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.
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.
Solvated dissipative electro-elastic network model of hydrated proteins.
Martin, Daniel R; Matyushov, Dmitry V
2012-10-28
Elastic network models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the network. In addition, the network is made heterogeneous and softened at the protein surface by accounting for hydration of the ionized residues. Solvation changes the network Hessian in two ways. Diagonal solvation terms soften the spring constants and off-diagonal dipole-dipole terms correlate displacements of the ionized residues. The model is used to formulate the response functions of the electrostatic potential and electric field appearing in theories of redox reactions and spectroscopy. We also formulate the dielectric response of the protein and find that solvation of the surface ionized residues leads to a slow relaxation peak in the dielectric loss spectrum, about two orders of magnitude slower than the main peak of protein relaxation. Finally, the solvated network is used to formulate the allosteric response of the protein to ion binding. The global thermodynamics of ion binding is not strongly affected by the network solvation, but it dramatically enhances conformational changes in response to placing a charge at the active site of the protein.
Di Paola, Luisa; Liang, Zhongjie; Giuliani, Alessandro
2017-01-01
The overall topology and interfacial interactions play key roles in understanding structural and functional principles of protein complexes. Elastic Network Model (ENM) and Protein Contact Network (PCN) are two widely used methods for high throughput investigation of structures and interactions within protein complexes. In this work, the comparative analysis of ENM and PCN relative to hemoglobin (Hb) was taken as case study. We examine four types of structural and dynamical paradigms, namely, conformational change between different states of Hbs, modular analysis, allosteric mechanisms studies, and interface characterization of an Hb. The comparative study shows that ENM has an advantage in studying dynamical properties and protein-protein interfaces, while PCN is better for describing protein structures quantitatively both from local and from global levels. We suggest that the integration of ENM and PCN would give a potential but powerful tool in structural systems biology. PMID:28243596
Elasticity of Poissonian fiber networks
NASA Astrophysics Data System (ADS)
Åström, J. A.; Mäkinen, J. P.; Alava, M. J.; Timonen, J.
2000-05-01
An effective-medium model is introduced for the elasticity of two-dimensional random fiber networks. These networks are commonly used as basic models of heterogeneous fibrous structures such as paper. Using the exact Poissonian statistics to describe the microscopic geometry of the network, the tensile modulus can be expressed by a single-parameter function. This parameter depends on the network density and fiber dimensions, which relate the macroscopic modulus to the relative importance of axial and bending deformations of the fibers. The model agrees well with simulation results and experimental findings. We also discuss the possible generalizations of the model.
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.
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
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.
Applying forces to elastic network models of large biomolecules using a haptic feedback device
NASA Astrophysics Data System (ADS)
Stocks, M. B.; Laycock, S. D.; Hayward, S.
2011-03-01
Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version.
Applying forces to elastic network models of large biomolecules using a haptic feedback device.
Stocks, M B; Laycock, S D; Hayward, S
2011-03-01
Elastic network models of biomolecules have proved to be relatively good at predicting global conformational changes particularly in large systems. Software that facilitates rapid and intuitive exploration of conformational change in elastic network models of large biomolecules in response to externally applied forces would therefore be of considerable use, particularly if the forces mimic those that arise in the interaction with a functional ligand. We have developed software that enables a user to apply forces to individual atoms of an elastic network model of a biomolecule through a haptic feedback device or a mouse. With a haptic feedback device the user feels the response to the applied force whilst seeing the biomolecule deform on the screen. Prior to the interactive session normal mode analysis is performed, or pre-calculated normal mode eigenvalues and eigenvectors are loaded. For large molecules this allows the memory and number of calculations to be reduced by employing the idea of the important subspace, a relatively small space of the first M lowest frequency normal mode eigenvectors within which a large proportion of the total fluctuation occurs. Using this approach it was possible to study GroEL on a standard PC as even though only 2.3% of the total number of eigenvectors could be used, they accounted for 50% of the total fluctuation. User testing has shown that the haptic version allows for much more rapid and intuitive exploration of the molecule than the mouse version.
Jang, Yunho; Jeong, Jay I; Kim, Moon K
2006-07-01
UMass Morph Server (UMMS) has been developed for the broad impact on the study of molecular dynamics (MD). The elastic network model (ENM) of a given macromolecule has been proven as a useful tool for analyzing thermal behaviors locally and predicting folding pathways globally. UMMS utilizes coarse-grained ENMs at various levels. These simplifications remarkably save computation time compared with all-atom MD simulations so that one can bring down massive computational problems from a supercomputer to a PC. To improve computational efficiency and physical reality of ENMs, the symmetry-constrained, rigid-cluster, hybrid and chemical-bond ENMs have been developed and implemented at UMMS. One can request both harmonic normal mode analysis of a single macromolecule and anharmonic pathway generation between two conformations of a same molecule using elastic network interpolation at http://biomechanics.ecs.umass.edu/umms.html.
Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation.
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.
Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation
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
A mass weighted chemical elastic network model elucidates closed form domain motions in proteins
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
Elastic network models capture the motions apparent within ensembles of RNA structures.
Zimmermann, Michael T; Jernigan, Robert L
2014-06-01
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.
Elastic network models capture the motions apparent within ensembles of RNA structures
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
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.
Robustness Elasticity in Complex Networks
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
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.
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.
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
Flexibility of the exportins Cse1p and Xpot depicted by elastic network model.
Hu, Mingwen; Kim, Byung
2011-07-01
Nucleocytoplasmic transport in eukaryotic cells involves many interactions between macromolecules, and has been an active area for many researchers. However, the precise mechanism still evades us and more efforts are needed to better understand it. In this study, the authors investigated exportins (Cse1p and Xpot) by elastic network interpolation (ENI) and elastic network based normal mode analysis (EN-NMA). Results of the study on Cse1p were in good agreement with the results obtained by molecular dynamics simulation in another study but with the benefit of time-efficiency. First, a formation of ring closure obtained by ENI was observed. Second, HEAT 1 to 3 and HEAT 14 to 17 had the largest values of root mean square deviation (RMSD) which indicated the flexibility of Cse1p during the transition. In the case of Xpot, a possible pathway from nuclear state to cytoplasmic state was shown, and the predicted pathway was also quantitatively analyzed in terms of RMSD. The results suggested two flexible regions of Xpot that might be important to the transporting mechanism. Moreover, the dominant mode of Xpot in the nuclear state obtained by EN-NMA not only showed the tendency to match the predicted pathway to the cytoplasmic state of Xpot, but also displayed the flexible regions of Xpot. A time-efficient computational approach was presented in this paper and the results indicated that the flexibility of tested exportins might be required to perform the biological function of transporting cargos.
Nonaffine rubber elasticity for stiff polymer networks.
Heussinger, Claus; Schaefer, Boris; Frey, Erwin
2007-09-01
We present a theory for the elasticity of cross-linked stiff polymer networks. Stiff polymers, unlike their flexible counterparts, are highly anisotropic elastic objects. Similar to mechanical beams, stiff polymers easily deform in bending, while they are much stiffer with respect to tensile forces ("stretching"). Unlike in previous approaches, where network elasticity is derived from the stretching mode, our theory properly accounts for the soft bending response. A self-consistent effective medium approach is used to calculate the macroscopic elastic moduli starting from a microscopic characterization of the deformation field in terms of "floppy modes"-low-energy bending excitations that retain a high degree of nonaffinity. The length scale characterizing the emergent nonaffinity is given by the "fiber length" lf, defined as the scale over which the polymers remain straight. The calculated scaling properties for the shear modulus are in excellent agreement with the results of recent simulations obtained in two-dimensional model networks. Furthermore, our theory can be applied to rationalize bulk rheological data in reconstituted actin networks.
Schröder, Gunnar F.; Brunger, Axel T.; Levitt, Michael
2008-01-01
Summary Structural studies of large proteins and protein assemblies are a difficult and pressing challenge in molecular biology. Experiments often yield only low-resolution or sparse data which are not sufficient to fully determine atomistic structures. We have developed a general geometry-based algorithm that efficiently samples conformational space under constraints imposed by low-resolution density maps obtained from electron microscopy or X-ray crystallography experiments. A deformable elastic network (DEN) is used to restrain the sampling to prior knowledge of an approximate structure. The DEN restraints dramatically reduce over-fitting, especially at low resolution. Cross-validation is used to optimally weight the structural information and experimental data. Our algorithm is robust even for noise-added density maps and has a large radius of convergence for our test case. The DEN restraints can also be used to enhance reciprocal space simulated annealing refinement. PMID:18073112
Filament-length-controlled elasticity in 3D fiber networks.
Broedersz, C P; Sheinman, M; Mackintosh, F C
2012-02-17
We present a model for disordered 3D fiber networks to study their linear and nonlinear elasticity. In contrast to previous 2D models, these 3D networks with binary crosslinks are underconstrained with respect to fiber stretching elasticity, suggesting that bending may dominate their response. We find that such networks exhibit a bending-dominated elastic regime controlled by fiber length, as well as a crossover to a stretch-dominated regime for long fibers. Finally, by extending the model to the nonlinear regime, we show that these networks become intrinsically nonlinear with a vanishing linear response regime in the limit of flexible or long filaments.
Elastic model of supercoiling.
Benham, C J
1977-01-01
An elastic model for the supercoiling of duplex DNA is developed. The simplest assumptions regarding the elastic properties of double-helical DNA (homogeneous, isotropic, of circular cross section, and remaining straight when unstressed) will generate two orders of superhelicity when stressed. Recent experimental results [Brady, G.W., Fein, D.B. & Brumberger, H. (1976) Nature 264, 231-234] suggest that in supercoiled DNA molecules there are regions where two distinct orders of supercoiling arise, as predicted by this model. PMID:267934
Zhao, Ziqing W; Xie, X Sunney; Ge, Hao
2016-03-24
Nucleotide-induced conformational closing of the finger domain of DNA polymerase is crucial for its catalytic action during DNA replication. Such large-amplitude molecular motion is often not fully accessible to either direct experimental monitoring or molecular dynamics simulations. However, a coarse-grained model can offer an informative alternative, especially for probing the relationship between conformational dynamics and catalysis. Here we investigate the dynamics of T7 DNA polymerase catalysis using a Langevin-type elastic network model incorporating detailed structural information on the open conformation without the substrate bound. Such a single-parameter model remarkably captures the induced conformational dynamics of DNA polymerase upon dNTP binding, and reveals its close coupling to the advancement toward transition state along the coordinate of the target reaction, which contributes to significant lowering of the activation energy barrier. Furthermore, analysis of stochastic catalytic rates suggests that when the activation energy barrier has already been significantly lowered and nonequilibrium relaxation toward the closed form dominates the catalytic rate, one must appeal to a picture of two-dimensional free energy surface in order to account for the full spectrum of catalytic modes. Our semiquantitative study illustrates the general role of conformational dynamics in achieving transition-state stabilization, and suggests that such an elastic network model, albeit simplified, possesses the potential to furnish significant mechanistic insights into the functioning of a variety of enzymatic systems.
Williams, Gareth; Toon, Andrew J
2010-12-01
Protein topology defined by the matrix of residue contacts has proved to be a fruitful basis for the study of protein dynamics. The widely implemented coarse-grained elastic network model of backbone fluctuations has been used to describe crystallographic temperature factors, allosteric couplings, and some aspects of the folding pathway. In the present study, we develop a model of protein dynamics based on the classical equations of motion of a damped network model (DNM) that describes the folding path from a completely unfolded state to the native conformation through a single-well potential derived purely from the native conformation. The kinetic energy gained through the collapse of the protein chain is dissipated through a friction term in the equations of motion that models the water bath. This approach is completely general and sufficiently fast that it can be applied to large proteins. Folding pathways for various proteins of different classes are described and shown to correlate with experimental observations and molecular dynamics and Monte Carlo simulations. Allosteric transitions between alternative protein structures are also modeled within the DNM through an asymmetric double-well potential.
Li, Hai Yan; Cao, Zan Xia; Zhao, Li Ling; Wang, Ji Hua
2013-05-21
The ribose-binding protein (RBP) is a sugar-binding bacterial periplasmic protein whose function is associated with a large allosteric conformational change from an open to a closed conformation upon binding to ribose. The open (ligand-free) and closed (ligand-bound) forms of RBP have been found. Here we investigate the conformational motions and residue fluctuations of the RBP by analyzing the modes of motion with two coarse-grained elastic network models, the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM). The calculated B-factors in both the calculated models are in good agreement with the experimentally determined B-factors in X-ray crystal structures. The slowest mode analysis by GNM shows that both forms have the same motion hinge axes around residues Ser103, Gln235, Asp264 and the two domains of both structures have similar fluctuation range. The superposition of the first three dominant modes of ANM, consisting of the rotating, bending and twisting motions of the two forms, accounts for large rearrangement of domains from the ligand-free (open) to ligand-bound (closed) conformation and thus constitutes a critical component of the RBP's functions. By analyzing cross-correlations between residue fluctuation and the difference-distance plot, it is revealed that the conformational change can be described as a rigid rotation of the two domains with respect to each other, whereas the internal structure of the two domains remains largely intact. The results directly indicate that the dominant dynamic characteristics of protein structures can be captured from their static native state using coarse-grained models.
Elastic response of filamentous networks with compliant crosslinks.
Sharma, A; Sheinman, M; Heidemann, K M; MacKintosh, F C
2013-11-01
Experiments have shown that elasticity of disordered filamentous networks with compliant crosslinks is very different from networks with rigid crosslinks. Here, we model and analyze filamentous networks as a collection of randomly oriented rigid filaments connected to each other by flexible crosslinks that are modeled as wormlike chains. For relatively large extensions we allow for enthalpic stretching of crosslink backbones. We show that for sufficiently high crosslink density, the network linear elastic response is affine on the scale of the filaments' length. The nonlinear regime can become highly nonaffine and is characterized by a divergence of the elastic modulus at finite strain. In contrast to the prior predictions, we do not find an asymptotic regime in which the differential elastic modulus scales linearly with the stress, although an approximate linear dependence can be seen in a transition from entropic to enthalpic regimes. We discuss our results in light of recent experiments.
Allosteric transitions of the maltose transporter studied by an elastic network model.
Li, Chun Hua; Yang, Yong Xiao; Su, Ji Guo; Liu, Bin; Tan, Jian Jun; Zhang, Xiao Yi; Wang, Cun Xin
2014-07-01
The maltose transporter from Escherichia coli is one of the ATP-binding cassette (ABC) transporters that utilize the energy from ATP hydrolysis to translocate substrates across cellular membranes. Until 2011, three crystal structures have been determined for maltose transporter at different states in the process of transportation. Here, based on these crystal structures, the allosteric pathway from the resting state (inward-facing) to the catalytic intermediate state (outward-facing) is studied by applying an adaptive anisotropic network model. The results suggest that the allosteric transitions proceed in a coupled way. The closing of the nucleotide-binding domains occurs first, and subsequently this conformational change is propagated to the transmembrane domains (TMD) via the EAA and EAS loops, and then to the maltose-binding protein, which facilitates the translocation of the maltose. It is also found that there exist nonrigid-body and asymmetric movements in the TMD. The cytoplasmic gate may only play the role of allosteric propagation during the transition from the pretranslocation to outward-facing states. In addition, the results show that the movment of the helical subdomain towards the RecA-like subdomain mainly occurs in the earlier stages of the transition. These results can provide some insights into the understanding of the mechanism of ABC transporters.
NASA Astrophysics Data System (ADS)
Kiyashchenko, D.; Smirnova, N.; Troyan, V.; Vallianatos, F.
2003-04-01
One of the important tools for seismic hazard risk assessment is study of the dynamic of properties of spatio-temporal distribution of the seismicity. We have performed simulation of the crack network development in elastic body under external stresses. The results of simulation show that the variations of several multifractal characteristics (correlation dimension, information dimension, higher order generalized fractal dimensions, the abscissa of the top of multifractal spectrum) contain information about evolution of the system towards main rupture. The validity of the results of simulations has been supported by the results of case studies of the seismicity catalogs for Japan and Southern California. Also the considered model of crack network evolution has reproduced such precursory phenomena as the decrease of b-values and the increase of the level of spatio-temporal correlations in the seismicity. Appreciable information on the pre-rupture evolution of fault (crack) network in the lithosphere could be provided by study of the properties of coda waves scattered by the faults and inhomogeneities of the considered seismically active region. We have incorporated the results of simulation of the crack network evolution and solution of 2D problem of elastic waves propagation in elastic media containing a number of cracks. We present the preliminary results of study of acoustic waves scattered in the elastic media by the crack network on different stages of the destruction process. The work is supported by the grant RFBR 02-05-65081, grant INTAS 99-1102 and Russian Programme Intergeophysica.
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
Strength reduction in electrical and elastic networks
NASA Astrophysics Data System (ADS)
Espinoza Ortiz, J. S.; Rajapakse, Chamith S.; Gunaratne, Gemunu H.
2002-10-01
Particular aspects of problems ranging from dielectric breakdown to metal-insulator transition can be studied using electrical or elastic networks. We present an expression for the mean breakdown strength of such networks. First, we introduce a method to evaluate the redistribution of current due to the removal of a finite number of elements from a hypercubic network of conductances. It is used to determine the reduction of breakdown strength due to a fracture of size κ. Numerical analysis is used to show that the analogous reduction due to random removal of elements from electrical and elastic networks follow a similar form. One possible application, namely the use of bone density as a diagnostic tool for osteoporosis, is discussed.
Su, Ji Guo; Han, Xiao Ming; Zhang, Xiao; Hou, Yan Xue; Zhu, Jian Zhuo; Wu, Yi Dong
2016-01-01
Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK2) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.
Properties of elastic percolating networks in isotropic media with arbitrary elastic constants
NASA Astrophysics Data System (ADS)
Pla, O.; Garcia-Molina, R.; Guinea, F.; Louis, E.
1990-06-01
The properties of diluted elastic media in two dimensions are investigated in an isotropic system in which the ratio between the two Lamé coefficients can be varied. Changes in the ratio between the continuum elastic constants induce significant variations in the behavior of the system away from the threshold for percolation, but not in the properties near the percolation transition. We discuss the results in both cases and their relevance to the definition of the universal properties of diluted elastic networks. It is shown that many features of interest, like the bulk modulus at intermediate concentrations of voids and the backbone, are very dependent on the microscopic details of the model, and not only on its macroscopic behavior. Thus, elastic percolation does not seem to have the same degree of universality as scalar percolation.
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
Breakdown Strength in Electrical and Elastic Random Networks
NASA Astrophysics Data System (ADS)
Espinoza Ortiz, Julio; Rajapakse, Chamith; Gunaratne, Gemunu
2003-03-01
Electrical or elastic networks provide a natural model to study transport processes such as dielectric breakdown to metal insulator transition in disordered inhomogeneous conductors. We present an expression for the mean breakdown strength of such networks. First, we introduce a method to evaluate the redistribution of current due to the removal of a finite number of elements from a hyper-cubic network of conductances. It is used to determine the reduction of breakdown strength due to a fracture of size κ. Numerical analysis is used to show that the analogous reduction due to random removal of elements from electrical and elastic networks follow a similar form. We discuss one possible application, namely the use of bone density as a diagnostic tools for osteoporosis.
