is a living material with a complex hierarchical structure which entails exceptional mechanical properties, including high fracture toughness, specific stiffness and strength. Bone tissue is essentially composed by two phases distributed in approximately 30-70%: an organic phase (mainly type I collagen and cells) and an inorganic phase (hydroxyapatite-HA-and water). The nanostructure of bone can be represented throughout three scale levels where different repetitive structural units or building blocks are found: at the first level, collagen molecules are arranged in a pentameric structure where mineral crystals grow in specific sites. This primary bone structure constitutes the mineralized collagen microfibril. A structural organization of inter-digitating microfibrils forms the mineralized collagen fibril which represents the second scale level. The third scale level corresponds to the mineralized collagen fibre which is composed by the binding of fibrils. The hierarchical nature of the bone tissue is largely responsible of their significant mechanical properties; consequently, this is a current outstanding research topic. Scarce works in literature correlates the elastic properties in the three scale levels at the bone nanoscale. The main goal of this work is to estimate the elastic properties of the bone tissue in a multiscale approach including a sensitivity analysis of the elastic behaviour at each length scale. This proposal is achieved by means of a novel hybrid multiscale modelling that involves neural network (NN) computations and finite elements method (FEM) analysis. The elastic properties are estimated using a neural network simulation that previously has been trained with the database results of the finite element models. In the results of this work, parametric analysis and averaged elastic constants for each length scale are provided. Likewise, the influence of the elastic constants of the tissue constituents is also depicted. Results highlight

  12. An elastic network model based on the structure of the red blood cell membrane skeleton.

    PubMed Central

    Hansen, J C; Skalak, R; Chien, S; Hoger, A

    1996-01-01

    A finite element network model has been developed to predict the macroscopic elastic shear modulus and the area expansion modulus of the red blood cell (RBC) membrane skeleton on the basis of its microstructure. The topological organization of connections between spectrin molecules is represented by the edges of a random Delaunay triangulation, and the elasticity of an individual spectrin molecule is represented by the spring constant, K, for a linear spring element. The model network is subjected to deformations by prescribing nodal displacements on the boundary. The positions of internal nodes are computed by the finite element program. The average response of the network is used to compute the shear modulus (mu) and area expansion modulus (kappa) for the corresponding effective continuum. For networks with a moderate degree of randomness, this model predicts mu/K = 0.45 and kappa/K = 0.90 in small deformations. These results are consistent with previous computational models and experimental estimates of the ratio mu/kappa. This model also predicts that the elastic moduli vary by 20% or more in networks with varying degrees of randomness. In large deformations, mu increases as a cubic function of the extension ratio lambda 1, with mu/K = 0.62 when lambda 1 = 1.5. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 7 FIGURE 8 FIGURE 9 FIGURE 10 FIGURE 11 FIGURE 12 FIGURE 13 FIGURE 14 FIGURE 15 FIGURE 16 FIGURE 17 FIGURE 18 FIGURE 20 FIGURE A1 FIGURE A2 FIGURE A3 PMID:8770194

  13. Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation

    PubMed Central

    Globisch, Christoph; Krishnamani, Venkatramanan; Deserno, Markus; Peter, Christine

    2013-01-01

    The major protective coat of most viruses is a highly symmetric protein capsid that forms spontaneously from many copies of identical proteins. Structural and mechanical properties of such capsids, as well as their self-assembly process, have been studied experimentally and theoretically, including modeling efforts by computer simulations on various scales. Atomistic models include specific details of local protein binding but are limited in system size and accessible time, while coarse grained (CG) models do get access to longer time and length scales but often lack the specific local interactions. Multi-scale models aim at bridging this gap by systematically connecting different levels of resolution. Here, a CG model for CCMV (Cowpea Chlorotic Mottle Virus), a virus with an icosahedral shell of 180 identical protein monomers, is developed, where parameters are derived from atomistic simulations of capsid protein dimers in aqueous solution. In particular, a new method is introduced to combine the MARTINI CG model with a supportive elastic network based on structural fluctuations of individual monomers. In the parametrization process, both network connectivity and strength are optimized. This elastic-network optimized CG model, which solely relies on atomistic data of small units (dimers), is able to correctly predict inter-protein conformational flexibility and properties of larger capsid fragments of 20 and more subunits. Furthermore, it is shown that this CG model reproduces experimental (Atomic Force Microscopy) indentation measurements of the entire viral capsid. Thus it is shown that one obvious goal for hierarchical modeling, namely predicting mechanical properties of larger protein complexes from models that are carefully parametrized on elastic properties of smaller units, is achievable. PMID:23613730

  14. Identifying essential pairwise interactions in elastic network model using the alpha shape theory.

    PubMed

    Xia, Fei; Tong, Dudu; Yang, Lifeng; Wang, Dayong; Hoi, Steven C H; Koehl, Patrice; Lu, Lanyuan

    2014-06-01

    Elastic network models (ENM) are based on the idea that the geometry of a protein structure provides enough information for computing its fluctuations around its equilibrium conformation. This geometry is represented as an elastic network (EN) that is, a network of links between residues. A spring is associated with each of these links. The normal modes of the protein are then identified with the normal modes of the corresponding network of springs. Standard approaches for generating ENs rely on a cutoff distance. There is no consensus on how to choose this cutoff. In this work, we propose instead to filter the set of all residue pairs in a protein using the concept of alpha shapes. The main alpha shape we considered is based on the Delaunay triangulation of the Cα positions; we referred to the corresponding EN as EN(∞). We have shown that heterogeneous anisotropic network models, called αHANMs, that are based on EN(∞) reproduce experimental B-factors very well, with correlation coefficients above 0.99 and root-mean-square deviations below 0.1 Å(2) for a large set of high resolution protein structures. The construction of EN(∞) is simple to implement and may be used automatically for generating ENs for all types of ENMs. PMID:24648309

  15. Experimental Study of Athermal Elastic Network Mechanics

    NASA Astrophysics Data System (ADS)

    Michel, Jonathan; Yunker, Peter

    Recently, significant theoretical effort has been directed towards understanding the mechanics of networks. Elastic networks are of inherent fundamental interest and serve as useful analogs for describing other physical systems. Recent applications include modeling of collagen and descriptions of jamming in granular media and glass formation. I propose to discuss ongoing experimental efforts to study mechanical properties of elastic networks, such as Young's modulus and ultimate strength, in the athermal limit. I will begin with the simple case of regular, isostatic crystalline lattices and proceed to studies of random, connected elastic networks of varying bond number for a given number of lattice sites, including both isostatic and sub-isostatic networks.

  16. Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives

    PubMed Central

    Yang, Lee-Wei; Chng, Choon-Peng

    2008-01-01

    In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of ‘open to close’ (open→close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series. PMID:19812764

  17. A mass weighted chemical elastic network model elucidates closed form domain motions in proteins

    PubMed Central

    Kim, Min Hyeok; Seo, Sangjae; Jeong, Jay Il; Kim, Bum Joon; Liu, Wing Kam; Lim, Byeong Soo; Choi, Jae Boong; Kim, Moon Ki

    2013-01-01

    An elastic network model (ENM), usually Cα coarse-grained one, has been widely used to study protein dynamics as an alternative to classical molecular dynamics simulation. This simple approach dramatically saves the computational cost, but sometimes fails to describe a feasible conformational change due to unrealistically excessive spring connections. To overcome this limitation, we propose a mass-weighted chemical elastic network model (MWCENM) in which the total mass of each residue is assumed to be concentrated on the representative alpha carbon atom and various stiffness values are precisely assigned according to the types of chemical interactions. We test MWCENM on several well-known proteins of which both closed and open conformations are available as well as three α-helix rich proteins. Their normal mode analysis reveals that MWCENM not only generates more plausible conformational changes, especially for closed forms of proteins, but also preserves protein secondary structures thus distinguishing MWCENM from traditional ENMs. In addition, MWCENM also reduces computational burden by using a more sparse stiffness matrix. PMID:23456820

  18. Elastic network models capture the motions apparent within ensembles of RNA structures

    PubMed Central

    Zimmermann, Michael T.; Jernigan, Robert L.

    2014-01-01

    The role of structure and dynamics in mechanisms for RNA becomes increasingly important. Computational approaches using simple dynamics models have been successful at predicting the motions of proteins and are often applied to ribonucleo-protein complexes but have not been thoroughly tested for well-packed nucleic acid structures. In order to characterize a true set of motions, we investigate the apparent motions from 16 ensembles of experimentally determined RNA structures. These indicate a relatively limited set of motions that are captured by a small set of principal components (PCs). These limited motions closely resemble the motions computed from low frequency normal modes from elastic network models (ENMs), either at atomic or coarse-grained resolution. Various ENM model types, parameters, and structure representations are tested here against the experimental RNA structural ensembles, exposing differences between models for proteins and for folded RNAs. Differences in performance are seen, depending on the structure alignment algorithm used to generate PCs, modulating the apparent utility of ENMs but not significantly impacting their ability to generate functional motions. The loss of dynamical information upon coarse-graining is somewhat larger for RNAs than for globular proteins, indicating, perhaps, the lower cooperativity of the less densely packed RNA. However, the RNA structures show less sensitivity to the elastic network model parameters than do proteins. These findings further demonstrate the utility of ENMs and the appropriateness of their application to well-packed RNA-only structures, justifying their use for studying the dynamics of ribonucleo-proteins, such as the ribosome and regulatory RNAs. PMID:24759093

  19. Identification of tail binding effect of kinesin-1 using an elastic network model.

    PubMed

    Kim, Jae In; Chang, Hyun Joon; Na, Sungsoo

    2015-10-01

    Kinesin is a motor protein that delivers cargo inside a cell. Kinesin has many different families, but they perform basically same function and have same motions. The walking motion of kinesin enables the cargo delivery inside the cell. Autoinhibition of kinesin is important because it explains how function of kinesin inside a cell is stopped. Former researches showed that tail binding is related to autoinhibition of kinesin. In this work, we performed normal mode analysis with elastic network model using different conformation of kinesin to determine the effect of tail binding by considering four models such as functional form, autoinhibited form, autoinhibited form without tail, and autoinhibited form with carbon structure. Our calculation of the thermal fluctuation and cross-correlation shows the change of tail-binding region in structural motion. Also strain energy of kinesin showed that elimination of tail binding effect leads the structure to have energetically similar behavior with the functional form. PMID:25676575

  20. Artificial neural network for modeling the elastic modulus of electrospun polycaprolactone/gelatin scaffolds.

    PubMed

    Vatankhah, Elham; Semnani, Dariush; Prabhakaran, Molamma P; Tadayon, Mahdi; Razavi, Shahnaz; Ramakrishna, Seeram

    2014-02-01

    Scaffolds for tissue engineering (TE) require the consideration of multiple aspects, including polymeric composition and the structure and mechanical properties of the scaffolds, in order to mimic the native extracellular matrix of the tissue. Electrospun fibers are frequently utilized in TE due to their tunable physical, chemical, and mechanical properties and porosity. The mechanical properties of electrospun scaffolds made from specific polymers are highly dependent on the processing parameters, which can therefore be tuned for particular applications. Fiber diameter and orientation along with polymeric composition are the major factors that determine the elastic modulus of electrospun nano- and microfibers. Here we have developed a neural network model to investigate the simultaneous effects of composition, fiber diameter and fiber orientation of electrospun polycaprolactone/gelatin mats on the elastic modulus of the scaffolds under ambient and simulated physiological conditions. The model generated might assist bioengineers to fabricate electrospun scaffolds with defined fiber diameters, orientations and constituents, thereby replicating the mechanical properties of the native target tissue. PMID:24075888

  1. Elastic regimes of subisostatic athermal fiber networks

    NASA Astrophysics Data System (ADS)

    Licup, A. J.; Sharma, A.; MacKintosh, F. C.

    2016-01-01

    Athermal models of disordered fibrous networks are highly useful for studying the mechanics of elastic networks composed of stiff biopolymers. The underlying network architecture is a key aspect that can affect the elastic properties of these systems, which include rich linear and nonlinear elasticity. Existing computational approaches have focused on both lattice-based and off-lattice networks obtained from the random placement of rods. It is not obvious, a priori, whether the two architectures have fundamentally similar or different mechanics. If they are different, it is not clear which of these represents a better model for biological networks. Here, we show that both approaches are essentially equivalent for the same network connectivity, provided the networks are subisostatic with respect to central force interactions. Moreover, for a given subisostatic connectivity, we even find that lattice-based networks in both two and three dimensions exhibit nearly identical nonlinear elastic response. We provide a description of the linear mechanics for both architectures in terms of a scaling function. We also show that the nonlinear regime is dominated by fiber bending and that stiffening originates from the stabilization of subisostatic networks by stress. We propose a generalized relation for this regime in terms of the self-generated normal stresses that develop under deformation. Different network architectures have different susceptibilities to the normal stress but essentially exhibit the same nonlinear mechanics. Such a stiffening mechanism has been shown to successfully capture the nonlinear mechanics of collagen networks.

  2. Elastic regimes of subisostatic athermal fiber networks.

    PubMed

    Licup, A J; Sharma, A; MacKintosh, F C

    2016-01-01

    Athermal models of disordered fibrous networks are highly useful for studying the mechanics of elastic networks composed of stiff biopolymers. The underlying network architecture is a key aspect that can affect the elastic properties of these systems, which include rich linear and nonlinear elasticity. Existing computational approaches have focused on both lattice-based and off-lattice networks obtained from the random placement of rods. It is not obvious, a priori, whether the two architectures have fundamentally similar or different mechanics. If they are different, it is not clear which of these represents a better model for biological networks. Here, we show that both approaches are essentially equivalent for the same network connectivity, provided the networks are subisostatic with respect to central force interactions. Moreover, for a given subisostatic connectivity, we even find that lattice-based networks in both two and three dimensions exhibit nearly identical nonlinear elastic response. We provide a description of the linear mechanics for both architectures in terms of a scaling function. We also show that the nonlinear regime is dominated by fiber bending and that stiffening originates from the stabilization of subisostatic networks by stress. We propose a generalized relation for this regime in terms of the self-generated normal stresses that develop under deformation. Different network architectures have different susceptibilities to the normal stress but essentially exhibit the same nonlinear mechanics. Such a stiffening mechanism has been shown to successfully capture the nonlinear mechanics of collagen networks. PMID:26871101

  3. Mechanics of elastic networks

    PubMed Central

    Norris, Andrew N.

    2014-01-01

    We consider a periodic lattice structure in d=2 or 3 dimensions with unit cell comprising Z thin elastic members emanating from a similarly situated central node. A general theoretical approach provides an algebraic formula for the effective elasticity of such frameworks. The method yields the effective cubic elastic constants for three-dimensional space-filling lattices with Z=4, 6, 8, 12 and 14, the last being the ‘stiffest’ lattice proposed by Gurtner & Durand (Gurtner & Durand 2014 Proc. R. Soc. A 470, 20130611. (doi:10.1098/rspa.2013.0611)). The analytical expressions provide explicit formulae for the effective properties of pentamode materials, both isotropic and anisotropic, obtained from the general formulation in the stretch-dominated limit for Z=d+1. PMID:25484608

  4. Robustness Elasticity in Complex Networks

    PubMed Central

    Matisziw, Timothy C.; Grubesic, Tony H.; Guo, Junyu

    2012-01-01

    Network robustness refers to a network’s resilience to stress or damage. Given that most networks are inherently dynamic, with changing topology, loads, and operational states, their robustness is also likely subject to change. However, in most analyses of network structure, it is assumed that interaction among nodes has no effect on robustness. To investigate the hypothesis that network robustness is not sensitive or elastic to the level of interaction (or flow) among network nodes, this paper explores the impacts of network disruption, namely arc deletion, over a temporal sequence of observed nodal interactions for a large Internet backbone system. In particular, a mathematical programming approach is used to identify exact bounds on robustness to arc deletion for each epoch of nodal interaction. Elasticity of the identified bounds relative to the magnitude of arc deletion is assessed. Results indicate that system robustness can be highly elastic to spatial and temporal variations in nodal interactions within complex systems. Further, the presence of this elasticity provides evidence that a failure to account for nodal interaction can confound characterizations of complex networked systems. PMID:22808060

  5. Modeling the bacterial flagellum by an elastic network of rigid bodies

    NASA Astrophysics Data System (ADS)

    Speier, C.; Vogel, R.; Stark, H.

    2011-08-01

    Bacteria such as Escherichia coli propel themselves by rotating a bundle of helical filaments, each driven by a rotary motor embedded in the cell membrane. Each filament is an assembly of thousands of copies of the protein flagellin which assumes two different states. We model the filament by an elastic network of rigid bodies that form bonds with one another according to a scheme suggested by Namba and Vondervistz (1997 Q. Rev. Biophys. 30 1-65) and add additional binding sites at the inner part of the rigid body. Our model reproduces the helical parameters of the 12 possible polymorphic configurations very well. We demonstrate that its energetical ground state corresponds to the normal helical form, usually observed in nature, only when inner and outer binding sites of the rigid body have a large axial displacement. This finding correlates directly to the elongated shape of the flagellin molecule. An Ising Hamiltonian in our model directly addresses the two states of the flagellin protein. It contains an external field that represents external parameters which allow us to alter the ground state of the filament.

  6. Global motions of the nuclear pore complex: insights from elastic network models.

    PubMed

    Lezon, Timothy R; Sali, Andrej; Bahar, Ivet

    2009-09-01

    The nuclear pore complex (NPC) is the gate to the nucleus. Recent determination of the configuration of proteins in the yeast NPC at approximately 5 nm resolution permits us to study the NPC global dynamics using coarse-grained structural models. We investigate these large-scale motions by using an extended elastic network model (ENM) formalism applied to several coarse-grained representations of the NPC. Two types of collective motions (global modes) are predicted by the ENMs to be intrinsically favored by the NPC architecture: global bending and extension/contraction from circular to elliptical shapes. These motions are shown to be robust against tested variations in the representation of the NPC, and are largely captured by a simple model of a toroid with axially varying mass density. We demonstrate that spoke multiplicity significantly affects the accessible number of symmetric low-energy modes of motion; the NPC-like toroidal structures composed of 8 spokes have access to highly cooperative symmetric motions that are inaccessible to toroids composed of 7 or 9 spokes. The analysis reveals modes of motion that may facilitate macromolecular transport through the NPC, consistent with previous experimental observations. PMID:19730674

  7. Strategy for designing broadband vibration isolation systems through exactly solvable models of graded elastic networks

    NASA Astrophysics Data System (ADS)

    Ng, Ka Ki; Chan, Wai Soen; Yu, Kin Wah

    2015-03-01

    Motivated by the need of seismic base isolation, we have proposed a strategy to design vibration isolation systems to achieve near-zero amplitude vibration under external excitations over a broad frequency band. The strategy combines two ideas from previous works: (i) zeros assignment for broadband epsilon-near-zero metamaterials [Sun, and Yu (2012)]; and (ii) the localization of vibrational modes in graded elastic networks [Xiao, Yakubo, and Yu (2006)]. Firstly, we aim to assign zeros (anti-resonance frequencies) over an operating frequency band. Starting from an exactly solvable model of zigzag diatomic chains, we demonstrate a one-to-one correspondence between the zeros and one type of the masses after solving the models. Hence, the zeros can be assigned at will by tuning the masses. Secondly, in order to achieve further vibrational suppression by gradon localization, a band overlapping picture is applied to tune the rest of the masses to an optimal value. The results can be generalized to 2D and 3D structures for more realistic applications.

  8. Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method.

    PubMed

    Su, Ji Guo; Qi, Li Sheng; Li, Chun Hua; Zhu, Yan Ying; Du, Hui Jing; Hou, Yan Xue; Hao, Rui; Wang, Ji Hua

    2014-08-01

    Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins. PMID:25215770

  9. Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method

    NASA Astrophysics Data System (ADS)

    Su, Ji Guo; Qi, Li Sheng; Li, Chun Hua; Zhu, Yan Ying; Du, Hui Jing; Hou, Yan Xue; Hao, Rui; Wang, Ji Hua

    2014-08-01

    Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins.

  10. Identification of key residues for protein conformational transition using elastic network model

    NASA Astrophysics Data System (ADS)

    Su, Ji Guo; Jin Xu, Xian; Hua Li, Chun; Chen, Wei Zu; Wang, Cun Xin

    2011-11-01

    Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase β, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

  11. On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion

    PubMed Central

    González, Àlex L.; Teixidó, Jordi; Borrell, José I.; Estrada-Tejedor, Roger

    2016-01-01

    Non-coding RNAs play a pivotal role in a number of diseases promoting an aberrant sequestration of nuclear RNA-binding proteins. In the particular case of myotonic dystrophy type 1 (DM1), a multisystemic autosomal dominant disease, the formation of large non-coding CUG repeats set up long-tract hairpins able to bind muscleblind-like proteins (MBNL), which trigger the deregulation of several splicing events such as cardiac troponin T (cTNT) and insulin receptor’s, among others. Evidence suggests that conformational changes in RNA are determinant for the recognition and binding of splicing proteins, molecular modeling simulations can attempt to shed light on the structural diversity of CUG repeats and to understand their pathogenic mechanisms. Molecular dynamics (MD) are widely used to obtain accurate results at atomistic level, despite being very time consuming, and they contrast with fast but simplified coarse-grained methods such as Elastic Network Model (ENM). In this paper, we assess the application of ENM (traditionally applied on proteins) for studying the conformational space of CUG repeats and compare it to conventional and accelerated MD conformational sampling. Overall, the results provided here reveal that ANM can provide useful insights into dynamic rCUG structures at a global level, and that their dynamics depend on both backbone and nucleobase fluctuations. On the other hand, ANM fail to describe local U-U dynamics of the rCUG system, which require more computationally expensive methods such as MD. Given that several limitations are inherent to both methods, we discuss here the usefulness of the current theoretical approaches for studying highly dynamic RNA systems such as CUG trinucleotide repeat overexpansions. PMID:27010216

  12. Postinstability models in elasticity

    NASA Technical Reports Server (NTRS)

    Zak, M.

    1984-01-01

    It is demonstrated that the instability caused by the failure of hyperbolicity in elasticity and associated with the problem of unpredictability in classical mechanics expresses the incompleteness of the original model of an elastic medium. The instability as well as the ill-posedness of the Cauchy problem are eliminated by reformulating the original model.

  13. Nonlinear elasticity of semiflexible filament networks.

    PubMed

    Meng, Fanlong; Terentjev, Eugene M

    2016-08-10

    We develop a continuum theory for equilibrium elasticity of a network of crosslinked semiflexible filaments, spanning the full range between flexible entropy-driven chains to stiff athermal rods. We choose the 3-chain constitutive model of network elasticity over several plausible candidates, and derive analytical expressions for the elastic energy at arbitrary strain, with the corresponding stress-strain relationship. The theory fits well to a wide range of experimental data on simple shear in different filament networks, quantitatively matching the differential shear modulus variation with stress, with only two adjustable parameters (which represent the filament stiffness and the pre-tension in the network, respectively). The general theory accurately describes the crossover between the positive and negative Poynting effect (normal stress on imposed shear) on increasing the stiffness of filaments forming the network. We discuss the network stability (the point of marginal rigidity) and the phenomenon of tensegrity, showing that filament pre-tension on crosslinking into the network determines the magnitude of linear modulus G0. PMID:27444846

  14. Modeling the collagen fibril network of biological tissues as a nonlinearly elastic material using a continuous volume fraction distribution function

    PubMed Central

    Shirazi, Reza; Vena, Pasquale; Sah, Robert L.; Klisch, Stephen M.

    2012-01-01

    Despite distinct mechanical functions, biological soft tissues have a common microstructure in which a ground matrix is reinforced by a collagen fibril network. The microstructural properties of the collagen network contribute to continuum mechanical tissue properties that are strongly anisotropic with tensile-compressive asymmetry. In this study, a novel approach based on a continuous distribution of collagen fibril volume fractions is developed to model fibril reinforced soft tissues as a nonlinearly elastic and anisotropic material. Compared with other approaches that use a normalized number of fibrils for the definition of the distribution function, this representation is based on a distribution parameter (i.e. volume fraction) that is commonly measured experimentally while also incorporating pre-stress of the collagen fibril network in a tissue natural configuration. After motivating the form of the collagen strain energy function, examples are provided for two volume fraction distribution functions. Consequently, collagen second-Piola Kirchhoff stress and elasticity tensors are derived, first in general form and then specifically for a model that may be used for immature bovine articular cartilage. It is shown that the proposed strain energy is a convex function of the deformation gradient tensor and, thus, is suitable for the formation of a polyconvex tissue strain energy function. PMID:23390357

  15. Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives.

    PubMed

    Yang, Lee-Wei; Chng, Choon-Peng

    2008-01-01

    In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of 'open to close' (open-->close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series. PMID:19812764

  16. Elasticity of fibrous networks under uniaxial prestress.

    PubMed

    Vahabi, Mahsa; Sharma, Abhinav; Licup, Albert James; van Oosten, Anne S G; Galie, Peter A; Janmey, Paul A; MacKintosh, Fred C

    2016-06-14

    We present theoretical and experimental studies of the elastic response of fibrous networks subjected to uniaxial strain. Uniaxial compression or extension is applied to extracellular networks of fibrin and collagen using a shear rheometer with free water in/outflow. Both uniaxial stress and the network shear modulus are measured. Prior work [van Oosten, et al., Sci. Rep., 2015, 6, 19270] has shown softening/stiffening of these networks under compression/extension, together with a nonlinear response to shear, but the origin of such behaviour remains poorly understood. Here, we study how uniaxial strain influences the nonlinear mechanics of fibrous networks. Using a computational network model with bendable and stretchable fibres, we show that the softening/stiffening behaviour can be understood for fixed lateral boundaries in 2D and 3D networks with comparable average connectivities to the experimental extracellular networks. Moreover, we show that the onset of stiffening depends strongly on the imposed uniaxial strain. Our study highlights the importance of both uniaxial strain and boundary conditions in determining the mechanical response of hydrogels. PMID:27174568

  17. Robust Heterogeneous Anisotropic Elastic Network Model Precisely Reproduces the Experimental B-factors of Biomolecules.

    PubMed

    Xia, Fei; Tong, Dudu; Lu, Lanyuan

    2013-08-13

    A computational method called the progressive fluctuation matching (PFM) is developed for constructing robust heterogeneous anisotropic network models (HANMs) for biomolecular systems. An HANM derived through the PFM approach consists of harmonic springs with realistic positive force constants, and yields the calculated B-factors that are basically identical to the experimental ones. For the four tested protein systems including crambin, trypsin inhibitor, HIV-1 protease, and lysozyme, the root-mean-square deviations between the experimental and the computed B-factors are only 0.060, 0.095, 0.247, and 0.049 Å(2), respectively, and the correlation coefficients are 0.99 for all. By comparing the HANM/ANM normal modes to their counterparts derived from both an atomistic force field and an NMR structure ensemble, it is found that HANM may provide more accurate results on protein dynamics. PMID:26584122

  18. Nonlinear Elasticity of Bottlebrush Networks and Gels

    NASA Astrophysics Data System (ADS)

    Dobrynin, Andrey; Cao, Zhen; Carrillo, Jan-Michael; Sheiko, Sergei

    2015-03-01

    Bottlebrush networks are examples of supersoft elastic materials that demonstrate highly nonlinear stress-strain behavior leading to material hardening with increasing deformation. Using molecular dynamics simulations and theoretical analysis we studied correlations between mechanical properties of bottlebrush networks and molecular parameters. Our simulations showed that both the network shear modulus G and the elongation at break decrease (onset of finite extensibility) with increasing the degree of polymerization (DP) of the side chains. The finite extensibility behavior is ascribed to the increase of the backbone elongation ratio β with DP of the side chains. Simulation results are in a good agreement with experimental observation of progressive softening of bottlebrush elastomers with increasing length of side chains and predictions of the nonlinear network deformation model which provides universal relationship between nonlinear network deformation modulus as a function of the first deformation invariant I1, bottlebrush backbone elongation ratio β, bottlebrush effective bending constant K and concentration of crosslinks. NSF DMR-1409710, DMR-1407645, DMR-1122483.

  19. Cross-Linked Fiber Network Embedded in Elastic Matrix

    PubMed Central

    Zhang, L.; Lake, S.P.; Barocas, V.H.; Shephard, M.S.; Picu, R.C.

    2013-01-01

    The mechanical behavior of a three-dimensional cross-linked fiber network embedded in matrix is studied in this work. The network is composed from linear elastic fibers which store energy only in the axial deformation mode, while the matrix is also isotropic and linear elastic. Such systems are encountered in a broad range of applications, from tissue to consumer products. As the matrix modulus increases, the network is constrained to deform more affinely. This leads to internal forces acting between the network and the matrix, which produce strong stress concentration at the network cross-links. This interaction increases the apparent modulus of the network and decreases the apparent modulus of the matrix. A model is developed to predict the effective modulus of the composite and its predictions are compared with numerical data for a variety of networks. PMID:24089623

  20. Computational Simulation of the Activation Cycle of Gα Subunit in the G Protein Cycle Using an Elastic Network Model

    PubMed Central

    Kim, Min Hyeok; Kim, Young Jin; Kim, Hee Ryung; Jeon, Tae-Joon; Choi, Jae Boong; Chung, Ka Young; Kim, Moon Ki

    2016-01-01

    Agonist-activated G protein-coupled receptors (GPCRs) interact with GDP-bound G protein heterotrimers (Gαβγ) promoting GDP/GTP exchange, which results in dissociation of Gα from the receptor and Gβγ. The GTPase activity of Gα hydrolyzes GTP to GDP, and the GDP-bound Gα interacts with Gβγ, forming a GDP-bound G protein heterotrimer. The G protein cycle is allosterically modulated by conformational changes of the Gα subunit. Although biochemical and biophysical methods have elucidated the structure and dynamics of Gα, the precise conformational mechanisms underlying the G protein cycle are not fully understood yet. Simulation methods could help to provide additional details to gain further insight into G protein signal transduction mechanisms. In this study, using the available X-ray crystal structures of Gα, we simulated the entire G protein cycle and described not only the steric features of the Gα structure, but also conformational changes at each step. Each reference structure in the G protein cycle was modeled as an elastic network model and subjected to normal mode analysis. Our simulation data suggests that activated receptors trigger conformational changes of the Gα subunit that are thermodynamically favorable for opening of the nucleotide-binding pocket and GDP release. Furthermore, the effects of GTP binding and hydrolysis on mobility changes of the C and N termini and switch regions are elucidated. In summary, our simulation results enabled us to provide detailed descriptions of the structural and dynamic features of the G protein cycle. PMID:27483005

  1. Nonlinear and heterogeneous elasticity of multiply-crosslinked biopolymer networks

    NASA Astrophysics Data System (ADS)

    Amuasi, H. E.; Heussinger, C.; Vink, R. L. C.; Zippelius, A.