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.
NASA Astrophysics Data System (ADS)
Bolgov, I.; Kaverzneva, T.; Kolesova, S.; Lazovskaya, T.; Stolyarov, O.; Tarkhov, D.
2016-11-01
The article deals with the problem of predicting of the temporal elongation law of the sample under dynamic loading. The determination of tensile behavior of samples under uniaxial loading is performed by a standard tensile method. The neural network approach is applied to construct an approximate elongation-force dependence using measurement data and posterior model of the dependence of rupture conditions on the neural network parameters. The considered approach can be used in the building industry.
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.
Na, Hyuntae; Jernigan, Robert L; Song, Guang
2015-10-01
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.
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.
Frappier, Vincent; Najmanovich, Rafael J
2014-04-01
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.
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.
Kameda, Takeru; Isami, Shuhei; Togashi, Yuichi; Nishimori, Hiraku; Sakamoto, Naoaki; Awazu, Akinori
2017-01-01
Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with consideration of sequence-dependent geometry, we propose elastic network models of DNA where each particle represents k nucleotides (1-particle-per-k-nucleotides, 1PkN). The models were adjusted according to profiles of the anisotropic fluctuations obtained from our previous 1-particle-per-1-nucleotide (1P1N) model, which was proven to reproduce such profiles of all-atom models. We confirmed that the 1P3N and 1P4N models are suitable for the analysis of detailed dynamics such as local twisting motion. The models are intended for the analysis of large structures, e.g., 10-nm fibers in the nucleus, and nucleoids of mitochondrial or phage DNA at low computational costs. As an example, we surveyed the physical characteristics of the whole mitochondrial human and Plasmodium falciparum genomes.
Kameda, Takeru; Isami, Shuhei; Togashi, Yuichi; Nishimori, Hiraku; Sakamoto, Naoaki; Awazu, Akinori
2017-01-01
Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with consideration of sequence-dependent geometry, we propose elastic network models of DNA where each particle represents k nucleotides (1-particle-per-k-nucleotides, 1PkN). The models were adjusted according to profiles of the anisotropic fluctuations obtained from our previous 1-particle-per-1-nucleotide (1P1N) model, which was proven to reproduce such profiles of all-atom models. We confirmed that the 1P3N and 1P4N models are suitable for the analysis of detailed dynamics such as local twisting motion. The models are intended for the analysis of large structures, e.g., 10-nm fibers in the nucleus, and nucleoids of mitochondrial or phage DNA at low computational costs. As an example, we surveyed the physical characteristics of the whole mitochondrial human and Plasmodium falciparum genomes. PMID:28382002
Sauerwald, Natalie; Zhang, She; Kingsford, Carl; Bahar, Ivet
2017-03-16
Understanding the three-dimensional (3D) architecture of chromatin and its relation to gene expression and regulation is fundamental to understanding how the genome functions. Advances in Hi-C technology now permit us to study 3D genome organization, but we still lack an understanding of the structural dynamics of chromosomes. The dynamic couplings between regions separated by large genomic distances (>50 Mb) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to model chromatin dynamics using Hi-C data. We show that the GNM can identify spatial couplings at multiple scales: it can quantify the correlated fluctuations in the positions of gene loci, find large genomic compartments and smaller topologically-associating domains (TADs) that undergo en bloc movements, and identify dynamically coupled distal regions along the chromosomes. We show that the predictions of the GNM correlate well with genome-wide experimental measurements. We use the GNM to identify novel cross-correlated distal domains (CCDDs) representing pairs of regions distinguished by their long-range dynamic coupling and show that CCDDs are associated with increased gene co-expression. Together, these results show that GNM provides a mathematically well-founded unified framework for modeling chromatin dynamics and assessing the structural basis of genome-wide observations.
Inferring a weighted elastic network from partial unfolding with coarse-grained simulations.
de Mendonça, Matheus R; Rizzi, Leandro G; Contessoto, Vinicius; Leite, Vitor B P; Alves, Nelson A
2014-01-01
A number of studies have demonstrated that simple elastic network models can reproduce experimental B-factors, providing insights into the structure-function properties of proteins. Here, we report a study on how to improve an elastic network model and explore its performance by predicting the experimental B-factors. Elastic network models are built on the experimental Cα coordinates, and they only take the pairs of Cα atoms within a given cutoff distance rc into account. These models describe the interactions by elastic springs with the same force constant. We have developed a method based on numerical simulations with a simple coarse-grained force field, to attribute weights to these spring constants. This method considers the time that two Cα atoms remain connected in the network during partial unfolding, establishing a means of measuring the strength of each link. We examined two different coarse-grained force fields and explored the computation of these weights by unfolding the native structures.
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
Su, Ji-Guo; Zhang, Xiao; Zhao, Shu-Xin; Li, Xing-Yuan; Hou, Yan-Xue; Wu, Yi-Dong; Zhu, Jian-Zhuo; An, Hai-Long
2015-08-04
BtuCD-BtuF from Escherichia coli is a binding protein-dependent adenosine triphosphate (ATP)-binding cassette (ABC) transporter system that uses the energy of ATP hydrolysis to transmit vitamin B12 across cellular membranes. Experimental studies have showed that during the transport cycle, the transporter undergoes conformational transitions between the "inward-facing" and "outward-facing" states, which results in the open-closed motions of the cytoplasmic gate of the transport channel. The opening-closing of the channel gate play critical roles for the function of the transporter, which enables the substrate vitamin B12 to be translocated into the cell. In the present work, the extent of opening of the cytoplasmic gate was chosen as a function-related internal coordinate. Then the mean-square fluctuation of the internal coordinate, as well as the cross-correlation between the displacement of the internal coordinate and the movement of each residue in the protein, were calculated based on the normal mode analysis of the elastic network model to analyze the function-related motions encoded in the structure of the system. In addition, the key residues important for the functional motions of the transporter were predicted by using a perturbation method. In order to facilitate the calculations, the internal coordinate was introduced as one of the axes of the coordinate space and the conventional Cartesian coordinate space was transformed into the internal/Cartesian space with linear approximation. All the calculations were carried out in this internal/Cartesian space. Our method can successfully identify the functional motions and key residues for the transporter BtuCD-BtuF, which are well consistent with the experimental observations.
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.
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.
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.
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.
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.
Rubber elasticity for percolation network consisting of Gaussian chains
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.
Hypo-Elastic Model for Lung Parenchyma
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.
A collagen and elastic network in the wing of the bat.
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
Fluctuation-stabilized marginal networks and anomalous entropic elasticity.
Dennison, M; Sheinman, M; Storm, C; MacKintosh, F C
2013-08-30
We study the elastic properties of thermal networks of Hookean springs. In the purely mechanical limit, such systems are known to have a vanishing rigidity when their connectivity falls below a critical, isostatic value. In this work, we show that thermal networks exhibit a nonzero shear modulus G well below the isostatic point and that this modulus exhibits an anomalous, sublinear dependence on temperature T. At the isostatic point, G increases as the square root of T, while we find G∝Tα below the isostatic point, where α≃0.8. We show that this anomalous T dependence is entropic in origin.
A mathematical model of elastic fin micromotors
NASA Astrophysics Data System (ADS)
Lu, Pin; Lee, Kwok Hong; Piang Lim, Siak; Dong, Shuxiang; Zhong Lin, Wu
2000-08-01
In the present work, a simplified mathematical model of ultrasonic elastic fin micromotors has been developed. According to the operating principle of this type of motor, the motions of a rotor in each cycle of the stator vibration are divided into several stages based on whether the fin tip and the stator are in contact with slip, contact without slip or separation. The equations of motion of the rotor in each stage are derived. The valid range of the model has been discussed through numerical examples. This work provides an initial effort to construct a model for the elastic fin motor by considering the dynamical deformation of the rotor as well as the intermittent contacts.
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.
Shape memory polymer network with thermally distinct elasticity and plasticity
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
NASA Astrophysics Data System (ADS)
Urayama, Kenji; Kawamura, Takanobu; Kohjiya, Shinzo
1996-09-01
We have investigated the degree of equilibrium swelling and the elastic modulus of networks prepared by end-linking oligo(dimethylsiloxane)s (ODMS) in solution as a function of polymer concentration at crosslinking. The molecular weight of ODMS is so low that entanglement couplings are not formed in uncrosslinked state. It has been found from the preparation concentration dependence of elastic modulus in preparation state that trapped entanglements are formed by the introduction of crosslinks, and those considerably contribute to elastic modulus, even if the prepolymers are not entangled in uncrosslinked state. The experimental results for preparation concentration dependence of the degree of equilibrium swelling and the elastic modulus of equilibrium swollen networks are compared with the theoretical predictions by the two theories, i.e., the affine model and the c* theorem. It has been clearly shown that the affine model describes well the experimental results, while the discrepancies between the experimental results and the predictions by the c* theorem are considerable. These results strongly suggest that preparation concentration should be regarded as a reference state, and the displacement of crosslinks moves affinely on swelling, while the complete disinterpenetration of network chains in equilibrium swollen state, which is a postulate of the c* theorem, does not occur.
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.
SAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein
Dony, Nicolas; Crowet, Jean Marc; Joris, Bernard; Brasseur, Robert; Lins, Laurence
2013-01-01
Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins. PMID:23722660
Rakshit, Sourav; Ananthasuresh, G K
2010-02-07
We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa-Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein, Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.
Continuum models for epitaxial growth with elasticity
NASA Astrophysics Data System (ADS)
Xiang, Yang
In heteroepitaxial growth, the mismatch between the lattice constants in the film and the substrate causes misfit strain in the film, making a flat surface unstable to small perturbations. This morphological instability is called Asaro-Tiller-Grinfeld (ATG) instability, which can drive the film to self-organize into nanostructures such as quantum wires or quantum dots. At low temperature, the surface consists of steps and facets, when the misfit strain causes step bunching, traditional continuum models for ATG instability does not apply directly. In the first part of this thesis, we derive a PDE model for step bunching by taking the continuum limit of the discrete models proposed by Tersoff et al and Duport et al. We study the linear instability of a uniform step train with small perturbations and compare our results with those of discrete models and continuum models for traditional ATG instability. We numerically study the nonlinear evolution of this instability and compare our results with those of discrete models. We also study the equilibrium shapes of step bunches and explain their coalescence. In the second part of this thesis, we derive a nonlinear approximate PDE for the ATG instability. In the ATG instability, the misfit strain is coupled with surface morphology and an elasticity problem must be solved numerically. Linear approximation is made in some cases such as when computing the equilibrium island shapes. Using the exact solution for a cycloid surface obtained by Chiu and Gao, we find that our nonlinear approximation has a wider range of applicability than linear approximation. Numerical simulation using our nonlinear PDE model predicts formation of a cusp-like surface morphology from initially small perturbations of flat surfaces, which agrees well with the result obtained by Spencer and Meiron by solving the elasticity problem numerically.
Li, Chunhua; Lv, Dashuai; Zhang, Lei; Yang, Feng; Wang, Cunxin; Su, Jiguo; Zhang, Yang
2016-07-07
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.
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.
Elastic network normal modes provide a basis for protein structure refinement
NASA Astrophysics Data System (ADS)
Gniewek, Pawel; Kolinski, Andrzej; Jernigan, Robert L.; Kloczkowski, Andrzej
2012-05-01
It is well recognized that thermal motions of atoms in the protein native state, the fluctuations about the minimum of the global free energy, are well reproduced by the simple elastic network models (ENMs) such as the anisotropic network model (ANM). Elastic network models represent protein dynamics as vibrations of a network of nodes (usually represented by positions of the heavy atoms or by the Cα atoms only for coarse-grained representations) in which the spatially close nodes are connected by harmonic springs. These models provide a reliable representation of the fluctuational dynamics of proteins and RNA, and explain various conformational changes in protein structures including those important for ligand binding. In the present paper, we study the problem of protein structure refinement by analyzing thermal motions of proteins in non-native states. We represent the conformational space close to the native state by a set of decoys generated by the I-TASSER protein structure prediction server utilizing template-free modeling. The protein substates are selected by hierarchical structure clustering. The main finding is that thermal motions for some substates, overlap significantly with the deformations necessary to reach the native state. Additionally, more mobile residues yield higher overlaps with the required deformations than do the less mobile ones. These findings suggest that structural refinement of poorly resolved protein models can be significantly enhanced by reduction of the conformational space to the motions imposed by the dominant normal modes.
An elastic rod model for anguilliform swimming.
McMillen, T; Holmes, P
2006-11-01
We develop a model for anguilliform (eel-like) swimming as an elastic rod actuated via time-dependent intrinsic curvature and subject to hydrodynamic drag forces, the latter as proposed by Taylor (in Proc Roy Proc Lond A 214:158-183, 1952). We employ a eometrically exact theory and discretize the resulting nonlinear partial differential evolution both to perform numerical simulations, and to compare with previous models consisting of chains of rigid links or masses connected by springs, dampers, and prescribed force generators representing muscles. We show that muscle activations driven by motoneuronal spike trains via calcium dynamics produce intrinsic curvatures corresponding to near-sinusoidal body shapes in longitudinally-uniform rods, but that passive elasticity causes Taylor's assumption of prescribed shape to fail, leading to time-periodic motions and lower speeds than those predicted Taylor (in Proc Roy Proc Lond A 214:158-183, 1952). We investigate the effects of bending stiffness, body geometry, and activation patterns on swimming speed, turning behavior, and acceleration to steady swimming. We show that laterally-uniform activation yields stable straight swimming and laterally differential activation levels lead to stable turns, and we argue that tapered bodies with reduced caudal (tail-end) activation (to produce uniform intrinsic curvature) swim faster than ones with uniform activation.
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.
Multicasting based optical inverse multiplexing in elastic optical network.
Guo, Bingli; Xu, Yingying; Zhu, Paikun; Zhong, Yucheng; Chen, Yuanxiang; Li, Juhao; Chen, Zhangyuan; He, Yongqi
2014-06-16
Optical multicasting based inverse multiplexing (IM) is introduced in spectrum allocation of elastic optical network to resolve the spectrum fragmentation problem, where superchannels could be split and fit into several discrete spectrum blocks in the intermediate node. We experimentally demonstrate it with a 1-to-7 optical superchannel multicasting module and selecting/coupling components. Also, simulation results show that, comparing with several emerging spectrum defragmentation solutions (e.g., spectrum conversion, split spectrum), IM could reduce blocking performance significantly but without adding too much system complexity as split spectrum. On the other hand, service fairness for traffic with different granularity of these schemes is investigated for the first time and it shows that IM performs better than spectrum conversion and almost as well as split spectrum, especially for smaller size traffic under light traffic intensity.
NASA Astrophysics Data System (ADS)
Zhu, Ruijie; Zhao, Yongli; Yang, Hui; Tan, Yuanlong; Chen, Haoran; Zhang, Jie; Jue, Jason P.
2016-08-01
Network virtualization can eradicate the ossification of the infrastructure and stimulate innovation of new network architectures and applications. Elastic optical networks (EONs) are ideal substrate networks for provisioning flexible virtual optical network (VON) services. However, as network traffic continues to increase exponentially, the capacity of EONs will reach the physical limitation soon. To further increase network flexibility and capacity, the concept of EONs is extended into the spatial domain. How to map the VON onto substrate networks by thoroughly using the spectral and spatial resources is extremely important. This process is called VON embedding (VONE).Considering the two kinds of resources at the same time during the embedding process, we propose two VONE algorithms, the adjacent link embedding algorithm (ALEA) and the remote link embedding algorithm (RLEA). First, we introduce a model to solve the VONE problem. Then we design the embedding ability measurement of network elements. Based on the network elements' embedding ability, two VONE algorithms were proposed. Simulation results show that the proposed VONE algorithms could achieve better performance than the baseline algorithm in terms of blocking probability and revenue-to-cost ratio.
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
The flow of power law fluids in elastic networks and porous media.
Sochi, Taha
2016-02-01
The flow of power law fluids, which include shear thinning and shear thickening as well as Newtonian as a special case, in networks of interconnected elastic tubes is investigated using a residual-based pore scale network modeling method with the employment of newly derived formulae. Two relations describing the mechanical interaction between the local pressure and local cross-sectional area in distensible tubes of elastic nature are considered in the derivation of these formulae. The model can be used to describe shear dependent flows of mainly viscous nature. The behavior of the proposed model is vindicated by several tests in a number of special and limiting cases where the results can be verified quantitatively or qualitatively. The model, which is the first of its kind, incorporates more than one major nonlinearity corresponding to the fluid rheology and conduit mechanical properties, that is non-Newtonian effects and tube distensibility. The formulation, implementation, and performance indicate that the model enjoys certain advantages over the existing models such as being exact within the restricting assumptions on which the model is based, easy implementation, low computational costs, reliability, and smooth convergence. The proposed model can, therefore, be used as an alternative to the existing Newtonian distensible models; moreover, it stretches the capabilities of the existing modeling approaches to reach non-Newtonian rheologies.
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.
Benefit of adaptive FEC in shared backup path protected elastic optical network.
Guo, Hong; Dai, Hua; Wang, Chao; Li, Yongcheng; Bose, Sanjay K; Shen, Gangxiang
2015-07-27
We apply an adaptive forward error correction (FEC) allocation strategy to an Elastic Optical Network (EON) operated with shared backup path protection (SBPP). To maximize the protected network capacity that can be carried, an Integer Linear Programing (ILP) model and a spectrum window plane (SWP)-based heuristic algorithm are developed. Simulation results show that the FEC coding overhead required by the adaptive FEC scheme is significantly lower than that needed by a fixed FEC allocation strategy resulting in higher network capacity for the adaptive strategy. The adaptive FEC allocation strategy can also significantly outperform the fixed FEC allocation strategy both in terms of the spare capacity redundancy and the average FEC coding overhead needed per optical channel. The proposed heuristic algorithm is efficient and not only performs closer to the ILP model but also does much better than the shortest-path algorithm.
Elastic models of defects in two-dimensional crystals
NASA Astrophysics Data System (ADS)
Kolesnikova, A. L.; Orlova, T. S.; Hussainova, I.; Romanov, A. E.
2014-12-01
Elastic models of defects in two-dimensional (2D) crystals are presented in terms of continuum mechanics. The models are based on the classification of defects, which is founded on the dimensionality of the specification region of their self-distortions, i.e., lattice distortions associated with the formation of defects. The elastic field of an infinitesimal dislocation loop in a film is calculated for the first time. The fields of the center of dilatation, dislocation, disclination, and circular inclusion in planar 2D elastic media, namely, nanofilms and graphenes, are considered. Elastic fields of defects in 2D and 3D crystals are compared.