    2015-08-01

    We simulate randomly crosslinked networks of biopolymers, characterizing linear and nonlinear elasticity under different loading conditions (uniaxial extension, simple shear, and pure shear). Under uniaxial extension, and upon entering the nonlinear regime, the network switches from a dilatant to contractile response. Analogously, under isochoric conditions (pure shear), the normal stresses change their sign. Both effects are readily explained with a generic weakly nonlinear elasticity theory. The elastic moduli display an intermediate super-stiffening regime, where moduli increase much stronger with applied stress σ than predicted by the force-extension relation of a single wormlike-chain ({G}{wlc}∼ {σ }3/2). We interpret this super-stiffening regime in terms of the reorientation of filaments with the maximum tensile direction of the deformation field. A simple model for the reorientation response gives an exponential stiffening, G∼ {{{e}}}σ , in qualitative agreement with our data. The heterogeneous, anisotropic structure of the network is reflected in correspondingly heterogeneous and anisotropic elastic properties. We provide a coarse-graining scheme to quantify the local anisotropy, the fluctuations of the elastic moduli, and the local stresses as a function of coarse-graining length. Heterogeneities of the elastic moduli are strongly correlated with the local density and increase with applied strain.

  2. Pulse wave propagation in a model human arterial network: Assessment of 1-D visco-elastic simulations against in vitro measurements

    PubMed Central

    Alastruey, Jordi; Khir, Ashraf W.; Matthys, Koen S.; Segers, Patrick; Sherwin, Spencer J.; Verdonck, Pascal R.; Parker, Kim H.; Peiró, Joaquim

    2011-01-01

    The accuracy of the nonlinear one-dimensional (1-D) equations of pressure and flow wave propagation in Voigt-type visco-elastic arteries was tested against measurements in a well-defined experimental 1:1 replica of the 37 largest conduit arteries in the human systemic circulation. The parameters required by the numerical algorithm were directly measured in the in vitro setup and no data fitting was involved. The inclusion of wall visco-elasticity in the numerical model reduced the underdamped high-frequency oscillations obtained using a purely elastic tube law, especially in peripheral vessels, which was previously reported in this paper [Matthys et al., 2007. Pulse wave propagation in a model human arterial network: Assessment of 1-D numerical simulations against in vitro measurements. J. Biomech. 40, 3476–3486]. In comparison to the purely elastic model, visco-elasticity significantly reduced the average relative root-mean-square errors between numerical and experimental waveforms over the 70 locations measured in the in vitro model: from 3.0% to 2.5% (p<0.012) for pressure and from 15.7% to 10.8% (p<0.002) for the flow rate. In the frequency domain, average relative errors between numerical and experimental amplitudes from the 5th to the 20th harmonic decreased from 0.7% to 0.5% (p<0.107) for pressure and from 7.0% to 3.3% (p<10−6) for the flow rate. These results provide additional support for the use of 1-D reduced modelling to accurately simulate clinically relevant problems at a reasonable computational cost. PMID:21724188

  3. Efficiency gain from elastic optical networks

    NASA Astrophysics Data System (ADS)

    Morea, Annalisa; Rival, Olivier

    2011-12-01

    We compare the cost-efficiency of optical networks based on mixed datarates (10, 40, 100Gb/s) and datarateelastic technologies. A European backbone network is examined under various traffic assumptions (volume of transported data per demand and total number of demands) to better understand the impact of traffic characteristics on cost-efficiency. Network dimensioning is performed for static and restorable networks (resilient to one-link failure). In this paper we will investigate the trade-offs between price of interfaces, reach and reconfigurability, showing that elastic solutions can be more cost-efficient than mixed-rate solutions because of the better compatibility between different datarates, increased reach of channels and simplified wavelength allocation.

  4. Variability of Fiber Elastic Moduli in Composite Random Fiber Networks Makes the Network Softer

    NASA Astrophysics Data System (ADS)

    Ban, Ehsan; Picu, Catalin

    2015-03-01

    Athermal fiber networks are assemblies of beams or trusses. They have been used to model mechanics of fibrous materials such as biopolymer gels and synthetic nonwovens. Elasticity of these networks has been studied in terms of various microstructural parameters such as the stiffness of their constituent fibers. In this work we investigate the elasticity of composite fiber networks made from fibers with moduli sampled from a distribution function. We use finite elements simulations to study networks made by 3D Voronoi and Delaunay tessellations. The resulting data collapse to power laws showing that variability in fiber stiffness makes fiber networks softer. We also support the findings by analytical arguments. Finally, we apply these results to a network with curved fibers to explain the dependence of the network's modulus on the variation of its structural parameters.

  5. Advantages of IP over elastic optical networks using multi-flow transponders from cost and equipment count aspects.

    PubMed

    Tanaka, Takafumi; Hirano, Akira; Jinno, Masahiko

    2014-01-13

    To evaluate the cost efficiency of IP over elastic optical network architectures, we use a multi-layer network design scheme that covers network to node equipment level. An evaluation in a static traffic environment shows that the multi-flow optical transponder-based elastic optical network reduces total cost as well as equipment counts compared to other elastic network models based on fixed-rate, mixed-line-rate and bandwidth-variable transponders. PMID:24514966

  6. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

    PubMed Central

    Na, Hyuntae; Jernigan, Robert L.; Song, Guang

    2015-01-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. PMID:26473491

  7. Drainage fracture networks in elastic solids with internal fluid generation

    NASA Astrophysics Data System (ADS)

    Kobchenko, Maya; Hafver, Andreas; Jettestuen, Espen; Galland, Olivier; Renard, François; Meakin, Paul; Jamtveit, Bjørn; Dysthe, Dag K.

    2013-06-01

    Experiments in which CO2 gas was generated by the yeast fermentation of sugar in an elastic layer of gelatine gel confined between two glass plates are described and analyzed theoretically. The CO2 gas pressure causes the gel layer to fracture. The gas produced is drained on short length scales by diffusion and on long length scales by flow in a fracture network, which has topological properties that are intermediate between river networks and hierarchical-fracture networks. A simple model for the experimental system with two parameters that characterize the disorder and the intermediate (river-fracture) topology of the network was developed and the results of the model were compared with the experimental results.

  8. Nonlinear elasticity of disordered fiber networks

    NASA Astrophysics Data System (ADS)

    Feng, Jingchen; Levine, Herbert; Mao, Xiaoming; Sander, Leonard M.

    One of the most striking mechanical properties in disordered biopolymer gels is strong nonlinearities. In the case of athermal gels (such as collagen- I) the nonlinearity has long been associated with a crossover from a bending dominated to a stretching dominated regime of elasticity. The physics of this crossover is related to the existence of a central-force isostatic point and to the small bending modulus for most gels. This crossover induces scaling behavior for the elastic moduli. In particular, for linear elasticity such a scaling law has been demonstrated by Broedersz et al. We generalize the scaling to the nonlinear regime with a two-parameter scaling law involving three critical exponents. We do numerical testing of the scaling law for two disordered lattice models, and find a good scaling collapse for the shear modulus in both the linear and nonlinear regimes. We compute all the critical exponents for the two lattice models and discuss the applicability of our results to real systems.

  9. Deformable elastic network refinement for low-resolution macromolecular crystallography

    SciTech Connect

    Schröder, Gunnar F.; Levitt, Michael; Brunger, Axel T.

    2014-09-01

    An overview of applications of the deformable elastic network (DEN) refinement method is presented together with recommendations for its optimal usage. Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  10. Scale-Dependent Nonaffine Elasticity of Semiflexible Polymer Networks

    NASA Astrophysics Data System (ADS)

    Atakhorrami, M.; Koenderink, G. H.; Palierne, J. F.; MacKintosh, F. C.; Schmidt, C. F.

    2014-02-01

    The cytoskeleton of eukaryotic cells provides mechanical support and governs intracellular transport. These functions rely on the complex mechanical properties of networks of semiflexible protein filaments. We study the impact of local network deformations on the scale-dependent mobility of probe particles in entangled networks of actin filaments using high-bandwidth microrheology. We find that micron-sized particles in these networks experience two opposing noncontinuum elastic effects: entropic depletion reduces the effective network rigidity, while local nonaffine deformations of the network substantially enhance the rigidity at low frequencies, eventually leading to a size-independent response and strong violation of the generalized Stokes formula. We show that a simple model of lateral bending of filaments embedded in a viscoelastic background leads to an intermediate scaling regime for the apparent elastic modulus G'(ω)˜ω9/16, closely matching the experiments. These results demonstrate that nonaffine bending deformations can be dominant for the mobility of objects of the size of vesicles and organelles in the cell.

  11. Domain Motions and Functionally-Key Residues of L-Alanine Dehydrogenase Revealed by an Elastic Network Model.

    PubMed

    Li, Xing-Yuan; Zhang, Jing-Chao; Zhu, Yan-Ying; Su, Ji-Guo

    2015-01-01

    Mycobacterium tuberculosis L-alanine dehydrogenase (L-MtAlaDH) plays an important role in catalyzing L-alanine to ammonia and pyruvate, which has been considered to be a potential target for tuberculosis treatment. In the present work, the functional domain motions encoded in the structure of L-MtAlaDH were investigated by using the Gaussian network model (GNM) and the anisotropy network model (ANM). The slowest modes for the open-apo and closed-holo structures of the enzyme show that the domain motions have a common hinge axis centered in residues Met133 and Met301. Accompanying the conformational transition, both the 1,4-dihydronicotinamide adenine dinucleotide (NAD)-binding domain (NBD) and the substrate-binding domain (SBD) move in a highly coupled way. The first three slowest modes of ANM exhibit the open-closed, rotation and twist motions of L-MtAlaDH, respectively. The calculation of the fast modes reveals the residues responsible for the stability of the protein, and some of them are involved in the interaction with the ligand. Then, the functionally-important residues relevant to the binding of the ligand were identified by using a thermodynamic method. Our computational results are consistent with the experimental data, which will help us to understand the physical mechanism for the function of L-MtAlaDH. PMID:26690143

  12. Nonlinear elasticity of cross-linked networks

    NASA Astrophysics Data System (ADS)

    John, Karin; Caillerie, Denis; Peyla, Philippe; Raoult, Annie; Misbah, Chaouqi

    2013-04-01

    Cross-linked semiflexible polymer networks are omnipresent in living cells. Typical examples are actin networks in the cytoplasm of eukaryotic cells, which play an essential role in cell motility, and the spectrin network, a key element in maintaining the integrity of erythrocytes in the blood circulatory system. We introduce a simple mechanical network model at the length scale of the typical mesh size and derive a continuous constitutive law relating the stress to deformation. The continuous constitutive law is found to be generically nonlinear even if the microscopic law at the scale of the mesh size is linear. The nonlinear bulk mechanical properties are in good agreement with the experimental data for semiflexible polymer networks, i.e., the network stiffens and exhibits a negative normal stress in response to a volume-conserving shear deformation, whereby the normal stress is of the same order as the shear stress. Furthermore, it shows a strain localization behavior in response to an uniaxial compression. Within the same model we find a hierarchy of constitutive laws depending on the degree of nonlinearities retained in the final equation. The presented theory provides a basis for the continuum description of polymer networks such as actin or spectrin in complex geometries and it can be easily coupled to growth problems, as they occur, for example, in modeling actin-driven motility.

  13. Dynamic Models of Robots with Elastic Hinges

    NASA Astrophysics Data System (ADS)

    Krakhmalev, O. N.

    2016-04-01

    Two dynamic models of robots with elastic hinges are considered. Dynamic models are the implementation of the method based on the Lagrange equation using the transformation matrices of elastic coordinates. Dynamic models make it possible to determine the elastic deviations from programmed motion trajectories caused by elastic deformations in hinges, which are taken into account in directions of change of the corresponding generalized coordinates. One model is the exact implementation of the Lagrange method and makes it possible to determine the total elastic deviation of the robot from the programmed motion trajectory. Another dynamic model is approximated and makes it possible to determine small elastic quasi-static deviations and elastic vibrations. The results of modeling the dynamics by two models are compared to the example of a two-link manipulator system. The considered models can be used when performing investigations of the mathematical accuracy of the robots.

  14. A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

    PubMed Central

    Frappier, Vincent; Najmanovich, Rafael J.

    2014-01-01

    Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and accuracy in different choices. In one extreme one finds accurate but slow molecular-dynamics based methods with all-atom representations and detailed atom potentials. On the other extreme, fast elastic network model (ENM) methods with Cα−only representations and simplified potentials that based on geometry alone, thus oblivious to protein sequence. Here we present ENCoM, an Elastic Network Contact Model that employs a potential energy function that includes a pairwise atom-type non-bonded interaction term and thus makes it possible to consider the effect of the specific nature of amino-acids on dynamics within the context of NMA. ENCoM is as fast as existing ENM methods and outperforms such methods in the generation of conformational ensembles. Here we introduce a new application for NMA methods with the use of ENCoM in the prediction of the effect of mutations on protein stability. While existing methods are based on machine learning or enthalpic considerations, the use of ENCoM, based on vibrational normal modes, is based on entropic considerations. This represents a novel area of application for NMA methods and a novel approach for the prediction of the effect of mutations. We compare ENCoM to a large number of methods in terms of accuracy and self-consistency. We show that the accuracy of ENCoM is comparable to that of the best existing methods. We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations. PMID:24762569

  15. Survivable virtual optical network embedding with probabilistic network-element failures in elastic optical networks

    NASA Astrophysics Data System (ADS)

    Yang, Hui; Cheng, Lei; Luo, Guangjun; Zhang, Jie; Zhao, Yongli; Ding, Huixia; Zhou, Jing; Wang, Yang

    2015-06-01

    The elastic optical networks can elastically allocate spectrum tailored for various bandwidth requirements. In addition, different virtual optical networks (VONs) formed by different applications or service providers need to be embedded on the common physical optical network, it brings virtual optical network embedding (VONE) problem. There is no precise standard to measure the survivability of VON from the failure probability view and take minimum VON failure probability as an objective in a VONE problem. In this paper, we investigate a survivable VONE problem from a new perspective. Considering probabilistic physical network-element failures, a novel metric, named virtual optical network failure probability (VON-FP), is introduced to evaluate the survivability of VONs in elastic optical networks. Moreover, a failure-probability-aware virtual optical network embedding (FPA-VONE) algorithm is proposed to deploy VONs on the physical network elements with small failure probability, and finally to decrease the VON-FP and enhance the spectrum utilization effectively.

  16. Energy distribution in disordered elastic networks

    NASA Astrophysics Data System (ADS)

    Plaza, Gustavo R.

    2010-09-01

    Disordered networks are found in many natural and artificial materials, from gels or cytoskeletal structures to metallic foams or bones. Here, the energy distribution in this type of networks is modeled, taking into account the orientation of the struts. A correlation between the orientation and the energy per unit volume is found and described as a function of the connectivity in the network and the relative bending stiffness of the struts. If one or both parameters have relatively large values, the struts aligned in the loading direction present the highest values of energy. On the contrary, if these have relatively small values, the highest values of energy can be reached in the struts oriented transversally. This result allows explaining in a simple way remodeling processes in biological materials, for example, the remodeling of trabecular bone and the reorganization in the cytoskeleton. Additionally, the correlation between the orientation, the affinity, and the bending-stretching ratio in the network is discussed.

  17. Elastic Optical Path Network Architecture: Framework for Spectrally-Efficient and Scalable Future Optical Networks

    NASA Astrophysics Data System (ADS)

    Jinno, Masahiko; Takara, Hidehiko; Sone, Yoshiaki; Yonenaga, Kazushige; Hirano, Akira

    This paper presents an elastic optical path network architecture as a novel networking framework to address the looming capacity crunch problem in internet protocol (IP) and optical networks. The basic idea is to introduce elasticity and adaptation into the optical domain to yield spectrally-efficient optical path accommodation, heightened network scalability through IP traffic offloading to the elastic optical layer, and enhanced survivability for serious disasters.

  18. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

    PubMed Central

    Kurkcuoglu, Zeynep; Doruker, Pemra

    2016-01-01

    Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7–15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4–3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its “parents” up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5–2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

  19. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins.

    PubMed

    Kurkcuoglu, Zeynep; Doruker, Pemra

    2016-01-01

    Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7-15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4-3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its "parents" up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5-2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

  20. Elastic modeling and migration in Earth models

    NASA Astrophysics Data System (ADS)

    Filhocunha, Carlos Alves

    Migration and inversion of marine seismic data using the elastic wave equation requires the transformation of the recorded pressure data into a vector particle-displacement field. This can be done easily when the recording geometry samples the wavefield both horizontally and vertically. However, only experimental surveys have cables located at different depths. Using a few assumptions, I derive a method for performing this transformation, which is applicable to standard surveys. The assumptions are: smooth water surface, cable nearly parallel to water surface, and perfect seismic-reflection at the water surface. Results in a realistic example, where these assumptions are only partially fulfilled, demonstrate that the method is robust. Elastic, reverse-time migration/inversion schemes in the space-time domain are usually implemented by finite-difference or finite-element methods. When imaging beyond structures, a dynamically accurate scheme must be used. For models characterized by layers with sharp boundaries, traditional finite-difference methods fail to correctly describe the dynamics of the propagation process. Failure comes from the lack of distinction between model and field variables; the same difference operator is applied to discontinuous (model) and continuous (wavefield) components. The problem is solved with a modified finite-difference scheme (dual-operator), which uses long operators for wave-fields, short operators for elastic parameters, Shoenberg-Muir (1989) equivalence relations, and a modified Virieux (1984) staggered grid scheme. Tests show that the dual-operator is dynamically more accurate than traditional finite-difference schemes and comparable to Haskell-Thomson schemes. In structurally complex media, accurate recovery of angle-dependent reflectivities requires elastic prestack migration. Mode separation can be done before or after depth extrapolation. Though more complex, the latter is more complete because it images mode-converted waves

  1. Elastic Modeling and Migration in Earth Models

    NASA Astrophysics Data System (ADS)

    Cunha, Carlos Alves, Filho

    Migration and inversion of marine seismic data using the elastic wave equation requires the transformation of the recorded pressure data into a vector particle-displacement field. This can be done easily when the recording geometry samples the wavefield both horizontally and vertically. However, only experimental surveys have cables located at different depths. Using a few assumptions, I derive a method for performing this transformation, which is applicable to standard surveys. The assumptions are: smooth water surface, cable nearly parallel to water surface, and perfect seismic -reflection at the water surface. Results in a realistic example, where these assumptions are only partially fulfilled, demonstrate that the method is robust. Elastic, reverse-time migration/inversion schemes in the space-time domain are usually implemented by finite -difference or finite-element methods. When imaging beyond structures, a dynamically accurate scheme must be used. For models characterized by layers with sharp boundaries traditional finite-difference methods fail to correctly describe the dynamics of the propagation process. Failure comes from the lack of distinction between model and field variables; the same difference operator is applied to discontinuous (model) and continuous (wavefield) components. The problem is solved with a modified finite-difference scheme (dual -operator), which uses long operators for wavefields, short operators for elastic parameters, Shoenberg-Muir (1989) equivalence relations and a modified Virieux (1984) staggered grid scheme. Tests show that the the dual-operator is dynamically more accurate than traditional finite-difference schemes and comparable to Haskell-Thomson schemes. In structurally complex media, accurate recovery of angle-dependent reflectivities requires elastic prestack migration. Mode separation can be done before or after depth extrapolation. Though more complex, the latter is more complete because it images mode

  2. A Mixed Protein Structure Network and Elastic Network Model Approach to Predict the Structural Communication in Biomolecular Systems: The PDZ2 Domain from Tyrosine Phosphatase 1E As a Case Study.

    PubMed

    Raimondi, Francesco; Felline, Angelo; Seeber, Michele; Mariani, Simona; Fanelli, Francesca

    2013-05-14

    Graph theory is being increasingly used to study the structural communication in biomolecular systems. This requires incorporating information on the system's dynamics, which is time-consuming and not suitable for high-throughput investigations. We propose a mixed Protein Structure Network (PSN) and Elastic Network Model (ENM)-based strategy, i.e., PSN-ENM, for fast investigation of allosterism in biological systems. PSN analysis and ENM-Normal Mode Analysis (ENM-NMA) are implemented in the structural analysis software Wordom, freely available at http://wordom.sourceforge.net/ . The method performs a systematic search of the shortest communication pathways that traverse a protein structure. A number of strategies to compare the structure networks of a protein in different functional states and to get a global picture of communication pathways are presented as well. The approach was validated on the PDZ2 domain from tyrosine phosphatase 1E (PTP1E) in its free (APO) and peptide-bound states. PDZ domains are, indeed, the systems whose structural communication and allosteric features are best characterized both in vitro and in silico. The agreement between predictions by the PSN-ENM method and in vitro evidence is remarkable and comparable to or higher than that reached by more time-consuming computational approaches tested on the same biological system. Finally, the PSN-ENM method was able to reproduce the salient communication features of unbound and bound PTP1E inferred from molecular dynamics simulations. High speed makes this method suitable for high throughput investigation of the communication pathways in large sets of biomolecular systems in different functional states. PMID:26583738

  3. Adaptive Quality of Transmission Control in Elastic Optical Network

    NASA Astrophysics Data System (ADS)

    Cai, Xinran

    Optical fiber communication is becoming increasingly important due to the burgeoning demand in the internet capacity. However, traditional wavelength division multiplexing (WDM) technique fails to address such demand because of its inefficient spectral utilization. As a result, elastic optical networking (EON) has been under extensive investigation recently. Such network allows sub-wavelength and super-wavelength channel accommodation, and mitigates the stranded bandwidth problem in the WDM network. In addition, elastic optical network is also able to dynamically allocate the spectral resources of the network based on channel conditions and impairments, and adaptively control the quality of transmission of a channel. This application requires two aspects to be investigated: an efficient optical performance monitoring scheme and networking control and management algorithms to reconfigure the network in a dynamic fashion. This thesis focuses on the two aspects discussed above about adaptive QoT control. We demonstrated a supervisory channel method for optical signal to noise ratio (OSNR) and chromatic dispersion (CD) monitoring. In addition, our proof-of-principle testbed experiments show successful impairment aware reconfiguration of the network with modulation format switching (MFS) only and MFS combined with lightpath rerouting (LR) for hundred-GHz QPSK superchannels undergoing time-varying OSNR impairment.

  4. Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patterns

    PubMed Central

    Childs, Dorothee; Grimbs, Sergio; Selbig, Joachim

    2015-01-01

    Motivation: Structural kinetic modelling (SKM) is a framework to analyse whether a metabolic steady state remains stable under perturbation, without requiring detailed knowledge about individual rate equations. It provides a representation of the system’s Jacobian matrix that depends solely on the network structure, steady state measurements, and the elasticities at the steady state. For a measured steady state, stability criteria can be derived by generating a large number of SKMs with randomly sampled elasticities and evaluating the resulting Jacobian matrices. The elasticity space can be analysed statistically in order to detect network positions that contribute significantly to the perturbation response. Here, we extend this approach by examining the kinetic feasibility of the elasticity combinations created during Monte Carlo sampling. Results: Using a set of small example systems, we show that the majority of sampled SKMs would yield negative kinetic parameters if they were translated back into kinetic models. To overcome this problem, a simple criterion is formulated that mitigates such infeasible models. After evaluating the small example pathways, the methodology was used to study two steady states of the neuronal TCA cycle and the intrinsic mechanisms responsible for their stability or instability. The findings of the statistical elasticity analysis confirm that several elasticities are jointly coordinated to control stability and that the main source for potential instabilities are mutations in the enzyme alpha-ketoglutarate dehydrogenase. Contact: dorothee.childs@embl.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072485

  5. A microchannel flow model for soft tissue elasticity

    NASA Astrophysics Data System (ADS)

    Parker, K. J.

    2014-08-01

    A number of advances, including imaging of tissue displacements, have increased our ability to make measurements of tissue elastic properties of animal and human tissues. Accordingly, the question is increasingly asked, ‘should our data be fit to a viscoelastic model, and if so which one?’ In this paper we focus solely on soft tissues in a functional (non-pathological) state, and develop a model of elastic behavior that is based on the flow of viscous fluids through the extensive network of tissue microchannels in response to applied stress. This behavior can be captured in a 2-parameter model, and the model appears to predict the stress-relaxation behavior and the dispersive shear wave behavior of bovine liver specimens and other soft tissues and phantoms. The relationship of the microchannel flow model to more traditional models is also examined.

  6. Rubber elasticity for percolation network consisting of Gaussian chains

    NASA Astrophysics Data System (ADS)

    Nishi, Kengo; Noguchi, Hiroshi; Sakai, Takamasa; Shibayama, Mitsuhiro

    2015-11-01

    A theory describing the elastic modulus for percolation networks of Gaussian chains on general lattices such as square and cubic lattices is proposed and its validity is examined with simulation and mechanical experiments on well-defined polymer networks. The theory was developed by generalizing the effective medium approximation (EMA) for Hookian spring network to Gaussian chain networks. From EMA theory, we found that the ratio of the elastic modulus at p, G to that at p = 1, G0, must be equal to G/G0 = (p - 2/f)/(1 - 2/f) if the position of sites can be determined so as to meet the force balance, where p is the degree of cross-linking reaction. However, the EMA prediction cannot be applicable near its percolation threshold because EMA is a mean field theory. Thus, we combine real-space renormalization and EMA and propose a theory called real-space renormalized EMA, i.e., REMA. The elastic modulus predicted by REMA is in excellent agreement with the results of simulations and experiments of near-ideal diamond lattice gels.

  7. Rubber Elasticity for percolation network consisting of Gaussian Chains

    NASA Astrophysics Data System (ADS)

    Nishi, Kengo; Shibayama, Mitsuhiro; Sakai, Takamasa

    A theory describing the elastic modulus for percolation networks of Gaussian chains on general lattices such as square and cubic lattices is proposed and its validity is examined with simulation and mechanical experiments on well-defined polymer networks. The theory was developed by generalizing the effective medium approximation for Hookian spring network (EMA) to Gaussian chain networks. From EMA theory, we found that the ratio of the elastic modulus at p, G to that at p = 1 ,G0, must be equal to G /G0 = (p - 2 / f) / (1 - 2 / f) if the position of sites can be determined so as to meet the force balance, where p is the degree of cross-linking reaction. However, the EMA prediction cannot be applicable near its percolation threshold because EMA is a mean field theory. Thus, we combine real-space renormalization and EMA, and propose a theory called real-space renormalized EMA, i.e., REMA. The elastic modulus predicted by REMA is in excellent agreement with the results of simulations and experiments of near-ideal diamond lattice gels.

  8. Rubber elasticity for percolation network consisting of Gaussian chains

    SciTech Connect

    Nishi, Kengo E-mail: sakai@tetrapod.t.u-tokyo.ac.jp Noguchi, Hiroshi; Shibayama, Mitsuhiro E-mail: sakai@tetrapod.t.u-tokyo.ac.jp; Sakai, Takamasa E-mail: sakai@tetrapod.t.u-tokyo.ac.jp

    2015-11-14

    A theory describing the elastic modulus for percolation networks of Gaussian chains on general lattices such as square and cubic lattices is proposed and its validity is examined with simulation and mechanical experiments on well-defined polymer networks. The theory was developed by generalizing the effective medium approximation (EMA) for Hookian spring network to Gaussian chain networks. From EMA theory, we found that the ratio of the elastic modulus at p, G to that at p = 1, G{sub 0}, must be equal to G/G{sub 0} = (p − 2/f)/(1 − 2/f) if the position of sites can be determined so as to meet the force balance, where p is the degree of cross-linking reaction. However, the EMA prediction cannot be applicable near its percolation threshold because EMA is a mean field theory. Thus, we combine real-space renormalization and EMA and propose a theory called real-space renormalized EMA, i.e., REMA. The elastic modulus predicted by REMA is in excellent agreement with the results of simulations and experiments of near-ideal diamond lattice gels.

  9. Rubber elasticity for percolation network consisting of Gaussian chains.

    PubMed

    Nishi, Kengo; Noguchi, Hiroshi; Sakai, Takamasa; Shibayama, Mitsuhiro

    2015-11-14

    A theory describing the elastic modulus for percolation networks of Gaussian chains on general lattices such as square and cubic lattices is proposed and its validity is examined with simulation and mechanical experiments on well-defined polymer networks. The theory was developed by generalizing the effective medium approximation (EMA) for Hookian spring network to Gaussian chain networks. From EMA theory, we found that the ratio of the elastic modulus at p, G to that at p = 1, G0, must be equal to G/G0 = (p - 2/f)/(1 - 2/f) if the position of sites can be determined so as to meet the force balance, where p is the degree of cross-linking reaction. However, the EMA prediction cannot be applicable near its percolation threshold because EMA is a mean field theory. Thus, we combine real-space renormalization and EMA and propose a theory called real-space renormalized EMA, i.e., REMA. The elastic modulus predicted by REMA is in excellent agreement with the results of simulations and experiments of near-ideal diamond lattice gels. PMID:26567682

  10. Dynamic Elasticity Model of Resilin Biopolymers

    NASA Astrophysics Data System (ADS)

    Hu, Xiao; Duki, Solomon

    2013-03-01

    Resilin proteins are `super elastic rubbers' in the flight and jumping systems of most insects, and can extend and retract millions of times. Natural resilin exhibits high resilience (> 95%) under high-frequency conditions, and could be stretched to over 300% of its original length with a low elastic modulus of 0.1-3 MPa. However, insight into the underlying molecular mechanisms responsible for resilin elasticity remains undefined. We report on the dynamic structure transitions and functions of full length resilin from fruit fly (D. melanogaster CG15920) and its different functional domains. A dynamic computational model is proposed to explain the super elasticity and energy conversion mechanisms of resilin, providing important insight into structure-function relationships for resilins, as well as other elastomeric proteins. A strong beta-turn transition was experimentally identified in the full length resilin and its non-elastic domains (Exon III). Changes in periodic long-range order were demonstrated during this transition, induced either by thermal or mechanical inputs, to confirm the universality of proposed mechanism. Further, this model offers new options for designing protein-based biopolymers with tunable material applications.

  11. Elastic model for dinucleosome structure and energy

    NASA Astrophysics Data System (ADS)

    Fatemi, Hashem; Khodabandeh, Fatemeh; Mohammad-Rafiee, Farshid

    2016-04-01

    The equilibrium structure of a dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem does not depend on the length of the linker DNA. In addition it is shown that the two histone octamers are almost perpendicular to each other, and the linker DNA in short lengths is almost straight. These findings could shed some light on the role of DNA elasticity in the chromatin structure.

  12. A collagen and elastic network in the wing of the bat.

    PubMed Central

    Holbrook, K A; Odland, G F

    1978-01-01

    Bundles of collagen fibrils, elastic fibres and fibroblasts are organized into a network that lies in the plane of a large portion of the bat wing. By ultrastructural (TEM and SEM) and biochemical analyses it was found that individual bundles of the net are similar to elastic ligaments. Although elastic fibres predominate, they are integrated and aligned in parallel with small bundles of collagen. A reticulum of fibroblasts, joined by focal junctions, forms a cellular framework throughout each bundle. Because of the unique features of the fibre bundles of the bat's wing, in particular their accessibility, and the parallel alignment of the collagen fibrils and elastic fibres in each easily isolatable fibre bundle, they should prove a most valuable model for connective tissue studies, particularly for the study of collagen-elastin interactions. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 Fig. 10 Fig. 11 Fig. 12 PMID:649500

  13. Hypo-Elastic Model for Lung Parenchyma

    SciTech Connect

    Freed, Alan D.; Einstein, Daniel R.