NASA Astrophysics Data System (ADS)
Dysthe, Dag Kristian; Kobchenko, Maya; Hafver, Andreas; Panahi, Hamed; Jamtveit, Bjørn; Renard, Francois
2014-05-01
Escape of internally generated fluids from low permeability elastic solids plays an important role in several natural environments. In geological systems, primary migration of hydrocarbons, dehydration of sediments and hydrated mantle rocks in subduction zones are examples where the existing permeability cannot accommodate transport of generated fluids in low permeability rocks and fluid pressure build-up may alter the permeability by fracturing. Fractures form and propagate in the rock due to internal pressure build-up. We have performed experiments on shales and model materials using X-ray microtomography, 2D imaging and pressure burst recordings to study the spatiotemporal evolution of drainage fracture networks and released fluids. The local growth of fractures due to internal pressure build up has been characterized and modeled. The spatial organization of the fracture networks have been characterized in a novel manner as intermediate between tree networks and hierarchical fracture networks. The dynamics of intermittent fluid release on the network show both periodic, 1/f and 1/f2 dependence of fluid release spectrum. Discrete element, algorithmic and finite element models have been used to reproduce different aspects of the drainage fracture network behavior.
Modeling shock waves in orthotropic elastic materials
NASA Astrophysics Data System (ADS)
Vignjevic, Rade; Campbell, James C.; Bourne, Neil K.; Djordjevic, Nenad
2008-08-01
A constitutive relationship for modeling of shock wave propagation in orthotropic materials is proposed for nonlinear explicit transient large deformation computer codes (hydrocodes). A procedure for separation of material volumetric compression (compressibility effects equation of state) from deviatoric strain effects is formulated, which allows for the consistent calculation of stresses in the elastic regime as well as in the presence of shock waves. According to this procedure the pressure is defined as the state of stress that results in only volumetric deformation, and consequently is a diagonal second order tensor. As reported by Anderson et al. [Comput. Mech. 15, 201 (1994)], the shock response of an orthotropic material cannot be accurately predicted using the conventional decomposition of the stress tensor into isotropic and deviatoric parts. This paper presents two different stress decompositions based on the assumption that the stress tensor is split into two components: one component is due to volumetric strain and the other is due to deviatoric strain. Both decompositions are rigorously derived. In order to test their ability to describe shock propagation in orthotropic materials, both algorithms were implemented in a hydrocode and their predictions were compared to experimental plate impact data. The material considered was a carbon fiber reinforced epoxy material, which was tested in both the through-thickness and longitudinal directions. The ψ decomposition showed good agreement with the physical behavior of the considered material, while the ζ decomposition significantly overestimated the longitudinal stresses.
Dynamics of enzymatic digestion of elastic fibers and networks under tension.
Araújo, Ascânio D; Majumdar, Arnab; Parameswaran, Harikrishnan; Yi, Eunice; Spencer, Jean L; Nugent, Matthew A; Suki, Béla
2011-06-07
We study the enzymatic degradation of an elastic fiber under tension using an anisotropic random-walk model coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series along which enzyme molecules can diffuse. Numerical simulations show that the fiber stiffness decreases exponentially with two distinct regimes. The time constant of the first regime decreases with increasing tension. Using a mean field calculation, we partition the time constant into geometrical, chemical and externally controllable factors, which is corroborated by the simulations. We incorporate the fiber model into a multiscale network model of the extracellular matrix and find that network effects do not mask the exponential decay of stiffness at the fiber level. To test these predictions, we measure the force relaxation of elastin sheets stretched to 20% uniaxial strain in the presence of elastase. The decay of force is exponential and the time constant is proportional to the inverse of enzyme concentration in agreement with model predictions. Furthermore, the fragment mass released into the bath during digestion is linearly related to enzyme concentration that is also borne out in the model. We conclude that in the complex extracellular matrix, feedback between the local rate of fiber digestion and the force the fiber carries acts to attenuate any spatial heterogeneity of digestion such that molecular processes manifest directly at the macroscale. Our findings can help better understand remodeling processes during development or in disease in which enzyme concentrations and/or mechanical forces become abnormal.
Flexible multi-dimensional modulation method for elastic optical networks
NASA Astrophysics Data System (ADS)
He, Zilong; Liu, Wentao; Shi, Sheping; Shen, Bailin; Chen, Xue; Gao, Xiqing; Zhang, Qi; Shang, Dongdong; Ji, Yongning; Liu, Yingfeng
2016-01-01
We demonstrate a flexible multi-dimensional modulation method for elastic optical networks. We compare the flexible multi-dimensional modulation formats PM-kSC-mQAM with traditional modulation formats PM-mQAM using numerical simulations in back-to-back and wavelength division multiplexed (WDM) transmission (50 GHz-spaced) scenarios at the same symbol rate of 32 Gbaud. The simulation results show that PM-kSC-QPSK and PM-kSC-16QAM can achieve obvious back-to-back sensitivity gain with respect to PM-QPSK and PM-16QAM at the expense of spectral efficiency reduction. And the WDM transmission simulation results show that PM-2SC-QPSK can achieve 57.5% increase in transmission reach compared to PM-QPSK, and 48.5% increase for PM-2SC-16QAM over PM-16QAM. Furthermore, we also experimentally investigate the back to back performance of PM-2SC-QPSK, PM-4SC-QPSK, PM-2SC-16QAM and PM-3SC-16QAM, and the experimental results agree well with the numerical simulations.
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.
Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.
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).
Studies in cutaneous aging: I. The elastic fiber network
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.
Shen, Zhi-shu; Hasegawa, Hiroshi; Sato, Ken-ichi; Tanaka, Takafumi; Hirano, Akira
2014-02-10
We propose a novel elastic optical path network where each specific bitrate signal uses its own dedicated fixed grid and one edge of its frequency grid is anchored at a specific frequency. Numerical evaluations using various bitrate signal patterns and network topologies show that the network proposal can almost match the performance of conventional flexible grid networks, while greatly mitigating the hardware requirements: it allows the use of the tunable filters for the fixed grid systems.
NASA Astrophysics Data System (ADS)
Ruiz, Franklin J.
This dissertation presents the results of using different inclusion and granular effective medium models and poroelasticity to predict the elastic properties of rocks with complex microstructures. Effective medium models account for the microstructure and texture of rocks, and can be used to predict the type of rock and microstructure from seismic velocities and densities. We introduce the elastic equivalency approach, using the differential effective medium model, to predict the effective elastic moduli of rocks and attenuation. We introduce the porous grain concept and develop rock physics models for rocks with microporosity. We exploit the porous grain concept to describe a variety of arrangements of uncemented and cemented grains with different degrees of hydraulic connectivity in the pore space. We first investigate the accuracy of the differential effective medium and self-consistent estimations of elastic properties of complex rock matrix using composites as analogs. We test whether the differential effective-medium (DEM) and self-consistent (SC) models can accurately estimate the elastic moduli of a complex rock matrix and compare the results with the average of upper and lower Hashin-Shtrikman bounds. We find that when the material microstructure is consistent with DEM, this model is more accurate than both SC and the bound-average method for a variety of inclusion aspect ratios, concentrations, and modulus contrasts. Based on these results, we next pose a question: can a theoretical inclusion model, specifically, the differential effective-medium model (DEM), be used to match experimental velocity data in rocks that are not necessarily made of inclusions (such as elastics)? We first approach this question by using empirical velocity-porosity equations as proxies for data. By finding a DEM inclusion aspect ratio (AR) to match these equations, we find that the required range of AR is remarkably narrow. Moreover, a constant AR of about 0.13 can be used to
Models for elastic shells with incompatible strains
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
NASA Astrophysics Data System (ADS)
Hamacher, Kay
2011-07-01
Biomolecular simulations have become a major tool in understanding biomolecules and their complexes. However, one can typically only investigate a few mutants or scenarios due to the severe computational demands of such simulations, leading to a great interest in method development to overcome this restriction. One way to achieve this is to reduce the complexity of the systems by an approximation of the forces acting upon the constituents of the molecule. The harmonic approximation used in elastic network models simplifies the physical complexity to the most reduced dynamics of these molecular systems. The reduced polymer modeled this way is typically comprised of mass points representing coarse-grained versions of, e.g., amino acids. In this work, we show how the computation of free energy contributions of contacts between two residues within the molecule can be reduced to a simple lookup operation in a precomputable matrix. Being able to compute such contributions is of great importance: protein design or molecular evolution changes introduce perturbations to these pair interactions, so we need to understand their impact. Perturbation to the interactions occurs 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 apply the new algorithm to (1) the bovine trypsin inhibitor, a well-known enzyme in biomedicine, and show the connection to folding properties and the hydrophobic collapse hypothesis and (2) the serine proteinase inhibitor CI-2 and show the correlation to Φ values to characterize folding importance. Furthermore, we discuss the computational complexity and show empirical results for the average case, sampled over a library of 77 structurally diverse proteins. We found a relative speedup of up to 10 000-fold for large proteins with respect to
All-optical OXC transition strategy from WDM optical network to elastic optical network.
Chen, Xin; Li, Juhao; Guo, Bingli; Zhu, Paikun; Tang, Ruizhi; Chen, Zhangyuan; He, Yongqi
2016-02-22
Elastic optical network (EON) has been proposed recently as a spectrum-efficient optical layer to adapt to rapidly-increasing traffic demands instead of current deployed wavelength-division-multiplexing (WDM) optical network. In contrast with conventional WDM optical cross-connect (OXCs) based on wavelength selective switches (WSSs), the EON OXCs are based on spectrum selective switches (SSSs) which are much more expensive than WSSs, especially for large-scale switching architectures. So the transition cost from WDM OXCs to EON OXCs is a major obstacle to realizing EON. In this paper, we propose and experimentally demonstrate a transition OXC (TOXC) structure based on 2-stage cascading switching architectures, which make full use of available WSSs in current deployed WDM OXCs to reduce number and port count of required SSSs. Moreover, we propose a contention-aware spectrum allocation (CASA) scheme for EON built with the proposed TOXCs. We show by simulation that the TOXCs reduce the network capital expenditure transiting from WDM optical network to EON about 50%, with a minor traffic blocking performance degradation and about 10% accommodated traffic number detriment compared with all-SSS EON OXC architectures.
Zhang, Jie; Yang, Hui; Zhao, Yongli; Ji, Yuefeng; Li, Hui; Lin, Yi; Li, Gang; Han, Jianrui; Lee, Young; Ma, Teng
2013-11-04
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.
The Modified Semidirect Onlay Technique With Articulated Elastic Model.
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.
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.
Body forces and pressures in elastic models of the myocardium.
Pierce, W H
1981-01-01
Tension strands are introduced to represent active myocardial fibers. They create one body force proportional to the divergence of the tension-direction vector, and a second equal to the tension divided by the radius of curvature. Explicit solutions to isotropic linearly elastic tensor equations with these body forces are found for the radially-symmetric, linearly-isotropic, elastic spherical heart with arbitrary radial body force. They confirm experiments showing supraluminal intramural pressures. Such pressures may affect coronary perfusion. A tension strand model which is a reasonable compromise between actual myofibrillar geometry and analytical simplicity is the iso-oblique, terminating, nonintersecting model. The body force from that or any other axially symmetric body force can be the forcing term for equations in which the heart is modeled as a thin, ellipsoidal, elastic membrane. PMID:7213931
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.
A mesoscopic network model for permanent set in crosslinked elastomers
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.
Entanglement effects in model polymer networks
NASA Astrophysics Data System (ADS)
Everaers, R.; Kremer, K.
The influence of topological constraints on the local dynamics in cross-linked polymer melts and their contribution to the elastic properties of rubber elastic systems are a long standing problem in statistical mechanics. Polymer networks with diamond lattice connectivity (Everaers and Kremer 1995, Everaers and Kremer 1996a) are idealized model systems which isolate the effect of topology conservation from other sources of quenched disorder. We study their behavior in molecular dynamics simulations under elongational strain. In our analysis we compare the measured, purely entropic shear moduli G to the predictions of statistical mechanical models of rubber elasticity, making extensive use of the microscopic structural and topological information available in computer simulations. We find (Everaers and Kremer 1995) that the classical models of rubber elasticity underestimate the true change in entropy in a deformed network significantly, because they neglect the tension along the contour of the strands which cannot relax due to entanglements (Everaers and Kremer (in preparation)). This contribution and the fluctuations in strained systems seem to be well described by the constrained mode model (Everaers 1998) which allows to treat the crossover from classical rubber elasticity to the tube model for polymer networks with increasing strand length within one transparant formalism. While this is important for the description of the effects we try to do a first quantitative step towards their explanation by topological considerations. We show (Everaers and Kremer 1996a) that for the comparatively short strand lengths of our diamond networks the topology contribution to the shear modulus is proportional to the density of entangled mesh pairs with non-zero Gauss linking number. Moreover, the prefactor can be estimated consistently within a rather simple model developed by Vologodskii et al. and by Graessley and Pearson, which is based on the definition of an entropic
Random networks of fibres display maximal heterogeneity in the distribution of elastic energy.
Aström, J A; Timonen, J; Myllys, M; Fellman, J; LeBell, J
2007-01-01
Above a small length scale, the distribution of local elastic energies in a material under an external load is typically Gaussian, and the dependence of the average elastic energy on strain defines the stiffness of the material. Some particular materials, such as granular packings, suspensions at the jamming transition, crumpled sheets and dense cellular aggregates, display under compression an exponential distribution of elastic energies, but also in this case the elastic properties are well defined. We demonstrate here that networks of fibres, which form uncorrelated non-fractal structures, have under external load a scale invariant distribution of elastic energy (epsilon) at the fibre-fibre contacts proportional to 1/epsilon. This distribution is much broader than any other distribution observed before for elastic energies in a material. We show that for small compressions it holds over 10 orders of magnitude in epsilon. In such a material a few 'hot spots' carry most of the elastic load. Consequently, these materials are highly susceptible to local irreversible deformations, and are thereby extremely efficient for damping vibrations.
Random networks of fibres display maximal heterogeneity in the distribution of elastic energy
NASA Astrophysics Data System (ADS)
Åström, J. A.; Timonen, J.; Myllys, M.; Fellman, J.; Lebell, J.
2007-01-01
Above a small length scale, the distribution of local elastic energies in a material under an external load is typically Gaussian, and the dependence of the average elastic energy on strain defines the stiffness of the material. Some particular materials, such as granular packings, suspensions at the jamming transition, crumpled sheets and dense cellular aggregates, display under compression an exponential distribution of elastic energies, but also in this case the elastic properties are well defined. We demonstrate here that networks of fibres, which form uncorrelated non-fractal structures, have under external load a scale invariant distribution of elastic energy (ɛ) at the fibre-fibre contacts proportional to 1/ɛ. This distribution is much broader than any other distribution observed before for elastic energies in a material. We show that for small compressions it holds over 10 orders of magnitude in ɛ. In such a material a few 'hot spots' carry most of the elastic load. Consequently, these materials are highly susceptible to local irreversible deformations, and are thereby extremely efficient for damping vibrations.
An elastic compound tube model for a single osteon.
Braidotti, P; Branca, F P; Sciubba, E; Stagni, L
1995-04-01
A model is developed whereby the secondary osteon--the dominant microstructural component of the cortical bone tissue--is considered as an n-layered cylinder with internal stresses in linear isotropic elasticity. An exact solution is obtained for a loading condition represented by a tensile-compressive force. The lengthening, the side deformation, and the strain energy of the system are explicitly calculated. The behavior of the main elastic quantities is illustrated by graphs. In particular, the important role played by the parity of the number of lamellae is revealed.
Elastic/viscoplastic constitutive model for fiber reinforced thermoplastic composites
NASA Technical Reports Server (NTRS)
Gates, T. S.; Sun, C. T.
1991-01-01
A constitutive model to describe the elastic/viscoplastic behavior of fiber-reinforced thermoplastic composites under plane stress conditions is presented. Formulations are given for quasi-static plasticity and time-dependent viscoplasticity. Experimental procedures required to generate the necessary material constants are explained, and the experimental data is compared to the predicted behavior.
Elastic model of a dislocation center for martensite nucleation
Vereshchagin, V.P.; Kashchenko, M.P.
1995-01-01
The possibility of spontaneous nucleation of a crystal of new phase when the original structure is metastable is usually connected with the catalyzing effect of defects playing the role of nucleation centers. In the case of the {gamma}{r_arrow}{alpha} martensite transformation in iron alloys, even individual dislocations can act as such defects, based on analysis of long-range elastic fields of isolated linear dislocations in a linearly elastic anisotropic continuum, the authors established the existence of a correlation between the geometric characteristics of the elastically deformed state in the vicinity of 60-degree and 30-degree dislocations and the structure and morphological characteristics of {alpha}-martensite observed in massive iron alloy samples. These results suggest that the dislocation affects the pathway of the martensite reaction and allows the authors to say that the specific characteristics of heterogeneous nucleation of new phase for the martensite mechanism of the {gamma}{r_arrow}{alpha} transformation involves singling out a single structural rearrangement variant which is suitable from the standpoint of adapation of the transforming lattice to the characteristic features of the elastically deformed state created by the dislocation. The possibilities for such adaption are limited by the crystallography of the transformation and the reactions of the surrounding austenite occurring when regular connections exist with the morphological characteristics of the martensite crystal, and are not necessarily compatible with the individual features of the elastic field of each dislocation. Considering this, the authors can introduce the concept of a dislocation center for nucleation of a martensite crystal about the region of the dislocation where conditions are realized which are favorable for the formation of a nucleus of martensite crystal of a certain shape and orientation, and they can develop an elastic model corresponding to this concept.
An elastic-viscous-plastic model for sea ice dynamics
Hunke, E.C.; Dukowicz, J.K.
1996-10-01
The standard model for sea ice dynamics treats the ice pack as a viscous-plastic material that flows plastically under typical stress conditions but behaves as a linear viscous fluid where strain rates are small and the ice becomes nearly rigid. Because of large viscosities in these regions, implicit numerical methods are necessary for timesteps larger than a few seconds. Current solution methods for these equations use iterative relaxation methods, which are time consuming, scale poorly with mesh resolution, and are not well adapted to parallel computation. To remedy this, we have developed and tested two separate methods. First, by demonstrating that the viscous-plastic rheology can be represented by a symmetric, negative definite matrix operator, we have implemented the faster and better behaved preconditioned conjugate gradient method. Second, realizing that only the response of the ice on time scales associated with wind forcing need be accurately resolved, we have modified the model to reduce to the viscous-plastic model at these time scales; at shorter time scales the adjustment process takes place by a numerically efficient elastic wave mechanism. This modification leads to a fully explicit numerical scheme which further improves the computational efficiency and is an advantage for implementations on parallel machines. Furthermore, we observe that the standard viscous-plastic model has poor dynamic response to forcing on a daily time scale, given the standard time step (1 day) used by the ice modeling community. In contrast, the explicit discretization of the elastic wave mechanism allows the elastic-viscous-plastic model to capture the ice response to variations in the imposed stress more accurately. Thus, the elastic-viscous-plastic model provides more accurate results for shorter time scales associated with physical forcing, reproduces viscous-plastic model behavior on longer time scales, and is computationally more efficient. 49 refs., 13 figs., 6 tabs.
Modeling the Citation Network by Network Cosmology
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
Modeling the citation network by network cosmology.