    2012-03-01

    A simple elastic isotropic constitutive model for the spongy tissue in lung is derived from the theory of hypoelasticity. The model is shown to exhibit a pressure dependent behavior that has been interpreted by some as indicating extensional anisotropy. In contrast, we show that this behavior arises natural from an analysis of isotropic hypoelastic invariants, and is a likely result of non-linearity, not anisotropy. The response of the model is determined analytically for several boundary value problems used for material characterization. These responses give insight into both the material behavior as well as admissible bounds on parameters. The model is characterized against published experimental data for dog lung. Future work includes non-elastic model behavior.

  14. Modeling orthotropic elasticity, localized plasticity and fracture in trabecular bone

    NASA Astrophysics Data System (ADS)

    O'Connor, D. T.; Elkhodary, K. I.; Fouad, Y.; Greene, M. S.; Sabet, F. A.; Qian, J.; Zhang, Y.; Liu, W. K.; Jasiuk, I.

    2016-05-01

    This work develops a model for the mechanical response of trabecular bone including plasticity, damage and fracture. It features a resultant lamellar orientation that captures trabecular strut anisotropic elasticity, and introduces asymmetric J2 plasticity with isotropic hardening to capture evolving strut tensile and compressive dissipative properties. A continuum compatibility based damage and fracture criterion is also proposed to model fracture surface generation. We investigated fracture of a trabecular bone network under a compressive load, for which failure modes of both tension and compression were identified at the strut level. The predicted trabecular network response was found to fall within the range of experimental results reported in literature. We also investigated the response of idealized struts under compression, tension and bending using our model. Individual struts were found to exhibit micro-buckling under compression and micro-necking under tension. These instabilities are however masked by the multiplicity and complexity of strut orientations at the trabecular network level.

  15. Modeling orthotropic elasticity, localized plasticity and fracture in trabecular bone

    NASA Astrophysics Data System (ADS)

    O'Connor, D. T.; Elkhodary, K. I.; Fouad, Y.; Greene, M. S.; Sabet, F. A.; Qian, J.; Zhang, Y.; Liu, W. K.; Jasiuk, I.

    2016-09-01

    This work develops a model for the mechanical response of trabecular bone including plasticity, damage and fracture. It features a resultant lamellar orientation that captures trabecular strut anisotropic elasticity, and introduces asymmetric J2 plasticity with isotropic hardening to capture evolving strut tensile and compressive dissipative properties. A continuum compatibility based damage and fracture criterion is also proposed to model fracture surface generation. We investigated fracture of a trabecular bone network under a compressive load, for which failure modes of both tension and compression were identified at the strut level. The predicted trabecular network response was found to fall within the range of experimental results reported in literature. We also investigated the response of idealized struts under compression, tension and bending using our model. Individual struts were found to exhibit micro-buckling under compression and micro-necking under tension. These instabilities are however masked by the multiplicity and complexity of strut orientations at the trabecular network level.

  16. Shape memory polymer network with thermally distinct elasticity and plasticity

    PubMed Central

    Zhao, Qian; Zou, Weike; Luo, Yingwu; Xie, Tao

    2016-01-01

    Stimuli-responsive materials with sophisticated yet controllable shape-changing behaviors are highly desirable for real-world device applications. Among various shape-changing materials, the elastic nature of shape memory polymers allows fixation of temporary shapes that can recover on demand, whereas polymers with exchangeable bonds can undergo permanent shape change via plasticity. We integrate the elasticity and plasticity into a single polymer network. Rational molecular design allows these two opposite behaviors to be realized at different temperature ranges without any overlap. By exploring the cumulative nature of the plasticity, we demonstrate easy manipulation of highly complex shapes that is otherwise extremely challenging. The dynamic shape-changing behavior paves a new way for fabricating geometrically complex multifunctional devices. PMID:26824077

  17. Elastic models of vocal fold tissues.

    PubMed

    Alipour-Haghighi, F; Titze, I R

    1991-09-01

    Elastic properties of canine vocal fold tissue (muscle and mucosa) were obtained through a series of experiments conducted in vitro and were modeled mathematically. The elastic properties play a significant role in quantitative analysis of vocal fold vibrations and theory of pitch control. Samples of vocalis muscle and mucosa were dissected and prepared from dog larynges a few minutes premortem and kept in a Krebs solution at a temperature of 37 +/- 1 degrees C and a pH of 7.4 +/- 0.05. Samples of muscle tissue and mucosa were stretched and released in a slow, sinusoidal fashion. Force and displacement of the samples were measured with a dual-servo system (ergometer). After digitization, stress-strain data for samples of muscle tissue and cover tissue were averaged. The stress-strain data were then fitted numerically by polynomial and exponential models. PMID:1939897

  18. Elastic model for crimped collagen fibrils

    NASA Technical Reports Server (NTRS)

    Freed, Alan D.; Doehring, Todd C.

    2005-01-01

    A physiologic constitutive expression is presented in algorithmic format for the nonlinear elastic response of wavy collagen fibrils found in soft connective tissues. The model is based on the observation that crimped fibrils in a fascicle have a three-dimensional structure at the micron scale that we approximate as a helical spring. The symmetry of this wave form allows the force/displacement relationship derived from Castigliano's theorem to be solved in closed form: all integrals become analytic. Model predictions are in good agreement with experimental observations for mitral-valve chordae tendinece.

  19. Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model.

    PubMed

    Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang

    2016-07-01

    Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules. PMID:27394096

  20. Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model

    NASA Astrophysics Data System (ADS)

    Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang

    2016-07-01

    Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction networks formed by connecting adjoining atomic contacts. It was shown that the adenine binding is critical to the folding of the add A-riboswitch while the removal of the ligand can result in drastic increase of the thermodynamic fluctuations especially in the junction regions between helix domains. Under the assumption that the native contacts with the highest thermodynamic fluctuations break first, the iterative GNM simulations showed that the unfolding process of the adenine-free add A-riboswitch starts with the denature of the terminal helix stem, followed by the loops and junctions involving ligand binding pocket, and then the central helix domains. Despite the simplified coarse-grained modeling, the unfolding dynamics and pathways are shown in close agreement with the results from atomic-level MD simulations and the NMR and single-molecule force spectroscopy experiments. Overall, the study demonstrates a new avenue to investigate the binding and folding dynamics of add A-riboswitch molecule which can be readily extended for other RNA molecules.

  1. Continuity Aware Spectrum Allocation Schemes for Virtual Optical Network Embedding in Elastic Optical Networks

    NASA Astrophysics Data System (ADS)

    Wang, Wei; Zhao, Yongli; He, Ruiying; Yu, Xiaosong; Zhang, Jie; Zheng, Haomian; Lin, Yi; Han, Jianrui

    2016-05-01

    Optical network virtualization has been studied as a promising technique for optical network resources provisioning. In the virtualization context of Elastic Optical Network (EON), Virtual Optical Network Embedding (VONE) is investigated as a key issue for allocating spectrum resources to VON requests. This paper discusses the continuity constraint for the VONE problem in EONs, and presents three continuity-aware spectrum allocation schemes according to strict and relaxed continuity constraints. We have demonstrated the proposed schemes on emulated testbed to verify the feasibility of composing VON with discontiguous spectrum resources. Additionally, the performances of the proposed schemes are compared via simulation in terms of blocking probability, spectrum resource utilization and discontinuity degree.

  2. Nonlinear Elasticity: From Single Chain to Networks and Gels

    NASA Astrophysics Data System (ADS)

    Dobrynin, Andrey; Carrillo, Jan-Michael; Mackintosh, Fred

    2014-03-01

    Biological and polymeric networks show highly nonlinear stress-strain behavior leading to material hardening with increasing deformation. Using a combination of theoretical analysis and molecular dynamics simulations we develop a model of network deformation that describes nonlinear mechanical properties of a broad variety of biological and polymeric networks and gels by relating their macroscopic strain-hardening behavior with molecular parameters of the network strands. The starting point of our approach is a nonlinear force/elongation relation for discrete chain model with varying bending rigidity. This theory provides a universal relationship between the strain-dependent network modulus and the network deformation as a function of the first invariant and chain elongation ratio that depends on a ratio of the unperturbed chain size to chain dimension in a fully extended conformation. The model predictions for the nonlinear shear modulus and differential shear modulus for uniaxial and shear deformations are in a very good agreement with both the results of molecular dynamics simulations of networks and with experimental data for biopolymer networks of actin, collagen, fibrin, vimentin, neurofilaments, and pectin. NSF-DMR-1004576

  3. Flexible wavelength de-multiplexer for elastic optical networking.

    PubMed

    Zhou, Rui; Gutierrez Pascual, M Deseada; Anandarajah, Prince M; Shao, Tong; Smyth, Frank; Barry, Liam P

    2016-05-15

    We report an injection locked flexible wavelength de-multiplexer (de-mux) that shows 24-h frequency stability of 1 kHz for optical comb-based elastic optical networking applications. We demonstrate 50 GHz, 87.5 GHz equal spacing and 6.25G-25G-50 GHz, 75G-50G-100 GHz unequal spacing for the de-multiplexer outputs. We also implement an unequally spaced (75G-50G-100 GHz), mixed symbol rate (12.5 GBaud and 40 GBaud) and modulation format (polarization division multiplexed quadrature phase shift keying and on-off keying) wavelength division multiplexed transmission system using the de-multiplexer outputs. The results show 0.6 dB receiver sensitivity penalty, at 7% hard decision forward error correction coding limit, of the 100 km transmitted de-mux outputs when compared to comb source seeding laser back-to-back. PMID:27176972

  4. Modeling an elastic swimmer driven at resonance

    NASA Astrophysics Data System (ADS)

    Yeh, Peter; Alexeev, Alexander

    2012-11-01

    Flexibility plays a vital role in the locomotion of aquatic animals. Using three dimensional computer simulations, we examine a flexible swimmer submerged in a viscous fluid with Reynolds number 100. The swimmer is modeled as a thin elastic rectangular plate, actuated at its leading edge to oscillate in a sinusoidal motion vertically at constant frequency and amplitude. The Lattice Boltzmann model is used to simulate an incompressible viscous fluid. The swimmer is free to move horizontally, and we measure the resulting steady state forward velocity, input power, and swimming performance. Our calculations reveal that both steady swimming velocity and performance strongly depend on the actuated frequency. Specifically, the maximum forward velocity is achieved near resonance, but the performance is maximized at a frequency about 1.8 times that at resonance. We visualize the vortex structures emerging in the fluid around swimmer and show how they contribute to the swimmer's forward motion.

  5. A neural network for controlling the configuration of frame structure with elastic members

    NASA Technical Reports Server (NTRS)

    Tsutsumi, Kazuyoshi

    1989-01-01

    A neural network for controlling the configuration of frame structure with elastic members is proposed. In the present network, the structure is modeled not by using the relative angles of the members but by using the distances between the joint locations alone. The relationship between the environment and the joints is also defined by their mutual distances. The analog neural network attains the reaching motion of the manipulator as a minimization problem of the energy constructed by the distances between the joints, the target, and the obstacles. The network can generate not only the final but also the transient configurations and the trajectory. This framework with flexibility and parallelism is very suitable for controlling the Space Telerobotic systems with many degrees of freedom.

  6. A model for compression-weakening materials and the elastic fields due to contractile cells

    NASA Astrophysics Data System (ADS)

    Rosakis, Phoebus; Notbohm, Jacob; Ravichandran, Guruswami

    2015-12-01

    We construct a homogeneous, nonlinear elastic constitutive law that models aspects of the mechanical behavior of inhomogeneous fibrin networks. Fibers in such networks buckle when in compression. We model this as a loss of stiffness in compression in the stress-strain relations of the homogeneous constitutive model. Problems that model a contracting biological cell in a finite matrix are solved. It is found that matrix displacements and stresses induced by cell contraction decay slower (with distance from the cell) in a compression weakening material than linear elasticity would predict. This points toward a mechanism for long-range cell mechanosensing. In contrast, an expanding cell would induce displacements that decay faster than in a linear elastic matrix.

  7. Deformation of an Elastic beam due to Viscous Flow in an Embedded Channel Network

    NASA Astrophysics Data System (ADS)

    Matia, Yoav; Gat, Amir

    2015-11-01

    Elastic deformation due to embedded fluidic networks is currently studied in the context of soft-actuators and soft-robotic applications. In this work, we analyze the time dependent interaction between elastic deformation of a slender beam and viscous flow within a long serpentine channel, embedded in the elastic structure. The channel is positioned asymmetrically with regard to the midplane of the elastic beam, and thus pressure within the channel creates a local moment deforming the beam. We focus on creeping flows and small deformations of the elastic beam and obtain, in leading order, a convection-diffusion equation governing the pressure-field within the serpentine channel. The beam time-dependent deformation is then obtained as a function of the pressure-field and the geometry of the embedded network. This relation enables the design of complex time-dependent deformation patterns of beams with embedded channel networks. Our theoretical results were illustrated and verified by numerical computations.

  8. Multipath protection for data center services in OpenFlow-based software defined elastic optical networks

    NASA Astrophysics Data System (ADS)

    Yang, Hui; Cheng, Lei; Yuan, Jian; Zhang, Jie; Zhao, Yongli; Lee, Young

    2015-06-01

    With the rapid growth of data center services, the elastic optical network is a very promising networking architecture to interconnect data centers because it can elastically allocate spectrum tailored for various bandwidth requirements. In case of a link failure, to ensure a high-level quality of service (QoS) for user request after the failure becomes a research focus. In light of it, in this paper, we propose and experimentally demonstrate multipath protection for data center services in OpenFlow-based software defined elastic optical network testbed aiming at improving network reliability. We first propose an OpenFlow-based software defined elastic optical network architecture for data center service protection. Then, based on the proposed architecture, multipath protection scheme is figured based on the importance level of the service. To implement the proposed scheme in the architecture, OpenFlow protocol is extended to support multipath protection in elastic optical network. The performance of our proposed multipath protection scheme is evaluated by means of experiment on our OpenFlow-based testbed. The feasibility of our proposed scheme is also demonstrated in software defined elastic optical networks.

  9. Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.

    PubMed

    Fossépré, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P

    2016-09-01

    Despite progress in computer modeling, most biological processes are still out of reach when using all-atom (AA) models. Coarse-grained (CG) models allow classical molecular dynamics (MD) simulations to be accelerated. Although simplification of spatial resolution at different levels is often investigated, simplification of the CG potential in itself has been less common. CG potentials are often similar to AA potentials. In this work, we consider the design and reliability of purely mechanical CG models of the μ opioid receptor (μOR), a G protein-coupled receptor (GPCR). In this sense, CG force fields (FF) consist of a set of holonomic constraints guided by an elastic network model (ENM). Even though ENMs are used widely to perform normal mode analysis (NMA), they are not often implemented as a single FF in the context of MD simulations. In this work, various ENM-like potentials were investigated by varying their force constant schemes and connectivity patterns. A method was established to systematically parameterize ENM-like potentials at different spatial resolutions by using AA data. To do so, new descriptors were introduced. The choice of conformation descriptors that also include flexibility information is important for a reliable parameterization of ENMs with different degrees of sensitivity. Hence, ENM-like potentials, with specific parameters, can be sufficient to accurately reproduce AA MD simulations of μOR at highly coarse-grained resolutions. Therefore, the essence of the flexibility properties of μOR can be captured with simple models at different CG spatial resolutions, opening the way to mechanical approaches to understanding GPCR functions. Graphical Abstract All atom structure, residue interaction network and coarse-grained elastic network models of the μ opioid receptor (μOR). PMID:27566318

  10. Determination of the elastic constants of a composite plate using wavelet transforms and neural networks

    NASA Astrophysics Data System (ADS)

    Yang, Jing; Cheng, Jianchun; Berthelot, Yves H.

    2002-03-01

    An inverse method based on a combination of the wavelet transform and artificial neural networks is presented. The method is used to recover the elastic constants of a fiber-reinforced composite plate from experimental measurements of ultrasonic Lamb waves generated and detected with lasers. In this method, the elastic constants are not recovered from the dispersion curves but rather directly from the measured waveforms. Transient waveforms obtained by numerical simulations for different elastic constants are used as input to train the neural network. The wavelet transform is used to extract the eigenvectors from the Lamb wave signals to simplify the structure of the neutral network. The eigenvectors are then introduced into a multilayer internally recurrent neural network with a back-propagation algorithm. Finally, experimental waveforms recoded on a titanium-graphite composite plate are used as input to recover the elastic constants of the material.

  11. Studies in cutaneous aging: I. The elastic fiber network

    SciTech Connect

    Braverman, I.M.; Fonferko, E.

    1982-05-01

    We studied by light and electron microscopy the elastic fibers in he sun exposed and sun protected skin of normal and psoriatic individuals of different ages in order to separate the changes of actinic damage from those of chronological aging. The sun exposed skin showed 2 types of elastic fiber abnormalities-one related to actinic damage and the other to chronological aging. The sun protected buttock skin showed only the latter. From ages 30 to 70, a minority of the elastic fibers exhibited abnormalities that appeared to represent a process of fiber disintegration. After age 70, the majority of elastic fibers showed these abnormalities. These abnormalities were present without accompanying inflammatory cells. Also, there was morphological evidence of continuing synthesis of elastic fibers during the lifetime of these subjects, except that from ages 50-93, the fibers appeared to be loosely, rather than compactly, assembled. Incubation of dermal slices from buttock skin of young adults with porcine pancreatic elastase and bovine chymotrypsin produced elastic fiber degradation that closely simulated the changes that were observed in aged sun protected skin. Researcher propose that one of the features of cutaneous aging is a slow, spontaneous, progressive degradative process inherent in the elastic fiber that can be enzymatically accelerated from decades to hours by elastase and chymotrypsin.

  12. Entropic elasticity of end adsorbed polymer chains: The spectrin network of red blood cells as C*-gel

    NASA Astrophysics Data System (ADS)

    Everaers, Ralf; Graham, Ian S.; Zuckermann, Martin J.; Sackmann, Erich

    1996-03-01

    We use Monte Carlo methods to investigate the end-to-end distance distribution and entropic elasticity of self-avoiding walks in a three-dimensional half-space with both ends adsorbed on the limiting surface. The obtained distributions are well described by the Redner-des Cloizeaux (RdC) ansatz q(x)=Cxθ exp(-(Kx)t), x being the rescaled length. Using the recent solution of the junction affine model for networks of RdC springs we apply the results to the cytoskeleton of the red blood cell (RBC), a two-dimensional network of spectrin molecules which is attached to the inner surface of the erythrocyte membrane. The shear moduli predicted for a noninteracting surface are in close agreement with simulation results by Boal for a bead-spring model of the spectrin network. Moreover, we calculate stress-strain relations for finite deformations. In particular for a network which is fully adsorbed on the bilayer we find a strongly nonlinear elastic response. Our results suggest that the elastic properties of RBCs cannot be obtained within the usual Gaussian models and depend sensitively on the degree of adsorption of the spectrin network.

  13. Modeling the effect of elastic point contact on dynamic response

    NASA Astrophysics Data System (ADS)

    Photiadis, Douglas M.; Goldstein, David J.; Willey, Jefferson M.

    2016-02-01

    We present a general, theoretical model describing the three-dimensional elastic behavior of point contacts. We provide a prescription for employing the model in a variety of physical systems and describe in detail how the model enables the use of lower-dimensional dynamic models while including approximate three-dimensional behavior of elastic point contacts. We conduct a series of experiments to validate the model for extensional and cantilever oscillators, and find good agreement between our measurements and the predictions of the model. We observe that the phenomenological effects of elastic point contacts can be significant and believe that our model will be useful to a broad range of research and engineering disciplines.

  14. Determination of elastic properties of a film-substrate system by using the neural networks

    NASA Astrophysics Data System (ADS)

    Xu, Baiqiang; Shen, Zhonghua; Ni, Xiaowu; Wang, Jijun; Guan, Jianfei; Lu, Jian

    2004-12-01

    An inverse method based on artificial neural network (ANN) is presented to determine the elastic properties of films from laser-genrated surface waves. The surface displacement responses are used as the inputs for the ANN model; the outputs of the ANN are the Young's modulus, density, Poisson's ratio, and thickness of the film. The finite element method is used to calculate the surface displacement responses in a film-substrate system. Levenberg Marquardt algorithm is used as numerical optimization to speed up the training process for the ANN model. In this method, the materials parameters are not recovered from the dispersion curves but rather directly from the transient surface displacement. We have also found that this procedure is very efficient for determining the materials parameters of layered systems.

  15. Experimental demonstration of elastic optical networks based on enhanced software defined networking (eSDN) for data center application.

    PubMed

    Zhang, Jie; Yang, Hui; Zhao, Yongli; Ji, Yuefeng; Li, Hui; Lin, Yi; Li, Gang; Han, Jianrui; Lee, Young; Ma, Teng

    2013-11-01

    Due to the high burstiness and high-bandwidth characteristics of the applications, data center interconnection by elastic optical networks have attracted much attention of network operators and service providers. Many data center applications require lower delay and higher availability with the end-to-end guaranteed quality of service. In this paper, we propose and implement a novel elastic optical network based on enhanced software defined networking (eSDN) architecture for data center application, by introducing a transport-aware cross stratum optimization (TA-CSO) strategy. eSDN can enable cross stratum optimization of application and elastic optical network stratum resources and provide the elastic physical layer parameter adjustment, e.g., modulation format and bandwidth. We have designed and verified experimentally software defined path provisioning on our testbed with four real OpenFlow-enabled elastic optical nodes for data center application. The overall feasibility and efficiency of the proposed architecture is also experimentally demonstrated and compared with individual CSO and physical layer adjustment strategies in terms of path setup/release/adjustment latency, blocking probability and resource occupation rate. PMID:24216922

  16. Models for elastic shells with incompatible strains

    PubMed Central

    Lewicka, Marta; Mahadevan, L.; Pakzad, Mohammad Reza

    2014-01-01

    The three-dimensional shapes of thin lamina, such as leaves, flowers, feathers, wings, etc., are driven by the differential strain induced by the relative growth. The growth takes place through variations in the Riemannian metric given on the thin sheet as a function of location in the central plane and also across its thickness. The shape is then a consequence of elastic energy minimization on the frustrated geometrical object. Here, we provide a rigorous derivation of the asymptotic theories for shapes of residually strained thin lamina with non-trivial curvatures, i.e. growing elastic shells in both the weakly and strongly curved regimes, generalizing earlier results for the growth of nominally flat plates. The different theories are distinguished by the scaling of the mid-surface curvature relative to the inverse thickness and growth strain, and also allow us to generalize the classical Föppl–von Kármán energy to theories of prestrained shallow shells. PMID:24808750

  17. A mesoscopic network model for permanent set in crosslinked elastomers

    SciTech Connect

    Weisgraber, T H; Gee, R H; Maiti, A; Clague, D S; Chinn, S; Maxwell, R S

    2009-01-29

    A mesoscopic computational model for polymer networks and composites is developed as a coarse-grained representation of the composite microstructure. Unlike more complex molecular dynamics simulations, the model only considers the effects of crosslinks on mechanical behavior. The elastic modulus, which depends only on the crosslink density and parameters in the bond potential, is consistent with rubber elasticity theory, and the network response satisfies the independent network hypothesis of Tobolsky. The model, when applied to a commercial filled silicone elastomer, quantitatively reproduces the experimental permanent set and stress-strain response due to changes in the crosslinked network from irradiation.

  18. Exploring elasticity and energy dissipation in mussel-inspired hydrogel transient networks

    NASA Astrophysics Data System (ADS)

    Grindy, Scott; Learsch, Robert; Holten-Andersen, Niels

    Dynamic, reversible crosslinks have been shown to specifically control the mechanical properties of a wide variety of mechanically tough and resilient biomaterials. We have shown that reversible histidine-metal ion interactions, known to contribute to the strong mechanical properties and self-healing nature of mussel byssal threads, can be used to control and engineer the temporally-hierarchical mechanical properties of model hydrogels orthogonally from the spatial structure of the material. Here, we explore the scaling relationships in our model networks to further inform our abilities to control the relative elasticity and energy dissipation on hierarchical timescales. Scaling arguments suggest that the elasticity is dominated by long-range entanglements, while the dissipation is controlled by the exchange kinetics of the transient crosslinks. Further, we show that by using UV light, we can further control the viscoelastic properties of our mussel-inspired hydrogels in situ. This process opens the door for creating biocompatible hydrogel materials with arbitrary spatial control over their viscoelastic mechanical properties. Overall, we show that by understanding the interplay between bio-inspired dynamic crosslinks and soft matter physics allows us to rationally design high-strength hydrogels for specific states of dynamic loading.

  19. Elasticity and photoelasticity relationships for polyethylene terephthalate fiber networks by molecular simulation.

    PubMed

    Nayak, Kapileswar; Das, Sushanta; Nanavati, Hemant

    2008-01-01

    We present a framework for the development of elasticity and photoelasticity relationships for polyethylene terephthalate fiber networks, incorporating aspects of the primary molecular structure. Semicrystalline polymeric fiber networks are modeled as sequentially arranged crystalline and amorphous regions. Rotational isomeric states-Monte Carlo simulations of amorphous chains of up to 360 bonds (degree of polymerization, DP=60), confined between and bridging infinite impenetrable crystalline walls, have been characterized by Omega, the probability density of the intercrystal separation h, and Deltabeta, the polarizability anisotropy. ln Omega and Deltabeta have been modeled as functions of h, yielding the chain deformation relationships. The development has been extended to the fiber network to yield the photoelasticity relationships. We execute our framework by fitting to experimental stress-elongation data and employing the single fitted parameter to directly predict the birefringence-elongation behavior, without any further fitting. Incorporating the effect of strain-induced crystallization into the framework makes it physically more meaningful and yields accurate predictions of the birefringence-elongation behavior. PMID:18190221

  20. Pore network microarchitecture influences human cortical bone elasticity during growth and aging.

    PubMed

    Bala, Yohann; Lefèvre, Emmanuelle; Roux, Jean-Paul; Baron, Cécile; Lasaygues, Philippe; Pithioux, Martine; Kaftandjian, Valérie; Follet, Hélène

    2016-10-01

    Cortical porosity is a major determinant of bone strength. Haversian and Volkmann׳s canals are׳seen' as pores in 2D cross-section but fashion a dynamic network of interconnected channels in 3D, a quantifiable footprint of intracortical remodeling. Given the changes in bone remodeling across life, we hypothesized that the 3D microarchitecture of the cortical pore network influences its stiffness during growth and ageing. Cubes of cortical bone of 2 mm side-length were harvested in the distal 1/3 of the fibula in 13 growing children (mean age±SD: 13±4 yrs) and 16 adults (age: 75±13 yrs). The cubes were imaged using desktop micro-CT (8.14µm isotropic voxel size). Pores were segmented as a solid to assess pore volume fraction, number, diameter, separation, connectivity and structure model index. Elastic coefficients were derived from measurements of ultrasonic bulk compression and shear wave velocities and apparent mass density. The pore volume fraction did not significantly differ between children and adults but originates from different microarchitectural patterns. Compared to children, adults had 42% (p=0.033) higher pore number that were more connected (Connective Density: +205%, p=0.001) with a 18% (p=0.007) lower pore separation. After accounting for the contribution of pore volume fraction, axial elasticity in traction-compression mode was significantly correlated with better connectivity in growing children and with pore separation among adults. The changes in intracortical remodeling across life alter the distribution, size and connectedness of the channels from which cortical void fraction originates. These alterations in pore network microarchitecture participate in changes in compressive and shear mechanical behavior, partly in a porosity-independent manner. The assessment of pore volume fraction (i.e., porosity) provides only a limited understanding of the role of cortical void volume fraction in its mechanical properties. PMID:27389322

  1. Model-based reconstructive elasticity imaging of deep venous thrombosis.

    PubMed

    Aglyamov, Salavat; Skovoroda, Andrei R; Rubin, Jonathan M; O'Donnell, Matthew; Emelianov, Stanislav Y

    2004-05-01

    Deep venous thrombosis (DVT) and its sequela, pulmonary embolism, is a significant clinical problem. Once detected, DVT treatment is based on the age of the clot. There are no good noninvasive methods, however, to determine clot age. Previously, we demonstrated that imaging internal mechanical strains can identify and possibly age thrombus in a deep vein. In this study the deformation geometry for DVT elasticity imaging and its effect on Young's modulus estimates is addressed. A model-based reconstruction method is presented to estimate elasticity in which the clot-containing vessel is modeled as a layered cylinder. Compared to an unconstrained approach in reconstructive elasticity imaging, the proposed model-based approach has several advantages: only one component of the strain tensor is used; the minimization procedure is very fast; the method is highly efficient because an analytic solution of the forward elastic problem is used; and the method is not very sensitive to the details of the external load pattern--a characteristic that is important for free-hand, external, surface-applied deformation. The approach was tested theoretically using a numerical model, and experimentally on both tissue-like phantoms and an animal model of DVT. Results suggest that elasticity reconstruction may prove to be a practical adjunct to triplex scanning to detect, diagnose, and stage DVT. PMID:15217230

  2. Modeling of Carbon Nanotube Composites Based on Nonlocal Elasticity Approach

    NASA Astrophysics Data System (ADS)

    Alavinasab, Ali; Jha, Ratneshwar; Ahmadi, G.

    2014-01-01

    Nonlocal continuum theory is studied for modeling stress distributions in nanocomposites. The second-order approximation in nonlocal theory is considered since the first-order approximation leads to an unacceptable solution. A representative volume element (RVE) of CNT composite is utilized to derive unknown constants in the nonlocal theory model. Stress distributions in RVE using nonlocal theory, classical elasticity, and finite element method are obtained. All three approaches yield the same force, but classical elasticity gives an incorrect value of first moment. Wave propagation studies show that the dispersion curve obtained by nonlocal theory is quite close to the atomic Born-von Karman model.

  3. The Modified Semidirect Onlay Technique With Articulated Elastic Model.

    PubMed

    Papazoglou, Efstratios; Diamantopoulou, Sofia

    2015-12-01

    The modified semidirect onlay technique with articulated elastic model involves the fabrication of a stone model that is quickly mounted on an articulator and it includes an elastic part that enables the fabrication of a restoration with proper occlusal anatomy. The technique overcomes the disadvantages of the direct technique such as polymerization shrinkage stress and difficulty in achieving proper contours and, compared to the indirect technique, treatment is completed in a single appointment, without laboratory cost. The novelty of the technique is that, since the restoration is fabricated on an articulated model it eliminates time for occlusal adjustments. PMID:26767243

  4. Modeling the Citation Network by Network Cosmology

    PubMed Central

    Xie, Zheng; Ouyang, Zhenzheng; Zhang, Pengyuan; Yi, Dongyun; Kong, Dexing

    2015-01-01

    Citation between papers can be treated as a causal relationship. In addition, some citation networks have a number of similarities to the causal networks in network cosmology, e.g., the similar in-and out-degree distributions. Hence, it is possible to model the citation network using network cosmology. The casual network models built on homogenous spacetimes have some restrictions when describing some phenomena in citation networks, e.g., the hot papers receive more citations than other simultaneously published papers. We propose an inhomogenous causal network model to model the citation network, the connection mechanism of which well expresses some features of citation. The node growth trend and degree distributions of the generated networks also fit those of some citation networks well. PMID:25807397

  5. Multiscale approach including microfibril scale to assess elastic constants of cortical bone based on neural network computation and homogenization method.