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.
Deconstruction and elastic {pi}{pi} scattering in Higgsless models
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.
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.
Orthotropic elastic shell model for buckling of microtubules.
Wang, C Y; Ru, C Q; Mioduchowski, A
2006-11-01
In view of the fact that microtubules exhibit strong anisotropic elastic properties, an orthotropic elastic shell model for microtubules is developed to study buckling behavior of microtubules. The predicted critical pressure is found to agree well with recent unexplained experimental data on pressure-induced buckling of microtubules [Needleman, Phys. Rev. Lett. 93, 198104 (2004); Biophys. J. 89, 3410 (2005)] which are lower than that predicted by the isotropic shell model by four orders of magnitude. General buckling behavior of microtubules under axial compression or radial pressure is studied. The results show that the isotropic shell model greatly overestimates the bucking loads of microtubules, except columnlike axially compressed buckling of long microtubules (of length-to-diameter ratio larger than, say, 150). In particular, the present results also offer a plausible explanation for the length dependency of flexibility of microtubules reported in the literature.
Mechanistic Constitutive Models for Rubber Elasticity and Viscoelasticity
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.
Split spectrum: a multi-channel approach to elastic optical networking.
Xia, Ming; Proietti, R; Dahlfort, Stefan; Yoo, S J B
2012-12-31
This paper introduces Split Spectrum, which enhances elastic optical networking by splitting a bulk traffic demand into multiple channels, when a single-channel transmission is prohibited by distance or spectrum availability. We performed transmission simulations to determine the maximum reach as a function of modulation format (dual polarization BPSK, QPSK, 16QAM), baud-rate (from 5 to 28 GBd), and number of ROADMs, for a Nyquist WDM super-channel with subcarrier spacing equal to 1.2 × baud-rate. Performance evaluation on two representative topologies shows that, compared to the previously proposed elastic optical networking, Split Spectrum doubles the zero-blocking load and achieves 100% higher network spectral efficiency at zero-blocking loads as a result of extended transmission distance and efficient utilization of spectrum fragments.
Phenomenological models of elastic nucleon scattering and predictions for LHC
NASA Astrophysics Data System (ADS)
Kašpar, Jan; Kundrát, Vojtěch; Lokajíček, Miloš; Procházka, Jiří
2011-02-01
The hitherto analyses of elastic collisions of charged nucleons involving common influence of Coulomb and hadronic scattering have been based practically on West and Yennie formula. However, this approach has been shown recently to be inadequate from experimental as well as theoretical points of view. The eikonal model enabling to determine physical characteristics in impact parameter space seems to be more pertinent. The contemporary phenomenological models admit, of course, different distributions of collision processes in the impact parameter space and cannot give any definite answer. Nevertheless, some predictions for the planned LHC energy that have been given on their basis may be useful, as well as the possibility of determining the luminosity from elastic scattering.
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.
Chaudhury, Manoj K; Finlay, John A; Chung, Jun Young; Callow, Maureen E; Callow, James A
2005-01-01
The effect of modulus and film thickness on the release of adhered spores and sporelings (young plants) of the green fouling alga Ulva (syn. Enteromorpha) was investigated. PDMS elastomers of constant thickness (100 microm) but different elastic moduli were prepared by varying cross-link density with functional silicone oligomers with degrees of polymerization ranging from 18-830. This provided a 50-fold range of modulus values between 0.2 and 9.4 MPa. Three PDMS coatings of different thicknesses were tested at constant elastic modulus (0.8 MPa). The data revealed no significant increase in percentage spore removal except at the lowest modulus of 0.2 MPa although sporelings released more readily at all but the highest modulus. The influence of coating thickness was also greater for the release of sporelings compared to spores. The release data are discussed in the light of fracture mechanics models that have been applied to hard fouling. New concepts appertaining to the release of soft fouling organisms are proposed, which take into account the deformation in the adhesive base of the adherand and deformation of the PDMS film.
Asymptotic modeling of assemblies of thin linearly elastic plates
NASA Astrophysics Data System (ADS)
Licht, Christian
2007-12-01
We derive various models of assemblies of thin linearly elastic plates by abutting or superposition through an asymptotic analysis taking into account small parameters associated with the size and the stiffness of the adhesive. They correspond to the linkage of two Kirchhoff-Love plates by a mechanical constraint which strongly depends on the magnitudes of the previous parameters. To cite this article: C. Licht, C. R. Mecanique 335 (2007).
The role of elastic compressibility in dynamic subduction models
NASA Astrophysics Data System (ADS)
Austmann, W.; Govers, R. M.
2013-12-01
Recent advances in geodynamic numerical models show a trend towards more realistic rheologies. The Earth is no longer modeled as a purely viscous fluid, but the effects of, for example, elasticity and plasticity are also included. However, by making such improvements, it is essential to include these more complex rheologies in a consistent way. Specifically, compressibility needs also to be included, an effect that is commonly neglected in numerical models. Recently, we showed that the effect of elastic compressibility is significant. This was done for a gravity driven cylinder in a homogeneous Maxwell fluid bounded by closed boundaries. For a fluid with a realistic compressibility (Poisson ratio equals 0.3), the settling velocity showed a discrepancy with the semi-analytical steady state incompressible solution of approximately 40%. The motion of the fluid was no longer restricted by a small region around the cylinder, but the motion of the cylinder compressed also the fluid near the bottom boundary. This compression decreased the resistance on the cylinder and resulted in a larger settling velocity. Here, we examine the influence of elastic compressibility in an oceanic subduction setting. The slab is driven by slab pull and a far field prescribed plate motion. Preliminary results indicate that elastic compressibility has a significant effect on the fluid motion. Differences with respect to nearly incompressible solution are most significant near material boundaries. In line with our earlier findings, the flow is increased in regions of confined flow, such as the mantle wedge or the subduction channel. As a consequence, an increasing compressibility results in a larger slab velocity. We seek to identify surface observables, such as topography and plate motion, that allow us to distinguish the compressible and incompressible behavior.
The role of elastic compressibility in dynamic subduction models
NASA Astrophysics Data System (ADS)
Austmann, Walter; Govers, Rob; Burov, Evgenii
2014-05-01
Recent advances in geodynamic numerical models show a trend towards more realistic rheologies. The Earth is no longer modeled as a purely viscous fluid, but the effects of, for example, elasticity and plasticity are also included. However, by making such improvements, it is essential to include these more complex rheologies in a consistent way. Specifically, compressibility needs also to be included, an effect that is commonly neglected in numerical models. Recently, we showed that the effect of elastic compressibility is significant. This was done for a gravity driven cylinder in a homogeneous Maxwell fluid bounded by closed boundaries. For a fluid with a realistic compressibility (Poisson ratio equals 0.3), the settling velocity showed a discrepancy with the semi-analytical steady state incompressible solution of approximately 40%. The motion of the fluid was no longer restricted by a small region around the cylinder, but the motion of the cylinder compressed also the fluid near the bottom boundary. This compression decreased the resistance on the cylinder and resulted in a larger settling velocity. Here, we examine the influence of elastic compressibility in an oceanic subduction setting. The slab is driven by slab pull and a far field prescribed plate motion. Preliminary results indicate that elastic compressibility has a significant effect on the fluid motion. Differences with respect to nearly incompressible solution are most significant near material boundaries. In line with our earlier findings, the flow is increased in regions of confined flow, such as the mantle wedge or the subduction channel. As a consequence, an increasing compressibility results in a larger slab velocity. We seek to identify surface observables, such as topography and plate motion, that allow us to distinguish the compressible and incompressible behavior.
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.
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.
Experimental flow studies in an elastic Y-model.
Mijovic, Budimir; Liepsch, Dieter
2003-01-01
To determine the causes and history of atherosclerosis it is necessary to understand the hemodynamic parameters of blood circulation. Hemodynamic parameters play an important role in the formation of atherosclerotic plaques, especially near bends and bifurcations where the flow separates from the wall. Here the flow is laminar and non-axial with eddies, secondary flow, flow separation and stagnation points. Stenoses are found predominantly in flow separation areas. Therefore, it is important to separately study the following flow parameters: steady and pulsatile flow, wall elasticity and non-Newtonian flow behavior of blood. A simplified silicon elastic y-model simulating the human carotid artery was used for the analysis of these parameters. This model can be used for numerical studies as well. Flow was visualized at steady flow using dyes and at pulsatile flow with a photoelastic apparatus and a birefringent solution. The local axial velocity at steady and pulsatile flow was determined with a one-component Laser-Doppler-Anemometer (LDA). Pulsatile flow was generated by a piston membrane pump. A glycerin-water solution was used to simulate the Newtonian flow behavior of blood. A DMSO-Separan water solution was used to simulate the non-Newtonian flow behavior. Pulsatile flow creates higher and lower shear rates so called oscillating shear rate compare to steady flow depending on the velocity amplitude. The non-Newtonian fluid showed a markedly different flow behavior than the Newtonian fluid especially in areas of flow separation. Shear gradients were calculated from these velocity measurements using a bicubic spline interpolation. Shear stresses were calculated from these velocity shear gradients and the viscosity of the non-Newtonian fluid at these shear gradients. At special areas, high shear stresses > 10 Pa were found. The elasticity of the model wall also influences the flow behavior. The measurements showed that the characteristics of pulsatile flow and the
Elastic modeling and steep dips: unraveling the reflected wavefield
Hoelting, C. J.; Gherasim, M.; House, L. S.; Marfurt, K. J.
2003-01-01
As part of a larger elastic numerical modeling project, we have been investigating how energy reflected from steeply dipping interfaces is recorded using typical multicomponent acquisition geometries. Specifically, we have been interpreting how rcflection events from the flanks of salt dome structures are distributed on 3C and 4C phones for vertical seismic profiles (VSPs) and ocean bottom seismic (OBS) or land surface surveys. The ultimate goal of this investigation is to improve the structural imaging of steeply dipping interfaces and eventually to evaluate the usc of the recorded elastic wavefield for fluid description near these interfaces. In the current work, we focus on a common assumption used when processing converted wave reflection seismic data that most PP energy is recorded on the vertical geophone and/or the hydrophone and that most PS energy is recorded on the horizontal geophones. This is a useful assumption when it is valid, because it eliminates the need for separation of the recorded wavefield into P and S wavetypes. Using two elastic models and different acquisition geometries, we examine the validity of this assumption in the presence of steeply dipping interfaces and discuss the implications for converted-wave and vector imaging of salt flanks.
Surface tension and the dodecahedron model for lung elasticity.
Kimmel, E; Budiansky, B
1990-05-01
Macroscopic elastic moduli governing the incremental deformations of lung parenchyma are calculated on the basis of a model for an individual lung element in the shape of a regular dodecahedron. Elastic stiffness within the element is provided by pin-jointed tension members along the edges of the dodecahedron, surface tension is incorporated into its pentagonal faces, and the influence of transpulmonary pressure is simulated by an externally applied hydrostatic tension. The analysis is based on a variational statement of nonlinear structural mechanics, and the results show how the moduli depend on the effective inflation pressure, the constitutive behavior of the idealized truss members, and the surface-area dependent surface tension. The theory is discussed in the light of available experimental information. A more general analysis is needed to account for the effects of structural as well as surface-tension hysteresis.
Dynamic on-demand defragmentation in flexible bandwidth elastic optical networks.
Yin, Yawei; Wen, Ke; Geisler, David J; Liu, Ruiting; Yoo, S J B
2012-01-16
While flexible bandwidth elastic optical networking is a promising direction for future networks, the spectral fragmentation problem in such a network inevitably raises the blocking probability and significantly degrades network performance. This paper addresses the spectral defragmentation problem using an auxiliary graph based approach, which transforms the problem into a matter of finding the maximum independent set (MIS) in the constructed auxiliary graph. The enabling technologies and defragmentation-capable node architectures, together with heuristic defragmentation algorithms are proposed and evaluated. Simulation results show that the proposed min-cost defragmentation algorithms can significantly reduce the blocking probability of incoming requests in a spectrally fragmented flexible bandwidth optical network, while substantially minimizing the number of disrupted connections.
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
Experimental demonstration of spectrum-sliced elastic optical path network (SLICE).
Kozicki, Bartłomiej; Takara, Hidehiko; Tsukishima, Yukio; Yoshimatsu, Toshihide; Yonenaga, Kazushige; Jinno, Masahiko
2010-10-11
We describe experimental demonstration of spectrum-sliced elastic optical path network (SLICE) architecture. We employ optical orthogonal frequency-division multiplexing (OFDM) modulation format and bandwidth-variable optical cross-connects (OXC) to generate, transmit and receive optical paths with bandwidths of up to 1 Tb/s. We experimentally demonstrate elastic optical path setup and spectrally-efficient transmission of multiple channels with bit rates ranging from 40 to 140 Gb/s between six nodes of a mesh network. We show dynamic bandwidth scalability for optical paths with bit rates of 40 to 440 Gb/s. Moreover, we demonstrate multihop transmission of a 1 Tb/s optical path over 400 km of standard single-mode fiber (SMF). Finally, we investigate the filtering properties and the required guard band width for spectrally-efficient allocation of optical paths in SLICE.
Elastic lattice modelling of seismic waves including a free surface
NASA Astrophysics Data System (ADS)
O`Brien, Gareth S.
2014-06-01
Elastic lattice methods (ELMs) have been shown to accurately model seismic wave propagation in a heterogeneous medium. These methods represent an elastic solid as a series of interconnected springs arranged on a lattice and recover a continuum wave equation in the long wavelength limit. However, in the case of a regular lattice, the recovery of the continuum equation depends on the symmetry of the lattice. By removing particles above a free surface this symmetry is broken. Therefore, this free surface implementation leads to errors when compared with a traction free boundary condition. The error between a traction free boundary condition and the ELMs grows as the Poisson's ratio deviates from 0.25. By modifying the interaction constants with a scalar, the error can be reduced while keeping the flexibility of the nearest neighbour interaction rule. We present results of simulations where modified spring constants reduce the misfit with a traction free boundary solution and hence increase the accuracy of the elastic lattice method solution on the free surface.
Phase-field elasticity model based on mechanical jump conditions
NASA Astrophysics Data System (ADS)
Schneider, Daniel; Tschukin, Oleg; Choudhury, Abhik; Selzer, Michael; Böhlke, Thomas; Nestler, Britta
2015-05-01
Computational models based on the phase-field method typically operate on a mesoscopic length scale and resolve structural changes of the material and furthermore provide valuable information about microstructure and mechanical property relations. An accurate calculation of the stresses and mechanical energy at the transition region is therefore indispensable. We derive a quantitative phase-field elasticity model based on force balance and Hadamard jump conditions at the interface. Comparing the simulated stress profiles calculated with Voigt/Taylor (Annalen der Physik 274(12):573, 1889), Reuss/Sachs (Z Angew Math Mech 9:49, 1929) and the proposed model with the theoretically predicted stress fields in a plate with a round inclusion under hydrostatic tension, we show the quantitative characteristics of the model. In order to validate the elastic contribution to the driving force for phase transition, we demonstrate the absence of excess energy, calculated by Durga et al. (Model Simul Mater Sci Eng 21(5):055018, 2013), in a one-dimensional equilibrium condition of serial and parallel material chains. To validate the driving force for systems with curved transition regions, we relate simulations to the Gibbs-Thompson equilibrium condition (Johnson and Alexander, J Appl Phys 59(8):2735, 1986).
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.
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
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.
A fast method for a generalized nonlocal elastic model
NASA Astrophysics Data System (ADS)
Du, Ning; Wang, Hong; Wang, Che
2015-09-01
We develop a numerical method for a generalized nonlocal elastic model, which is expressed as a composition of a Riesz potential operator with a fractional differential operator, by composing a collocation method with a finite difference discretization. By carefully exploring the structure of the coefficient matrix of the numerical method, we develop a preconditioned fast Krylov subspace method, which reduces the computations to (Nlog N) per iteration and the memory to O (N). The use of the preconditioner significantly reduces the number of iterations, and the preconditioner can be inverted in O (Nlog N) computations. Numerical results show the utility of the method.
Accurate numerical solutions for elastic-plastic models. [LMFBR
Schreyer, H. L.; Kulak, R. F.; Kramer, J. M.
1980-03-01
The accuracy of two integration algorithms is studied for the common engineering condition of a von Mises, isotropic hardening model under plane stress. Errors in stress predictions for given total strain increments are expressed with contour plots of two parameters: an angle in the pi plane and the difference between the exact and computed yield-surface radii. The two methods are the tangent-predictor/radial-return approach and the elastic-predictor/radial-corrector algorithm originally developed by Mendelson. The accuracy of a combined tangent-predictor/radial-corrector algorithm is also investigated.
A 3D Orthotropic Elastic Continuum Damage Material Model
English, Shawn Allen; Brown, Arthur A.
2013-08-01
A three dimensional orthotropic elastic constitutive model with continuum damage is implemented for polymer matrix composite lamina. Damage evolves based on a quadratic homogeneous function of thermodynamic forces in the orthotropic planes. A small strain formulation is used to assess damage. In order to account for large deformations, a Kirchhoff material formulation is implemented and coded for numerical simulation in Sandia’s Sierra Finite Element code suite. The theoretical formulation is described in detail. An example of material parameter determination is given and an example is presented.
Multi-scale modelling of elastic moduli of trabecular bone
Hamed, Elham; Jasiuk, Iwona; Yoo, Andrew; Lee, YikHan; Liszka, Tadeusz
2012-01-01
We model trabecular bone as a nanocomposite material with hierarchical structure and predict its elastic properties at different structural scales. The analysis involves a bottom-up multi-scale approach, starting with nanoscale (mineralized collagen fibril) and moving up the scales to sub-microscale (single lamella), microscale (single trabecula) and mesoscale (trabecular bone) levels. Continuum micromechanics methods, composite materials laminate theory and finite-element methods are used in the analysis. Good agreement is found between theoretical and experimental results. PMID:22279160
A nonlocal elastic anisotropic shell model for microtubule buckling behaviors in cytoplasm
NASA Astrophysics Data System (ADS)
Gao, Yuanwen; An, Le
2010-07-01
The buckling behaviors of microtubules (MTs) in a living cell have been studied based on the nonlocal anisotropic shell theory and Stokes flow theory. The analytical expressions for the buckling load and the growth rate of the buckling are obtained and discussed. In addition, the pressure on MTs, resulting from cytosol motion, is derived on the basis of the Stokes flow theory. The influences of filament network elasticity and the shear modulus of MTs, especially the cytosol viscosity and MT small scale effects on MT buckling behaviors, are investigated. The analytical results show that the MT buckling growth rate increases with the MT small scale parameter, while decreases as the filament network elastic modulus, the MT shear modulus and cytoplasm viscosity increase. Although the cytosol viscosity has a significant influence on the value of the growth rate, it shows little effects on the range of the axial wave number of buckling as well as the critical axial wave number that corresponds to the maximal growth rate. Finally, the MT buckling growth rates have been calculated using the beam model, the isotropic shell model, and the anisotropic shell model. The results indicate that using the anisotropy shell theory to model the buckling behavior of MTs is necessary.