    PubMed

    Barkaoui, Abdelwahed; Chamekh, Abdessalem; Merzouki, Tarek; Hambli, Ridha; Mkaddem, Ali

    2014-03-01

    The complexity and heterogeneity of bone tissue require a multiscale modeling to understand its mechanical behavior and its remodeling mechanisms. In this paper, a novel multiscale hierarchical approach including microfibril scale based on hybrid neural network (NN) computation and homogenization equations was developed to link nanoscopic and macroscopic scales to estimate the elastic properties of human cortical bone. The multiscale model is divided into three main phases: (i) in step 0, the elastic constants of collagen-water and mineral-water composites are calculated by averaging the upper and lower Hill bounds; (ii) in step 1, the elastic properties of the collagen microfibril are computed using a trained NN simulation. Finite element calculation is performed at nanoscopic levels to provide a database to train an in-house NN program; and (iii) in steps 2-10 from fibril to continuum cortical bone tissue, homogenization equations are used to perform the computation at the higher scales. The NN outputs (elastic properties of the microfibril) are used as inputs for the homogenization computation to determine the properties of mineralized collagen fibril. The mechanical and geometrical properties of bone constituents (mineral, collagen, and cross-links) as well as the porosity were taken in consideration. This paper aims to predict analytically the effective elastic constants of cortical bone by modeling its elastic response at these different scales, ranging from the nanostructural to mesostructural levels. Our findings of the lowest scale's output were well integrated with the other higher levels and serve as inputs for the next higher scale modeling. Good agreement was obtained between our predicted results and literature data. PMID:24123969

  6. Elastic-plastic models for multi-site damage

    NASA Technical Reports Server (NTRS)

    Actis, Ricardo L.; Szabo, Barna A.

    1994-01-01

    This paper presents recent developments in advanced analysis methods for the computation of stress site damage. The method of solution is based on the p-version of the finite element method. Its implementation was designed to permit extraction of linear stress intensity factors using a superconvergent extraction method (known as the contour integral method) and evaluation of the J-integral following an elastic-plastic analysis. Coarse meshes are adequate for obtaining accurate results supported by p-convergence data. The elastic-plastic analysis is based on the deformation theory of plasticity and the von Mises yield criterion. The model problem consists of an aluminum plate with six equally spaced holes and a crack emanating from each hole. The cracks are of different sizes. The panel is subjected to a remote tensile load. Experimental results are available for the panel. The plasticity analysis provided the same limit load as the experimentally determined load. The results of elastic-plastic analysis were compared with the results of linear elastic analysis in an effort to evaluate how plastic zone sizes influence the crack growth rates. The onset of net-section yielding was determined also. The results show that crack growth rate is accelerated by the presence of adjacent damage, and the critical crack size is shorter when the effects of plasticity are taken into consideration. This work also addresses the effects of alternative stress-strain laws: The elastic-ideally-plastic material model is compared against the Ramberg-Osgood model.

  7. Model for the elastic behavior near intermartensitic transitions

    NASA Astrophysics Data System (ADS)

    Dai, Liyang; Cullen, James; Wuttig, Manfred

    2005-05-01

    Transitions between different martensitic states have been observed in Ni0.50Mn0.284Ga0.216 using elastic constant measurements. In this paper, we develop a model to explain the reentrant behavior based on a Landau expansion of the free energy in strain space. Here, we assume that the coefficient of the third-order term as well as the second-order term has significant temperature dependence. This assumption results in a C' versus temperature in good agreement with observation. The model and possible modifications to it are discussed and compared to the elastic constant data.

  8. Modeling and Feed-Forward Control of Structural Elastic Robots

    NASA Astrophysics Data System (ADS)

    Reiner, M.; Otter, M.; Ulbrich, H.

    2010-09-01

    In this paper an approach for modeling and control of robots with elasticities in power trains and in structural parts is presented and experimentally verified. For this purpose object-oriented, nonlinear models are developed in the modeling language Modelica. A system theoretical study of the generated models shows that a direct inversion of the models, due to the unstable zero dynamics, is not possible. Therefore an algorithm for the approximate inversion is developed. With this inversion method an approximate inverse model considering structural elasticity for a 6-axis robot is created and verified for the control of the robot. The new control leads to a considerable improvement of the driving characteristics of the robot in the experiment.

  9. Model analysis of tidal volume response to inspiratory elastic loads.

    PubMed

    Zin, W A; Rossi, A; Zocchi, L; Milic-Emili, J

    1984-07-01

    Based on experimental inspiratory driving pressure waveforms and active respiratory impedance data of anesthetized cats, we made model predictions of the factors that determine the immediate (first loaded breath) intrinsic (i.e., nonneural) tidal volume compensation to added inspiratory elastic loads. The time course of driving pressure (P) was given by P = atb, where a is the pressure at 1 s from onset of inspiration and represents the intensity of neuromuscular drive, t is time, and b is an index of the shape of the driving pressure wave. For a given active respiratory impedance, tidal volume compensation to added elastic loads decreases with increasing inspiratory duration and decreasing value of b but is independent of a. We have also assessed the validity of the "effective elastance" (Lynne-Davies et al., J. Appl. Physiol. 30: 512-516, 1971) as a predictor of tidal volume responses to elastic loads. In absence of vagal feedback, the effective elastance appears to be a reliable predictor, except for short inspiratory duration and a very high intrinsic resistance. PMID:6469787

  10. Modelling fracture orientations in reservoirs with photo-elastic techniques

    SciTech Connect

    Rawnsley, K.; Auzias, V.; Petit, J.P.

    1995-08-01

    Fractures within a reservoir can be divided into two types: faults, which result from shear displacement, and tension fractures which result from opening mode displacement. Tension fractures develop perpendicular to the minimal principal stress and so represent an image of the stress field orientation prevailing during their development. In reservoirs tension fractures are not observed by standard seismic techniques and can only be observed very locally in core or suitable well bore images. Frequently tension fracture orientations vary within and between wells. For this reason the extrapolation of tension fracture orientations between wells can be complicated. We present a method based on photo-elastic techniques that can model complex tension fracture patterns. Photo-elastic techniques permit the modelling of a stress field in a faulted strata and have shown that variations in tension fracture orientation may often be linked to stress field perturbations due to faults. The photo-elastic model consists of a rectangular plate of transparent polymer into which narrow slots with various frictional properties can be engineered to represent faults. The plate is loaded in a compression cell and light is transmitted through the plate via two polarizers and the directions of the stress field trajectories can be determined. Applications of photo-elastic modelling of tension fracture orientations to both outcrop and reservoir data are presented. The reservoir example consists of a horizontal well with continuous fracture data obtained from core and Formation Micro-Scanner logs. It is shown that the stress field at the seismic fault scale can be related to the large scale variations in the fracture pattern in the well. Smaller scale variations in the well fracture orientations are simulated by down scaling the photo-elastic model from seismic scale faults to include mostly sub-seismic faults near the well.

  11. The role of mode of delivery on elastic fiber architecture and vaginal vault elasticity: a rodent model study

    PubMed Central

    Downing, Keith; Billah, Mubashir; Raparia, Eva; Shah, Anup; Silverstein, Moshe; Ahmad, Amanda; Boutis, Gregory S.

    2013-01-01

    We report on an experimental study of the role of mode of delivery and pregnancy on the architecture of vaginal elastic fibers and vaginal vault elasticity in female Sprague-Dawley rats. In primiparous rats submitted to spontaneous or Cesarean delivery and virgin rats submitted to simulated delivery, the tortuosity of elastic fibers (defined as the ratio of length to end-to-end distance) was observed to decrease when measured two days to two weeks postpartum. In addition, the measured tortuosity of elastic fibers in multiparous rats was greater than that of virgin rats. The tortuosity of elastic fibers of all rats measured at two days postpartum were found to be similar to that of multiparous rats. At two weeks postpartum the measured tortuosity of vaginal elastic fibers was indistinguishable from virgin rats, regardless of the delivery method. Borrowing from the field of polymer physics, a model is suggested that connects elastic fiber tortuosity to the resulting tension under an applied stress; fibers having high tortuosity are expected to provide less structural support than more linear, low tortuosity fibers. To probe the macroscopic effects in elasticity due to architectural changes observed in elastic fibers, we have measured the stiffness of the vaginal vault in each cohort using a pressure-infusion system. The vaginal vault stiffness of all primiparous rats measured two weeks postpartum was greater than that measured two days postpartum. In addition, the vaginal vault of virgin rats was stiffer than that of multiparous rats. These observations confirmed that vaginal vault elastic fibers undergo significant remodeling due to pregnancy and parturition, and that the complex remodeling may be a significant contributor to tissue elasticity. Remarkably, regardless of the mode of delivery or simulated tissue trauma, elastic fiber tortuosity is observed to decrease from two days to two weeks postpartum indicating the onset of repair and recovery of tissue stiffness

  12. Modelling Elastic Media With Arbitrary Shapes Using the Wavelet Transform

    NASA Astrophysics Data System (ADS)

    Rosa, J. W.; Cardoso, F. A.; Rosa, J. W.; Aki, K.

    2004-12-01

    We extend the new method proposed by Rosa et al. (2001) for the study of elastic bodies with complete arbitrary shapes. The method was originally developed for modelling 2-D elastic media with the application of the wavelet transform, and was extended to cases where discontinuities simulated geologic faults between two different elastic media. In addition to extending the method for the study of bodies with complete arbitrary shapes, we also test new transforms with the objective of making the related matrices more compact, which are also applied to the most general case of the method. The basic method consists of the discretization of the polynomial expansion for the boundary conditions of the 2-D problem involving the stress and strain relations for the media. This parameterization leads to a system of linear equations that should be solved for the determination of the expansion coefficients, which are the model parameters, and their determination leads to the solution of the problem. Despite the fact that the media we studied originally were 2-D bodies, the result of the application of this new method can be viewed as an approximate solution to some specific 3-D problems. Among the motivations for developing this method are possible geological applications (that is, the study of tectonic plates and geologic faults) and simulations of the elastic behaviour of materials in several other fields of science. The wavelet transform is applied with two main objectives, namely to decrease the error related to the truncation of the polynomial expansion and to make the system of linear equations more compact for computation. Having validated this method for the original 2-D elastic media, we plan that this extension to elastic bodies with complete arbitrary shapes will enable it to be even more attractive for modelling real media. Reference Rosa, J. W. C., F. A. C. M. Cardoso, K. Aki, H. S. Malvar, F. A. V. Artola, and J. W. C. Rosa, Modelling elastic media with the

  13. Deconstruction and elastic ππ scattering in Higgsless models

    NASA Astrophysics Data System (ADS)

    Chivukula, R. Sekhar; Simmons, Elizabeth H.; He, Hong-Jian; Kurachi, Masafumi; Tanabashi, Masaharu

    2007-02-01

    We study elastic pion-pion scattering in global linear moose models and apply the results to a variety of Higgsless models in flat and anti-de Sitter (AdS) space using the equivalence theorem. In order to connect the global moose to Higgsless models, we first introduce a block-spin transformation which corresponds, in the continuum, to the freedom to perform coordinate transformations in the Higgsless model. We show that it is possible to make an “f-flat” deconstruction in which all of the f-constants fj of the linear moose model are identical; the phenomenologically relevant f-flat models are those in which the coupling constants of the groups at either end of the moose are small—corresponding to the global linear moose. In studying pion-pion scattering, we derive various sum rules, including one analogous to the Kawarabayashi-Suzuki-Riazuddin-Fayyazuddin (KSRF) relation, and use them in evaluating the low-energy and high-energy forms of the leading elastic partial-wave scattering amplitudes. We obtain elastic unitarity bounds as a function of the mass of the lightest KK mode and discuss their physical significance.

  14. Deconstruction and elastic {pi}{pi} scattering in Higgsless models

    SciTech Connect

    Chivukula, R. Sekhar; Simmons, Elizabeth H.; He, Hong-Jian; Kurachi, Masafumi; Tanabashi, Masaharu

    2007-02-01

    We study elastic pion-pion scattering in global linear moose models and apply the results to a variety of Higgsless models in flat and anti-de Sitter (AdS) space using the equivalence theorem. In order to connect the global moose to Higgsless models, we first introduce a block-spin transformation which corresponds, in the continuum, to the freedom to perform coordinate transformations in the Higgsless model. We show that it is possible to make an 'f-flat' deconstruction in which all of the f-constants f{sub j} of the linear moose model are identical; the phenomenologically relevant f-flat models are those in which the coupling constants of the groups at either end of the moose are small--corresponding to the global linear moose. In studying pion-pion scattering, we derive various sum rules, including one analogous to the Kawarabayashi-Suzuki-Riazuddin-Fayyazuddin (KSRF) relation, and use them in evaluating the low-energy and high-energy forms of the leading elastic partial-wave scattering amplitudes. We obtain elastic unitarity bounds as a function of the mass of the lightest KK mode and discuss their physical significance.

  15. NEXT-GENERATION NUMERICAL MODELING: INCORPORATING ELASTICITY, ANISOTROPY AND ATTENUATION

    SciTech Connect

    S. LARSEN; ET AL

    2001-03-01

    A new effort has been initiated between the Department of Energy (DOE) and the Society of Exploration Geophysicists (SEG) to investigate what features the next generation of numerical seismic models should contain that will best address current technical problems encountered during exploration in increasingly complex geologies. This collaborative work is focused on designing and building these new models, generating synthetic seismic data through simulated surveys of various geometries, and using these data to test and validate new and improved seismic imaging algorithms. The new models will be both 2- and 3-dimensional and will include complex velocity structures as well as anisotropy and attenuation. Considerable attention is being focused on multi-component acoustic and elastic effects because it is now widely recognized that converted phases could play a vital role in improving the quality of seismic images. An existing, validated 3-D elastic modeling code is being used to generate the synthetic data. Preliminary elastic modeling results using this code are presented here along with a description of the proposed new models that will be built and tested.

  16. Modeling universal dynamics of cell spreading on elastic substrates.

    PubMed

    Fan, Houfu; Li, Shaofan

    2015-11-01

    A three-dimensional (3D) multiscale moving contact line model is combined with a soft matter cell model to study the universal dynamics of cell spreading over elastic substrates. We have studied both the early stage and the late stage cell spreading by taking into account the actin tension effect. In this work, the cell is modeled as an active nematic droplet, and the substrate is modeled as a St. Venant Kirchhoff elastic medium. A complete 3D simulation of cell spreading has been carried out. The simulation results show that the spreading area versus spreading time at different stages obeys specific power laws, which is in good agreement with experimental data and theoretical prediction reported in the literature. Moreover, the simulation results show that the substrate elasticity may affect force dipole distribution inside the cell. The advantage of this approach is that it combines the hydrodynamics of actin retrograde flow with moving contact line model so that it can naturally include actin tension effect resulting from actin polymerization and actomyosin contraction, and thus it might be capable of simulating complex cellular scale phenomenon, such as cell spreading or even crawling. PMID:25850888

  17. Mechanistic Constitutive Models for Rubber Elasticity and Viscoelasticity

    SciTech Connect

    Puso, M

    2003-01-21

    Physically based models which describe the finite strain behavior of vulcanized rubber are developed. Constitutive laws for elasticity and viscoelasticity are derived by integrating over orientation space the forces due to each individual polymer chain. A novel scheme is presented which effectively approximates these integrals in terms of strain and strain invariants. In addition, the details involving the implementation of such models into a quasi-static large strain finite element formulation are provided. In order to account for the finite extensibility of a molecular chain, Langevin statistics is used to model the chain response. The classical statistical model of rubber assumes that polymer chains interact only at the chemical crosslinks. It is shown that such model when fitted for uniaxial tension data cannot fit compression or equibiaxial data. A model which incorporates the entanglement interactions of surrounding chains, in addition to the finite extensibility of the chains, is shown to give better predictions than the classical model. The technique used for approximating the orientation space integral was applied to both the classical and entanglement models. A viscoelasticity model based on the force equilibration process as described by Doi and Edwards is developed. An assumed form for the transient force in the chain is postulated. The resulting stress tensor is composed of an elastic and a viscoelastic portion with the elastic stress given by the proposed entanglement model. In order to improve the simulation of experimental data, it was found necessary to include the effect of unattached or dangling polymer chains in the viscoelasticity model. The viscoelastic effect of such chains is the manifestation of a disengagement process. This disengagement model for unattached polymer chains motivated an empirical model which was very successful in simulating the experimental results considered.

  18. Efficient routing and spectrum assignment in elastic optical networks with time scheduled traffic

    NASA Astrophysics Data System (ADS)

    Qiu, Yang; Fan, Zheyu; Chan, Chun-Kit

    2016-07-01

    Elastic optical networks (EONs) employ dynamic routing and spectrum assignment (RSA) algorithms to support diverse services and heterogeneous requests. However, these RSA algorithms may possibly induce spectrum fragments when allocating spectrum to accommodate different service requests. Therefore, such induced spectrum fragments should also be regarded as spectrum consumption besides the allocated spectrum by RSA algorithms. In this paper, by additionally considering the holding times of lightpaths and service connections, we first introduce a comprehensive spectrum consumption model to simultaneously investigate both the allocated and the fragmented spectrum consumptions. Then we solve this model in both static and dynamic traffic scenarios, by either formulating the RSA problem with time-scheduled traffic or introducing a time-aware spectrum-efficient heuristics algorithm. Since no defragmentation is executed in spectrum allocation, the proposed RSA algorithm requires no traffic disruption and can be realized more easily in reality. Simulation results show that the proposed algorithm reduces the comprehensive spectrum consumption and has lower bandwidth blocking probability than the typical first-fit RSA algorithm.

  19. Performance evaluation of time-aware enhanced software defined networking (TeSDN) for elastic data center optical interconnection.

    PubMed

    Yang, Hui; Zhang, Jie; Zhao, Yongli; Ji, Yuefeng; Li, Hui; Lin, Yi; Li, Gang; Han, Jianrui; Lee, Young; Ma, Teng

    2014-07-28

    Data center interconnection with elastic optical networks is a promising scenario to meet the high burstiness and high-bandwidth requirements of data center services. We previously implemented enhanced software defined networking over elastic optical network for data center application [Opt. Express 21, 26990 (2013)]. On the basis of it, this study extends to consider the time-aware data center service scheduling with elastic service time and service bandwidth according to the various time sensitivity requirements. A novel time-aware enhanced software defined networking (TeSDN) architecture for elastic data center optical interconnection has been proposed in this paper, by introducing a time-aware resources scheduling (TaRS) scheme. The TeSDN can accommodate the data center services with required QoS considering the time dimensionality, and enhance cross stratum optimization of application and elastic optical network stratums resources based on spectrum elasticity, application elasticity and time elasticity. The overall feasibility and efficiency of the proposed architecture is experimentally verified on our OpenFlow-based testbed. The performance of TaRS scheme under heavy traffic load scenario is also quantitatively evaluated based on TeSDN architecture in terms of blocking probability and resource occupation rate. PMID:25089383

  20. Self-consistent Modeling of Elastic Anisotropy in Shale

    NASA Astrophysics Data System (ADS)

    Kanitpanyacharoen, W.; Wenk, H.; Matthies, S.; Vasin, R.

    2012-12-01

    Elastic anisotropy in clay-rich sedimentary rocks has increasingly received attention because of significance for prospecting of petroleum deposits, as well as seals in the context of nuclear waste and CO2 sequestration. The orientation of component minerals and pores/fractures is a critical factor that influences elastic anisotropy. In this study, we investigate lattice and shape preferred orientation (LPO and SPO) of three shales from the North Sea in UK, the Qusaiba Formation in Saudi Arabia, and the Officer Basin in Australia (referred to as N1, Qu3, and L1905, respectively) to calculate elastic properties and compare them with experimental results. Synchrotron hard X-ray diffraction and microtomography experiments were performed to quantify LPO, weight proportions, and three-dimensional SPO of constituent minerals and pores. Our preliminary results show that the degree of LPO and total amount of clays are highest in Qu3 (3.3-6.5 m.r.d and 74vol%), moderately high in N1 (2.4-5.6 m.r.d. and 70vol%), and lowest in L1905 (2.3-2.5 m.r.d. and 42vol%). In addition, porosity in Qu3 is as low as 2% while it is up to 6% in L1605 and 8% in N1, respectively. Based on this information and single crystal elastic properties of mineral components, we apply a self-consistent averaging method to calculate macroscopic elastic properties and corresponding seismic velocities for different shales. The elastic model is then compared with measured acoustic velocities on the same samples. The P-wave velocities measured from Qu3 (4.1-5.3 km/s, 26.3%Ani.) are faster than those obtained from L1905 (3.9-4.7 km/s, 18.6%Ani.) and N1 (3.6-4.3 km/s, 17.7%Ani.). By making adjustments for pore structure (aspect ratio) and single crystal elastic properties of clay minerals, a good agreement between our calculation and the ultrasonic measurement is obtained.

  1. Modeling and Processing of Continuous 3D Elastic Wavefield Data

    NASA Astrophysics Data System (ADS)

    Milkereit, B.; Bohlen, T.

    2001-12-01

    Continuous seismic wavefields are excited by earthquake clustering, induced seismicity in reservoirs, and mining. In hydrocarbon reservoirs, for example, pore pressure changes and fluid flow (mass transfer) will cause incremental deviatoric stresses sufficient to trigger and sustain seismic activity. Here we address three aspects of seismic wavefields in three-dimensional heterogeneous media triggered by distributed sources in space and time: forward modeling, multichannel data processing, and source location imaging. A power law distribution of seismic sources (such as the Gutenberg-Richter law) is used for the modeling of viscoelastic/elastic wave propagation through a realistic earth model. 3D modeling provides new insight in the interaction of multi-source wavefields and the role of scale-dependend elastic model parameters on transmitted and reflected/back-scattered wavefields. There exists a strong correlation between the spatial properties of the compressional, shear wave and density perturbations and the lateral correlation length of the resulting reflected or transmitted seismic wavefields. Modeling is based on the implementation of 3D elastic/viscoelastic FD codes on massive parallel and/or distributed computing resources using MPI (message passing interface). For parallelization, large grid 3D earth models are decomposed into subvolume processing elements whereby each processing element is updating the wavefield within its portion of the grid. Processing of continuous seismic wavefields excited by multiple distributed sources is based on a combination of crosscorrelated or slowness-transformed array data and Kirchhoff or reverse time migration for source location or source volume imaging. The appearance of slowness in both migration and array data processing suggests the possibility of combining them into a single process. In order to place further constraints on the migration, the directivity properties of 3-component receiver arrays can be included in

  2. Supersymmetric sigma model of disordered, isotropic, elastic media

    NASA Astrophysics Data System (ADS)

    Photiadis, Douglas

    The supersymmetry method proposed by Efetov in 1983 has been enormously successful at describing a broad range of phenomena involving disorder, providing a framework for understanding and going beyond the successes of random matrix theory and allowing a calculation of the slowing of diffusion as the Anderson transition is approached. The original model described the propagation of a scalar wave in a disordered medium, and subsequent work extended these ideas to classical waves, optical or elastic, with the approximation that the wave propagation can be similarly described by a scalar theory. Such a theory cannot however account correctly for scattering between different polarizations. A direct attempt to derive a supersymmetric model describing elastic waves results in a non-renormalizable field theory, and poses substantial difficulties. We have obtained a supersymmetric sigma model by considering the dual model which describes a generalized superstress field. The model enables one to fully account for the different wave types and polarizations in the medium. We will present our recent results in this area, including model predictions for the obtained diffusion constants, and the effects of renormalization to first order. This research was funded by the Office of Naval Research.

  3. Hybrid Simulation Modeling to Estimate U.S. Energy Elasticities

    NASA Astrophysics Data System (ADS)

    Baylin-Stern, Adam C.

    This paper demonstrates how an U.S. application of CIMS, a technologically explicit and behaviourally realistic energy-economy simulation model which includes macro-economic feedbacks, can be used to derive estimates of elasticity of substitution (ESUB) and autonomous energy efficiency index (AEEI) parameters. The ability of economies to reduce greenhouse gas emissions depends on the potential for households and industry to decrease overall energy usage, and move from higher to lower emissions fuels. Energy economists commonly refer to ESUB estimates to understand the degree of responsiveness of various sectors of an economy, and use estimates to inform computable general equilibrium models used to study climate policies. Using CIMS, I have generated a set of future, 'pseudo-data' based on a series of simulations in which I vary energy and capital input prices over a wide range. I then used this data set to estimate the parameters for transcendental logarithmic production functions using regression techniques. From the production function parameter estimates, I calculated an array of elasticity of substitution values between input pairs. Additionally, this paper demonstrates how CIMS can be used to calculate price-independent changes in energy-efficiency in the form of the AEEI, by comparing energy consumption between technologically frozen and 'business as usual' simulations. The paper concludes with some ideas for model and methodological improvement, and how these might figure into future work in the estimation of ESUBs from CIMS. Keywords: Elasticity of substitution; hybrid energy-economy model; translog; autonomous energy efficiency index; rebound effect; fuel switching.

  4. Multiscale, structure-based modeling for the elastic mechanical behavior of arterial walls.

    PubMed

    Stylianopoulos, Triantafyllos; Barocas, Victor H

    2007-08-01

    Passive elastic behavior of arterial wall remains difficult to model. Although phenomenological and structural models exist, the question of how the three-dimensional network structure of the collagen in the artery determines its mechanical properties is still open. A model is presented that incorporates a collagen network as well as the noncollagenous material that comprise the artery. The collagen architecture is represented as a network of interconnected fibers, and a neo-Hookean constitutive equation is used to describe the contribution of the noncollagenous matrix. The model is multiscale in that volume-averaging theory is applied to the collagen network, and it is structural in that parameters of the microstructure of the collagen network were considered instead of a macroscopic constitutive law. The computational results provided a good fit to published experimental data for decellularized porcine carotid arteries. The model predicted increased circumferential compliance for increased axial stretch, consistent with previously published reports, and a relatively small sensitivity to open angle. Even at large extensions, the model predicted that the noncollagenous matrix would be in compression, preventing collapse of the collagen network. The incorporation of fiber-fiber interactions led to an accurate model of artery wall behavior with relatively few parameters. The counterintuitive result that the noncollagenous component is in compression during extension and inflation of the tissue suggests that the collagen is important even at small strains, with the noncollagenous components supporting the network, but not resisting the load directly. More accurate representation of the microstructure of the artery wall is needed to explore this issue further. PMID:17655483

  5. Elastic Model Transitions Using Quadratic Inequality Constrained Least Squares

    NASA Technical Reports Server (NTRS)

    Orr, Jeb S.

    2012-01-01

    A technique is presented for initializing multiple discrete finite element model (FEM) mode sets for certain types of flight dynamics formulations that rely on superposition of orthogonal modes for modeling the elastic response. Such approaches are commonly used for modeling launch vehicle dynamics, and challenges arise due to the rapidly time-varying nature of the rigid-body and elastic characteristics. By way of an energy argument, a quadratic inequality constrained least squares (LSQI) algorithm is employed to e ect a smooth transition from one set of FEM eigenvectors to another with no requirement that the models be of similar dimension or that the eigenvectors be correlated in any particular way. The physically unrealistic and controversial method of eigenvector interpolation is completely avoided, and the discrete solution approximates that of the continuously varying system. The real-time computational burden is shown to be negligible due to convenient features of the solution method. Simulation results are presented, and applications to staging and other discontinuous mass changes are discussed

  6. Elastic laboratory measurements and modeling of saturated basalts

    NASA Astrophysics Data System (ADS)

    Adam, Ludmila; Otheim, Thomas

    2013-03-01

    Understanding the elastic behavior of basalt is important to seismically monitor volcanoes, subsea basalts, and carbon sequestration in basalt. We estimate the elastic properties of basalt samples from the Snake River Plain, Idaho, at ultrasonic (0.8 MHz) and seismic (2-300 Hz) frequencies. To test the sensitivity of seismic waves to the fluid content in the pore structure, measurements are performed at three saturation conditions: saturated with liquid CO2, water, and dry. When CO2 replaces water, the P-wave velocity drops, on average, by 10%. Vesicles and cracks, observed in the rock microstructure, control the relaxation of pore-fluid pressures in the rock as a wave propagates. The bulk and shear moduli of basalts saturated with liquid CO2 are not frequency dependent, suggesting that fluid pore pressures are in equilibrium between 2 Hz and 0.8 MHz. However, when samples are water saturated, the bulk modulus of the rock is frequency dependent. Modeling with Gassmann's equations predicts the measured saturated rock bulk modulus for all fluids for frequencies below 20 Hz but underpredicts the water-saturated basalt bulk modulus for frequencies greater than 20 Hz. The most likely reason is that the pore-fluid pressures are unrelaxed. Instead, the ultrasonic frequency rock moduli are modeled with high-frequency elastic theories of squirt flow and Kuster-Toksöz (KT). Although KT's model is based on idealized pore shapes, a combination of spheres (vesicles) and penny-shaped cracks (fractures) interpreted and quantified from petrographical data predicts the ultrasonic dry and saturated rock moduli for the measured basalts.

  7. Dynamics of Elastic Beams with Embedded Fluid-Filled Parallel-Channel Networks

    PubMed Central

    Gat, Amir D.

    2015-01-01

    Abstract A pressurized fluid-filled parallel-channel network embedded in an elastic beam, asymmetrically to the neutral plane, will create a deformation field within the beam. Deformation due to embedded fluidic networks is currently studied in the context of soft actuators and soft-robotic applications. Expanding on this concept, configurations can be designed so that the pressure in the channel network is created directly from external forces acting on the beam, and thus can be viewed as passive solid–fluid composite structures. We approximate the deformation of such structures and relate the fluid pressure and geometry of the network to a continuous deformation-field function. This enables the design of networks creating steady arbitrary deformation fields as well as to eliminate deformation created by external time-varying forces, thus increasing the effective rigidity of the beam. In addition, by including the effects of the deformation created by the channel network on the beam inertia, we can modify the response of the beam to external time-varying forces. We present a scheme to design channel networks that create predefined oscillating deformation patterns in response to external oscillating forces. The ability to include inertial effects is relevant to the design of dynamic soft robots and soft actuators. Our results are illustrated and validated by numerical computations.

  8. Elastic tracking versus neural network tracking for very high multiplicity problems

    SciTech Connect

    Harlander, M.; Gyulassy, M.

    1991-04-01

    A new Elastic Tracking (ET) algorithm is proposed for finding tracks in very high multiplicity and noisy environments. It is based on a dynamical reinterpretation and generalization of the Radon transform and is related to elastic net algorithms for geometrical optimization. ET performs an adaptive nonlinear fit to noisy data with a variable number of tracks. Its numerics is more efficient than that of the traditional Radon or Hough transform method because it avoids binning of phase space and the costly search for valid minima. Spurious local minima are avoided in ET by introducing a time-dependent effective potential. The method is shown to be very robust to noise and measurement error and extends tracking capabilities to much higher track densities than possible via local road finding or even the novel Denby-Peterson neural network tracking algorithms. 12 refs., 2 figs.

  9. Distinct Tensile Response of Model Semi-flexible Elastomer Networks

    NASA Astrophysics Data System (ADS)

    Aguilera-Mercado, Bernardo M.; Cohen, Claude; Escobedo, Fernando A.