An Elastic Model of Blebbing in Nuclear Lamin Meshworks
NASA Astrophysics Data System (ADS)
Funkhouser, Chloe; Sknepnek, Rastko; Shimi, Takeshi; Goldman, Anne; Goldman, Robert; Olvera de La Cruz, Monica
2013-03-01
A two-component continuum elastic model is introduced to analyze a nuclear lamin meshwork, a structural element of the lamina of the nuclear envelope. The main component of the lamina is a meshwork of lamin protein filaments providing mechanical support to the nucleus and also playing a role in gene expression. Abnormalities in nuclear shape are associated with a variety of pathologies, including some forms of cancer and Hutchinson-Gilford progeria syndrome, and are often characterized by protruding structures termed nuclear blebs. Nuclear blebs are rich in A-type lamins and may be related to pathological gene expression. We apply the two-dimensional elastic shell model to determine which characteristics of the meshwork could be responsible for blebbing, including heterogeneities in the meshwork thickness and mesh size. We find that if one component of the lamin meshwork, rich in A-type lamins, has a tendency to form a larger mesh size than that rich in B-type lamins, this is sufficient to cause segregation of the lamin components and also to form blebs rich in A-type lamins. The model produces structures with comparable morphologies and mesh size distributions as the lamin meshworks of real, pathological nuclei. Funded by US DoE Award DEFG02-08ER46539 and by the DDR&E and AFOSR under Award FA9550-10-1-0167; simulations performed on NU Quest cluster
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.
Elastic-wave velocity in marine sediments with gas hydrates: Effective medium modeling
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.
Modeling, design, and optimization of Mindwalker series elastic joint.
Wang, Shiqian; Meijneke, Cor; van der Kooij, Herman
2013-06-01
Weight and power autonomy are limiting the daily use of wearable exoskeleton. Lightweight, efficient and powerful actuation system are not easy to achieve. Choosing the right combinations of existing technologies, such as battery, gear and motor is not a trivial task. In this paper, we propose an optimization framework by setting up a power-based quasi-static model of the exoskeleton joint drivetrain. The goal is to find the most efficient and lightweight combinations. This framework can be generalized for other similar applications by extending or accommodating the model to their own needs. We also present the Mindwalker exoskeleton joint, for which a novel series elastic actuator, consisting of a ballscrew-driven linear actuator and a double spiral spring, was developed and tested. This linear actuator is capable of outputting 960 W power and the exoskeleton joint can output 100 Nm peak torque continuously. The double spiral spring can sense torque between 0.08Nm and 100 Nm and it exhibits linearity of 99.99%, with no backlash or hysteresis. The series elastic joint can track a chirp torque profile with amplitude of 100 Nm over 6 Hz (large torque bandwidth) and for small torque (2 Nm peak-to-peak), it has a bandwidth over 38 Hz. The integrated exoskeleton joint, including the ballscrew-driven linear actuator, the series spring, electronics and the metal housing which hosts these components, weighs 2.9 kg.
Elastic tracking versus neural network tracking for very high multiplicity problems
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.
Effective-medium theory of elastic waves in random networks of rods.
Katz, J I; Hoffman, J J; Conradi, M S; Miller, J G
2012-06-01
We formulate an effective medium (mean field) theory of a material consisting of randomly distributed nodes connected by straight slender rods, hinged at the nodes. Defining wavelength-dependent effective elastic moduli, we calculate both the static moduli and the dispersion relations of ultrasonic longitudinal and transverse elastic waves. At finite wave vector k the waves are dispersive, with phase and group velocities decreasing with increasing wave vector. These results are directly applicable to networks with empty pore space. They also describe the solid matrix in two-component (Biot) theories of fluid-filled porous media. We suggest the possibility of low density materials with higher ratios of stiffness and strength to density than those of foams, aerogels, or trabecular bone.
Crosslinked actin networks show liquid crystal elastomer behaviour, including soft-mode elasticity
NASA Astrophysics Data System (ADS)
Dalhaimer, Paul; Discher, Dennis E.; Lubensky, Tom C.
2007-05-01
Actin filament networks with protein crosslinks of distinct length and flexibility resemble liquid crystal elastomers. We simulate actin filament systems with flexible crosslinkers of varying length and connectivity to understand general phase behaviour and elasticity. Simulated networks with very short filaments and long crosslinkers resemble the cytoskeleton of the red blood cell and remain isotropic in compression and shear, seeming well-suited to blood flow. In contrast, networks with longer filaments as found in many cell types show three regimes of nematic phase behaviour dependent on crosslinker length: (1) `loose' networks are isotropic at zero stress but align under compression or shear; (2) `semi-loose' networks are nematic at low stress but become isotropic under dilation and (3) `tight' networks possess a locked-in nematic order as represented by the cytoskeleton of the outer hair cell in the ear, for which anisotropic compliance directs sound propagation. Furthermore, for a subset of loose networks with `periodic' connections among filaments, extremely soft stress-strain behaviour is found, as predicted for liquid crystal elastomers.
Dynamics of Elastic Beams with Embedded Fluid-Filled Parallel-Channel Networks
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. PMID:27625914
Hanson, David E
2011-08-07
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.
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.
A Double Scattering Analytical Model For Elastic Recoil Detection Analysis
Barradas, N. P.; Lorenz, K.; Alves, E.; Darakchieva, V.
2011-06-01
We present an analytical model for calculation of double scattering in elastic recoil detection measurements. Only events involving the beam particle and the recoil are considered, i.e. 1) an ion scatters off a target element and then produces a recoil, and 2) an ion produces a recoil which then scatters off a target element. Events involving intermediate recoils are not considered, i.e. when the primary ion produces a recoil which then produces a second recoil. If the recoil element is also present in the stopping foil, recoil events in the stopping foil are also calculated. We included the model in the standard code for IBA data analysis NDF, and applied it to the measurement of hydrogen in Si.
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.
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].
Modelling and simulation of substrate elasticity sensing in stem cells.
Zeng, Xiaowei; Li, Shaofan
2011-05-01
Recently, we have developed a multiscale soft matter cell model aiming at improving the understanding of mechanotransduction mechanism of stem cells, which is responsible for information exchange between cells and their extracellular environment. In this paper, we report the preliminary results of our research on multiscale modelling and simulation of soft contact and adhesion of stem cells. The proposed multiscale soft matter cell model may be used to model soft contact and adhesion between cells and their extracellular substrates. To the authors' best knowledge, this may be the first time that a soft matter model has been developed for cell contact and adhesion. Moreover, we have developed and implemented a Lagrange-type meshfree Galerkin formulation and related computational algorithms for the proposed cell model. Comparison study with experimental data has been conducted to validate the parameters of the cell model. By using the soft matter cell model, we have simulated the soft adhesive contact process between cells and extracellular substrates. The simulation shows that the cell can sense substrate elasticity by responding it in different manners from cell spreading to cell contact configuration and molecular conformation changes.
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.
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.
Elastic properties of compressed cryocrystals in a deformed atom model
NASA Astrophysics Data System (ADS)
Gorbenko, Ie. Ie.; Zhikharev, I. V.; Troitskaya, E. P.; Chabanenko, Val. V.; Pilipenko, E. A.
2013-06-01
A model with deformed atom shells was built to investigate the elastic properties of rare-gas Ne and Kr crystals under high pressure. It is shown that the observed deviation from the Cauchy relation δ cannot be adequately reproduced when taking into account only the many-body interaction. The individual pressure dependence of δ is the result of competition of the many-body interaction and the quadrupole interaction associated with the quadrupole-type deformation of electron shells of the atoms during the displacement of the nuclei. Each kind of interaction makes a strongly pressure dependent contribution to δ. In the case of Ne and Kr, contributions of these interactions are compensated to a good precision, providing δ being almost constant against pressure.
Dynamic Visco-elastic Buckling Analysis for Airway Model
NASA Astrophysics Data System (ADS)
Bando, Kiyoshi; Ohba, Kenkichi; Yamanoi, Yuta
In order to clarify the mechanism by which the lung airway narrows during an asthma attack, dynamic buckling analysis of the wall was conducted. The wall was modeled using a visco-elastic thin-walled circular cylinder of the Voigt model for the planestress state. A governing equation for dynamic buckling was derived, and in the equation, the contraction of smooth muscle was replaced by uniform inward transmural pressure. The non-dimensional parameters for the buckling wave number n were nondimensional retardation time τ, non-dimensional increasing velocity of inward transmural pressure β, thickness radius ratio α2, radius length ratio η, density ratio ζ, and Poisson's ratio ν. The validity of the theoretical model was confirmed by comparing the calculated wave number with that obtained from the experiment, in which a silicone rubber tube blended with silicone potting gel was used as the in vitro airway model. In addition, the wave number n increased with β. It was necessary to consider the damping effect of the tube model or the airway wall, and n increased by 1.5 to 2 due to the additional mass effect of surrounding tissues of the basement membrane in the airway wall.
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.
An Elastic Plastic Contact Model with Strain Hardening for the LAMMPS Granular Package
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.
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
Evolution of a fracture network in an elastic medium with internal fluid generation and expulsion
NASA Astrophysics Data System (ADS)
Kobchenko, Maya; Hafver, Andreas; Jettestuen, Espen; Renard, François; Galland, Olivier; Jamtveit, Bjørn; Meakin, Paul; Dysthe, Dag Kristian
2014-11-01
A simple and reproducible analog experiment was used to simulate fracture formation in a low-permeability elastic solid during internal fluid/gas production, with the objective of developing a better understanding of the mechanisms that control the dynamics of fracturing, fracture opening and closing, and fluid transport. In the experiment, nucleation, propagation, and coalescence of fractures within an elastic gelatin matrix, confined in a Hele-Shaw cell, occurred due to CO2 production via fermentation of sugar, and it was monitored by optical means. We first quantified how a fracture network develops, and then how intermittent fluid transport is controlled by the dynamics of opening and closing of fractures. The gas escape dynamics exhibited three characteristic behaviors: (1) Quasiperiodic release of gas with a characteristic frequency that depends on the gas production rate but not on the system size. (2) A 1 /f power spectrum for the fluctuations in the total open fracture area over an intermediate range of frequencies (f ), which we attribute to collective effects caused by interaction between fractures in the drainage network. (3) A 1 /f2 power spectrum was observed at high frequencies, which can be explained by the characteristic behavior of single fractures.
Evolution of a fracture network in an elastic medium with internal fluid generation and expulsion.
Kobchenko, Maya; Hafver, Andreas; Jettestuen, Espen; Renard, François; Galland, Olivier; Jamtveit, Bjørn; Meakin, Paul; Dysthe, Dag Kristian
2014-11-01
A simple and reproducible analog experiment was used to simulate fracture formation in a low-permeability elastic solid during internal fluid/gas production, with the objective of developing a better understanding of the mechanisms that control the dynamics of fracturing, fracture opening and closing, and fluid transport. In the experiment, nucleation, propagation, and coalescence of fractures within an elastic gelatin matrix, confined in a Hele-Shaw cell, occurred due to CO_{2} production via fermentation of sugar, and it was monitored by optical means. We first quantified how a fracture network develops, and then how intermittent fluid transport is controlled by the dynamics of opening and closing of fractures. The gas escape dynamics exhibited three characteristic behaviors: (1) Quasiperiodic release of gas with a characteristic frequency that depends on the gas production rate but not on the system size. (2) A 1/f power spectrum for the fluctuations in the total open fracture area over an intermediate range of frequencies (f), which we attribute to collective effects caused by interaction between fractures in the drainage network. (3) A 1/f^{2} power spectrum was observed at high frequencies, which can be explained by the characteristic behavior of single fractures.
Directed network discovery with dynamic network modelling.
Anzellotti, Stefano; Kliemann, Dorit; Jacoby, Nir; Saxe, Rebecca
2017-02-16
Cognitive tasks recruit multiple brain regions. Understanding how these regions influence each other (the network structure) is an important step to characterize the neural basis of cognitive processes. Often, limited evidence is available to restrict the range of hypotheses a priori, and techniques that sift efficiently through a large number of possible network structures are needed (network discovery). This article introduces a novel modelling technique for network discovery (Dynamic Network Modelling or DNM) that builds on ideas from Granger Causality and Dynamic Causal Modelling introducing three key changes: (1) efficient network discovery is implemented with statistical tests on the consistency of model parameters across participants, (2) the tests take into account the magnitude and sign of each influence, and (3) variance explained in independent data is used as an absolute (rather than relative) measure of the quality of the network model. In this article, we outline the functioning of DNM, we validate DNM in simulated data for which the ground truth is known, and we report an example of its application to the investigation of influences between regions during emotion recognition, revealing top-down influences from brain regions encoding abstract representations of emotions (medial prefrontal cortex and superior temporal sulcus) onto regions engaged in the perceptual analysis of facial expressions (occipital face area and fusiform face area) when participants are asked to switch between reporting the emotional valence and the age of a face.
Constitutive modelling of composite biopolymer networks.
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.
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.
Modeling the elastic energy of alloys: Potential pitfalls of continuum treatments.
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
Modeling the elastic energy of alloys: Potential pitfalls of continuum treatments
NASA Astrophysics Data System (ADS)
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
NASA Astrophysics Data System (ADS)
Zhu, Ruijie; Zhao, Yongli; Yang, Hui; Yu, Xiaosong; Zhang, Jie; Yousefpour, Ashkan; Wang, Nannan; Jue, Jason P.
2016-12-01
In this paper, we propose a multi-path fragmentation-aware routing, modulation and spectrum assignment algorithm (RMSA) for advance reservation (AR) and immediate reservation (IR) requests in elastic optical networks. Immediate reservation requests should be provided with service immediately, while advance reservation requests have specific starting times and holding times. As lightpaths are set up and torn down, fragmentation may occur in both spectrum and time domains. To decrease the two-dimensional fragmentation and to solve the problem of resource scarcity, we propose splitting requests into different parts and transferring these parts along one or more paths utilizing sliceable bandwidth variable transponders. We first introduce a model to solve the problem and propose a two-dimensional fragmentation occurrence measurement in spectrum and time domains. Then we propose a multi-path fragmentation-aware RMSA algorithm (MPFA). Simulation results show that MPFA can achieve better performance than existing algorithms in terms of blocking probability and spectrum utilization.
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…
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.
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.
Double porosity modeling in elastic wave propagation for reservoir characterization
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.
Assessment of distributed arterial network models.
Segers, P; Stergiopulos, N; Verdonck, P; Verhoeven, R
1997-11-01
The aim of this study is to evaluate the relative importance of elastic non-linearities, viscoelasticity and resistance vessel modelling on arterial pressure and flow wave contours computed with distributed arterial network models. The computational results of a non-linear (time-domain) and a linear (frequency-domain) mode were compared using the same geometrical configuration and identical upstream and downstream boundary conditions and mechanical properties. pressures were computed at the ascending aorta, brachial and femoral artery. In spite of the identical problem definition, computational differences were found in input impedance modulus (max. 15-20%), systolic pressure (max. 5%) and pulse pressure (max. 10%). For the brachial artery, the ratio of pulse pressure to aortic pulse pressure was practically identical for both models (3%), whereas for the femoral artery higher values are found for the linear model (+10%). The aortic/brachial pressure transfer function indicates that pressure harmonic amplification is somewhat higher in the linear model for frequencies lower than 6 Hz while the opposite is true for higher frequencies. These computational disparities were attributed to conceptual model differences, such as the treatment of geometric tapering, rather than to elastic or convective non-linearities. Compared to the effect of viscoelasticity, the discrepancy between the linear and non-linear model is of the same importance. At peripheral locations, the correct representation of terminal impedance outweight the computational differences between the linear and non-linear models.
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.
Visualizing tropoelastin in a long-term human elastic fibre cell culture model
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
Model Diagnostics for Bayesian Networks
ERIC Educational Resources Information Center
Sinharay, Sandip
2006-01-01
Bayesian networks are frequently used in educational assessments primarily for learning about students' knowledge and skills. There is a lack of works on assessing fit of Bayesian networks. This article employs the posterior predictive model checking method, a popular Bayesian model checking tool, to assess fit of simple Bayesian networks. A…
Introduction to physical properties and elasticity models: Chapter 20
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.
A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces
Zhou, Y. C.; Holst, Michael; McCammon, J. Andrew
2008-01-01
In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods. PMID:19461946
Zhou, Y C; Holst, Michael; McCammon, J Andrew
2008-04-01
In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods.
Rubber elasticity: Solution of the James-Guth model
NASA Astrophysics Data System (ADS)
Eichinger, B. E.
2015-05-01
The solution of the many-body statistical mechanical theory of elasticity formulated by James and Guth in the 1940s [H. M. James, J. Chem. Phys. 15, 651 (1947)], 10.1063/1.1746624 is presented. The remarkable aspect of the solution is that it gives an elastic free energy that is essentially equivalent to that developed by Flory over a period of several decades.
New, higher-order, elasticity-based micromechanics model
Williams, T. O.
2003-01-01
The formulation for a new homogenization theory is presented. The theory utilizes a higher-order, elasticity-based cell analysis of a periodic array of unit cells. The unit cell is discretized into subregions or subcells. The displacement field within each subcell is approximated by an (truncated) eigenfunction function expansion of up to fifth order. The governing equations are developed by satisfying the pointwise governing equations of geometrically linear continuum mechanics exactly up through the given order of the subcell displacement fields. The specified governing equations are valid for any type of constitutive model used to describe the behavior of the material in a subcell. The fifth order theory is subsequently reduced to a third order theory. The appropriate reduction of the fifth and third order theories to the first order theory (which corresponds to a variant of the original method of cells (MOC) (Aboudi, 1991) theory) is outlined. The 3D ECM theory correctly reduces to the 2D ECM theory microstructures and the exact 1D theory for bilaminated structures. Comparison of the predicted bulk and local responses with published results indicates that the theory accurately predicts both types of responses. Furthermore, it is shown that the higher order fields introduced coupling effects between the local fields that can result in substantial changes in the predicted bulk inelastic response of a composite.
Freeze fracturing of elastic porous media: a mathematical model
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
A Dynamic Space-Time Network Flow Model for City Traffic Congestion.
1983-10-01
both the constant demand and elastic demand models a static set of origin destination demands is assumed to exist. This may be a valid long run...determined for each situation. II. A TWO ATTRIBUTE DINAMIC NETWORK FLOW MODEL In this section a two attribute network flow model which is dynamic, i.e
NASA Astrophysics Data System (ADS)
Liu, Huanlin; Li, Yuan; Peng, Han; Huang, Jun; Kong, Deqian
2017-01-01
Resolving the optical multicast contention in optical switch node is an effective approach to improve the performance of elastic optical multicast switch. An optical node architecture integrating with output shared all-optical Orthogonal Frequency Division Multiplexing (OFDM) network coding technology and shared feedback fiber delay lines (FDLs) buffer is designed. And a time-frequency joint scheduling strategy (TFJSS) is proposed. In TFJSS, the maximal weighted independent set algorithm is used to select the output packets with no overlapping spectrum among the contending multicast packets. The remaining contention packets are compressed by OFDM network coding with all-optical XOR operation. Hence, the contention is avoided in spectrum domain by encoding the contending unicast/multicast packets and changing the carrier frequency of encoded packets. If the network coding cannot successfully resolve the contending packets, the shared feedback FDLs are called to address the contention in time domain. Compared with the existing node architecture and scheduling algorithm, the simulation results show that the proposed architecture and the TFJSS can reduce the packet loss probability with low delay largely.