    2011-03-01

    Through coarse-grained molecular modeling, we study how the elastic response strongly depends upon nanostructural heterogeneities in model networks made of semi-flexible chains exhibiting both regular and realistic connectivity. Idealized regular polymer networks have been shown to display a peculiar elastic response similar to that of super-tough natural materials (e.g., organic adhesives inside abalone shells). We investigate the impact of chain stiffness, and the effect of including tri-block copolymer chains, on the network's topology and elastic response. We find in some systems a dual tensile response: a liquid-like behavior at small deformations, and a distinct saw-tooth shaped stress-strain curve at moderate to large deformations. Additionally, stiffer regular networks exhibit a marked hysteresis over loading-unloading cycles that can be deleted by heating-cooling cycles or by performing deformations along different axes. Furthermore, small variations of chain stiffness may entirely change the nature of the network's tensile response from an entropic to an enthalpic elastic regime, and micro-phase separation of different blocks within elastomer networks may significantly enhance their mechanical strength. This work was supported by the American Chemical Society.

  10. Model neural networks

    SciTech Connect

    Kepler, T.B.

    1989-01-01

    After a brief introduction to the techniques and philosophy of neural network modeling by spin glass inspired system, the author investigates several properties of these discrete models for autoassociative memory. Memories are represented as patterns of neural activity; their traces are stored in a distributed manner in the matrix of synaptic coupling strengths. Recall is dynamic, an initial state containing partial information about one of the memories evolves toward that memory. Activity in each neuron creates fields at every other neuron, the sum total of which determines its activity. By averaging over the space of interaction matrices with memory constraints enforced by the choice of measure, we show that the exist universality classes defined by families of field distributions and the associated network capacities. He demonstrates the dominant role played by the field distribution in determining the size of the domains of attraction and present, in two independent ways, an expression for this size. He presents a class of convergent learning algorithms which improve upon known algorithms for producing such interaction matrices. He demonstrates that spurious states, or unexperienced memories, may be practically suppressed by the inducement of n-cycles and chaos. He investigates aspects of chaos in these systems, and then leave discrete modeling to implement the analysis of chaotic behavior on a continuous valued network realized in electronic hardware. In each section he combine analytical calculation and computer simulations.

  11. Elastic response of DNA molecules under the action of interfacial traction and stretching: An elastic thin rod model

    NASA Astrophysics Data System (ADS)

    Xiao, Ye; Huang, Zaixing; Qiang, Lei; Gao, Jun

    2015-11-01

    In a multivalent salt solution, a segment of DNA is modeled as an elastic rod subjected to the interfacial traction. The shooting method is used to calculate the equilibrium configurations of condensed DNA under the action of the longitudinal end-force and interfacial traction simultaneously. The results show that the shapes of DNA are mainly determined by the competition between the interfacial energy and elastic strain energy of stretching. The change of end-to-end distance with the longitudinal end-force is consistent with the worm-like chain (WLC) model. The higher the concentration is, the stronger the condensation of DNA.

  12. The molecular kink paradigm for rubber elasticity: Numerical simulations of explicit polyisoprene networks at low to moderate tensile strains

    NASA Astrophysics Data System (ADS)

    Hanson, David E.

    2011-08-01

    Based on recent molecular dynamics and ab initio simulations of small isoprene molecules, we propose a new ansatz for rubber elasticity. We envision a network chain as a series of independent molecular kinks, each comprised of a small number of backbone units, and the strain as being imposed along the contour of the chain. We treat chain extension in three distinct force regimes: (Ia) near zero strain, where we assume that the chain is extended within a well defined tube, with all of the kinks participating simultaneously as entropic elastic springs, (II) when the chain becomes sensibly straight, giving rise to a purely enthalpic stretching force (until bond rupture occurs) and, (Ib) a linear entropic regime, between regimes Ia and II, in which a force limit is imposed by tube deformation. In this intermediate regime, the molecular kinks are assumed to be gradually straightened until the chain becomes a series of straight segments between entanglements. We assume that there exists a tube deformation tension limit that is inversely proportional to the chain path tortuosity. Here we report the results of numerical simulations of explicit three-dimensional, periodic, polyisoprene networks, using these extension-only force models. At low strain, crosslink nodes are moved affinely, up to an arbitrary node force limit. Above this limit, non-affine motion of the nodes is allowed to relax unbalanced chain forces. Our simulation results are in good agreement with tensile stress vs. strain experiments.

  13. Modelling apical constriction in epithelia using elastic shell theory.

    PubMed

    Jones, Gareth Wyn; Chapman, S Jonathan

    2010-06-01

    Apical constriction is one of the fundamental mechanisms by which embryonic tissue is deformed, giving rise to the shape and form of the fully-developed organism. The mechanism involves a contraction of fibres embedded in the apical side of epithelial tissues, leading to an invagination or folding of the cell sheet. In this article the phenomenon is modelled mechanically by describing the epithelial sheet as an elastic shell, which contains a surface representing the continuous mesh formed from the embedded fibres. Allowing this mesh to contract, an enhanced shell theory is developed in which the stiffness and bending tensors of the shell are modified to include the fibres' stiffness, and in which the active effects of the contraction appear as body forces in the shell equilibrium equations. Numerical examples are presented at the end, including the bending of a plate and a cylindrical shell (modelling neurulation) and the invagination of a spherical shell (modelling simple gastrulation). PMID:19859751

  14. The kinesin walk: a dynamic model with elastically coupled heads.

    PubMed Central

    Derényi, I; Vicsek, T

    1996-01-01

    Recently individual two-headed kinesin molecules have been studied in in vitro motility assays revealing a number of their peculiar transport properties. In this paper we propose a simple and robust model for the kinesin stepping process with elastically coupled Brownian heads that show all of these properties. The analytic and numerical treatment of our model results in a very good fit to the experimental data and practically has no free parameters. Changing the values of the parameters in the restricted range allowed by the related experimental estimates has almost no effect on the shape of the curves and results mainly in a variation of the zero load velocity that can be directly fitted to the measured data. In addition, the model is consistent with the measured pathway of the kinesin ATPase. PMID:8692894

  15. Elastic-wave velocity in marine sediments with gas hydrates: Effective medium modeling

    USGS Publications Warehouse

    Helgerud, M.B.; Dvorkin, J.; Nur, A.; Sakai, A.; Collett, T.

    1999-01-01

    We offer a first-principle-based effective medium model for elastic-wave velocity in unconsolidated, high porosity, ocean bottom sediments containing gas hydrate. The dry sediment frame elastic constants depend on porosity, elastic moduli of the solid phase, and effective pressure. Elastic moduli of saturated sediment are calculated from those of the dry frame using Gassmann's equation. To model the effect of gas hydrate on sediment elastic moduli we use two separate assumptions: (a) hydrate modifies the pore fluid elastic properties without affecting the frame; (b) hydrate becomes a component of the solid phase, modifying the elasticity of the frame. The goal of the modeling is to predict the amount of hydrate in sediments from sonic or seismic velocity data. We apply the model to sonic and VSP data from ODP Hole 995 and obtain hydrate concentration estimates from assumption (b) consistent with estimates obtained from resistivity, chlorinity and evolved gas data. Copyright 1999 by the American Geophysical Union.

  16. Constitutive modelling of composite biopolymer networks.

    PubMed

    Fallqvist, B; Kroon, M

    2016-04-21

    The mechanical behaviour of biopolymer networks is to a large extent determined at a microstructural level where the characteristics of individual filaments and the interactions between them determine the response at a macroscopic level. Phenomena such as viscoelasticity and strain-hardening followed by strain-softening are observed experimentally in these networks, often due to microstructural changes (such as filament sliding, rupture and cross-link debonding). Further, composite structures can also be formed with vastly different mechanical properties as compared to the individual networks. In this present paper, we present a constitutive model presented in a continuum framework aimed at capturing these effects. Special care is taken to formulate thermodynamically consistent evolution laws for dissipative effects. This model, incorporating possible anisotropic network properties, is based on a strain energy function, split into an isochoric and a volumetric part. Generalisation to three dimensions is performed by numerical integration over the unit sphere. Model predictions indicate that the constitutive model is well able to predict the elastic and viscoelastic response of biological networks, and to an extent also composite structures. PMID:26851172

  17. Modelling of poro-visco-elastic biological systems

    NASA Astrophysics Data System (ADS)

    Bilotsky, Y.; Gasik, M.

    2015-09-01

    The research of mechanical properties of poro-visco-elastic biomaterials is an important task, especially for tailoring the best conditions for in-growth and healing of implants. In this work we analysed the behaviour of biomaterials under different static and dynamic loading regimes, in "dry" and "wet" conditions. Retrieved data revealed nonlinear relations between applied force and resulting deformation, with time and frequency dependence. These features were described by a nonlinear model, which reasonably fits mentioned peculiarities. The simplified model was validated with numerical simulations using COMSOL software. Upon validation it allows incorporation of the experimental data obtained by biomechanical spectroscopy towards prediction of biomaterials behaviour in "in vitro" conditions, with the purpose to extrapolate to clinically-relevant environment.

  18. Folding model calculations for 6He+12C elastic scattering

    NASA Astrophysics Data System (ADS)

    Awad, A. Ibraheem

    2016-03-01

    In the framework of the double folding model, we used the α+2n and di-triton configurations for the nuclear matter density of the 6He nucleus to generate the real part of the optical potential for the system 6He+12C. As an alternative, we also use the high energy approximation to generate the optical potential for the same system. The derived potentials are employed to analyze the elastic scattering differential cross section at energies of 38.3, 41.6 and 82.3 MeV/u. For the imaginary part of the potential we adopt the squared Woods-Saxon form. The obtained results are compared with the corresponding measured data as well as with available results in the literature. The calculated total reaction cross sections are investigated and compared with the optical limit Glauber model description.

  19. Relating Cohesive Zone Model to Linear Elastic Fracture Mechanics

    NASA Technical Reports Server (NTRS)

    Wang, John T.

    2010-01-01

    The conditions required for a cohesive zone model (CZM) to predict a failure load of a cracked structure similar to that obtained by a linear elastic fracture mechanics (LEFM) analysis are investigated in this paper. This study clarifies why many different phenomenological cohesive laws can produce similar fracture predictions. Analytical results for five cohesive zone models are obtained, using five different cohesive laws that have the same cohesive work rate (CWR-area under the traction-separation curve) but different maximum tractions. The effect of the maximum traction on the predicted cohesive zone length and the remote applied load at fracture is presented. Similar to the small scale yielding condition for an LEFM analysis to be valid. the cohesive zone length also needs to be much smaller than the crack length. This is a necessary condition for a CZM to obtain a fracture prediction equivalent to an LEFM result.

  20. Elasticity-based targeted growth models of morphogenesis.

    PubMed

    Alford, Patrick W

    2015-01-01

    Embryonic tissue mechanics play an important role in regulating morphogenesis during organ formation, both in a bottom-up sense, where changes in gene expression drive mechanical shape changes, and in a top-down sense, where perturbations in tissue mechanics feed back to drive changes in gene expression. In growing tissues that can generate internal forces and have complex geometries, like those in the embryo, it can often be difficult to empirically determine the mechanical state of the tissue, let alone the relationships between gene expression and mechanical behavior. Mathematical models can be used to fill this gap. Here, we discuss elasticity-based models for growing tissues with a specific focus on targeted growth in embryonic tissues. PMID:25245704

  1. A study of self-propelled elastic cylindrical micro-swimmers using modeling and computation

    NASA Astrophysics Data System (ADS)

    Shi, Lingling; Čanić, Sunčica; Quaini, Annalisa; Pan, Tsorng-Whay

    2016-06-01

    We study propulsion of micro-swimmers in 3D creeping flow. The swimmers are assumed to be made of elastic cylindrical hollow tubes. The swimming is generated by the contractions of the tube's elastic membrane walls producing a traveling wave in the form of a "step-function" traversing the swimmer from right to left, propelling the swimmer from left to right. The problem is motivated by medical applications such as drug delivery. The influence of several non-dimensional design parameters on the velocity of the swimmer is investigated, including the swimmer aspect ratio, and the amplitude of the traveling wave relative to the swimmer radius. An immersed boundary method based on a finite element method approach is successfully combined with an elastic spring network model to simulate the two-way fluid-structure interaction coupling between the elastic cylindrical tube and the flow of a 3D viscous, incompressible fluid. To gain a deeper insight into the influence of various parameters on the swimmer speed, a reduced 1D fluid-structure interaction model was derived and validated. It was found that fast swimmers are those with large tube aspect ratios, and with the amplitude of the traveling wave which is roughly 50% of the reference swimmer radius. It was shown that the speed of our "optimal swimmer" is around 1.5 swimmer lengths per second, which is at the top of the class of all currently manufactured micro-swimmers swimming in low Reynolds number flows (Re =10-6), reported in [11].

  2. Modeling growth paths of interacting crack pairs in elastic media.

    PubMed

    Ghelichi, Ramin; Kamrin, Ken

    2015-10-28

    The problem of predicting the growth of a system of cracks, each crack influencing the growth of the others, arises in multiple fields. We develop an analytical framework toward this aim, which we apply to the 'En-Passant' family of crack growth problems, in which a pair of initially parallel, offset cracks propagate nontrivially toward each other under far-field opening stress. We utilize boundary integral and perturbation methods of linear elasticity, linear elastic fracture mechanics, and common crack opening criteria to calculate the first analytical model for curved En-Passant crack paths. The integral system is reduced under a hierarchy of approximations, producing three methods of increasing simplicity for computing crack paths. The last such method is a major highlight of this work, using an asymptotic matching argument to predict crack paths based on superposition of simple, single-crack fields. Within the corresponding limits of the three methods, all three are shown to agree with each other. We provide comparisons to exact results and existing experimental data to verify certain approximation steps. PMID:26330342

  3. Network model with structured nodes

    NASA Astrophysics Data System (ADS)

    Frisco, Pierluigi

    2011-08-01

    We present a network model in which words over a specific alphabet, called structures, are associated to each node and undirected edges are added depending on some distance measure between different structures. This model shifts the underlying principle of network generation from a purely mathematical one to an information-based one. It is shown how this model differs from the Barábasi-Albert and duplication models and how it can generate networks with topological features similar to biological networks: power law degree distribution, low average path length, clustering coefficient independent from the network size, etc. Two biological networks: S. cerevisiae gene network and E. coli protein-protein interaction network, are replicated using this model.

  4. Probing the cross-effect of strains in non-linear elasticity of nearly regular polymer networks by pure shear deformation.

    PubMed

    Katashima, Takuya; Urayama, Kenji; Chung, Ung-il; Sakai, Takamasa

    2015-05-01

    The pure shear deformation of the Tetra-polyethylene glycol gels reveals the presence of an explicit cross-effect of strains in the strain energy density function even for the polymer networks with nearly regular structure including no appreciable amount of structural defect such as trapped entanglement. This result is in contrast to the expectation of the classical Gaussian network model (Neo Hookean model), i.e., the vanishing of the cross effect in regular networks with no trapped entanglement. The results show that (1) the cross effect of strains is not dependent on the network-strand length; (2) the cross effect is not affected by the presence of non-network strands; (3) the cross effect is proportional to the network polymer concentration including both elastically effective and ineffective strands; (4) no cross effect is expected exclusively in zero limit of network concentration in real polymer networks. These features indicate that the real polymer networks with regular network structures have an explicit cross-effect of strains, which originates from some interaction between network strands (other than entanglement effect) such as nematic interaction, topological interaction, and excluded volume interaction. PMID:25956121

  5. Survivable VON mapping with ambiguity similitude for differentiable maximum shared capacity in elastic optical networks

    NASA Astrophysics Data System (ADS)

    Yang, Hui; Zhu, Xiaoxu; Bai, Wei; Zhao, Yongli; Zhang, Jie; Liu, Zhu; Zhou, Ziguan; Ou, Qinghai

    2016-09-01

    Virtualization is considered to be a promising solution to support various emerging applications. This paper illustrates the problem of virtual mapping from a new perspective, and mainly focuses on survivable mapping of virtual networks and the potential trade-off between spectral resource usage effectiveness and failure resilience level. We design an optimum shared protection mapping (OSPM) scheme in elastic optical networks. A differentiable maximum shared capacity of each frequency slot is defined to more efficiently shared protection resource. In order to satisfy various assessment standards, a metric called ambiguity similitude is defined for the first time to give insight on the optimizing difficulty. Simulation results are presented to compare the outcome of the novel OSPM algorithm with traditional dedicated link protection and maximum shared protection mapping. By synthetic analysis, OSPM outperforms the other two schemes in terms of striking a perfect balance among blocking probability, resources utilization, protective success rate, and spectrum redundancy.

  6. A Morpho-Elastic Model of Hyphal Tip Growth in Filamentous Organisms

    NASA Astrophysics Data System (ADS)

    Goriely, A.; Tabor, M.; Tongen, A.

    The growth of filamentous cells is modeled through the use of exact, nonlinear, elasticity theory for shells and membranes. The biomechanical model is able to capture the generic features of growth of a broad array of cells including actinomycetes, fungi, and root hairs. It also provides the means of studying the effects of external surface stresses. The growth mechanism is modeled by a process of incremental elastic growth in which the cell wall responds elastically to the continuous addition of new material.

  7. Elasticity of fractal materials using the continuum model with non-integer dimensional space

    NASA Astrophysics Data System (ADS)

    Tarasov, Vasily E.

    2015-01-01

    Using a generalization of vector calculus for space with non-integer dimension, we consider elastic properties of fractal materials. Fractal materials are described by continuum models with non-integer dimensional space. A generalization of elasticity equations for non-integer dimensional space, and its solutions for the equilibrium case of fractal materials are suggested. Elasticity problems for fractal hollow ball and cylindrical fractal elastic pipe with inside and outside pressures, for rotating cylindrical fractal pipe, for gradient elasticity and thermoelasticity of fractal materials are solved.

  8. Computational Model of Three Dimensional Elastic Wing Driven by Muscles

    NASA Astrophysics Data System (ADS)

    Wang, Z. Jane; Cowen, Nathaniel; Peskin, Charles S.; Childress, Stephen W.

    2003-11-01

    The flapping wing motion observed in nature results from couplings of muscles, flexible wing structures, and unsteady flows. Previously we have studied the unsteady flows and forces of a rigid two dimensional wing undergoing prescribed motion similar to kinematics observed in insects, as a means of understanding basic unsteady aerodynamic mechanisms. In this talk, we describe our recent progress in constructing a more realistic model insect, which consists of a pair of elastic wings immersed in fluids, and is driven by periodically contracting 'muscles'. A natural computational framework for such a system is the immersed boundary method, which is used here. We present simulations of flapping flight at Reynolds number 10^2, in the same range as that of fruitflies and butterflies.

  9. Modeling of thermal stresses in elastic multilayer coating systems

    NASA Astrophysics Data System (ADS)

    Gao, Chunxue; Zhao, Zhiwei; Li, Xuehua

    2015-02-01

    The performance and reliability of multilayer coating systems are strongly influenced by thermal stresses. The present study develops an alternative analytical model to predict the thermal stresses in elastic multilayer coating systems. An exact closed-form solution is obtained which is independent of the number of coating layers. In addition, with the definition of the coordinate system, the closed-form solution is concisely formulated. Specific results are calculated for thermal stresses in HfO2/SiO2 multilayer optical coatings, and a finite element analysis is performed to confirm the analytical results. The two results agree fairly well with each other. Also, when the thicknesses of the coating layers are much less than the substrate thickness, the approximate solution is obtained based on the exact closed-form solution, and its accuracy is examined.

  10. Shape Selection in the non-Euclidean Model of Elasticity

    NASA Astrophysics Data System (ADS)

    Gemmer, John

    In this dissertation we investigate the behavior of radially symmetric non-Euclidean plates of thickness t with constant negative Gaussian curvature. We present a complete study of these plates using the Foppl-von Karman and Kirchhoff reduced theories of elasticity. Motivated by experimental results, we focus on deformations with a periodic profile. For the Foppl-von Karman model, we prove rigorously that minimizers of the elastic energy converge to saddle shaped isometric immersions. In studying this convergence, we prove rigorous upper and lower bounds for the energy that scale like the thickness t squared. Furthermore, for deformation with n-waves we prove that the lower bound scales like nt2 while the upper bound scales like n2t2. We also investigate the scaling with thickness of boundary layers where the stretching energy is concentrated with decreasing thickness. For the Kichhoff model, we investigate isometric immersions of disks with constant negative curvature into R2, and the minimizers for the bending energy, i.e. the L2 norm of the principal curvatures over the class of W2,2 isometric immersions. We show the existence of smooth immersions of arbitrarily large geodesic balls in the hyperbolic plane into Euclidean space. In elucidating the connection between these immersions and the non-existence/singularity results of Hilbert and Amsler, we obtain a lower bound for the L infinity norm of the principal curvatures for such smooth isometric immersions. We also construct piecewise smooth isometric immersions that have a periodic profile, are globally W2,2, and numerically have lower bending energy than their smooth counterparts. The number of periods in these configurations is set by the condition that the principal curvatures of the surface remain finite and grow approximately exponentially with the radius of the disc.

  11. Dynamic optical resource allocation for mobile core networks with software defined elastic optical networking.

    PubMed

    Zhao, Yongli; Chen, Zhendong; Zhang, Jie; Wang, Xinbo

    2016-07-25

    Driven by the forthcoming of 5G mobile communications, the all-IP architecture of mobile core networks, i.e. evolved packet core (EPC) proposed by 3GPP, has been greatly challenged by the users' demands for higher data rate and more reliable end-to-end connection, as well as operators' demands for low operational cost. These challenges can be potentially met by software defined optical networking (SDON), which enables dynamic resource allocation according to the users' requirement. In this article, a novel network architecture for mobile core network is proposed based on SDON. A software defined network (SDN) controller is designed to realize the coordinated control over different entities in EPC networks. We analyze the requirement of EPC-lightpath (EPCL) in data plane and propose an optical switch load balancing (OSLB) algorithm for resource allocation in optical layer. The procedure of establishment and adjustment of EPCLs is demonstrated on a SDON-based EPC testbed with extended OpenFlow protocol. We also evaluate the OSLB algorithm through simulation in terms of bandwidth blocking ratio, traffic load distribution, and resource utilization ratio compared with link-based load balancing (LLB) and MinHops algorithms. PMID:27464120

  12. Size effects and internal length scales in the elasticity of random fiber networks

    NASA Astrophysics Data System (ADS)

    Picu, Catalin; Berkache, Kamel; Shahsavari, Ali; Ganghoffer, Jean-Francois

    Random fiber networks are the structural element of many biological and man-made materials, including connective tissue, various consumer products and packaging materials. In all cases of practical interest the scale at which the material is used and the scale of the fiber diameter or the mean segment length of the network are separated by several orders of magnitude. This precludes solving boundary value problems defined on the scale of the application while resolving every fiber in the system, and mandates the development of continuum equivalent models. To this end, we study the intrinsic geometric and mechanical length scales of the network and the size effect associated with them. We consider both Cauchy and micropolar continuum models and calibrate them based on the discrete network behavior. We develop a method to predict the characteristic length scales of the problem and the minimum size of a representative element of the network based on network structural parameters and on fiber properties.

  13. Asymptotic analysis of mathematical models for elastic composite media

    NASA Astrophysics Data System (ADS)

    Serkov, S. K.

    The main subject of the thesis is the asymptotic analysis of models in mechanics of composite materials. It is based on the extension of the theory of the Polya-Szego tensors to the problems of homogenization and fracture. Such a technique allows one to obtain an asymptotic solution to a problem where most of numerical algorithms fail due to the presence of a singular perturbation. As a result of this work, a number of interesting effects have been found in optimization of composites and inverse problems of crack-inclusion interaction. Chapter 1 is an introductory chapter that contains the main definitions and bibliographical remarks. In Chapter 2 the Polya-Szego dipole tensors are employed for analysis of plane elasticity problems in non-homogeneous media. Classes of equivalence for defects (cavities and rigid inclusions) are specified for the Laplace and Navier operators: composite materials with defects of the same class have the same effective elastic moduli. Explicit asymptotic formulae for the effective compliance matrices of dilute composites are obtained. The problem of the optimal cavity shape is analyzed in Chapter 3. The analysis uses the Polya-Szego tensors calculated in Chapter 2. A new type of structure which is optimal for shear loading has been found. Properties of the optimal cavity are described. The crack-inclusion interaction problem considered in Chapter 4 has been solved by the asymptotic methods. An analysis of crack trajectories is performed in Chapter 5 for different types of defects and interface conditions. The algorithm employs the Polya-Szego tensors as integral characteristics describing the defect. Comparison with experimental data (Ceramic Centre, Bologna) is presented. In Chapter 6 we use the method of compound asymptotic expansions to treat the homogenization problem for thin-walled composites. The technique of boundary layer fields is employed to derive the junction condition in the region connecting thin walls. The asymptotic

  14. An Elastic Plastic Contact Model with Strain Hardening for the LAMMPS Granular Package

    SciTech Connect

    Kuhr, Bryan; Brake, Matthew Robert; Lechman, Jeremy B.

    2015-03-01

    The following details the implementation of an analytical elastic plastic contact model with strain hardening for normal im pacts into the LAMMPS granular package. The model assumes that, upon impact, the co llision has a period of elastic loading followed by a period of mixed elastic plas tic loading, with contributions to each mechanism estimated by a hyperbolic seca nt weight function. This function is implemented in the LAMMPS source code as the pair style gran/ep/history. Preliminary tests, simulating the pouring of pure nickel spheres, showed the elastic/plastic model took 1.66x as long as similar runs using gran/hertz/history.

  15. Elastic deformation and failure in protein filament bundles: atomistic simulations and coarse-grained modeling

    PubMed Central

    Hammond, N. A.

    2008-01-01

    The synthetic peptide RAD16-II has shown promise in tissue engineering and drug delivery. It has been studied as a vehicle for cell delivery and controlled release of IGF-1 to repair infarcted cardiac tissue, and as a scaffold to promote capillary formation for an in vitro model of angiogenesis. The structure of RAD16-II is hierarchical, with monomers forming long β-sheets that pair together to form filaments; filaments form bundles approximately 30–60 nm in diameter; branching networks of filament bundles form macroscopic gels. We investigate the mechanics of shearing between the two β-sheets constituting one filament, and between cohered filaments of RAD16-II. This shear loading is found in filament bundle bending or in tensile loading of fibers composed of partial-length filaments. Molecular dynamics simulations show that time to failure is a stochastic function of applied shear stress, and that for a given loading time behavior is elastic for sufficiently small shear loads. We propose a coarse-grained model based on Langevin dynamics that matches molecular dynamics results and facilities extending simulations in space and time. The model treats a filament as an elastic string of particles, each having potential energy that is a periodic function of its position relative to the neighboring filament. With insight from these simulations, we discuss strategies for strengthening RAD16-II and similar materials. PMID:18440063

  16. On the neural network calculation of the Lamé coefficients through eigenvalues of the elasticity operator

    NASA Astrophysics Data System (ADS)

    Ossandón, Sebastián; Reyes, Camilo

    2016-02-01

    A new numerical method is presented with the purpose to calculate the Lamé coefficients, associated with an elastic material, through eigenvalues of the elasticity operator. The finite element method is used to solve repeatedly, using different Lamé coefficients values, the direct problem by training a direct radial basis neural network. A map of eigenvalues, as a function of the Lamé constants, is then obtained. This relationship is later inverted and refined by training an inverse radial basis neural network, allowing calculation of mentioned coefficients. A numerical example is presented to prove the effectiveness of this novel method.

  17. Global model for the lithospheric strength and effective elastic thickness

    NASA Astrophysics Data System (ADS)

    Tesauro, Magdala; Kaban, Mikhail K.; Cloetingh, Sierd A. P. L.

    2013-08-01

    Global distribution of the strength and effective elastic thickness (Te) of the lithosphere are estimated using physical parameters from recent crustal and lithospheric models. For the Te estimation we apply a new approach, which provides a possibility to take into account variations of Young modulus (E) within the lithosphere. In view of the large uncertainties affecting strength estimates, we evaluate global strength and Te distributions for possible end-member 'hard' (HRM) and a 'soft' (SRM) rheology models of the continental crust. Temperature within the lithosphere has been estimated using a recent tomography model of Ritsema et al. (2011), which has much higher horizontal resolution than previous global models. Most of the strength is localized in the crust for the HRM and in the mantle for the SRM. These results contribute to the long debates on applicability of the "crème brulée" or "jelly-sandwich" model for the lithosphere structure. Changing from the SRM to HRM turns most of the continental areas from the totally decoupled mode to the fully coupled mode of the lithospheric layers. However, in the areas characterized by a high thermal regime and thick crust, the layers remain decoupled even for the HRM. At the same time, for the inner part of the cratons the lithospheric layers are coupled in both models. Therefore, rheological variations lead to large changes in the integrated strength and Te distribution in the regions characterized by intermediate thermal conditions. In these areas temperature uncertainties have a greater effect, since this parameter principally determines rheological behavior. Comparison of the Te estimates for both models with those determined from the flexural loading and spectral analysis shows that the 'hard' rheology is likely applicable for cratonic areas, whereas the 'soft' rheology is more representative for young orogens.

  18. Atomistic modeling of diffusional phasetransformations with elastic strain

    SciTech Connect

    Mason, D R; Rudd, R E; Sutton, A P

    2003-10-31

    Phase transformations in 2xxx series aluminium alloys (Al-Cu-Mg) are investigated with an off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strain around misfitting atoms and vacancies. Atomic interactions are modelled by Finnis-Sinclair potentials constructed for these simulations. Vacancy diffusion is modelled by comparing the energies of trial states, where the system is partially relaxed for each trial state. No special requirements are made about the description of atomic interactions, making our approach suitable for more fundamentally based models such as tight binding if sufficient computational resources are available. Only a limited precision is required for the energy of each trial state, determined by the value of kBT. Since the change in the relaxation displacement field caused by a vacancy hop decays as 1/r{sup 3} , it is sufficient to determine the next move by relaxing only those atoms in a sphere of finite radius centred on the moving vacancy. However, once the next move has been selected, the entire system is relaxed. Simulations of the early stages of phase separation in Al-Cu with elastic relaxation show an enhanced rate of clustering compared to those performed on the same system with a rigid lattice.

  19. Modeling the dynamics of a tracer particle in an elastic active gel

    NASA Astrophysics Data System (ADS)

    Ben-Isaac, E.; Fodor, É.; Visco, P.; van Wijland, F.; Gov, Nir S.

    2015-07-01

    The internal dynamics of active gels both in artificial (in vitro) model systems and inside the cytoskeleton of living cells has been extensively studied with experiments of recent years. These dynamics are probed using tracer particles embedded in the network of biopolymers together with molecular motors, and distinct nonthermal behavior is observed. We present a theoretical model of the dynamics of a trapped active particle, which allows us to quantify the deviations from equilibrium behavior, using both analytic and numerical calculations. We map the different regimes of dynamics in this system and highlight the different manifestations of activity: breakdown of the virial theorem and equipartition, different elasticity-dependent "effective temperatures," and distinct non-Gaussian distributions. Our results shed light on puzzling observations in active gel experiments and provide physical interpretation of existing observations, as well as predictions for future studies.

  20. Modeling the dynamics of a tracer particle in an elastic active gel.

    PubMed

    Ben-Isaac, E; Fodor, É; Visco, P; van Wijland, F; Gov, Nir S

    2015-07-01

    The internal dynamics of active gels both in artificial (in vitro) model systems and inside the cytoskeleton of living cells has been extensively studied with experiments of recent years. These dynamics are probed using tracer particles embedded in the network of biopolymers together with molecular motors, and distinct nonthermal behavior is observed. We present a theoretical model of the dynamics of a trapped active particle, which allows us to quantify the deviations from equilibrium behavior, using both analytic and numerical calculations. We map the different regimes of dynamics in this system and highlight the different manifestations of activity: breakdown of the virial theorem and equipartition, different elasticity-dependent "effective temperatures," and distinct non-Gaussian distributions. Our results shed light on puzzling observations in active gel experiments and provide physical interpretation of existing observations, as well as predictions for future studies. PMID:26274211

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

    PubMed

    Baskaran, Arvind; Ratsch, Christian; Smereka, Peter

    2015-12-01

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

  2. Critical review of elastic and plastic thermal contact conductance models and comparison with experiment

    SciTech Connect

    Sridhar, M.R.; Yovanovich, M.M. )

    1993-01-01

    More than 450 thermal contact resistance data points obtained from isotropic conforming rough surfaces for five different materials; Ni200, SS304, two Zirconium alloys and Al6061 have been compared with the existing elastic and plastic models. For the first time data have been reduced to a dimensionless form assuming both elastic as well as plastic deformation. Normally data were compared with either the elastic model or the plastic model assuming a type of deformation a priori. The relative merits of different models and the surface factors influencing the mode of deformation are still not clear. Hence the aim of the present work was to compare most of the models available in the literature with themselves as well as with isotropic data. Comparison showed that generally smoother surfaces deform elastically and rougher ones plastically. However there are some data sets which compare well with both the elastic as well as the plastic models. 20 refs.

  3. The Elastic Body Model: A Pedagogical Approach Integrating Real Time Measurements and Modelling Activities

    ERIC Educational Resources Information Center

    Fazio, C.; Guastella, I.; Tarantino, G.

    2007-01-01

    In this paper, we describe a pedagogical approach to elastic body movement based on measurements of the contact times between a metallic rod and small bodies colliding with it and on modelling of the experimental results by using a microcomputer-based laboratory and simulation tools. The experiments and modelling activities have been built in the…

  4. Estimation of Elastic Modulus of Intact Rocks by Artificial Neural Network

    NASA Astrophysics Data System (ADS)

    Ocak, Ibrahim; Seker, Sadi Evren

    2012-11-01

    The modulus of elasticity of intact rock ( E i) is an important rock property that is used as an input parameter in the design stage of engineering projects such as dams, slopes, foundations, tunnel constructions and mining excavations. However, it is sometimes difficult to determine the modulus of elasticity in laboratory tests because high-quality cores are required. For this reason, various methods for predicting E i have been popular research topics in recently published literature. In this study, the relationships between the uniaxial compressive strength, unit weight ( γ) and E i for different types of rocks were analyzed, employing an artificial neural network and 195 data obtained from laboratory tests carried out on cores obtained from drilling holes within the area of three metro lines in Istanbul, Turkey. Software was developed in Java language using Weka class libraries for the study. To determine the prediction capacity of the proposed technique, the root-mean-square error and the root relative squared error indices were calculated as 0.191 and 92.587, respectively. Both coefficients indicate that the prediction capacity of the study is high for practical use.

  5. An elastic model of partial budding of retroviruses

    NASA Astrophysics Data System (ADS)

    Zhang, Rui; Nguyen, Toan

    2008-03-01

    Retroviruses are characterized by their unique infection strategy of reverse transcription, in which the genetic information flows from RNA back to DNA. The most well known representative is the human immunodeficiency virus (HIV). Unlike budding of traditional enveloped viruses, retrovirus budding happens together with the formation of spherical virus capsids at the cell membrane. Led by this unique budding mechanism, we proposed an elastic model of retrovirus budding in this work. We found that if the lipid molecules of the membrane are supplied fast enough from the cell interior, the budding always proceeds to completion. In the opposite limit, there is an optimal size of partially budded virions. The zenith angle of these partially spherical capsids, α, is given by α˜(2̂/κσ)^1/4, where κ is the bending modulus of the membrane, σ is the surface tension of the membrane, and τ characterizes the strength of capsid protein interaction. If τ is large enough such that α˜π, the budding is complete. Our model explained many features of retrovirus partial budding observed in experiments.

  6. Double porosity modeling in elastic wave propagation for reservoir characterization

    SciTech Connect

    Berryman, J. G., LLNL

    1998-06-01

    Phenomenological equations for the poroelastic behavior of a double porosity medium have been formulated and the coefficients in these linear equations identified. The generalization from a single porosity model increases the number of independent coefficients from three to six for an isotropic applied stress. In a quasistatic analysis, the physical interpretations are based upon considerations of extremes in both spatial and temporal scales. The limit of very short times is the one most relevant for wave propagation, and in this case both matrix porosity and fractures behave in an undrained fashion. For the very long times more relevant for reservoir drawdown,the double porosity medium behaves as an equivalent single porosity medium At the macroscopic spatial level, the pertinent parameters (such as the total compressibility) may be determined by appropriate field tests. At the mesoscopic scale pertinent parameters of the rock matrix can be determined directly through laboratory measurements on core, and the compressibility can be measured for a single fracture. We show explicitly how to generalize the quasistatic results to incorporate wave propagation effects and how effects that are usually attributed to squirt flow under partially saturated conditions can be explained alternatively in terms of the double-porosity model. The result is therefore a theory that generalizes, but is completely consistent with, Biot`s theory of poroelasticity and is valid for analysis of elastic wave data from highly fractured reservoirs.

  7. Piezoresistive Sensor with High Elasticity Based on 3D Hybrid Network of Sponge@CNTs@Ag NPs.

    PubMed

    Zhang, Hui; Liu, Nishuang; Shi, Yuling; Liu, Weijie; Yue, Yang; Wang, Siliang; Ma, Yanan; Wen, Li; Li, Luying; Long, Fei; Zou, Zhengguang; Gao, Yihua

    2016-08-31

    Pressure sensors with high elasticity are in great demand for the realization of intelligent sensing, but there is a need to develope a simple, inexpensive, and scalable method for the manufacture of the sensors. Here, we reported an efficient, simple, facile, and repeatable "dipping and coating" process to manufacture a piezoresistive sensor with high elasticity, based on homogeneous 3D hybrid network of carbon nanotubes@silver nanoparticles (CNTs@Ag NPs) anchored on a skeleton sponge. Highly elastic, sensitive, and wearable sensors are obtained using the porous structure of sponge and the synergy effect of CNTs/Ag NPs. Our sensor was also tested for over 2000 compression-release cycles, exhibiting excellent elasticity and cycling stability. Sensors with high performance and a simple fabrication process are promising devices for commercial production in various electronic devices, for example, sport performance monitoring and man-machine interfaces. PMID:27482721

  8. Visualizing tropoelastin in a long-term human elastic fibre cell culture model

    PubMed Central

    Halm, M.; Schenke-Layland, K.; Jaspers, S.; Wenck, H.; Fischer, F.

    2016-01-01

    Elastin is an essential protein found in a variety of tissues where resilience and flexibility are needed, such as the skin and the heart. When aiming to engineer suitable implants, elastic fibres are needed to allow adequate tissue renewal. However, the visualization of human elastogenesis remains in the dark. To date, the visualization of human tropoelastin (TE) production in a human cell context and its fibre assembly under live cell conditions has not been achieved. Here, we present a long-term cell culture model of human dermal fibroblasts expressing fluorescence-labelled human TE. We employed a lentiviral system to stably overexpress Citrine-labelled TE to build a fluorescent fibre network. Using immunofluorescence, we confirmed the functionality of the Citrine-tagged TE. Furthermore, we visualized the fibre assembly over the course of several days using confocal microscopy. Applying super resolution microscopy, we were able to investigate the inner structure of the elastin–fibrillin-1 fibre network. Future investigations will allow the tracking of TE produced under various conditions. In tissue engineering applications the fluorescent fibre network can be visualized under various conditions or it serves as a tool for investigating fibre degradation processes in disease-in-a-dish-models. PMID:26842906

  9. Simple model for directed networks

    NASA Astrophysics Data System (ADS)

    Morelli, Luis G.

    2003-06-01

    We study a model for directed networks based on the Watts-Stogatz model for small-world phenomena. We focus on some topological aspects of directed networks inspired in food web theory, namely, the fraction of basal and top nodes in the network and node level distributions. We argue that in directed networks basal nodes play an important role, collecting information or resources from the environment. We give analytical expressions for the fraction of basal and top nodes for the model, and study the node level distributions with numerical simulations.

  10. Introduction to physical properties and elasticity models: Chapter 20

    USGS Publications Warehouse

    Dvorkin, Jack; Helgerud, Michael B.; Waite, William F.; Kirby, Stephen H.; Nur, Amos

    2003-01-01

    Estimating the in situ methane hydrate volume from seismic surveys requires knowledge of the rock physics relations between wave speeds and elastic moduli in hydrate/sediment mixtures. The elastic moduli of hydrate/sediment mixtures depend on the elastic properties of the individual sedimentary particles and the manner in which they are arranged. In this chapter, we present some rock physics data currently available from literature. The unreferenced values in Table I were not measured directly, but were derived from other values in Tables I and II using standard relationships between elastic properties for homogeneous, isotropic material. These derivations allow us to extend the list of physical property estimates, but at the expense of introducing uncertainties due to combining property values measured under different physical conditions. This is most apparent in the case of structure II (sII) hydrate for which very few physical properties have been measured under identical conditions.

  11. Freeze fracturing of elastic porous media: a mathematical model

    PubMed Central

    Vlahou, I.; Worster, M. G.

    2015-01-01

    We present a mathematical model of the fracturing of water-saturated rocks and other porous materials in cold climates. Ice growing inside porous rocks causes large pressures to develop that can significantly damage the rock. We study the growth of ice inside a penny-shaped cavity in a water-saturated porous rock and the consequent fracturing of the medium. Premelting of the ice against the rock, which results in thin films of unfrozen water forming between the ice and the rock, is one of the dominant processes of rock fracturing. We find that the fracture toughness of the rock, the size of pre-existing faults and the undercooling of the environment are the main parameters determining the susceptibility of a medium to fracturing. We also explore the dependence of the growth rates on the permeability and elasticity of the medium. Thin and fast-fracturing cracks are found for many types of rocks. We consider how the growth rate can be limited by the existence of pore ice, which decreases the permeability of a medium, and propose an expression for the effective ‘frozen’ permeability. PMID:25792954

  12. Complex Networks in Psychological Models

    NASA Astrophysics Data System (ADS)

    Wedemann, R. S.; Carvalho, L. S. A. V. D.; Donangelo, R.

    We develop schematic, self-organizing, neural-network models to describe mechanisms associated with mental processes, by a neurocomputational substrate. These models are examples of real world complex networks with interesting general topological structures. Considering dopaminergic signal-to-noise neuronal modulation in the central nervous system, we propose neural network models to explain development of cortical map structure and dynamics of memory access, and unify different mental processes into a single neurocomputational substrate. Based on our neural network models, neurotic behavior may be understood as an associative memory process in the brain, and the linguistic, symbolic associative process involved in psychoanalytic working-through can be mapped onto a corresponding process of reconfiguration of the neural network. The models are illustrated through computer simulations, where we varied dopaminergic modulation and observed the self-organizing emergent patterns at the resulting semantic map, interpreting them as different manifestations of mental functioning, from psychotic through to normal and neurotic behavior, and creativity.

  13. Assortative model for social networks.

    PubMed

    Catanzaro, Michele; Caldarelli, Guido; Pietronero, Luciano

    2004-09-01

    In this Brief Report we present a version of a network growth model, generalized in order to describe the behavior of social networks. The case of study considered is the preprint archive at cul.arxiv.org. Each node corresponds to a scientist, and a link is present whenever two authors wrote a paper together. This graph is a nice example of degree-assortative network, that is, to say a network where sites with similar degree are connected to each other. The model presented is one of the few able to reproduce such behavior, giving some insight on the microscopic dynamics at the basis of the graph structure. PMID:15524673

  14. A staggered-grid convolutional differentiator for elastic wave modelling

    NASA Astrophysics Data System (ADS)

    Sun, Weijia; Zhou, Binzhong; Fu, Li-Yun

    2015-11-01

    The computation of derivatives in governing partial differential equations is one of the most investigated subjects in the numerical simulation of physical wave propagation. An analytical staggered-grid convolutional differentiator (CD) for first-order velocity-stress elastic wave equations is derived in this paper by inverse Fourier transformation of the band-limited spectrum of a first derivative operator. A taper window function is used to truncate the infinite staggered-grid CD stencil. The truncated CD operator is almost as accurate as the analytical solution, and as efficient as the finite-difference (FD) method. The selection of window functions will influence the accuracy of the CD operator in wave simulation. We search for the optimal Gaussian windows for different order CDs by minimizing the spectral error of the derivative and comparing the windows with the normal Hanning window function for tapering the CD operators. It is found that the optimal Gaussian window appears to be similar to the Hanning window function for tapering the same CD operator. We investigate the accuracy of the windowed CD operator and the staggered-grid FD method with different orders. Compared to the conventional staggered-grid FD method, a short staggered-grid CD operator achieves an accuracy equivalent to that of a long FD operator, with lower computational costs. For example, an 8th order staggered-grid CD operator can achieve the same accuracy of a 16th order staggered-grid FD algorithm but with half of the computational resources and time required. Numerical examples from a homogeneous model and a crustal waveguide model are used to illustrate the superiority of the CD operators over the conventional staggered-grid FD operators for the simulation of wave propagations.

  15. Elastic Coupling of Nascent apCAM Adhesions to Flowing Actin Networks

    PubMed Central

    Mejean, Cecile O.; Schaefer, Andrew W.; Buck, Kenneth B.; Kress, Holger; Shundrovsky, Alla; Merrill, Jason W.; Dufresne, Eric R.; Forscher, Paul

    2013-01-01

    Adhesions are multi-molecular complexes that transmit forces generated by a cell’s acto-myosin networks to external substrates. While the physical properties of some of the individual components of adhesions have been carefully characterized, the mechanics of the coupling between the cytoskeleton and the adhesion site as a whole are just beginning to be revealed. We characterized the mechanics of nascent adhesions mediated by the immunoglobulin-family cell adhesion molecule apCAM, which is known to interact with actin filaments. Using simultaneous visualization of actin flow and quantification of forces transmitted to apCAM-coated beads restrained with an optical trap, we found that adhesions are dynamic structures capable of transmitting a wide range of forces. For forces in the picoNewton scale, the nascent adhesions’ mechanical properties are dominated by an elastic structure which can be reversibly deformed by up to 1 µm. Large reversible deformations rule out an interface between substrate and cytoskeleton that is dominated by a number of stiff molecular springs in parallel, and favor a compliant cross-linked network. Such a compliant structure may increase the lifetime of a nascent adhesion, facilitating signaling and reinforcement. PMID:24039928

  16. Hybrid routing and spectrum assignment algorithms based on distance-adaptation combined coevolution and heuristics in elastic optical networks

    NASA Astrophysics Data System (ADS)

    Ding, Zhe; Xu, Zhanqi; Zeng, Xiaodong; Ma, Tao; Yang, Fan

    2014-04-01

    By adopting the orthogonal frequency division multiplexing technology, spectrum-sliced elastic optical path networks can offer flexible bandwidth to each connection request and utilize the spectrum resources efficiently. The routing and spectrum assignment (RSA) problems in SLICE networks are solved by using heuristic algorithms in most prior studies and addressed by intelligent algorithms in few investigations. The performance of RSA algorithms can be further improved if we could combine such two types of algorithms. Therefore, we propose three hybrid RSA algorithms: DACE-GMSF, DACE-GLPF, and DACE-GEMkPSF, which are the combination of the heuristic algorithm and coevolution based on distance-adaptive policy. In the proposed algorithms, we first groom the connection requests, then sort the connection requests by using the heuristic algorithm (most subcarriers first, longest path first, and extended most k paths' slots first), and finally search the approximately optimal solution with the coevolutionary policy. We present a model of the RSA problem by using integral linear programming, and key elements in the proposed algorithms are addressed in detail. Simulations under three topologies show that the proposed hybrid RSA algorithms can save spectrum resources efficiently.

  17. Shared end-to-content backup path protection in k-node (edge) content connected elastic optical datacenter networks.

    PubMed

    Li, Xin; Huang, Shanguo; Yin, Shan; Guo, Bingli; Zhao, Yongli; Zhang, Jie; Zhang, Min; Gu, Wanyi

    2016-05-01

    To quantitatively measure content connectivity and provide protection for different kinds of content, the concept of k-node (edge) content connectivity is proposed recently. Based on k-node (edge) content connectivity, k-node (edge) content connected elastic optical datacenter network (KC-EODN) is proposed to design disaster-resilient and spectrum-efficient optical datacenter networks. In KC-EODN, k independent end-to-content paths are established for each request. However, it will consume too much resource to assign dedicated spectrum for each end-to-content path. Spectrum sharing among multiple end-to-content paths of different requests can greatly improve resource efficiency. In this paper, a novel perfect matching based sharing principle among multiple end-to-content paths of different requests is proposed. Based on the new proposed sharing principle, we present the shared end-to-content backup path protection (SEBPP) scheme for KC-EODN. Integer linear program (ILP) model and heuristic algorithms are designed for SEBPP scheme with the objective of minimizing the total of working and backup spectrum resources. Numerical results show that the proposed SEBPP scheme can greatly reduce spectrum consumption while ensuring the survivability against natural disaster and multi-failures. PMID:27137559

  18. Modeling thermal-mechanical behavior of networks with reconfigurable crosslinks

    NASA Astrophysics Data System (ADS)

    Yang, Jeh-Chang; Meng, Yuan; Anthamatten, Mitchell

    Actively moving polymers nearly always involve the storage or release of mechanical energy using external stimuli. Thermomechanical experiments were conducted on well-defined chemical networks bearing both permanent and light-reconfigurable covalent junctions. Experimental data include stress relaxation and mechanical creep during photoinduced network reconfiguration as well as equilibrium stress-strain behavior of reprogrammed networks. Physical models of elastic networks were applied to describe thermomechanical behavior during and after bond re-formation while under external stress. The role of dangling ends in influencing competitive network mechanics is evaluated to explain observed phenomena and discrepancies between theory and data. Understanding how process path is related to the equilibrium thermomechanics of such reprogrammed networks is important to engineering shape actuator driven by crystallization. Nsf ECCS-1530540.

  19. Rigid-plug elastic-water model for transient pipe flow with entrapped air pocket

    SciTech Connect

    Zhou, Ling; Liu, Prof. Deyou; Karney, Professor Byran W.; Zhang, Qin Fen; OU, CHANGQI

    2011-01-01

    Pressure transients in a rapidly filling pipe with an entrapped air pocket are investigated analytically. A rigid-plug elastic water model is developed by applying elastic water hammer to the majority of the water column while applying rigid water analysis to a small portion near the air-water interface, which avoids effectively the interpolation error of previous approaches. Moreover, another two simplified models are introduced respectively based on constant water length and by neglecting water elasticity. Verification of the three models is confirmed by experimental results. Calculations show that the simplification of constant water length is feasible for small air pockets. The complete rigid water model is appropriate for cases with large initial air volume. The rigid-plug elastic model can predict all the essential features for the entire range of initial air fraction considered in this study, and it is the effective model for analysis of pressure transients of entrapped air.

  20. Analysis of Nonlinear Poro-Elastic and Poro-Visco-Elastic Models

    NASA Astrophysics Data System (ADS)

    Bociu, Lorena; Guidoboni, Giovanna; Sacco, Riccardo; Webster, Justin T.

    2016-07-01

    We consider the initial and boundary value problem for a system of partial differential equations describing the motion of a fluid-solid mixture under the assumption of full saturation. The ability of the fluid phase to flow within the solid skeleton is described by the permeability tensor, which is assumed here to be a multiple of the identity and to depend nonlinearly on the volumetric solid strain. In particular, we study the problem of the existence of weak solutions in bounded domains, accounting for non-zero volumetric and boundary forcing terms. We investigate the influence of viscoelasticity on the solution functional setting and on the regularity requirements for the forcing terms. The theoretical analysis shows that different time regularity requirements are needed for the volumetric source of linear momentum and the boundary source of traction depending on whether or not viscoelasticity is present. The theoretical results are further investigated via numerical simulations based on a novel dual mixed hybridized finite element discretization. When the data are sufficiently regular, the simulations show that the solutions satisfy the energy estimates predicted by the theoretical analysis. Interestingly, the simulations also show that, in the purely elastic case, the Darcy velocity and the related fluid energy might become unbounded if indeed the data do not enjoy the time regularity required by the theory.

  1. Campus network security model study

    NASA Astrophysics Data System (ADS)

    Zhang, Yong-ku; Song, Li-ren

    2011-12-01

    Campus network security is growing importance, Design a very effective defense hacker attacks, viruses, data theft, and internal defense system, is the focus of the study in this paper. This paper compared the firewall; IDS based on the integrated, then design of a campus network security model, and detail the specific implementation principle.

  2. Elastic body spline technique for feature point generation and face modeling.

    PubMed

    Kuo, Chung J; Hung, Jui-Hsin; Tsai, Meng-Han; Shih, Po-Liang

    2005-12-01

    Due to the advent of MPEG-4 standard, facial animation has been receiving significant attention lately. A common approach for facial animation is to use the mesh model. The physics-based transformation, elastic body spline (EBS), has been proposed to deform the facial mesh model and generate realistic expression by assuming the whole facial image has the same elastic property. In this paper, we partition facial images into different regions and propose an iterative algorithm to find the elastic property of each facial region. By doing so, we can obtain the EBS for mesh vertices in the facial mesh model such that facial animation can be more realistically achieved. PMID:16370468

  3. Modeling viscoelastic networks and cell deformation in the context of the immersed boundary method

    SciTech Connect

    Bottino, D.C.

    1998-11-20

    The author presents a straightforward numerical technique for modeling passive viscoelastic networks, such as the actin cytoskeleton of ameboid cells, in the context of the immersed boundary method. The technique involves modeling the cytoskeletal material as a network of dynamic elastic links immersed in the ambient cytosol. Linking rules of varying complexity allow the numerical network to exhibit varying degrees of viscosity, elasticity, shear thinning, and thixotropy (stress-overshoot). A series of simulated viscometer tests are used to analyze the mechanical properties of the model networks and the effects of input parameters on these properties. The numerical network is then used in the context of a full-cell model involving simulated micropipette aspiration. These micropipette aspiration tests indicate that the immersed boundary method--with the added enhancement of the viscoelastic network model presented here--can be developed into a versatile tool for studying the free-boundary deformations of passively stressed and actively moving ameboid cells.

  4. On the origin of Gaussian network theory in the thermo/chemo-responsive shape memory effect of amorphous polymers undergoing photo-elastic transition

    NASA Astrophysics Data System (ADS)

    Lu, Haibao; Huang, Wei Min; Leng, Jinsong

    2016-06-01

    Amorphous polymers are normally isotropic in their physical properties, however, upon stress their structural randomness is disturbed and they become anisotropic. There is a close connection between the optical anisotropy and the elastic (or mechanical) anisotropy, since both are related to the type of symmetry exhibited by the molecular structure. On the origin of Gaussian network theory, a phenomenological constitutive framework was proposed to study the photo-elastic transition and working mechanism of the thermo-/chemo-responsive shape-memory effect (SME) in amorphous shape memory polymers (SMPs). Optically refractive index was initially employed to couple the stress, strain and the anisotropy of the random link in macromolecule chain. Based on the Arrhenius law, a constitutive framework was then applied for the temperature dependence of optical (or elastic or mechanical) anisotropy according to the fictive temperature parameter. Finally, the phenomenological photo-elastic model was proposed to quantitatively identify the influential factors behind the thermo-/chemo-responsive SME in SMPs, of which the shape recovery behavior is predicted and verified by the available experimental data reported in the literature.

  5. Evaluation of massless-spring modeling of suspension-line elasticity during the parachute unfurling process

    NASA Technical Reports Server (NTRS)

    Poole, L. R.; Huckins, E. K., III

    1972-01-01

    A general theory on mathematical modeling of elastic parachute suspension lines during the unfurling process was developed. Massless-spring modeling of suspension-line elasticity was evaluated in detail. For this simple model, equations which govern the motion were developed and numerically integrated. The results were compared with flight test data. In most regions, agreement was satisfactory. However, poor agreement was obtained during periods of rapid fluctuations in line tension.

  6. Transient Networks and Dense Colloidal Suspensions: From Viscous Flow to Elastic Instabilities

    NASA Astrophysics Data System (ADS)

    Bouchaud, Elisabeth

    2013-03-01

    In order to analyze the mechanical response of viscoelastic materials in highly non-linear regimes, we have designed a new kind of Hele-Shaw cell where both viscous liquids and soft elastic solids can be tested at a controlled loading rate. We first consider model Maxwell liquids - characterized by a single relaxation time - with the project of benchmarking the response of complex, glassy systems. We use several solutions of microemulsions connected by telechelic polymers. We show that these materials undergo instability in a broad range of loading rates. At low rates, this instability is shown to be of the viscous Saffman-Taylor type. At high rates, we observe a purely elastic bulk instability discovered recently in the context of soft elastomers. A microfluidic version of our cell makes it possible to study the response of colloidal suspensions. We use more or less concentrated PNIPA aqueous solutions for which temperature controls the volume fraction. Observations are interpreted in the light of our understanding of their viscoelastic properties. This work was done in collaboration with Maxime Lefranc, Baudouin Saintyves, Olivier Dauchot and Serge Mora. It was funded by ANR, France.

  7. A micromechanical damage and fracture model for polymers based on fractional strain-gradient elasticity

    NASA Astrophysics Data System (ADS)

    Heyden, S.; Li, B.; Weinberg, K.; Conti, S.; Ortiz, M.

    2015-01-01

    We formulate a simple one-parameter macroscopic model of distributed damage and fracture of polymers that is amenable to a straightforward and efficient numerical implementation. We show that the macroscopic model can be rigorously derived, in the sense of optimal scaling, from a micromechanical model of chain elasticity and failure regularized by means of fractional strain-gradient elasticity. In particular, we derive optimal scaling laws that supply a link between the single parameter of the macroscopic model, namely, the critical energy-release rate of the material, and micromechanical parameters pertaining to the elasticity and strength of the polymer chains and to the strain-gradient elasticity regularization. We show how the critical energy-release rate of specific materials can be determined from test data. Finally, we demonstrate the scope and fidelity of the model by means of an example of application, namely, Taylor-impact experiments of polyurea 1000 rods.

  8. Neural network modeling of emotion

    NASA Astrophysics Data System (ADS)

    Levine, Daniel S.

    2007-03-01

    This article reviews the history and development of computational neural network modeling of cognitive and behavioral processes that involve emotion. The exposition starts with models of classical conditioning dating from the early 1970s. Then it proceeds toward models of interactions between emotion and attention. Then models of emotional influences on decision making are reviewed, including some speculative (not and not yet simulated) models of the evolution of decision rules. Through the late 1980s, the neural networks developed to model emotional processes were mainly embodiments of significant functional principles motivated by psychological data. In the last two decades, network models of these processes have become much more detailed in their incorporation of known physiological properties of specific brain regions, while preserving many of the psychological principles from the earlier models. Most network models of emotional processes so far have dealt with positive and negative emotion in general, rather than specific emotions such as fear, joy, sadness, and anger. But a later section of this article reviews a few models relevant to specific emotions: one family of models of auditory fear conditioning in rats, and one model of induced pleasure enhancing creativity in humans. Then models of emotional disorders are reviewed. The article concludes with philosophical statements about the essential contributions of emotion to intelligent behavior and the importance of quantitative theories and models to the interdisciplinary enterprise of understanding the interactions of emotion, cognition, and behavior.

  9. A Network Synthesis Model for Generating Protein Interaction Network Families

    PubMed Central

    Sahraeian, Sayed Mohammad Ebrahim; Yoon, Byung-Jun

    2012-01-01

    In this work, we introduce a novel network synthesis model that can generate families of evolutionarily related synthetic protein–protein interaction (PPI) networks. Given an ancestral network, the proposed model generates the network family according to a hypothetical phylogenetic tree, where the descendant networks are obtained through duplication and divergence of their ancestors, followed by network growth using network evolution models. We demonstrate that this network synthesis model can effectively create synthetic networks whose internal and cross-network properties closely resemble those of real PPI networks. The proposed model can serve as an effective framework for generating comprehensive benchmark datasets that can be used for reliable performance assessment of comparative network analysis algorithms. Using this model, we constructed a large-scale network alignment benchmark, called NAPAbench, and evaluated the performance of several representative network alignment algorithms. Our analysis clearly shows the relative performance of the leading network algorithms, with their respective advantages and disadvantages. The algorithm and source code of the network synthesis model and the network alignment benchmark NAPAbench are publicly available at http://www.ece.tamu.edu/bjyoon/NAPAbench/. PMID:22912671

  10. Elastic properties of alpha quartz and the alkali halides based on an interatomic force model.

    NASA Technical Reports Server (NTRS)

    Weidner, D. J.; Simmons, G.

    1972-01-01

    A two-body central-force atomic model can be used to describe accurately the elastic properties of alpha quartz if the nontetrahedral O:O forces are included. The strength of the Si:O interaction has little effect on the bulk modulus. The technique is sufficiently general to allow calculations of the elastic properties of a specified structure under arbitrary pressure from a complete description of the interatomic forces. The elastic constants for the NaCl structure and the CsCl structure are examined. Our model includes two-body, central, anion-anion, anion-cation, and electrostatic interactions.

  11. 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.

  12. The Elastic Behaviour of Sintered Metallic Fibre Networks: A Finite Element Study by Beam Theory

    PubMed Central

    Bosbach, Wolfram A.

    2015-01-01

    Background The finite element method has complimented research in the field of network mechanics in the past years in numerous studies about various materials. Numerical predictions and the planning efficiency of experimental procedures are two of the motivational aspects for these numerical studies. The widespread availability of high performance computing facilities has been the enabler for the simulation of sufficiently large systems. Objectives and Motivation In the present study, finite element models were built for sintered, metallic fibre networks and validated by previously published experimental stiffness measurements. The validated models were the basis for predictions about so far unknown properties. Materials and Methods The finite element models were built by transferring previously published skeletons of fibre networks into finite element models. Beam theory was applied as simplification method. Results and Conclusions The obtained material stiffness isn’t a constant but rather a function of variables such as sample size and boundary conditions. Beam theory offers an efficient finite element method for the simulated fibre networks. The experimental results can be approximated by the simulated systems. Two worthwhile aspects for future work will be the influence of size and shape and the mechanical interaction with matrix materials. PMID:26569603

  13. Freight Network Equilibrium Model revisited: the Freight Network Modeling System

    SciTech Connect

    Tobin, R.L.