Universality in Nonlinear Elasticity of Biological and Polymeric Networks and Gels
NASA Astrophysics Data System (ADS)
Carrillo, Jan-Michael; Dobrynin, Andrey
2011-03-01
Networks and gels are part of our everyday experience starting from automotive tires and rubber bands to biological tissues and cells. Biological and polymeric networks show remarkably high deformability at relatively small stresses and can sustain reversible deformations up to ten times of their initial size. A distinctive feature of these materials is highly nonlinear stress-strain curves leading to material hardening with increasing deformation. This differentiates networks and gels from conventional materials, such as metals and glasses, showing linear stress-strain relationship in the reversible deformation regime. Using theoretical analysis and molecular dynamics simulations we propose and test a model 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. This model provides a universal relationship between the strain-dependent network modulus and the network deformation and explains strain-hardening of natural rubber, synthetic polymeric networks, and biopolymer networks of actin, collagen, fibrin, vimentin and neurofilaments. NSF: DMR-1004576.
Elastic-Net Copula Granger Causality for Inference of Biological Networks
Siyal, Mohammad Yakoob
2016-01-01
Aim In bioinformatics, the inference of biological networks is one of the most active research areas. It involves decoding various complex biological networks that are responsible for performing diverse functions in human body. Among these networks analysis, most of the research focus is towards understanding effective brain connectivity and gene networks in order to cure and prevent related diseases like Alzheimer and cancer respectively. However, with recent advances in data procurement technology, such as DNA microarray analysis and fMRI that can simultaneously process a large amount of data, it yields high-dimensional data sets. These high dimensional dataset analyses possess challenges for the analyst. Background Traditional methods of Granger causality inference use ordinary least-squares methods for structure estimation, which confront dimensionality issues when applied to high-dimensional data. Apart from dimensionality issues, most existing methods were designed to capture only the linear inferences from time series data. Method and Conclusion In this paper, we address the issues involved in assessing Granger causality for both linear and nonlinear high-dimensional data by proposing an elegant form of the existing LASSO-based method that we call “Elastic-Net Copula Granger causality”. This method provides a more stable way to infer biological networks which has been verified using rigorous experimentation. We have compared the proposed method with the existing method and demonstrated that this new strategy outperforms the existing method on all measures: precision, false detection rate, recall, and F1 score. We have also applied both methods to real HeLa cell data and StarPlus fMRI datasets and presented a comparison of the effectiveness of both methods. PMID:27792750
On a molecular statistical basis for Ogden's model of rubber elasticity
NASA Astrophysics Data System (ADS)
Ehret, Alexander E.
2015-05-01
In this paper, a link is established between the statistical theory of long chain molecules and Ogden's phenomenological model of rubber elasticity. It has been shown by several authors in the past that many invariant-based phenomenological models for rubber-like materials are related to the classical statistical theories. The essential means to reach this reconciliation were methods to account for a non-affine deformation of polymer chains in the network, appropriate techniques to calculate their averaged response, and an approximation of the inverse Langevin function appearing in the non-Gaussian statistical theory. It is shown in this paper that the very same approach, if appropriately implemented, allows to express the strain-energy function of Ogden's material in terms of physical constants characterising the polymer chain and network, together with few additional parameters that account for the non-affine deformation of the polymer chains. Particularly, it is shown that Ogden's model can be represented as a non-affine non-Gaussian 3-chain model with topological constraints.
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.
Generative model for feedback networks
NASA Astrophysics Data System (ADS)
White, Douglas R.; Kejžar, Nataša; Tsallis, Constantino; Farmer, Doyne; White, Scott
2006-01-01
We propose a model for network formation and study some of its statistical properties. The motivation for the model comes from the growth of several kinds of real networks (i.e., kinship and trading networks, networks of corporate alliances, networks of autocatalytic chemical reactions). These networks grow either by establishing closer connections by adding links in the existing network or by adding new nodes. A node in these networks lacks the information of the entire network. In order to establish a closer connection to other nodes it starts a search in the neighboring part of the network and waits for a possible feedback from a distant node that received the “searching signal.” Our model imitates this behavior by growing the network via the addition of a link that creates a cycle in the network or via the addition of a new node with a link to the network. The forming of a cycle creates feedback between the two ending nodes. After choosing a starting node, a search is made for another node at a suitable distance; if such a node is found, a link is established between this and the starting node, otherwise (such a node cannot be found) a new node is added and is linked to the starting node. We simulate this algorithm and find that we cannot reject the hypothesis that the empirical degree distribution is a q -exponential function, which has been used to model long-range processes in nonequilibrium statistical mechanics.
NASA Astrophysics Data System (ADS)
Yong, Peng; Huang, Jianping; Li, Zhenchun; Liao, Wenyuan; Qu, Luping; Li, Qingyang; Liu, Peijun
2016-12-01
In finite difference (FD) method, numerical dispersion is the dominant factor influencing the accuracy of seismic modeling. Various optimized FD schemes for scalar wave modeling have been proposed to reduce grid dispersion, while the optimized time-space domain FD schemes for elastic wave modeling have not been fully investigated yet. In this paper, an optimized FD scheme with Equivalent Staggered Grid (ESG) for elastic modelling has been developed. We start from the constant P- and S-wave speed elastic wave equations and then deduce analytical plane wave solutions in the wavenumber domain with eigenvalue decomposition method. Based on the elastic plane wave solutions, three new time-space domain dispersion relations of ESG elastic modeling are obtained, which are represented by three equations corresponding to P-, S- and converted wave terms in the elastic equations, respectively. By using these new relations, we can study the dispersion errors of different spatial FD terms independently. The dispersion analysis showed that different spatial FD terms have different errors. It is therefore suggested that different FD coefficients to be used to approximate the three spatial derivative terms. In addition, the relative dispersion error in L2-norm is minimized through optimizing FD coefficients using Newton's method. Synthetic examples have demonstrated that this new optimal FD schemes have superior accuracy for elastic wave modeling compared to Taylor-series expansion and optimized space domain FD schemes.
NASA Astrophysics Data System (ADS)
Yong, Peng; Huang, Jianping; Li, Zhenchun; Liao, Wenyuan; Qu, Luping; Li, Qingyang; Liu, Peijun
2017-02-01
In finite-difference (FD) method, numerical dispersion is the dominant factor influencing the accuracy of seismic modelling. Various optimized FD schemes for scalar wave modelling have been proposed to reduce grid dispersion, while the optimized time-space domain FD schemes for elastic wave modelling have not been fully investigated yet. In this paper, an optimized FD scheme with Equivalent Staggered Grid (ESG) for elastic modelling has been developed. We start from the constant P- and S-wave speed elastic wave equations and then deduce analytical plane wave solutions in the wavenumber domain with eigenvalue decomposition method. Based on the elastic plane wave solutions, three new time-space domain dispersion relations of ESG elastic modelling are obtained, which are represented by three equations corresponding to P-, S- and converted-wave terms in the elastic equations, respectively. By using these new relations, we can study the dispersion errors of different spatial FD terms independently. The dispersion analysis showed that different spatial FD terms have different errors. It is therefore suggested that different FD coefficients to be used to approximate the three spatial derivative terms. In addition, the relative dispersion error in L2-norm is minimized through optimizing FD coefficients using Newton's method. Synthetic examples have demonstrated that this new optimal FD schemes have superior accuracy for elastic wave modelling compared to Taylor-series expansion and optimized space domain FD schemes.
Rigid-plug elastic-water model for transient pipe flow with entrapped air pocket
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.
Analysis of Nonlinear Poro-Elastic and Poro-Visco-Elastic Models
NASA Astrophysics Data System (ADS)
Bociu, Lorena; Guidoboni, Giovanna; Sacco, Riccardo; Webster, Justin T.
2016-12-01
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.
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.
Elastic coupling of nascent apCAM adhesions to flowing actin networks.
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.
Li, Xin; Huang, Shanguo; Yin, Shan; Guo, Bingli; Zhao, Yongli; Zhang, Jie; Zhang, Min; Gu, Wanyi
2016-05-02
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.
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.
Effect of matrix elasticity on the continuous foaming of food models.
Narchi, I; Vial, Ch; Djelveh, G
2008-12-01
The aim is to understand the effect of matrix elasticity on continuous foaming using food models based on glucose syrup. This was modified by adding polyacrylamide (PAA) with 2% whey protein isolate (WPI) or Tween 80 as foaming agents. Foaming was conducted in a stirred column. Rotation speed N and gas-to-liquid flow ratio (G/L) were varied. Overrun, average bubble size d (32), texture and stability were measured using densimetry, image analysis, and rheometry, respectively. Experimental results showed that 0.01% PAA did not modify the viscosity of 2% WPI models, but conferred low elastic behavior. PAA (0.05%) doubled matrix viscosity and drastically increased elasticity. The increase of elasticity became slower for further PAA addition. Foaming experiments demonstrated that theoretical overrun could not be achieved for inelastic WPI models in two cases: for high viscosity and low N, as dispersion effectiveness was reduced; for high G/L and N because of enhanced coalescence. Matrix elasticity was shown to increase overrun at constant viscosity for high G/L by enhancing interface stabilization. However, in elastic models, gas dispersion was more difficult and d (32) was higher than in inelastic fluids of similar viscosity. Finally, when the limiting step was dispersion, foaming was shown to be negatively affected by matrix elasticity.
Magneto-elastic oscillator: Modeling and analysis with nonlinear magnetic interaction
NASA Astrophysics Data System (ADS)
Kumar, K. Aravind; Ali, Shaikh Faruque; Arockiarajan, A.
2017-04-01
The magneto-elastically buckled beam is a classic example of a nonlinear oscillator that exhibits chaotic motions. This system serves as a model to analyze the motion of elastic structures in magnetic fields. The system follows a sixth order magneto-elastic potential and may have up to five static equilibrium positions. However, often the non-dimensional Duffing equation is used to approximate the system, with the coefficients being derived from experiments. In few other instances, numerical methods are used to evaluate the magnetic field values. These field values are then used to approximate the nonlinear magnetic restoring force. In this manuscript, we derive analytical closed form expressions for the magneto-elastic potential and the nonlinear restoring forces in the system. Such an analytical formulation would facilitate tracing the effect of change in a parameter, such as the magnet dimension, on the dynamics of the system. The model is derived assuming a single mode approximation, taking into account the effect of linear elastic and nonlinear magnetic forces. The developed model is then numerically simulated to show that it is accurate in capturing the system dynamics and bifurcation of equilibrium positions. The model is validated through experiments based on forced vibrations of the magneto-elastic oscillator. To gather further insights about the magneto-elastic oscillator, a parametric study has been conducted based on the field strength of the magnets and the distance between the magnets and the results are reported.
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.
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.
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.
14O+p elastic scattering in a microscopic cluster model
Descouvemont, P.; Baye, D.; Leo, F.
2006-04-26
The 14O+p elastic scattering is analyzed in a fully microscopic cluster model. With the Resonating Group Method associated with the microscopic R-matrix theory, phase shifts and cross sections are calculated. Data on 16O+p are used to test the precision of the model. For the 14O+p elastic scattering, an excellent agreement is found with recent experimental data. Resonances properties in 15F are discussed.
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.
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.
A modified elastic foundation contact model for application in 3D models of the prosthetic knee.
Pérez-González, Antonio; Fenollosa-Esteve, Carlos; Sancho-Bru, Joaquín L; Sánchez-Marín, Francisco T; Vergara, Margarita; Rodríguez-Cervantes, Pablo J
2008-04-01
Different models have been used in the literature for the simulation of surface contact in biomechanical knee models. However, there is a lack of systematic comparisons of these models applied to the simulation of a common case, which will provide relevant information about their accuracy and suitability for application in models of the implanted knee. In this work a comparison of the Hertz model (HM), the elastic foundation model (EFM) and the finite element model (FEM) for the simulation of the elastic contact in a 3D model of the prosthetic knee is presented. From the results of this comparison it is found that although the nature of the EFM offers advantages when compared with that of the HM for its application to realistic prosthetic surfaces, and when compared with the FEM in CPU time, its predictions can differ from FEM in some circumstances. These differences are considerable if the comparison is performed for prescribed displacements, although they are less important for prescribed loads. To solve these problems a new modified elastic foundation model (mEFM) is proposed that maintains basically the simplicity of the original model while producing much more accurate results. In this paper it is shown that this new mEFM calculates pressure distribution and contact area with accuracy and short computation times for toroidal contacting surfaces. Although further work is needed to confirm its validity for more complex geometries the mEFM is envisaged as a good option for application in 3D knee models to predict prosthetic knee performance.
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.
Henager, Charles H.; Nguyen, Ba Nghiep; Kurtz, Richard J.; Ferraris, Monica; Katoh, Yutai
2015-06-30
The international fusion community designed miniature torsion specimens for joint testing and irradiation in test reactors with limited irradiation volumes since SiC and SiC-composites used in fission or fusion environments require joining methods for assembling systems. Torsion specimens fail out-of-plane when joints are strong and when elastic moduli are comparable to SiC, which causes difficulties in determining shear strengths for many joints or for comparing unirradiated and irradiated joints. A finite element damage model was developed to treat elastic joints such as SiC/Ti3SiC2+SiC and elastic-plastic joints such as SiC/epoxy and steel/epoxy. The model uses constitutive shear data and is validated using epoxy joint data. The elastic model indicates fracture is likely to occur within the joined pieces to cause out-of-plane failures for miniature torsion specimens when a certain modulus and strength ratio between the joint material and the joined material exists. Lower modulus epoxy joints always fail in plane and provide good model validation.
Modeling Network Interdiction Tasks
2015-09-17
facilities. Social networks, whether through online tools such as Facebook and Twitter or via real connections such as family and work relationships...routes to avoid tariffs, taxes or tolls. In addition, when it is determined that a portion of a communications network has been hacked or compromised, it
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++.
Assortative model for social networks
NASA Astrophysics Data System (ADS)
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.
Elastic properties of compressed rare-gas crystals in a model of deformable atoms
NASA Astrophysics Data System (ADS)
Gorbenko, Ie. Ie.; Troitskaya, E. P.; Pilipenko, E. A.
2017-01-01
The elastic properties of compressed Ne, Ar, Kr, and Xe rare-gas crystals were studied in a model of deformable and polarizable atoms. The second-order Fuchs elasticity moduli, their pressure derivatives, and the Zener elastic anisotropy ratio were calculated with allowance for three-body interaction and quadrupole deformation in electron shells within a wide pressure range. Comparison with the experiment and results of other authors was performed. In xenon at a compression of 0.6, the shear modulus B 44 was observed to become zero, thus corresponding to the FCC-HCP transition at 75 GPa.
New theoretical considerations in polymer rheology: Elastic breakdown of chain entanglement network
NASA Astrophysics Data System (ADS)
Wang, Shi-Qing; Ravindranath, Sham; Wang, Yangyang; Boukany, Pouyan
2007-08-01
Recent experimental evidence has motivated us to present a set of new theoretical considerations and to provide a rationale for interpreting the intriguing flow phenomena observed in entangled polymer solutions and melts [P. Tapadia and S. Q. Wang, Phys. Rev. Lett. 96, 016001 (2006); 96, 196001 (2006); S. Q. Wang et al., ibid. 97, 187801 (2006)]. Three forces have been recognized to play important roles in controlling the response of a strained entanglement network. During flow, an intermolecular locking force fiml arises and causes conformational deformation in each load-bearing strand between entanglements. The chain deformation builds up a retractive force fretract within each strand. Chain entanglement prevails in quiescence because a given chain prefers to stay interpenetrating into other chains within its pervaded volume so as to enjoy maximum conformational entropy. Since each strand of length lent has entropy equal to kBT, the disentanglement criterion is given by fretract>fent~kBT/lent in the case of interrupted deformation. This condition identifies fent as a cohesive force. Imbalance among these forces causes elastic breakdown of the entanglement network. For example, an entangled polymer yields during continuous deformation when the declining fiml cannot sustain the elevated fretract. This opposite trend of the two forces is at the core of the physics governing a ``cohesive'' breakdown at the yield point (i.e., the stress overshoot) in startup flow. Identifying the yield point as the point of force imbalance, we can also rationalize the recently observed striking scaling behavior associated with the yield point in continuous deformation of both shear and extension.
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.
NASA Astrophysics Data System (ADS)
Liu, Huanlin; Zhang, Mingjia; Yi, Pengfei; Chen, Yong
2016-12-01
In order to address the problems of spectrum fragmentation and low sharing degree of spectrum resources in survivable elastic optical networks, an improved algorithm, called shared path protection by reconstructing sharable bandwidth based on spectrum segmentation (SPP-RSB-SS), is proposed in the paper. In the SPP-RSB-SS algorithm, for reducing the number of spectrum fragmentations and improving the success rate of spectrum allocation, the whole spectrum resource is partitioned into several spectrum segments. And each spectrum segment is allocated to the requests with the same bandwidth requirement in priority. Meanwhile, the protection path with higher spectrum sharing degree is selected through optimizing the link cost function and reconstructing sharable bandwidth. Hence, the protection path can maximize the sharable spectrum usage among multiple protection paths. The simulation results indicate that the SPP-RSB-SS algorithm can increase the sharing degree of protection spectrum effectively. Furthermore, the SPP-RSB-SS algorithm can enhance the spectrum utilization, and reduce the bandwidth blocking probability significantly.
The Elastic Behaviour of Sintered Metallic Fibre Networks: A Finite Element Study by Beam Theory
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
Substitution and price elasticity estimates using inter-countrypooled data in a translog cost model
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.
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.
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.
Automated Measurement and Statistical Modeling of Elastic Laminae in Arteries
Xu, Hai; Hu, Jin-Jia; Humphrey, Jay D.; Liu, Jyh-Charn
2010-01-01
Structural features of elastic laminae within arteries can provide vital information for both the mechanobiology and the biomechanics of the wall. In this paper, we propose, test, and illustrate a new computer-based scheme for automated analysis of regional distributions of elastic laminae thickness, inter-lamellar distances, and fragmentation (furcation points) from standard histological images. Our scheme eliminates potential artifacts produced by tissue cutting, automatically aligns tissue according to physiologic orientations, and performs cross-sectional measurements along radial directions. A statistical randomized complete block design (RCBD) and F-test were used to assess potential (non)-uniformity of lamellar thicknesses and separations along both radial and circumferential directions. Illustrative results for both normotensive and hypertensive thoracic porcine aorta revealed marked heterogeneity along the radial direction in nearly stress-free samples. Clearly, regional measurements can provide more detailed information about morphologic changes that cannot be gained by globally averaged evaluations alone. We also found that quantifying Furcation Point densities offers new information about potential elastin fragmentation, particularly in response to increased loading due to hypertension. PMID:20221934
Calculations of isothermal elastic constants in the phase-field crystal model
NASA Astrophysics Data System (ADS)
Pisutha-Arnond, N.; Chan, V. W. L.; Elder, K. R.; Thornton, K.