    1984-01-01

    The Freight Network Equilibrium Model (FNEM) was developed to study potential coal transportation impacts that could result from widespread conversion of boilers to use coal for fuel, as mandated under the Powerplant and Industrial Fuel Use Act of 1978. Continued improvement of FNEM and creation of auxiliary software and data during applications of the model in various transportation analyses led to the development of the Freight Network Modeling System, a general and flexible modeling system designed to have wide applicability to a variety of freight transportation analyses. It consists of compatible network data bases, data management software, models of freight transportation, report generators, and graphics output. The network data include US rail, water, highway, and pipeline systems. Data management software automates the task of setting up a study network of appropriate detail in appropriate regions of the country. The major analytical tools in the system are FNEM and Shortest Path Analysis and Display (SPAD); FNEM is predictive and simulates decisions of both shippers and carriers, taking into account the competition for transportation facilities; SPAD is a simpler model that optimizes routings of single shipments. Output for both FNEM and SPAD includes detailed routings, cost and delay estimates for all shipments, and data on total traffic levels. SPAD can be used interactively with routes displayed graphically. 13 references, 10 figures, 2 tables.

  14. Identification of thin elastic isotropic plate parameters applying Guided Wave Measurement and Artificial Neural Networks

    NASA Astrophysics Data System (ADS)

    Pabisek, Ewa; Waszczyszyn, Zenon

    2015-12-01

    A new hybrid computational system for material identification (HCSMI) is presented, developed for the identification of homogeneous, elastic, isotropic plate parameters. Attention is focused on the construction of dispersion curves, related to Lamb waves. The main idea of the system HCSMI lies in separation of two essential basic computational stages, corresponding to direct or inverse analyses. In the frame of the first stage an experimental dispersion curve DCexp is constructed, applying Guided Wave Measurement (GWM) technique. Then, in the other stage, corresponding to the inverse analysis, an Artificial Neural Network (ANN) is trained 'off line'. The substitution of results of the first stage, treated as inputs of the ANN, gives the values of identified plate parameters. In such a way no iteration is needed, unlike to the classical approach. In such an approach, the "distance" between the approximate experimental curves DCexp and dispersion curves DCnum obtained in the direct analysis, is iteratively minimized. Two case studies are presented, corresponding either to measurements in laboratory tests or those related to pseudo-experimental noisy data of computer simulations. The obtained results prove high numerical efficiency of HCSMI, applied to the identification of aluminum plate parameters.

  15. POLICY VARIATION, LABOR SUPPLY ELASTICITIES, AND A STRUCTURAL MODEL OF RETIREMENT

    PubMed Central

    MANOLI, DAY; MULLEN, KATHLEEN J.; WAGNER, MATHIS

    2015-01-01

    This paper exploits a combination of policy variation from multiple pension reforms in Austria and administrative data from the Austrian Social Security Database. Using the policy changes for identification, we estimate social security wealth and accrual elasticities in individuals’ retirement decisions. Next, we use these elasticities to estimate a dynamic programming model of retirement decisions. Finally, we use the estimated model to examine the labor supply and welfare consequences of potential social security reforms. PMID:26472916

  16. Adaptive Models for Gene Networks

    PubMed Central

    Shin, Yong-Jun; Sayed, Ali H.; Shen, Xiling

    2012-01-01

    Biological systems are often treated as time-invariant by computational models that use fixed parameter values. In this study, we demonstrate that the behavior of the p53-MDM2 gene network in individual cells can be tracked using adaptive filtering algorithms and the resulting time-variant models can approximate experimental measurements more accurately than time-invariant models. Adaptive models with time-variant parameters can help reduce modeling complexity and can more realistically represent biological systems. PMID:22359614

  17. 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

  18. Fractional-order elastic models of cartilage: A multi-scale approach

    NASA Astrophysics Data System (ADS)

    Magin, Richard L.; Royston, Thomas J.

    2010-03-01

    The objective of this research is to develop new quantitative methods to describe the elastic properties (e.g., shear modulus, viscosity) of biological tissues such as cartilage. Cartilage is a connective tissue that provides the lining for most of the joints in the body. Tissue histology of cartilage reveals a multi-scale architecture that spans a wide range from individual collagen and proteoglycan molecules to families of twisted macromolecular fibers and fibrils, and finally to a network of cells and extracellular matrix that form layers in the connective tissue. The principal cells in cartilage are chondrocytes that function at the microscopic scale by creating nano-scale networks of proteins whose biomechanical properties are ultimately expressed at the macroscopic scale in the tissue's viscoelasticity. The challenge for the bioengineer is to develop multi-scale modeling tools that predict the three-dimensional macro-scale mechanical performance of cartilage from micro-scale models. Magnetic resonance imaging (MRI) and MR elastography (MRE) provide a basis for developing such models based on the nondestructive biomechanical assessment of cartilage in vitro and in vivo. This approach, for example, uses MRI to visualize developing proto-cartilage structure, MRE to characterize the shear modulus of such structures, and fractional calculus to describe the dynamic behavior. Such models can be extended using hysteresis modeling to account for the non-linear nature of the tissue. These techniques extend the existing computational methods to predict stiffness and strength, to assess short versus long term load response, and to measure static versus dynamic response to mechanical loads over a wide range of frequencies (50-1500 Hz). In the future, such methods can perhaps be used to help identify early changes in regenerative connective tissue at the microscopic scale and to enable more effective diagnostic monitoring of the onset of disease.

  19. Simplified models of biological networks.

    PubMed

    Sneppen, Kim; Krishna, Sandeep; Semsey, Szabolcs

    2010-01-01

    The function of living cells is controlled by complex regulatory networks that are built of a wide diversity of interacting molecular components. The sheer size and intricacy of molecular networks of even the simplest organisms are obstacles toward understanding network functionality. This review discusses the achievements and promise of a bottom-up approach that uses well-characterized subnetworks as model systems for understanding larger networks. It highlights the interplay between the structure, logic, and function of various types of small regulatory circuits. The bottom-up approach advocates understanding regulatory networks as a collection of entangled motifs. We therefore emphasize the potential of negative and positive feedback, as well as their combinations, to generate robust homeostasis, epigenetics, and oscillations. PMID:20192769

  20. Coarse grain modeling of imperfect networks and gels

    NASA Astrophysics Data System (ADS)

    Sliozberg, Yelena; Chantawansri, Tanya; Sirk, Timothy; Andzelm, Jan; Mrozek, Randy; Lenhart, Joseph

    2013-03-01

    There is a strong interest in chemically and physically cross-linked entangled polymer networks and gels due to their tailorability in respect to both mechanical and structural properties. Even so, these properties are sensitive to imperfections in the polymer networks, such as dangling ends and loops. Computational modeling is a viable tool to understand the effects of these imperfections on properties in a controlled environment, in which specific defects can be systematically created and varied. In this study, we have employed generic bead-spring models of flexible chains to study a chemically and physically cross-linked network. Our results will show the importance defects, such as dangling ends and loops, on the mechanical and structural properties of these networks. We will also discuss the effects of these defects on the time-dependent elastic modulus. The simulation results qualitatively agree with experimental results and the other theoretical predictions.

  1. Numerical solution of an elastic and viscoelastic gravitational models by the finite element method

    NASA Astrophysics Data System (ADS)

    Arjona Almodóvar, A.; Chacón Rebollo, T.; Gómez Marmol, M.

    2014-12-01

    Volcanic areas present a lower effective viscosity than usually in the Earth's crust. Both the elastic-gravitational and the viscoelastic-gravitational models allow the computation of gravity, deformation, and gravitational potential changes in order to investigate crustal deformations of Earth (see for instance Battaglia & Segall, 2004; Fernández et al. 1999, 2001; Rundle 1980 and 1983). These models can be represented by a coupled system of linear parabolic (for the elastic deformations), hyperbolic (for the viscoelastic deformations) and elliptic partial differential equations (for gravitational potential changes) (see for instance Arjona et al. 2008 and 2010). The existence and uniqueness of weak solutions for both the elastic-gravitational and viscoelastic-gravitational problem was demonstrated in Arjona et al. (2008 and 2014). The stabilization to solutions of the associated stationary system was proved in Arjona and Díaz (2007). Here we consider the internal source as response to the effect of a pressurized magma reservoir into a multilayered, elastic-gravitational and viscoelastic-gravitational earth model. We introduce the numerical analysis of a simplified steady elastic-gravitational model, solved by means of the finite element method. We also present some numerical tests in realistic situations that confirm the predictions of theoretical order of convergence. Finally, we describe the methodology for both the elastic-gravitational and the viscoelastic-gravitational models using 2D and 3D test examples performed with FreeFEM++.

  2. The modified Black-Scholes model via constant elasticity of variance for stock options valuation

    NASA Astrophysics Data System (ADS)

    Edeki, S. O.; Owoloko, E. A.; Ugbebor, O. O.

    2016-02-01

    In this paper, the classical Black-Scholes option pricing model is visited. We present a modified version of the Black-Scholes model via the application of the constant elasticity of variance model (CEVM); in this case, the volatility of the stock price is shown to be a non-constant function unlike the assumption of the classical Black-Scholes model.

  3. How can cells sense the elasticity of a substrate? An analysis using a cell tensegrity model.

    PubMed

    De Santis, G; Lennon, A B; Boschetti, F; Verhegghe, B; Verdonck, P; Prendergast, P J

    2011-01-01

    A eukaryotic cell attaches and spreads on substrates, whether it is the extracellular matrix naturally produced by the cell itself, or artificial materials, such as tissue-engineered scaffolds. Attachment and spreading require the cell to apply forces in the nN range to the substrate via adhesion sites, and these forces are balanced by the elastic response of the substrate. This mechanical interaction is one determinant of cell morphology and, ultimately, cell phenotype. In this paper we use a finite element model of a cell, with a tensegrity structure to model the cytoskeleton of actin filaments and microtubules, to explore the way cells sense the stiffness of the substrate and thereby adapt to it. To support the computational results, an analytical 1D model is developed for comparison. We find that (i) the tensegrity hypothesis of the cytoskeleton is sufficient to explain the matrix-elasticity sensing, (ii) cell sensitivity is not constant but has a bell-shaped distribution over the physiological matrix-elasticity range, and (iii) the position of the sensitivity peak over the matrix-elasticity range depends on the cytoskeletal structure and in particular on the F-actin organisation. Our model suggests that F-actin reorganisation observed in mesenchymal stem cells (MSCs) in response to change of matrix elasticity is a structural-remodelling process that shifts the sensitivity peak towards the new value of matrix elasticity. This finding discloses a potential regulatory role of scaffold stiffness for cell differentiation. PMID:22048898

  4. Specimen-specific multi-scale model for the anisotropic elastic constants of human cortical bone

    PubMed Central

    Deuerling, Justin M.; Yue, Weimin; Espinoza Orías, Alejandro A.; Roeder, Ryan K.

    2009-01-01

    The anisotropic elastic constants of human cortical bone were predicted using a specimen-specific micromechanical model that accounted for structural parameters across multiple length scales. At the nano-scale, the elastic constants of the mineralized collagen fibril were estimated from measured volume fractions of the constituent phases, namely apatite crystals and Type I collagen. The elastic constants of the extracellular matrix (ECM) were predicted using the measured orientation distribution function (ODF) for the apatite crystals to average the contribution of misoriented mineralized collagen fibrils. Finally, the elastic constants of cortical bone tissue were determined by accounting for the measured volume fraction of Haversian porosity within the ECM. Model predictions using the measured apatite crystal ODF were not statistically different from experimental measurements for both the magnitude and anisotropy of elastic constants. In contrast, model predictions using common idealized assumptions of perfectly aligned or randomly oriented apatite crystals were significantly different from the experimental measurements. A sensitivity analysis indicated that the apatite crystal volume fraction and ODF were the most influential structural parameters affecting model predictions of the magnitude and anisotropy, respectively, of elastic constants. PMID:19664772

  5. Substitution and price elasticity estimates using inter-countrypooled data in a translog cost model

    SciTech Connect

    Roy, Joyashree; Sanstad, Alan H.; Sathaye, Jayant A.; Khaddaria,Raman

    2006-06-01

    Pooled data across several developing countries and the U.S. were used to estimate long-run substitution and price elasticities ina translog framework for the paper, iron and steel, and aggregatemanufacturing industries. While the quality of the estimates variesacross the several industry-specific models, the results suggest highervalues for these elasticities than appear commonly used in integratedassessment models. Estimates of own-price elasticities of energy rangefrom - 0.80 to - 1.76 and are comparable to estimates from previouseconometric studies in the context of developed countries (- 0.77 to -0.87). Substitution elasticities show wider variation across countriesand industries. For energy and capital they range from -1.96 to 9.80, forlabor and energy from 2.61 to 7.11, and for energy and material from -0.26 to 2.07.

  6. Computational fluid dynamics modeling of airflow inside lungs using heterogenous anisotropic lung tissue elastic properties.

    PubMed

    Ilegbusi, Olusegun; Li, Ziang; Min, Yugang; Meeks, Sanford; Kupelian, Patrick; Santhanam, Anand P

    2012-01-01

    The aim of this paper is to model the airflow inside lungs during breathing and its fluid-structure interaction with the lung tissues and the lung tumor using subject-specific elastic properties. The fluid-structure interaction technique simultaneously simulates flow within the airway and anisotropic deformation of the lung lobes. The three-dimensional (3D) lung geometry is reconstructed from the end-expiration 3D CT scan datasets of humans with lung cancer. The lung is modeled as a poro-elastic medium with anisotropic elastic property (non-linear Young's modulus) obtained from inverse lung elastography of 4D CT scans for the same patients. The predicted results include the 3D anisotropic lung deformation along with the airflow pattern inside the lungs. The effect is also presented of anisotropic elasticity on both the spatio-temporal volumetric lung displacement and the regional lung hysteresis. PMID:22356987

  7. Self-consistent modeling of visco-elastic polycrystals: Application to irradiation creep and growth

    NASA Astrophysics Data System (ADS)

    Turner, P. A.; Tomé, C. N.

    1993-07-01

    w EPRESENT a model that permits the simulation of the transient response of polycrystalline aggregates to externally imposed loads and temperature gradients. The mechanical response of the constitutive grains includes elastic, Newtonian (linearly viscous), thermal and growth terms. The formulation explicitly accounts for the anisotropy in the elastic, creep, thermal and growth properties of both grains and polycrystals, and describes the time evolution of the overall visco-elastic moduli and of the internal stresses. It also provides, as limit cases, the correct overall elastic, thermal, creep and growth moduli of the polycrystal. The model is applied to analyse the characteristics of irradiation creep and growth in reactor tubes subjected to hydrostatic pressure. The influence of texture, grain anisotropy, grain shape and thermal stresses over the predicted polycrystal response, and expecially over the transient regime, is analysed in detail.

  8. Phase field modeling of fracture in rubbery polymers. Part I: Finite elasticity coupled with brittle failure

    NASA Astrophysics Data System (ADS)

    Miehe, Christian; Schänzel, Lisa-Marie

    2014-04-01

    This work presents a new phase field model for rate-independent crack propagation in rubbery polymers at large strains and considers details of its numerical implementation. The approach accounts for micro-mechanically based features of both the elastic bulk response as well as the crack toughness of idealized polymer networks. The proposed diffusive crack modeling based on the introduction of a crack phase field overcomes difficulties associated with the computational realization of sharp crack discontinuities, in particular when it comes to complex crack topologies. The crack phase field governs a crack density function, which describes the macroscopic crack surface in the polymer per unit of the reference volume. It provides the basis for the constitutive modeling of a degrading free energy storage and a crack threshold function with a Griffith-type critical energy release rate, that governs the crack propagation in the polymer. Both the energy storage as well as the critical energy release due to fracture can be related to classical statistical network theories of polymers. The proposed framework of diffusive fracture in polymers is formulated in terms of a rate-type variational principle that determines the evolution of the coupled primary variable fields, i.e. the deformation field and the crack phase field. On the computational side, we outline a staggered solution procedure based on a one-pass operator split of the coupled equations, that successively updates in a typical time step the crack phase field and the displacement field. Such a solution algorithm is extremely robust, easy to implement and ideally suited for engineering problems. We finally demonstrate the performance of the phase field formulation of fracture at large strains by means of representative numerical examples.

  9. Data modeling of network dynamics

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger M.; Handley, James W.; Faucheux, Jeffery P.; Harris, Brad

    2004-01-01

    This paper highlights Data Modeling theory and its use for text data mining as a graphical network search engine. Data Modeling is then used to create a real-time filter capable of monitoring network traffic down to the port level for unusual dynamics and changes in business as usual. This is accomplished in an unsupervised fashion without a priori knowledge of abnormal characteristics. Two novel methods for converting streaming binary data into a form amenable to graphics based search and change detection are introduced. These techniques are then successfully applied to 1999 KDD Cup network attack data log-on sessions to demonstrate that Data Modeling can detect attacks without prior training on any form of attack behavior. Finally, two new methods for data encryption using these ideas are proposed.

  10. Modeling elastic momentum transfer cross-sections from mobility data

    NASA Astrophysics Data System (ADS)

    Nikitović, Ž. D.; Stojanović, V. D.; Raspopović, Z. M.

    2016-04-01

    In this letter we present a new method to simply obtain the elastic momentum transfer cross-section which predicts a maximum of reduced mobility and its sensitivity to the temperature variation at low energies. We first determined the transport cross-section which resembles mobility data for similar closed-shell systems by using the Monte Carlo method. Second, we selected the most probable reactive processes and compiled cross-sections from experimental and theoretical data. At the end, an elastic momentum transfer cross-section is obtained by subtracting the compiled cross-sections from the momentum transfer cross-section, taking into account the effects of the angular scattering distributions. Finally, the cross-section set determined in such a way is used as an input in a final Monte Carlo code run, to calculate the flux and bulk reduced mobility for Ne+ + CF4 which were discussed as functions of the reduced electric field E/N (N is the gas density) for the temperature T = 300 K.

  11. Ising model for distribution networks

    NASA Astrophysics Data System (ADS)

    Hooyberghs, H.; Van Lombeek, S.; Giuraniuc, C.; Van Schaeybroeck, B.; Indekeu, J. O.

    2012-01-01

    An elementary Ising spin model is proposed for demonstrating cascading failures (breakdowns, blackouts, collapses, avalanches, etc.) that can occur in realistic networks for distribution and delivery by suppliers to consumers. A ferromagnetic Hamiltonian with quenched random fields results from policies that maximize the gap between demand and delivery. Such policies can arise in a competitive market where firms artificially create new demand, or in a solidarity environment where too high a demand cannot reasonably be met. Network failure in the context of a policy of solidarity is possible when an initially active state becomes metastable and decays to a stable inactive state. We explore the characteristics of the demand and delivery, as well as the topological properties, which make the distribution network susceptible of failure. An effective temperature is defined, which governs the strength of the activity fluctuations which can induce a collapse. Numerical results, obtained by Monte Carlo simulations of the model on (mainly) scale-free networks, are supplemented with analytic mean-field approximations to the geometrical random field fluctuations and the thermal spin fluctuations. The role of hubs versus poorly connected nodes in initiating the breakdown of network activity is illustrated and related to model parameters.

  12. A microstructurally informed model for the mechanical response of three-dimensional actin networks

    PubMed Central

    KWON, R.Y.; LEW, A.J.; JACOBS, C.R.

    2008-01-01

    We propose a class of microstructurally informed models for the linear elastic mechanical behavior of cross-linked polymer networks such as the actin cytoskeleton. Salient features of the models include the possibility to represent anisotropic mechanical behavior resulting from anisotropic filament distributions, and a power-law scaling of the mechanical properties with the filament density. Mechanical models within the class are parameterized by seven different constants. We demonstrate a procedure for determining these constants using finite element models of three-dimensional actin networks. Actin filaments and cross-links were modeled as elastic rods, and the networks were constructed at physiological volume fractions and at the scale of an image voxel. We show the performance of the model in estimating the mechanical behavior of the networks over a wide range of filament densities and degrees of anisotropy. PMID:18568835

  13. Elastic block model for the Betic-Rif Arc from inversion of GPS data

    NASA Astrophysics Data System (ADS)

    Khazaradze, Giorgi; Asensio, Eva; Echeverria, Anna; McCaffrey, Robert

    2014-05-01

    This work provides an updated kinematic block model for the Betic-Rif region in western Mediterranean based on the compilation of the most recent GPS measurements. The study zone includes the tectonic plate boundary between the Nubia and Eurasia plates, where the exact boundary between the two plates is diffuse. The complexity of the plate boundary in the Betic-Rif arc is also evidenced by: i) broad spatial distribution of seismicity; ii) variety of focal mechanisms; iii) non-uniform crustal deformation field deduced from GPS observations. In this study we compiled the GPS results obtained from the Topo-Iberia CGPS network consisting of 25 CGPS sites (21 in Spain and 4 on Morocco) with the previously published GPS velocities from the region. The GPS velocities from various sources were transformed into a common Eurasia reference frame using the VELROT routine of the GAMIT/GLOBK software from MIT. The resulting GPS velocities were complemented with the seismic and geologic information. A kinematic model of the elastic blocks was obtained by the inversion of these data using the TDEFNODE software. Specifically, we used the GPS derived horizontal velocities, geologic fault slip rates, transform fault azimuths, and earthquake-derived fault slip vector azimuths to invert for block angular velocities, creep and locking on block-bounding faults, permanent strain rates within the blocks. Our preferred model includes 5 blocks, from which the 2 blocks represent the stable part of the Eurasia and Nubia plates. The 3 remaining blocks roughly represent the following 3 domains: 1) Rif mountains, straight of Gibraltar and western Alboran sea (RAWB block); internal zone of the eastern Betics (EBET block) and external zone of the eastern Betics and the eastern Alboran sea (block ESTE). Our modeling results show that the majority of the deformation is absorbed between the blocks EBET and RAWB, where the estimated slip rates reach 3.9 mm/yr, indicating mainly right-lateral motion

  14. Thermal Network Modelling Handbook

    NASA Technical Reports Server (NTRS)

    1972-01-01

    Thermal mathematical modelling is discussed in detail. A three-fold purpose was established: (1) to acquaint the new user with the terminology and concepts used in thermal mathematical modelling, (2) to present the more experienced and occasional user with quick formulas and methods for solving everyday problems, coupled with study cases which lend insight into the relationships that exist among the various solution techniques and parameters, and (3) to begin to catalog in an orderly fashion the common formulas which may be applied to automated conversational language techniques.

  15. Spatial Models for Virtual Networks

    NASA Astrophysics Data System (ADS)

    Janssen, Jeannette

    This paper discusses the use of spatial graph models for the analysis of networks that do not have a direct spatial reality, such as web graphs, on-line social networks, or citation graphs. In a spatial graph model, nodes are embedded in a metric space, and link formation depends on the relative position of nodes in the space. It is argued that spatial models form a good basis for link mining: assuming a spatial model, the link information can be used to infer the spatial position of the nodes, and this information can then be used for clustering and recognition of node similarity. This paper gives a survey of spatial graph models, and discusses their suitability for link mining.

  16. Performance evaluation of data center service localization based on virtual resource migration in software defined elastic optical network.

    PubMed

    Yang, Hui; Zhang, Jie; Ji, Yuefeng; Tan, Yuanlong; Lin, Yi; Han, Jianrui; Lee, Young

    2015-09-01

    Data center interconnection with elastic optical network is a promising scenario to meet the high burstiness and high-bandwidth requirements of data center services. In our previous work, we implemented cross stratum optimization of optical network and application stratums resources that allows to accommodate data center services. In view of this, this study extends the data center resources to user side to enhance the end-to-end quality of service. We propose a novel data center service localization (DCSL) architecture based on virtual resource migration in software defined elastic data center optical network. A migration evaluation scheme (MES) is introduced for DCSL based on the proposed architecture. The DCSL can enhance the responsiveness to the dynamic end-to-end data center demands, and effectively reduce the blocking probability to globally optimize optical network and application resources. The overall feasibility and efficiency of the proposed architecture are experimentally verified on the control plane of our OpenFlow-based enhanced SDN testbed. The performance of MES scheme under heavy traffic load scenario is also quantitatively evaluated based on DCSL architecture in terms of path blocking probability, provisioning latency and resource utilization, compared with other provisioning scheme. PMID:26368410

  17. Boundary conditions between poro-elastic medium and pure fluid in multi-scale modelling

    NASA Astrophysics Data System (ADS)

    Lacis, Ugis; Bagheri, Shervin

    2015-11-01

    Accurate modelling of porous and poro-elastic media has been a long standing issue in geophysics, fluid mechanics, and biology. There has been a notable development of continuous models for both porous and poro-elastic materials, nevertheless there is still an on-going debate about the modelling of effective boundary conditions between different types of media, such as, poro-elastic medium and free fluid, porous medium and solid wall. Some recent works have rigorously treated interface between porous medium and free fluid, however, there have been no detailed investigation regarding the interface between poro-elastic medium and free fluid. We use the multi-scale modelling to arrive with averaged, effective macroscopic equations for description of a poro-elastic medium. Then we investigate the interface in detail and arrive with effective boundary conditions. To validate our model, we construct direct numerical simulations using an immersed boundary (IB) method. The IB method is beforehand validated with respect to theoretical predictions for Darcy's flow in porous materials with a given pore structure.

  18. An Elastic-Plastic Damage Model for Long-Fiber Thermoplastics

    SciTech Connect

    Nguyen, Ba Nghiep; Kunc, Vlastimil

    2009-08-11

    This article proposes an elastic-plastic damage model that combines micromechanical modeling with continuum damage mechanics to predict the stress-strain response of injection-molded long-fiber thermoplastics. The model accounts for distributions of orientation and length of elastic fibers embedded in a thermoplastic matrix whose behavior is elastic-plastic and damageable. The elastic-plastic damage behavior of the matrix is described by the modified Ramberg-Osgood relation and the three-dimensional damage model in deformation assuming isotropic hardening. Fiber/matrix debonding is accounted for using a parameter that governs the fiber/matrix interface compliance. A linear relationship between this parameter and the matrix damage variable is assumed. First, the elastic-plastic damage behavior of the reference aligned-fiber composite containing the same fiber volume fraction and length distribution as the actual composite is computed using an incremental Eshelby-Mori-Tanaka mean field approach. The incremental response of the latter is then obtained from the solution for the aligned-fiber composite by averaging over all fiber orientations. The model is validated against the experimental stress-strain results obtained for long-glass-fiber/polypropylene specimens.

  19. An elastic-perfectly plastic flow model for finite element analysis of perforated materials

    SciTech Connect

    Jones, D.P.; Gordon, J.L.; Hutula, D.N.; Banas, D.; Newman, J.B.

    1999-02-01

    This paper describes the formulation of an elastic-perfectly plastic flow theory applicable to equivalent solid [EQS] modeling of perforated materials. An equilateral triangular array of circular penetrations is considered. The usual assumptions regarding geometry and loading conditions applicable to the development of elastic constants for EQS modeling of perforated plates are considered to apply here. An elastic-perfectly plastic [EPP] EQS model is developed for a collapse surface that includes fourth-order stress terms. The fourth order yield function has been shown to be appropriate for plates with a triangular array of circular holes. A complete flow model is formulated using the consistent tangent modulus approach based on the fourth order yield function.

  20. The impact of ice I rheology on interior models of Ganymede: The elastic vs. the visco-elastic case

    NASA Astrophysics Data System (ADS)

    Steinbrügge, Gregor; Hussmann, Hauke; Sohl, Frank; Oberst, Jürgen

    2015-04-01

    Many investigations on key processes of icy satellites are driven by the rheological behavior of planetary ices. Future missions to Jupiter's icy moons (e.g. JUICE / Europa clipper) aimed at constraining the thickness of the outer ice shell using radio science and/or laser altimetry will have to address this problem. We investigate for the case of Ganymede under which conditions the ice I viscosity could be constrained by measuring the phase-lag of the tidal response using laser altimetry. In the absence of seismic data, interior structure models are constrained by the satellite's mean density and mean moment-of-inertia factor. One key observable to reduce the ambiguity of the corresponding structural models is the measurement of the dynamic response of the satellite's outer ice shells to tidal forces exerted by Jupiter and characterized by the body tide surface Love numbers h2 and k2. The Love number k2 measures the variation of the gravitational potential due to tidally induced internal redistribution of mass and can be inferred from radio science experiments. The Love number h2 is a measure for the tide-induced radial displacement of the satellite's surface. It is an advantage that Ganymede's surface displacement Love number h2 can be expected to be measured with a high accuracy using laser altimetry (Steinbrügge et al., 2014). However, the determination of the resulting ice thickness further depends on the possible existence of a liquid subsurface water ocean and on the tidally effective rheology of the outer ice shell (Moore and Schubert, 2003). Here, we distinguish between an elastic, visco-elastic or even fluid behavior in the sense of the Maxwell model and alternative rheological models. In the case of Ganymede the fluid case would imply high ice temperatures which are at odds with thermal equilibrium models calculated by Spohn and Schubert (2003). However the visco-elastic case is still possible. Laboratory measurements of ice I (e.g. Sotin et al., 1998

  1. Polymer networks: Modeling and applications

    NASA Astrophysics Data System (ADS)

    Masoud, Hassan

    Polymer networks are an important class of materials that are ubiquitously found in natural, biological, and man-made systems. The complex mesoscale structure of these soft materials has made it difficult for researchers to fully explore their properties. In this dissertation, we introduce a coarse-grained computational model for permanently cross-linked polymer networks than can properly capture common properties of these materials. We use this model to study several practical problems involving dry and solvated networks. Specifically, we analyze the permeability and diffusivity of polymer networks under mechanical deformations, we examine the release of encapsulated solutes from microgel capsules during volume transitions, and we explore the complex tribological behavior of elastomers. Our simulations reveal that the network transport properties are defined by the network porosity and by the degree of network anisotropy due to mechanical deformations. In particular, the permeability of mechanically deformed networks can be predicted based on the alignment of network filaments that is characterized by a second order orientation tensor. Moreover, our numerical calculations demonstrate that responsive microcapsules can be effectively utilized for steady and pulsatile release of encapsulated solutes. We show that swollen gel capsules allow steady, diffusive release of nanoparticles and polymer chains, whereas gel deswelling causes burst-like discharge of solutes driven by an outward flow of the solvent initially enclosed within a shrinking capsule. We further demonstrate that this hydrodynamic release can be regulated by introducing rigid microscopic rods in the capsule interior. We also probe the effects of velocity, temperature, and normal load on the sliding of elastomers on smooth and corrugated substrates. Our friction simulations predict a bell-shaped curve for the dependence of the friction coefficient on the sliding velocity. Our simulations also illustrate

  2. Size-dependent elastic properties of crystalline polymers via a molecular mechanics model

    NASA Astrophysics Data System (ADS)

    Zhao, Junhua; Guo, Wanlin; Zhang, Zhiliang; Rabczuk, Timon

    2011-12-01

    An analytical molecular mechanics model is developed to obtain the size-dependent elastic properties of crystalline polyethylene. An effective "stick-spiral" model is adopted in the polymer chain. Explicit equations are derived from the Lennard-Jones potential function for the van der Waals force between any two polymer chains. By using the derived formulas, the nine size-dependent elastic constants are investigated systematically. The present analytical results are in reasonable agreement with those from present united-atom molecular dynamics simulations. The established analytical model provides an efficient route for mechanical characterization of crystalline polymers and related materials toward nanoelectromechanical applications.

  3. The design, analysis and experimental evaluation of an elastic model wing

    NASA Technical Reports Server (NTRS)

    Cavin, R. K., III; Thisayakorn, C.