2013-01-01
The phase-field crystal (PFC) method is an emerging coarse-grained atomistic model that can be used to predict material properties. In this work, we describe procedures for calculating isothermal elastic constants using the PFC method. We find that the conventional procedures used in the PFC method for calculating the elastic constants are inconsistent with those defined from a theory of thermoelasticity of stressed materials. Therefore we present an alternative procedure for calculating the elastic constants that are consistent with the definitions from the thermoelasticity theory, and show that the two procedures result in different predictions. Furthermore, we employ a thermodynamic formulation of stressed solids to quantify the differences between the elastic constants obtained from the two procedures in terms of thermodynamic quantities such as the pressure evaluated at the undeformed state.
Singh, Amit Raj; Granek, Rony
2016-10-14
We study DNA denaturation by integrating elasticity - as described by the Gaussian network model - with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.
NASA Astrophysics Data System (ADS)
Singh, Amit Raj; Granek, Rony
2016-10-01
We study DNA denaturation by integrating elasticity — as described by the Gaussian network model — with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.
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.
Nonequilibrium model on Apollonian networks.
Lima, F W S; Moreira, André A; Araújo, Ascânio D
2012-11-01
We investigate the majority-vote model with two states (-1,+1) and a noise parameter q on Apollonian networks. The main result found here is the presence of the phase transition as a function of the noise parameter q. Previous results on the Ising model in Apollonian networks have reported no presence of a phase transition. We also studied the effect of redirecting a fraction p of the links of the network. By means of Monte Carlo simulations, we obtained the exponent ratio γ/ν, β/ν, and 1/ν for several values of rewiring probability p. The critical noise q{c} and U were also calculated. Therefore, the results presented here demonstrate that the majority-vote model belongs to a different universality class than equilibrium Ising model on Apollonian network.
A three-dimensional computational model of collagen network mechanics.
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.
An Elastic-Plastic Damage Model for Long-Fiber Thermoplastics
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.
Ice-shelf tidal deflections modelled with a full 3D elastic model
NASA Astrophysics Data System (ADS)
Konovalov, Yuri
2014-05-01
Ice-shelf flexure modelling was performed using a full 3D finite-difference elastic model, which takes into account sub-ice-shelf seawater flow. The numerical experiments were carried out for the thin plate of ice with changing ice thickness (with trapezoidal profile along the center line). The sub-ice seawater flow was described by the wave channel equation (Holdsworth and Glynn, 1978). In the model ice shelf flexures result from variations in the incoming (outgoing) sea water flux, which flows into (out of) the sub-ice-shelf channel. The numerical experiments were carried out for harmonic incoming seawater fluxes and the ice-shelf flexures were obtained for tidal ocean impacts and for different ice-shelf spatial extents. References Bassis J.N., Fricker H.A., Coleman R., Minster J.-B.: An investigation into the forces that drive ice-shelf rift propagation on the Amery Ice Shelf, East Antarcyica. J. of Glaciol. 54 (184): 17-27, 2008. Holdsworth G and Glynn J.: Iceberg calving from floating glaciers by a vibrating mechanism. Nature. 274, 464-466, 1978. Konovalov Y. V.: Ice-shelf resonance deflections modelled with a 2D elastic centre-line model. Physical Review & Research International, 4(1), 9-29, 2014. Vaughan D.G.: Tidal flexure at ice shelf margins. J. Geophys. Res. 100(B4), 6213-6224, 2002.
Geophysical models of heat and fluid flow in damageable poro-elastic continua
NASA Astrophysics Data System (ADS)
Roubíček, Tomáš
2017-03-01
A rather general model for fluid and heat transport in poro-elastic continua undergoing possibly also plastic-like deformation and damage is developed with the goal to cover various specific models of rock rheology used in geophysics of Earth's crust. Nonconvex free energy at small elastic strains, gradient theories (in particular the concept of second-grade nonsimple continua), and Biot poro-elastic model are employed, together with possible large displacement due to large plastic-like strains evolving during long time periods. Also the additive splitting is justified in stratified situations which are of interest in modelling of lithospheric crust faults. Thermodynamically based formulation includes entropy balance (in particular the Clausius-Duhem inequality) and an explicit global energy balance. It is further outlined that the energy balance can be used to ensure, under suitable data qualification, existence of a weak solution and stability and convergence of suitable approximation schemes at least in some particular situations.
An elastic failure model of indentation damage. [of brittle structural ceramics
NASA Technical Reports Server (NTRS)
Liaw, B. M.; Kobayashi, A. S.; Emery, A. F.
1984-01-01
A mechanistically consistent model for indentation damage based on elastic failure at tensile or shear overloads, is proposed. The model accommodates arbitrary crack orientation, stress relaxation, reduction and recovery of stiffness due to crack opening and closure, and interfacial friction due to backward sliding of closed cracks. This elastic failure model was implemented by an axisymmetric finite element program which was used to simulate progressive damage in a silicon nitride plate indented by a tungsten carbide sphere. The predicted damage patterns and the permanent impression matched those observed experimentally. The validation of this elastic failure model shows that the plastic deformation postulated by others is not necessary to replicate the indentation damage of brittle structural ceramics.
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
Henager, Charles H.; Nguyen, Ba Nghiep; Kurtz, Richard J.; Roosendaal, Timothy J.; Borlaug, Brennan A.; Ferraris, Monica; Ventrella, Andrea; Katoh, Yutai
2015-03-01
The use of SiC and SiC-composites in fission or fusion environments requires joining methods for assembling systems. The international fusion community designed miniature torsion specimens for joint testing and irradiation in test reactors with limited irradiation volumes. These torsion specimens fail out-of-plane when joints are strong and when elastic moduli are within a certain range compared to SiC, which causes difficulties in determining shear strengths for joints or for comparing unirradiated and irradiated joints. A finite element damage model was developed that indicates fracture is likely to occur within the joined pieces to cause out-of-plane failures for miniature torsion specimens when a certain modulus and strength ratio between the joint material and the joined material exists. The model was extended to treat elastic-plastic joints such as SiC/epoxy and steel/epoxy joints tested as validation of the specimen design.
Yang, Hui; Zhang, Jie; Ji, Yuefeng; Tan, Yuanlong; Lin, Yi; Han, Jianrui; Lee, Young
2015-09-07
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.
Mobility Model for Tactical Networks
NASA Astrophysics Data System (ADS)
Rollo, Milan; Komenda, Antonín
In this paper a synthetic mobility model which represents behavior and movement pattern of heterogeneous units in disaster relief and battlefield scenarios is proposed. These operations usually take place in environment without preexisting communication infrastructure and units thus have to be connected by wireless communication network. Units cooperate to fulfill common tasks and communication network has to serve high amount of communication requests, especially data, voice and video stream transmissions. To verify features of topology control, routing and interaction protocols software simulations are usually used, because of their scalability, repeatability and speed. Behavior of all these protocols relies on the mobility model of the network nodes, which has to resemble real-life movement pattern. Proposed mobility model is goal-driven and provides support for various types of units, group mobility and realistic environment model with obstacles. Basic characteristics of the mobility model like node spatial distribution and average node degree were analyzed.
NASA Astrophysics Data System (ADS)
Merlet, Benoît
2015-08-01
We study the thin-shell limit of the nonlinear elasticity model for vesicles introduced in part I. We consider vesicles of width with elastic energy of order . In this regime, we show that the limit model is a bending theory for generalized hypersurfaces—namely, co-dimension one oriented varifolds without boundary. Up to a positive factor, the limit functional is the Willmore energy. In the language of -convergence, we establish a compactness result, a lower bound result and the matching upper bound in the smooth case.
Dynamic elastic properties from micro-CT images: modeling and experimental validation
NASA Astrophysics Data System (ADS)
Lebedev, M.; Pervukhina, M.; de Paula, O.; Clennell, B.; Gurevich, B.
2009-04-01
Knowledge of the elastic properties of rocks is a key factor in seismic interpretation. Elastic properties of rock are determined by its microstructure and their prediction relies on the availability of accurate microstructural models. X-ray computer tomography (CT) as a unique non-destructive technique is becoming a powerful tool in geophysics research which reveals detailed 3D microstructure of rock with special resolution of 1 micron. Recent breakthrough in computational capabilities allows simulation of elastic properties directly using the micro-CT images. In this study we simulate acoustic velocities of sandstones, based on high resolution 3D images and compare simulation results with ultrasonic measurements. Synchrotron images of two sandstones are segmented to separate grain from pore space. The porosity obtained as a result of the segmentation process is compared with the measured porosity for the segmentation quality control. Parallel 3D finite difference (FD) code is used to simulate elastic wave propagation through the digitized two phase media where the total solid phase is supposed to have elastic properties of intact quartz and the pore space is either dry or saturated with water. Attenuation and dispersion of acoustic velocities are obtained at a range of frequencies. The numerical results noticeably overestimate velocities obtained at laboratory experiments at ultrasonic frequencies. The discrepancy can be explained with the fact that grain contacts have strong effect on elastic moduli and are the most speculative part of the simulations. To validate our FD code and calibrate the properties of grain contacts, we simulated elastic wave propagation in aluminum foam with porosity of 40%. All grain contacts in the foam are "solid" and its microstructure is similar to that of moldic carbonates. Preliminary results of FD modeling and comparison with experiment of carbonates are presented as well.
NASA Astrophysics Data System (ADS)
García-Pelagio, Karla P.; Santamaría-Holek, Ivan; Bloch, Robert J.; Ortega, Alicia; González-Serratos, Hugo
2010-12-01
Two of the most important proteins linking the contractile apparatus and costameres at the sarcolemma of skeletal muscle fibers are dystrophin and desmin. We have developed an elastic model of the proteins that link the sarcolemma to the myofibrils. This is a distributed model, with an elastic constant, k, that includes the main protein components of the costameres. The distributed spring model is composed of parallel units attached in series. To test the model, we performed experiments in which we applied negative pressure, generated by an elastimeter, to a small area of the sarcolemma from single myofiber. The negative pressure formed a bleb of variable height, dependent on the pressure applied. We normalized our measurements of k in dystrophin-null (mdx) and desmin-null (des-/-) mice to the value we obtained for wild type (WT) mice, which was set at 1.0. The relative experimental value for the stiffness of myofibers from mice lacking dystrophin or desmin was 0.5 and 0.7, respectively. The theoretical k values of the individual elements were obtained using neural networks (NN), in which the input was the k value for each parallel spring component and the output was the solution of each resulting parallel system. We compare the experimental values of k in control and mutant muscles to the theoretical values obtained by NN for each protein. Computed theoretical values were 0.4 and 0.8 for dystrophin- and desmin-null muscles, respectively, and 0.9 for WT, in reasonable agreement with our experimental results. This suggests that, although it is a simplified spring model solved by NN, it provides a good approximation of the distribution of spring elements and the elastic constants of the proteins that form the costameres. Our results show that dystrophin is the protein that contributes more than any other to the strength of the connections between the sarcolemma and the contractile apparatus, the costameres.
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.
Network growth models and genetic regulatory networks
NASA Astrophysics Data System (ADS)
Foster, D. V.; Kauffman, S. A.; Socolar, J. E. S.
2006-03-01
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with the innovation of new links, allowing for the possibility that input and output links from a newly created node may have different probabilities of survival. We find some counterintuitive trends as the parameters are varied, including the broadening of the in-degree distribution when the probability for retaining input links is decreased. We also find that both the scaling of transcription factors with genome size and the measured degree distributions for genes in yeast can be reproduced by the growth algorithm if and only if a special seed is used to initiate the process.
Network growth models and genetic regulatory networks
NASA Astrophysics Data System (ADS)
Socolar, Joshua; Foster, David; Kauffman, Stuart
2006-03-01
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new links, allowing for the possibility that input and output links from a newly created node may have different probabilities of survival. We find some counterintuitive trends as parameters are varied, including the broadening of indegree distribution when the probability for retaining input links is decreased. We also find that both the scaling of transcription factors with genome size and the measured degree distributions for genes in yeast can be reproduced by the growth algorithm if and only if a special seed is used to initiate the process.
Non-Newtonian bile flow in elastic cystic duct: one- and three-dimensional modeling.
Li, W G; Luo, X Y; Chin, S B; Hill, N A; Johnson, A G; Bird, N C
2008-11-01
Bile flow is thought to play an essential role in the pathophysiological genesis of cholelithiasis (gallstone formation) and in gallbladder pain. In this paper, we extend our previous study of the human biliary system (Li et al., 2007, J. Biomech. Eng., 129:164-173) to include two important factors: the non-Newtonian properties of bile, and elastic deformation of the cystic duct. A one-dimensional (1D) model is analyzed and compared with three-dimensional (3D) fluid-structure interaction simulations. It is found that non-Newtonian bile raises resistance to the flow of bile, which can be augmented significantly by the elastic deformation (collapse) of the cystic duct. We also show that the 1D model predicts the pressure drop of the cystic duct flow well for all cases considered (Newtonian or non-Newtonian flow, rigid or elastic ducts), when compared with the full 3D simulations.
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.
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.
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.
Quantifying the contribution of actin networks to the elastic strength of fibroblasts.
Ananthakrishnan, Revathi; Guck, Jochen; Wottawah, Falk; Schinkinger, Stefan; Lincoln, Bryan; Romeyke, Maren; Moon, Tess; Käs, Josef
2006-09-21
The structural models created to understand the cytoskeletal mechanics of cells in suspension are described here. Suspended cells can be deformed by well-defined surface stresses in an Optical Stretcher [Guck, J., Ananthakrishnan, R., Mahmood, H., Moon, T.J., Cunningham, C.C., Käs, J., 2001. The optical stretcher: a novel laser tool to micromanipulate cells. Biophys. J. 81(2), 767-784], a two-beam optical trap designed for the contact-free deformation of cells. Suspended cells have a well-defined cytoskeleton, displaying a radially symmetric actin cortical network underlying the cell membrane with no actin stress fibers, and microtubules and intermediate filaments in the interior. Based on experimental data using suspended fibroblasts, we create two structural models: a thick shell actin cortex model that describes cell deformation for a localized stress distribution on these cells and a three-layered model that considers the entire cytoskeleton when a broad stress distribution is applied. Applying the models to data, we obtain a (actin) cortical shear moduli G of approximately 220 Pa for normal fibroblasts and approximately 185 Pa for malignantly transformed fibroblasts. Additionally, modeling the cortex as a transiently crosslinked isotropic actin network, we show that actin and its crosslinkers must be co-localized into a tight shell to achieve these cortical strengths. The similar moduli values and cortical actin and crosslinker densities but different deformabilities of the normal and cancerous cells suggest that a cell's structural strength is not solely determined by cytoskeletal composition but equally importantly by (actin) cytoskeletal architecture via differing cortical thicknesses. We also find that although the interior structural elements (microtubules, nucleus) contribute to the deformed cell's exact shape via their loose coupling to the cortex, it is the outer actin cortical shell (and its thickness) that mainly determines the cell's structural
Fazzalari, Nicola L.
2009-01-01
Elastic fibres are critical constituents of dynamic biological structures that functionally require elasticity and resilience. The network of elastic fibres in the anulus fibrosus of the intervertebral disc is extensive, however until recently, the majority of histological, biochemical and biomechanical studies have focussed on the roles of other extracellular matrix constituents such as collagens and proteoglycans. The resulting lack of detailed descriptions of elastic fibre network architecture and mechanical function has limited understanding of the potentially important contribution made by elastic fibres to healthy disc function and their possible roles in the progression of disc degeneration. In addition, it has made it difficult to postulate what the consequences of elastic fibre related disorders would be for intervertebral disc behaviour, and to develop treatments accordingly. In this paper, we review recent and historical studies which have examined both the structure and the function of the human lumbar anulus fibrosus elastic fibre network, provide a synergistic discussion in an attempt to clarify its potentially critical contribution both to normal intervertebral disc behaviour and the processes relating to its degeneration, and recommend critical areas for future research. PMID:19263091
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.
An approach for modeling vulnerability of the network of networks
NASA Astrophysics Data System (ADS)
Zhang, Jianhua; Song, Bo; Zhang, Zhaojun; Liu, Haikuan
2014-10-01
In this paper, a framework is given to model the network of networks and to investigate the vulnerability of the network of networks subjected to failures. Because there are several redundant systems in infrastructure systems, the dependent intensity between two networks is introduced and adopted to discuss the vulnerability of the interdependent infrastructure networks subjected to failures. Shanghai electrified rail transit network is used to illustrate the feasibility and effectiveness of the proposed framework. Because the rail network is dependent on the power grid and communication network, the corresponding power grid and communication network are also included in this system. Meanwhile the failures to the power grid and communication network are utilized to investigate the vulnerability of the rail network. The results show that the rail network strongly depends on the power grid and weakly depends on the communication network, and the transport functionality loss of the rail network increases with the increase of dependent intensity. Meanwhile the highest betweenness node-based attack to the power grid and the largest degree node-based attack to the communication network can result in the most functionality losses to the rail network. Moreover, the functionality loss of the rail network has the smallest value when the tolerance parameter of the power grid equals 0.75 and the critical nodes of the power grid and communication network can be obtained by simulations.
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.
Klöppel, Thomas; Wall, Wolfgang A
2011-07-01
A novel finite element approach is presented to simulate the mechanical behavior of human red blood cells (RBC, erythrocytes). As the RBC membrane comprises a phospholipid bilayer with an intervening protein network, we propose to model the membrane with two distinct layers. The fairly complex characteristics of the very thin lipid bilayer are represented by special incompressible solid shell elements and an anisotropic viscoelastic constitutive model. Properties of the protein network are modeled with an isotropic hyperelastic third-order material. The elastic behavior of the model is validated with existing optical tweezers studies with quasi-static deformations. Employing material parameters consistent with literature, simulation results are in excellent agreement with experimental data. Available models in literature neglect either the surface area conservation of the RBC membrane or realistic loading conditions of the optical tweezers experiments. The importance of these modeling assumptions, that are both included in this study, are discussed and their influence quantified. For the simulation of the dynamic motion of RBC, the model is extended to incorporate the cytoplasm. This is realized with a monolithic fully coupled fluid-structure interaction simulation, where the fluid is described by the incompressible Navier-Stokes equations in an arbitrary Lagrangian Eulerian framework. It is shown that both membrane viscosity and cytoplasm viscosity have significant influence on simulation results. Characteristic recovery times and energy dissipation for varying strain rates in dynamic laser trap experiments are calculated for the first time and are found to be comparable with experimental data.
Proxy model materials to simulate the elastic properties of digested municipal sludge.