    1974-01-01

    An elastic orbiter model was developed to evaluate the effectiveness of aeroelasticity computer programs. The elasticity properties were introduced by constructing beam-like straight wings for the wind tunnel model. A standard influence coefficient mathematical model was used to estimate aeroelastic effects analytically. In general good agreement was obtained between the empirical and analytical estimates of the deformed shape. However, in the static aeroelasticity case, it was found that the physical wing exhibited less bending and more twist than was predicted by theory.

  4. New features of vault architecture and dynamics revealed by novel refinement using the deformable elastic network approach.

    PubMed

    Casañas, Arnau; Querol-Audí, Jordi; Guerra, Pablo; Pous, Joan; Tanaka, Hideaki; Tsukihara, Tomitake; Verdaguer, Nuria; Fita, Ignasi

    2013-06-01

    The vault particle, with a molecular weight of about 10 MDa, is the largest ribonucleoprotein that has been described. The X-ray structure of intact rat vault has been solved at a resolution of 3.5 Å [Tanaka et al. (2009), Science, 323, 384-388], showing an overall barrel-shaped architecture organized into two identical moieties, each consisting of 39 copies of the major vault protein (MVP). The model deposited in the PDB includes 39 MVP copies (half a vault) in the crystal asymmetric unit. A 2.1 Å resolution structure of the seven N-terminal repeats (R1-7) of MVP has also been determined [Querol-Audí et al. (2009), EMBO J. 28, 3450-3457], revealing important discrepancies with respect to the MVP models for repeats R1 and R2. Here, the re-refinement of the vault structure by incorporating the high-resolution information available for the R1-7 domains, using the deformable elastic network (DEN) approach and maintaining strict 39-fold noncrystallographic symmetry is reported. The new refinement indicates that at the resolution presently available the MVP shell can be described well as only one independent subunit organized with perfect D39 molecular symmetry. This refinement reveals that significant rearrangements occur in the N-terminus of MVP during the closing of the two vault halves and that the 39-fold symmetry breaks in the cap region. These results reflect the highly dynamic nature of the vault structure and represent a necessary step towards a better understanding of the biology and regulation of this particle. PMID:23695250

  5. Shear-stress fluctuations in self-assembled transient elastic networks

    NASA Astrophysics Data System (ADS)

    Wittmer, J. P.; Kriuchevskyi, I.; Cavallo, A.; Xu, H.; Baschnagel, J.

    2016-06-01

    Focusing on shear-stress fluctuations, we investigate numerically a simple generic model for self-assembled transient networks formed by repulsive beads reversibly bridged by ideal springs. With Δ t being the sampling time and t(f ) ˜1 /f the Maxwell relaxation time (set by the spring recombination frequency f ), the dimensionless parameter Δ x =Δ t /t(f ) is systematically scanned from the liquid limit (Δ x ≫1 ) to the solid limit (Δ x ≪1 ) where the network topology is quenched and an ensemble average over m -independent configurations is required. Generalizing previous work on permanent networks, it is shown that the shear-stress relaxation modulus G (t ) may be efficiently determined for all Δ x using the simple-average expression G (t ) =μA-h (t ) with μA=G (0 ) characterizing the canonical-affine shear transformation of the system at t =0 and h (t ) the (rescaled) mean-square displacement of the instantaneous shear stress as a function of time t . This relation is compared to the standard expression G (t ) =c ˜(t ) using the (rescaled) shear-stress autocorrelation function c ˜(t ) . Lower bounds for the m configurations required by both relations are given.

  6. Shear-stress fluctuations in self-assembled transient elastic networks.

    PubMed

    Wittmer, J P; Kriuchevskyi, I; Cavallo, A; Xu, H; Baschnagel, J

    2016-06-01

    Focusing on shear-stress fluctuations, we investigate numerically a simple generic model for self-assembled transient networks formed by repulsive beads reversibly bridged by ideal springs. With Δt being the sampling time and t_{☆}(f)∼1/f the Maxwell relaxation time (set by the spring recombination frequency f), the dimensionless parameter Δx=Δt/t_{☆}(f) is systematically scanned from the liquid limit (Δx≫1) to the solid limit (Δx≪1) where the network topology is quenched and an ensemble average over m-independent configurations is required. Generalizing previous work on permanent networks, it is shown that the shear-stress relaxation modulus G(t) may be efficiently determined for all Δx using the simple-average expression G(t)=μ_{A}-h(t) with μ_{A}=G(0) characterizing the canonical-affine shear transformation of the system at t=0 and h(t) the (rescaled) mean-square displacement of the instantaneous shear stress as a function of time t. This relation is compared to the standard expression G(t)=c[over ̃](t) using the (rescaled) shear-stress autocorrelation function c[over ̃](t). Lower bounds for the m configurations required by both relations are given. PMID:27415324

  7. Elasticity analyses of size-based red and white abalone matrix models: management and conservation.

    PubMed

    Rogers-Bennett, Laura; Leaf, Robert T

    2006-02-01

    Prospective elasticity analyses have been used to aid in the management of fished species and the conservation of endangered species. Elasticities were examined for deterministic size-based matrix models of red abalone, Haliotis rufescens, and white abalone, H. sorenseni, to evaluate which size classes influenced population growth (lambda) the most. In the red abalone matrix, growth transitions were determined from a tag recapture study and grouped into nine size classes. In the white abalone matrix, abalone growth was determined from a laboratory study and grouped into five size classes. Survivorship was estimated from tag recapture data for red abalone using a Jolly-Seber model with size as a covariate and used for both red and white abalone. Reproduction estimates for both models used averages of the number of mature eggs produced by female red and white abalone in each size class from four-year reproduction studies. Population growth rate (lambda) was set to 1.0, and the first-year survival (larval survival through to the first size class) was estimated by iteration. Survival elasticities were higher than fecundity elasticities in both the red and white matrix models. The sizes classes with the greatest survival elasticities, and therefore the most influence on population growth in the model, were the sublegal red abalone (150-178 mm) and the largest white abalone size class (140-175 mm). For red abalone, the existing minimum legal size (178 mm) protects the size class the model suggests is critical to population growth. Implementation of education programs for novice divers coupled with renewed enforcement may serve to minimize incidental mortality of the critical size class. For white abalone, conservation efforts directed at restoring adults may have more of an impact on population growth than efforts focusing on juveniles. Our work is an example of how prospective elasticity analyses of size-structured matrix models can be used to quantitatively evaluate

  8. Bayesian Networks for Social Modeling

    SciTech Connect

    Whitney, Paul D.; White, Amanda M.; Walsh, Stephen J.; Dalton, Angela C.; Brothers, Alan J.

    2011-03-28

    This paper describes a body of work developed over the past five years. The work addresses the use of Bayesian network (BN) models for representing and predicting social/organizational behaviors. The topics covered include model construction, validation, and use. These topics show the bulk of the lifetime of such model, beginning with construction, moving to validation and other aspects of model ‘critiquing’, and finally demonstrating how the modeling approach might be used to inform policy analysis. To conclude, we discuss limitations of using BN for this activity and suggest remedies to address those limitations. The primary benefits of using a well-developed computational, mathematical, and statistical modeling structure, such as BN, are 1) there are significant computational, theoretical and capability bases on which to build 2) ability to empirically critique the model, and potentially evaluate competing models for a social/behavioral phenomena.

  9. Composite model for the anisotropic elastic moduli of lean oil shale

    SciTech Connect

    Rundle, J.B.; Schuler, K.W.

    1981-02-01

    A model to predict the anisotropic elastic moduli of lean oil shale is formulated. Deformation of a homogeneous ellipsoidal inclusion in a host matrix is used as the basis for computing the deformation of the composite. Both inclusions and the host rock are presumed to be separately isotropic. Anisotropy of the composite arises from the nonspherical shape of the kerogen inclusions. Six parameters are needed to quantify the model fully: 2 elastic moduli for the host rock, 2 for the inclusions, the kerogen content, and the inclusion aspect ratio. The model is compared to a set of statically measured elastic moduli. Good agreement with lean oil shale data was found. However, some systematic differences appear in comparison with moduli measured ultrasonically. 20 references.

  10. Theoretical modeling for neutron elastic scattering angular distribution in the fast energy range

    SciTech Connect

    Kawano, Toshihiko

    2010-12-07

    One of the major issues of neutron scattering modeling in the fast energy range is the contribution of compound elastic and inelastic scattering to the total scattering process. The compound component may become large at very low energies where the angular distribution becomes 90-degree symmetric in the center-of-mass system. Together with the shape elastic component, the elastic scattering gives slightly forward-peaked angular distributions in the fast energy range. This anisotropic angular distribution gives high sensitivities to many important nuclear reactor characteristics, such as criticality and neutron shielding. In this talk we describe how the anisotropic angular distributions are calculated within the statistical model framework, including the case where strongly coupled channels exist, by combining the coupled-channels theory with the Hauser-Feshbach model. This unique capability extension will have significant advantages in understanding the neutron scattering process for deformed nuclei, like uranium or plutonium, on which advanced nuclear energy applications center.

  11. On the influence of model parametrization in elastic full waveform tomography

    NASA Astrophysics Data System (ADS)

    Köhn, D.; De Nil, D.; Kurzmann, A.; Przebindowska, A.; Bohlen, T.

    2012-10-01

    Elastic Full Waveform Tomography (FWT) aims to reduce the misfit between recorded and modelled data, to deduce a very detailed model of elastic material parameters in the underground. The choice of the elastic model parameters to be inverted affects the convergence and quality of the reconstructed subsurface model. Using the Cross-Triangle-Squares (CTS) model three elastic parametrizations, Lamé parameters m1 = [λ, μ, ρ], seismic velocities m2 = [Vp, Vs, ρ] and seismic impedances m3 = [Ip, Is, ρ] for far-offset reflection seismic acquisition geometries with explosive point sources and free-surface condition are studied. In each CTS model the three elastic parameters are assigned to three different geometrical objects that are spatially separated. The results of the CTS model study reveal a strong requirement of a sequential frequency inversion from low to high frequencies to reconstruct the density model. Using only high-frequency data, cross-talk artefacts have an influence on the quantitative reconstruction of the material parameters, while for a sequential frequency inversion only structural artefacts, representing the boundaries of different model parameters, are present. During the inversion, the Lamé parameters, seismic velocities and impedances could be reconstructed well. However, using the Lamé parametrization ?-artefacts are present in the λ model, while similar artefacts are suppressed when using seismic velocities or impedances. The density inversion shows the largest ambiguity for all parametrizations. However, the artefacts are again more dominant, when using the Lamé parameters and suppressed for seismic velocity and impedance parametrization. The afore mentioned results are confirmed for a geologically more realistic modified Marmousi-II model. Using a conventional streamer acquisition geometry the P-velocity, S-velocity and density models of the subsurface were reconstructed successfully and are compared with the results of the Lam

  12. Stochastic reduced order computational model of structures having numerous local elastic modes in low frequency dynamics

    NASA Astrophysics Data System (ADS)

    Arnoux, A.; Batou, A.; Soize, C.; Gagliardini, L.

    2013-08-01

    This paper is devoted to the construction of a stochastic reduced order computational model of structures having numerous local elastic modes in low frequency dynamics. We are particularly interested in automotive vehicles which are made up of stiff parts and flexible components. This type of structure is characterized by the fact that it exhibits, in the low frequency range, not only the classical global elastic modes but also numerous local elastic modes which cannot easily be separated from the global elastic modes. To solve this difficult problem, an innovative method has recently been proposed for constructing a reduced order computational dynamical model adapted to this particular situation for the low frequency range. Then a new adapted generalized eigenvalue problem is introduced and allows a global vector basis to be constructed for the global displacements space. This method requires to decompose the domain of the structure into sub-domains. Such a decomposition is carried out using the Fast Marching Method. This global vector basis is then used to construct the reduced order computational model. Since there are model uncertainties induced by modeling errors in the computational model, the nonparametric probabilistic approach of uncertainties is used and implemented in the reduced order computational model. The methodology is applied to a complex computational model of an automotive vehicle.

  13. Tuition Elasticity of the Demand for Higher Education among Current Students: A Pricing Model.

    ERIC Educational Resources Information Center

    Bryan, Glenn A.; Whipple, Thomas W.

    1995-01-01

    A pricing model is offered, based on retention of current students, that colleges can use to determine appropriate tuition. A computer-based model that quantifies the relationship between tuition elasticity and projected net return to the college was developed and applied to determine an appropriate tuition rate for a small, private liberal arts…

  14. Elastic pp Scattering at LHC Energies in Various Multi-Pomeron Exchange Models

    NASA Astrophysics Data System (ADS)

    Novikov, Ivan; Shabelski, Yuli

    2012-10-01

    We consider the data for elastic pp scattering in the framework of Regge theory in various models of multiple Pomeron exchanges: quasi-eikonal approach and two-channel approach. The results of the model calculations are compared with the experimental data presented by the TOTEM collaboration.

  15. A random interacting network model for complex networks

    NASA Astrophysics Data System (ADS)

    Goswami, Bedartha; Shekatkar, Snehal M.; Rheinwalt, Aljoscha; Ambika, G.; Kurths, Jürgen

    2015-12-01

    We propose a RAndom Interacting Network (RAIN) model to study the interactions between a pair of complex networks. The model involves two major steps: (i) the selection of a pair of nodes, one from each network, based on intra-network node-based characteristics, and (ii) the placement of a link between selected nodes based on the similarity of their relative importance in their respective networks. Node selection is based on a selection fitness function and node linkage is based on a linkage probability defined on the linkage scores of nodes. The model allows us to relate within-network characteristics to between-network structure. We apply the model to the interaction between the USA and Schengen airline transportation networks (ATNs). Our results indicate that two mechanisms: degree-based preferential node selection and degree-assortative link placement are necessary to replicate the observed inter-network degree distributions as well as the observed inter-network assortativity. The RAIN model offers the possibility to test multiple hypotheses regarding the mechanisms underlying network interactions. It can also incorporate complex interaction topologies. Furthermore, the framework of the RAIN model is general and can be potentially adapted to various real-world complex systems.

  16. A random interacting network model for complex networks

    PubMed Central

    Goswami, Bedartha; Shekatkar, Snehal M.; Rheinwalt, Aljoscha; Ambika, G.; Kurths, Jürgen

    2015-01-01

    We propose a RAndom Interacting Network (RAIN) model to study the interactions between a pair of complex networks. The model involves two major steps: (i) the selection of a pair of nodes, one from each network, based on intra-network node-based characteristics, and (ii) the placement of a link between selected nodes based on the similarity of their relative importance in their respective networks. Node selection is based on a selection fitness function and node linkage is based on a linkage probability defined on the linkage scores of nodes. The model allows us to relate within-network characteristics to between-network structure. We apply the model to the interaction between the USA and Schengen airline transportation networks (ATNs). Our results indicate that two mechanisms: degree-based preferential node selection and degree-assortative link placement are necessary to replicate the observed inter-network degree distributions as well as the observed inter-network assortativity. The RAIN model offers the possibility to test multiple hypotheses regarding the mechanisms underlying network interactions. It can also incorporate complex interaction topologies. Furthermore, the framework of the RAIN model is general and can be potentially adapted to various real-world complex systems. PMID:26657032

  17. A random interacting network model for complex networks.

    PubMed

    Goswami, Bedartha; Shekatkar, Snehal M; Rheinwalt, Aljoscha; Ambika, G; Kurths, Jürgen

    2015-01-01

    We propose a RAndom Interacting Network (RAIN) model to study the interactions between a pair of complex networks. The model involves two major steps: (i) the selection of a pair of nodes, one from each network, based on intra-network node-based characteristics, and (ii) the placement of a link between selected nodes based on the similarity of their relative importance in their respective networks. Node selection is based on a selection fitness function and node linkage is based on a linkage probability defined on the linkage scores of nodes. The model allows us to relate within-network characteristics to between-network structure. We apply the model to the interaction between the USA and Schengen airline transportation networks (ATNs). Our results indicate that two mechanisms: degree-based preferential node selection and degree-assortative link placement are necessary to replicate the observed inter-network degree distributions as well as the observed inter-network assortativity. The RAIN model offers the possibility to test multiple hypotheses regarding the mechanisms underlying network interactions. It can also incorporate complex interaction topologies. Furthermore, the framework of the RAIN model is general and can be potentially adapted to various real-world complex systems. PMID:26657032

  18. Research on the model of home networking

    NASA Astrophysics Data System (ADS)

    Yun, Xiang; Feng, Xiancheng

    2007-11-01

    It is the research hotspot of current broadband network to combine voice service, data service and broadband audio-video service by IP protocol to transport various real time and mutual services to terminal users (home). Home Networking is a new kind of network and application technology which can provide various services. Home networking is called as Digital Home Network. It means that PC, home entertainment equipment, home appliances, Home wirings, security, illumination system were communicated with each other by some composing network technology, constitute a networking internal home, and connect with WAN by home gateway. It is a new network technology and application technology, and can provide many kinds of services inside home or between homes. Currently, home networking can be divided into three kinds: Information equipment, Home appliances, Communication equipment. Equipment inside home networking can exchange information with outer networking by home gateway, this information communication is bidirectional, user can get information and service which provided by public networking by using home networking internal equipment through home gateway connecting public network, meantime, also can get information and resource to control the internal equipment which provided by home networking internal equipment. Based on the general network model of home networking, there are four functional entities inside home networking: HA, HB, HC, and HD. (1) HA (Home Access) - home networking connects function entity; (2) HB (Home Bridge) Home networking bridge connects function entity; (3) HC (Home Client) - Home networking client function entity; (4) HD (Home Device) - decoder function entity. There are many physical ways to implement four function entities. Based on theses four functional entities, there are reference model of physical layer, reference model of link layer, reference model of IP layer and application reference model of high layer. In the future home network

  19. Elastic epsilon/sup + -/-He scattering with the use of the model-potential method

    SciTech Connect

    Khan, P.; Datta, S.K.; Bhattacharyya, D.; Ghosh, A.S.

    1984-06-01

    A model-potential method has been used to evaluate the elastic e/sup + -/-He scattering at the low-incident energies. The potential contains one parameter to include the effect of short-range correlation. The results for the elastic e/sup + -/-He scattering have been obtained using the same parameter. Two model exchange potentials, one for s wave and the other for higher partial waves, have been employed. The present results are in good agreement with the measured values and refined theoretical predictions.

  20. The permeability and elastic moduli of tuff from Campi Flegrei, Italy: implications for ground deformation modelling

    NASA Astrophysics Data System (ADS)

    Heap, M. J.; Baud, P.; Meredith, P. G.; Vinciguerra, S.; Reuschlé, T.

    2014-01-01

    The accuracy of ground deformation modelling at active volcanoes is a principal requirement in volcanic hazard mitigation. However, the reliability of such models relies on the accuracy of the rock physical property (permeability and elastic moduli) input parameters. Unfortunately, laboratory-derived values on representative rocks are usually rare. To this end we have performed a systematic laboratory study on the influence of pressure and temperature on the permeability and elastic moduli of samples from the two most widespread lithified pyroclastic deposits at the Campi Flegrei volcanic district, Italy. Our data show that the water permeability of Neapolitan Yellow Tuff and a tuff from the Campanian Ignimbrite differ by about 1.5 orders of magnitude. As pressure (depth) increases beyond the critical point for inelastic pore collapse (at an effective pressure of 10-15 MPa, or a depth of about 750 m), permeability and porosity decrease significantly, and ultrasonic wave velocities and dynamic elastic moduli increase significantly. Increasing the thermal stressing temperature increases the permeability and decreases the ultrasonic wave velocities and dynamic elastic moduli of the Neapolitan Yellow Tuff; whereas the tuff from the Campanian Ignimbrite remains unaffected. This difference is due to the presence of thermally unstable zeolites within the Neapolitan Yellow Tuff. For both rocks we also find, under the same pressure conditions, that the dynamic (calculated from ultrasonic wave velocities) and static (calculated from triaxial stress-strain data) elastic moduli differ significantly. The choice of elastic moduli in ground deformation modelling is therefore an important consideration. While we urge that these new laboratory data should be considered in routine ground deformation modelling, we highlight the challenges for ground deformation modelling based on the heterogeneous nature (vertically and laterally) of the rocks that comprise the caldera at Campi

  1. Quantitative Modeling of Coupled Piezo-Elastodynamic Behavior of Piezoelectric Actuators Bonded to an Elastic Medium for Structural Health Monitoring: A Review

    PubMed Central

    Huang, Guoliang; Song, Fei; Wang, Xiaodong

    2010-01-01

    Elastic waves, especially guided waves, generated by a piezoelectric actuator/sensor network, have shown great potential for on-line health monitoring of advanced aerospace, nuclear, and automotive structures in recent decades. Piezoelectric materials can function as both actuators and sensors in these applications due to wide bandwidth, quick response and low costs. One of the most fundamental issues surrounding the effective use of piezoelectric actuators is the quantitative evaluation of the resulting elastic wave propagation by considering the coupled piezo-elastodynamic behavior between the actuator and the host medium. Accurate characterization of the local interfacial stress distribution between the actuator and the host medium is the key issue for the problem. This paper presents a review of the development of analytical, numerical and hybrid approaches for modeling of the coupled piezo-elastodynamic behavior. The resulting elastic wave propagation for structural health monitoring is also summarized. PMID:22319319

  2. Fictitious Domain Methods for Fracture Models in Elasticity.

    NASA Astrophysics Data System (ADS)

    Court, S.; Bodart, O.; Cayol, V.; Koko, J.

    2014-12-01

    As surface displacements depend non linearly on sources location and shape, simplifying assumptions are generally required to reduce computation time when inverting geodetic data. We present a generic Finite Element Method designed for pressurized or sheared cracks inside a linear elastic medium. A fictitious domain method is used to take the crack into account independently of the mesh. Besides the possibility of considering heterogeneous media, the approach permits the evolution of the crack through time or more generally through iterations: The goal is to change the less things we need when the crack geometry is modified; In particular no re-meshing is required (the boundary conditions at the level of the crack are imposed by Lagrange multipliers), leading to a gain of computation time and resources with respect to classic finite element methods. This method is also robust with respect to the geometry, since we expect to observe the same behavior whatever the shape and the position of the crack. We present numerical experiments which highlight the accuracy of our method (using convergence curves), the optimality of errors, and the robustness with respect to the geometry (with computation of errors on some quantities for all kind of geometric configurations). We will also provide 2D benchmark tests. The method is then applied to Piton de la Fournaise volcano, considering a pressurized crack - inside a 3-dimensional domain - and the corresponding computation time and accuracy are compared with results from a mixed Boundary element method. In order to determine the crack geometrical characteristics, and pressure, inversions are performed combining fictitious domain computations with a near neighborhood algorithm. Performances are compared with those obtained combining a mixed boundary element method with the same inversion algorithm.

  3. From Process Modeling to Elastic Property Prediction for Long-Fiber Injection-Molded Thermoplastics

    SciTech Connect

    Nguyen, Ba Nghiep; Kunc, Vlastimil; Frame, Barbara J.; Phelps, Jay; Tucker III, Charles L.; Bapanapalli, Satish K.; Holbery, James D.; Smith, Mark T.

    2007-09-13

    This paper presents an experimental-modeling approach to predict the elastic properties of long-fiber injection-molded thermoplastics (LFTs). The approach accounts for fiber length and orientation distributions in LFTs. LFT samples were injection-molded for the study, and fiber length and orientation distributions were measured at different locations for use in the computation of the composite properties. The current fiber orientation model was assessed to determine its capability to predict fiber orientation in LFTs. Predicted fiber orientations for the studied LFT samples were also used in the calculation of the elastic properties of these samples, and the predicted overall moduli were then compared with the experimental results. The elastic property prediction was based on the Eshelby-Mori-Tanaka method combined with the orientation averaging technique. The predictions reasonably agree with the experimental LFT data

  4. Probabilistic logic modeling of network reliability for hybrid network architectures

    SciTech Connect

    Wyss, G.D.; Schriner, H.K.; Gaylor, T.R.

    1996-10-01

    Sandia National Laboratories has found that the reliability and failure modes of current-generation network technologies can be effectively modeled using fault tree-based probabilistic logic modeling (PLM) techniques. We have developed fault tree models that include various hierarchical networking technologies and classes of components interconnected in a wide variety of typical and atypical configurations. In this paper we discuss the types of results that can be obtained from PLMs and why these results are of great practical value to network designers and analysts. After providing some mathematical background, we describe the `plug-and-play` fault tree analysis methodology that we have developed for modeling connectivity and the provision of network services in several current- generation network architectures. Finally, we demonstrate the flexibility of the method by modeling the reliability of a hybrid example network that contains several interconnected ethernet, FDDI, and token ring segments. 11 refs., 3 figs., 1 tab.

  5. A general one-dimension nonlinear magneto-elastic coupled constitutive model for magnetostrictive materials

    SciTech Connect

    Zhang, Da-Guang; Li, Meng-Han; Zhou, Hao-Miao

    2015-10-15

    For magnetostrictive rods under combined axial pre-stress and magnetic field, a general one-dimension nonlinear magneto-elastic coupled constitutive model was built in this paper. First, the elastic Gibbs free energy was expanded into polynomial, and the relationship between stress and strain and the relationship between magnetization and magnetic field with the polynomial form were obtained with the help of thermodynamic relations. Then according to microscopic magneto-elastic coupling mechanism and some physical facts of magnetostrictive materials, a nonlinear magneto-elastic constitutive with concise form was obtained when the relations of nonlinear strain and magnetization in the polynomial constitutive were instead with transcendental functions. The comparisons between the prediction and the experimental data of different magnetostrictive materials, such as Terfenol-D, Metglas and Ni showed that the predicted magnetostrictive strain and magnetization curves were consistent with experimental results under different pre-stresses whether in the region of low and moderate field or high field. Moreover, the model can fully reflect the nonlinear magneto-mechanical coupling characteristics between magnetic, magnetostriction and elasticity, and it can effectively predict the changes of material parameters with pre-stress and bias field, which is useful in practical applications.

  6. Low-Dimensional Generalized Coordinate Models of Large-Deformation Elastic Joints

    NASA Astrophysics Data System (ADS)

    Odhner, Lael; Dollar, Aaron

    2012-02-01

    In the field of robotics, it is increasingly common to use elastic elements such as rods, beams or sheets to allow motion between the rigid links of a robot, rather than conventional sliding mechanisms such as pin joints. Although these elastic joints are simpler to manufacture, especially at meso- and micro-scales, representational simplicity is sacrificed. It is far easier to compute the Lagrangian of a robot using joint angles as generalized coordinates, rather than by considering the large-deformation continuum behavior of elastic joints. In this talk, we will discuss our work toward finding accurate, low-dimensional discretizations of elastic joint mechanics, suitable for use in generalized coordinate models of robot kinematics and dynamics. We use modally parameterized backbone curves to describe the kinematic configuration of the elastic joints, and compute the energy associated with deformation using rod and shell theory. In the plane, only three smooth deformation modes are sufficient to describe Euler-Bernoulli bending of 90 degrees to within 1 percent. Parametric models for the three-dimensional motion of sheet hinges are more complex, but can be simplified significantly using boundary conditions and constraints imposed by ruled surface assumptions.

  7. Plant Growth Models Using Artificial Neural Networks

    NASA Technical Reports Server (NTRS)

    Bubenheim, David

    1997-01-01

    In this paper, we descrive our motivation and approach to devloping models and the neural network architecture. Initial use of the artificial neural network for modeling the single plant process of transpiration is presented.

  8. To what extent can cortical bone millimeter-scale elasticity be predicted by a two-phase composite model with variable porosity?

    PubMed

    Granke, Mathilde; Grimal, Quentin; Parnell, William J; Raum, Kay; Gerisch, Alf; Peyrin, Françoise; Saïed, Amena; Laugier, Pascal

    2015-01-01

    An evidence gap exists in fully understanding and reliably modeling the variations in elastic anisotropy that are observed at the millimeter scale in human cortical bone. The porosity (pore volume fraction) is known to account for a large part, but not all, of the elasticity variations. This effect may be modeled by a two-phase micromechanical model consisting of a homogeneous matrix pervaded by cylindrical pores. Although this model has been widely used, it lacks experimental validation. The aim of the present work is to revisit experimental data (elastic coefficients, porosity) previously obtained from 21 cortical bone specimens from the femoral mid-diaphysis of 10 donors and test the validity of the model by proposing a detailed discussion of its hypotheses. This includes investigating to what extent the experimental uncertainties, pore network modeling, and matrix elastic properties influence the model's predictions. The results support the validity of the two-phase model of cortical bone which assumes that the essential source of variations of elastic properties at the millimeter-scale is the volume fraction of vascular porosity. We propose that the bulk of the remaining discrepancies between predicted stiffness coefficients and experimental data (RMSE between 6% and 9%) is in part due to experimental errors and part due to small variations of the extravascular matrix properties. More significantly, although most of the models that have been proposed for cortical bone were based on several homogenization steps and a large number of variable parameters, we show that a model with a single parameter, namely the volume fraction of vascular porosity, is a suitable representation for cortical bone. The results could provide a guide to build specimen-specific cortical bone models. This will be of interest to analyze the structure-function relationship in bone and to design bone-mimicking materials. PMID:25462527

  9. Elastic Properties of Human Osteon and Osteonal Lamella Computed by a Bidirectional Micromechanical Model and Validated by Nanoindentation.

    PubMed

    Korsa, Radim; Lukes, Jaroslav; Sepitka, Josef; Mares, Tomas

    2015-08-01

    Knowledge of the anisotropic elastic properties of osteon and osteonal lamellae provides a better understanding of various pathophysiological conditions, such as aging, osteoporosis, osteoarthritis, and other degenerative diseases. For this reason, it is important to investigate and understand the elasticity of cortical bone. We created a bidirectional micromechanical model based on inverse homogenization for predicting the elastic properties of osteon and osteonal lamellae of cortical bone. The shape, the dimensions, and the curvature of osteon and osteonal lamellae are described by appropriately chosen curvilinear coordinate systems, so that the model operates close to the real morphology of these bone components. The model was used to calculate nine orthotropic elastic constants of osteonal lamellae. The input values have the elastic properties of a single osteon. We also expressed the dependence of the elastic properties of the lamellae on the angle of orientation. To validate the model, we performed nanoindentation tests on several osteonal lamellae. We compared the experimental results with the calculated results, and there was good agreement between them. The inverted model was used to calculate the elastic properties of a single osteon, where the input values are the elastic constants of osteonal lamellae. These calculations reveal that the model can be used in both directions of homogenization, i.e., direct homogenization and also inverse homogenization. The model described here can provide either the unknown elastic properties of a single lamella from the known elastic properties at the level of a single osteon, or the unknown elastic properties of a single osteon from the known elastic properties at the level of a single lamella. PMID:25901781

  10. Modeling the Dynamics of Compromised Networks

    SciTech Connect

    Soper, B; Merl, D M

    2011-09-12

    Accurate predictive models of compromised networks would contribute greatly to improving the effectiveness and efficiency of the detection and control of network attacks. Compartmental epidemiological models have been applied to modeling attack vectors such as viruses and worms. We extend the application of these models to capture a wider class of dynamics applicable to cyber security. By making basic assumptions regarding network topology we use multi-group epidemiological models and reaction rate kinetics to model the stochastic evolution of a compromised network. The Gillespie Algorithm is used to run simulations under a worst case scenario in which the intruder follows the basic connection rates of network traffic as a method of obfuscation.