Eshtiaghi, Nicky; Markis, Flora; Baudez, Jean-Christophe; Slatter, Paul
2013-10-01
The elastic rheological properties of sludge are complex and evolve with time as a result of ageing and microbial activity. Due to the peculiar nature of sludge, this makes the measurement of physical parameters difficul. The challenge is to identify a reference material that can be used as a proxy for industrial process design or optimization. In this study, respectively the mixtures of 0.5%, 0.7% and 1% glass beads suspension in water have been added to 0.5%, 0.7% and 1% carbopol dissolved in water and neutralized with NaOH to prepare gel, at different ratios. Elastic and loss moduli have been determined for different glass bead suspension ratios in the range of 0%-80%. The results showed that there is a critical glass bead suspension/carbopol ratio at which the elastic properties of the mixture changes dramatically. The elastic properties of these model mixtures of different glass bead/carbopol ratio suspensions are compared with the elastic property of municipal sludge sampled from a Melbourne Waste Water Treatment Plant, and similarity established.
Three-dimensional elasticity models for buckling of anisotropic and auxetic beams and plates
NASA Astrophysics Data System (ADS)
Hamad, Eltigani
The three-dimensional elasticity model is developed to determine the critical buckling load for isotropic, anisotropic, and auxetic beams and plates. Different beam theories are studied and compared to the elasticity theory. The study was based on the assessment of those beam theories using different beam cross-sections and boundary conditions. The elasticity theory for anisotropic beams obtained well results for large slenderness ratios when it compared with Euler-Bernoulli theory which is considered in this study the main area of comparison study. For small values of slenderness ratio the elasticity theory obtained significant difference than the Euler-Bernoulli theory, which means that Euler-Bernoulli is weaker when it is used for short beams than long beams. The orientation of the anisotropy behavior is also studied and has showed how the buckling load can be changed due to the orientation of the elasticity modulus. The auxetic beams behave differently than the anisotropic behavior, it gives results higher and lower than the Euler-Bernoulli theory according to the slenderness ratio and the Poisson's ratio values. A significant behavior was noticed in using beams with negative Poisson's the ratio which can be useful in structure mechanics field.
NASA Astrophysics Data System (ADS)
Koutsoumaris, C. Chr.; Eptaimeros, K. G.; Zisis, T.; Tsamasphyros, G. J.
2016-12-01
The nonlocal theory of elasticity is widely employed to the study of nanoscale problems. The differential approach of Eringen's nonlocal beam theory has been widely used to solve problems whose size effect is substantial in structures. However, in the case of Euler-Bernoulli beam theory (EBBT), this approach reveals inconsistencies that do not allow for the energy functional formulation. To avoid these inconsistencies, an alternative route is to use the integral form of nonlocal elasticity. This study revolves around the nonlocal integral beam model for various attenuation functions with the intention to explore the static response of a beam (or a nanobeam) for different types of loadings and boundary conditions (BC).
NASA Astrophysics Data System (ADS)
Carter, B.; Chachoua, E.; Chamel, N.
2006-01-01
This work develops the dynamics of a perfectly elastic solid model for application to the outer crust of a magnetised neutron star. Particular attention is given to the Noether identities responsible for energy-momentum conservation, using a formulation that is fully covariant, not only (as is usual) in a fully relativistic treatment but also (sacrificing accuracy and elegance for economy of degrees of gravitational freedom) in the technically more complicated case of the Newtonian limit. The results are used to obtain explicit (relativistic and Newtonian) formulae for the propagation speeds of generalised (Alfven type) magneto-elastic perturbation modes.
Modeling ventricular function during cardiac assist: does time-varying elastance work?
Vandenberghe, Stijn; Segers, Patrick; Steendijk, Paul; Meyns, Bart; Dion, Robert A E; Antaki, James F; Verdonck, Pascal
2006-01-01
The time-varying elastance theory of Suga et al. is widely used to simulate left ventricular function in mathematical models and in contemporary in vitro models. We investigated the validity of this theory in the presence of a left ventricular assist device. Left ventricular pressure and volume data are presented that demonstrate the heart-device interaction for a positive-displacement pump (Novacor) and a rotary blood pump (Medos). The Novacor was implanted in a calf and used in fixed-rate mode (85 BPM), whereas the Medos was used at several flow levels (0-3 l/min) in seven healthy sheep. The Novacor data display high beat-to-beat variations in the amplitude of the elastance curve, and the normalized curves deviate strongly from the typical bovine curve. The Medos data show how the maximum elastance depends on the pump flow level. We conclude that the original time-varying elastance theory insufficiently models the complex hemodynamic behavior of a left ventricle that is mechanically assisted, and that there is need for an updated ventricular model to simulate the heart-device interaction.
A spline-based parameter and state estimation technique for static models of elastic surfaces
NASA Technical Reports Server (NTRS)
Banks, H. T.; Daniel, P. L.; Armstrong, E. S.
1983-01-01
Parameter and state estimation techniques for an elliptic system arising in a developmental model for the antenna surface in the Maypole Hoop/Column antenna are discussed. A computational algorithm based on spline approximations for the state and elastic parameters is given and numerical results obtained using this algorithm are summarized.
Nonlinear Visco-Elastic Response of Composites via Micro-Mechanical Models
NASA Technical Reports Server (NTRS)
Gates, Thomas S.; Sridharan, Srinivasan
2005-01-01
Micro-mechanical models for a study of nonlinear visco-elastic response of composite laminae are developed and their performance compared. A single integral constitutive law proposed by Schapery and subsequently generalized to multi-axial states of stress is utilized in the study for the matrix material. This is used in conjunction with a computationally facile scheme in which hereditary strains are computed using a recursive relation suggested by Henriksen. Composite response is studied using two competing micro-models, viz. a simplified Square Cell Model (SSCM) and a Finite Element based self-consistent Cylindrical Model (FECM). The algorithm is developed assuming that the material response computations are carried out in a module attached to a general purpose finite element program used for composite structural analysis. It is shown that the SSCM as used in investigations of material nonlinearity can involve significant errors in the prediction of transverse Young's modulus and shear modulus. The errors in the elastic strains thus predicted are of the same order of magnitude as the creep strains accruing due to visco-elasticity. The FECM on the other hand does appear to perform better both in the prediction of elastic constants and the study of creep response.
NASA Astrophysics Data System (ADS)
Gilabert, F. A.; Roux, J.-N.; Castellanos, A.
2008-09-01
The quasistatic behavior of a simple two-dimensional model of a cohesive powder under isotropic loads is investigated by discrete element simulations. We ignore contact plasticity and focus on the effect of geometry and collective rearrangements on the material behavior. The loose packing states, as assembled and characterized in a previous numerical study [Gilabert, Roux, and Castellanos, Phys. Rev. E 75, 011303 (2007)], are observed, under growing confining pressure P , to undergo important structural changes, while solid fraction Φ irreversibly increases (typically, from 0.4-0.5 to 0.75-0.8). The system state goes through three stages, with different forms of the plastic consolidation curve, i.e., Φ as a function of the growing reduced pressure P*=Pa/F0 , defined with adhesion force F0 and grain diameter a . In the low-confinement regime (I), the system undergoes negligible plastic compaction, and its structure is influenced by the assembling process. In regime II the material state is independent of initial conditions, and the void ratio varies linearly with lnP [i.e., Δ(1/Φ)=λΔ(lnP*) ], as described in the engineering literature. Plasticity index λ is reduced in the presence of a small rolling resistance (RR). In the last stage of compaction (III), Φ approaches an asymptotic, maximum solid fraction Φmax , as a power law Φmax-Φ∝(P*)-α , with α≃1 , and properties of cohesionless granular packs are gradually retrieved. Under consolidation, while the range ξ of fractal density correlations decreases, force patterns reorganize from self-balanced clusters to force chains, with correlative evolutions of force distributions, and elastic moduli increase by a large amount. Plastic deformation events correspond to very small changes in the network topology, while the denser regions tend to move like rigid bodies. Elastic properties are dominated by the bending of thin junctions in loose systems. For growing RR those tend to form particle chains, the
Aidun, J.B.; Addessio, F.L.
1995-11-01
The theoretical basis of the homogenization technique developed by Aboudi is presented and assessed. Given the constitutive relations of the constituents, this technique provides an equivalent, homogeneous, constitutive model of unidirectional, continuous-fiber-reinforced composites. The expressions that comprise the first-order version of the technique are given special attention as this treatment has considerable practical value. Nonlinear elasticity effects are added to it. This extension increases the accuracy of numerical simulations of high strain-rate loadings. It is particularly important for any dynamic loading in which shock waves might be produced, including crash safety, armor, and munitions applications. Examples illustrate that elastic nonlinearity can make substantial contributions at strains of only a few per cent. These contributions are greatest during post-yield inelastic deformation. The micromechanics-based homogenization technique is shown to facilitate use of an efficient approximate treatment of elastic nonlinearity in composites with isotropic matrix materials.
On the the Contact Lens Problem: Modeling Rigid and Elastic Beams on Thin Films
NASA Astrophysics Data System (ADS)
Trinh, Philippe; Wilson, Stephen; Stone, Howard
2011-11-01
Generally, contact lenses are prescribed by the practitioner to fit each individual patient's eye, but these fitting-philosophies are based on empirical studies and a certain degree of trial-and-error. A badly fitted lens can cause a range of afflictions, which varies from mild dry-eye-discomfort, to more serious corneal diseases. Thus, at this heart of this problem, is the question of how a rigid or elastic plate interacts with the free-surface of a thin viscous film. In this talk, we present several mathematical models for the study of these plate-and-fluid problems. Asymptotic and numerical results are described, and we explain the role of elasticity, surface tension, viscosity, and pressure in determining the equilibrium solutions. Finally, we discuss the implications of our work on the contact lens problem, as well as on other coating processes which involve elastic substrates.
Modeling of Distributed Sensing of Elastic Waves by Fiber-Optic Interferometry
Agbodjan Prince, Just; Kohl, Franz; Sauter, Thilo
2016-01-01
This paper deals with the transduction of strain accompanying elastic waves in solids by firmly attached optical fibers. Stretching sections of optical fibers changes the time required by guided light to pass such sections. Exploiting interferometric techniques, highly sensitive fiber-optic strain transducers are feasible based on this fiber-intrinsic effect. The impact on the actual strain conversion of the fiber segment’s shape and size, as well as its inclination to the elastic wavefront is studied. FEM analyses show that severe distortions of the interferometric response occur when the attached fiber length spans a noticeable fraction of the elastic wavelength. Analytical models of strain transduction are presented for typical transducer shapes. They are used to compute input-output relationships for the transduction of narrow-band strain pulses as a function of the mechanical wavelength. The described approach applies to many transducers depending on the distributed interaction with the investigated object. PMID:27608021
Modeling of Distributed Sensing of Elastic Waves by Fiber-Optic Interferometry.
Agbodjan Prince, Just; Kohl, Franz; Sauter, Thilo
2016-09-06
This paper deals with the transduction of strain accompanying elastic waves in solids by firmly attached optical fibers. Stretching sections of optical fibers changes the time required by guided light to pass such sections. Exploiting interferometric techniques, highly sensitive fiber-optic strain transducers are feasible based on this fiber-intrinsic effect. The impact on the actual strain conversion of the fiber segment's shape and size, as well as its inclination to the elastic wavefront is studied. FEM analyses show that severe distortions of the interferometric response occur when the attached fiber length spans a noticeable fraction of the elastic wavelength. Analytical models of strain transduction are presented for typical transducer shapes. They are used to compute input-output relationships for the transduction of narrow-band strain pulses as a function of the mechanical wavelength. The described approach applies to many transducers depending on the distributed interaction with the investigated object.
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.
Modeling non-crystalline networks
NASA Astrophysics Data System (ADS)
Lei, Ming
In this thesis, the author reports the modeling of both the static and the dynamical aspects of non-crystalline networks. Porous silicon and silica have attracted attention recently due to their unusual photoelectronic properties. Porosity is central to these striking properties which are not present in non-porous silicon and silica. We propose an algorithm that is effective in building fully-coordinated amorphous networks that are discontinuous in certain regions---that is, they contain large voids of mesoscopic or macroscopic dimensions. Such networks can be both porous and amorphous, and can also be finite in certain dimensions. Voids of arbitrary shapes and sizes are first superimposed on a crystalline silicon network. The atoms in the pore regions are removed. Local "defects" are created, then eliminated, as pairs of them are brought together by a defect migration process. The network is fully coordinated after the defect migration process. The Wooten Winer Weaire (WWW) algorithm, is then applied to make the network amorphous. Oxygen is inserted on every silicon-silicon bond to create a porous silica network. Silica networks in the form of an amorphous fiber and an amorphous film are created by this procedure. Distortions due to surface effects are investigated. The local atomic arrangement in these discontinuous networks is similar to that in bulk amorphous silica. Covalent bond lengths and angles in amorphous networks do not vary much because of the high energies associated with bond length and angle distortions. Therefore, they can be viewed as constraints that do not change with time in any significant way. Proteins, viewed as another type of non-crystalline network, are glued together by covalent bonds, hydrogen bonds, hydrophobic interactions, and other interactions. The concentration of constraints in some regions of the proteins are so high that these regions are rigid. The other regions are flexible. The flexible regions of protein can exhibit large
Global communications network modeling tools
NASA Astrophysics Data System (ADS)
Cohen, Marc A.; Baraniuk, Steven P.
The authors are developing a list of requirements for a general computer-aided engineering tool which will support the design and evaluation of global communications networks into the next decade. The target applications of this tool include simulating the operation of large C3I networks, including both terrestrial and space segments. Hierarchical modeling and specification strategies, based on those in OPNET, will be the core of the tool architecture. A key modeling requirement is the determination of link closure, based on node dynamics and orientation. Specification of satellite orbits will be based on the six classical orbital elements, and will feature graphical feedback in the form of azimuth/elevation plots. Detailed terrestrial scenario specification will be supported, including the deployment of fixed ground, mobile ground, and airborne nodes. Decision support features will generate graphical views of node and network variables, including availability plots and connectivity maps.
A thermodynamic model of thermal end elastic properties of curium
NASA Astrophysics Data System (ADS)
Povzner, A. A.; Filanovich, A. N.; Oskina, V. A.
2013-11-01
A self-consistent thermodynamic model of curium is developed. In the framework of this model the temperature dependencies of heat capacity, coefficient of thermal expansion, bulk modulus and Debye temperature of Cm are calculated. It is shown that the phonon anharmonicity of Cm is weaker than in the case of Np and δ-Pu, but stronger than in lanthanides.
Elastic and thermal expansion asymmetry in dense molecular materials.
Burg, Joseph A; Dauskardt, Reinhold H
2016-09-01
The elastic modulus and coefficient of thermal expansion are fundamental properties of elastically stiff molecular materials and are assumed to be the same (symmetric) under both tension and compression loading. We show that molecular materials can have a marked asymmetric elastic modulus and coefficient of thermal expansion that are inherently related to terminal chemical groups that limit molecular network connectivity. In compression, terminal groups sterically interact to stiffen the network, whereas in tension they interact less and disconnect the network. The existence of asymmetric elastic and thermal expansion behaviour has fundamental implications for computational approaches to molecular materials modelling and practical implications on the thermomechanical strains and associated elastic stresses. We develop a design space to control the degree of elastic asymmetry in molecular materials, a vital step towards understanding their integration into device technologies.
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
NASA Astrophysics Data System (ADS)
Wang, Fu; Liu, Bo; Zhang, Lijia; Xin, Xiangjun; Tian, Qinghua; Zhang, Qi; Rao, Lan; Tian, Feng; Luo, Biao; Liu, Yingjun; Tang, Bao
2016-10-01
Elastic Optical Networks are considered to be a promising technology for future high-speed network. In this paper, we propose a RSA algorithm based on the ant colony optimization of minimum consecutiveness loss (ACO-MCL). Based on the effect of the spectrum consecutiveness loss on the pheromone in the ant colony optimization, the path and spectrum of the minimal impact on the network are selected for the service request. When an ant arrives at the destination node from the source node along a path, we assume that this path is selected for the request. We calculate the consecutiveness loss of candidate-neighbor link pairs along this path after the routing and spectrum assignment. Then, the networks update the pheromone according to the value of the consecutiveness loss. We save the path with the smallest value. After multiple iterations of the ant colony optimization, the final selection of the path is assigned for the request. The algorithms are simulated in different networks. The results show that ACO-MCL algorithm performs better in blocking probability and spectrum efficiency than other algorithms. Moreover, the ACO-MCL algorithm can effectively decrease spectrum fragmentation and enhance available spectrum consecutiveness. Compared with other algorithms, the ACO-MCL algorithm can reduce the blocking rate by at least 5.9% in heavy load.
Tan, Hung Nguyen; Inoue, Takashi; Kurosu, Takayuki; Namiki, Shu
2013-08-26
We propose the use of Nyquist OTDM-WDM signal for highly efficient, fully elastic all-optical networks. With the possibility of generation of ultra-coarse yet flexible granular channels, Nyquist OTDM-WDM can eliminate guard-bands in conventional WDM systems, and hence improves the spectral efficiency in network perspective. In this paper, transmission and pass-drop operations of mixed baudrate Nyquist OTDM-WDM channels from 43 Gbaud to dual-polarization 344 Gbaud are successfully demonstrated over 320 km fiber link with four FlexGrid-compatible WSS nodes. A stable clock recovery is also carried out for different baudrate Nyquist OTDMs by optical null-header insertion technique.
Cho, Hyun Woo; Kim, Sang Won; Kim, Jeongmin; Kim, Un Jeong; Im, Kyuhyun; Park, Jong-Jin; Sung, Bong June
2016-05-21
We investigate how the electrical conductance of microfibers (made of polymers and conductive nanofillers) decreases upon uniaxial deformation by performing both experiments and simulations. Even though various elastic conductors have been developed due to promising applications for deformable electronic devices, the mechanism at a molecular level for electrical conductance change has remained elusive. Previous studies proposed that the decrease in electrical conductance would result from changes in either distances or contact numbers between conductive fillers. In this work, we prepare microfibers of single walled carbon nanotubes (SWCNTs)/polyvinyl alcohol composites and investigate the electrical conductance and the orientation of SWCNTs upon uniaxial deformation. We also perform extensive Monte Carlo simulations, which reproduce experimental results for the relative decrease in conductance and the SWCNTs orientation. We investigate the electrical networks of SWCNTs in microfibers and find that the decrease in the electrical conductance upon uniaxial deformation should be attributed to a subtle change in the topological structure of the electrical network.
Tissue elasticity measurement method using forward and inversion algorithms
NASA Astrophysics Data System (ADS)
Lee, Jong-Ha; Won, Chang-Hee; Park, Hee-Jun; Ku, Jeonghun; Heo, Yun Seok; Kim, Yoon-Nyun
2013-03-01
Elasticity is an important indicator of tissue health, with increased stiffness pointing to an increased risk of cancer. We investigated a tissue elasticity measurement method using forward and inversion algorithms for the application of early breast tumor identification. An optical based elasticity measurement system is developed to capture images of the embedded lesions using total internal reflection principle. From elasticity images, we developed a novel method to estimate the elasticity of the embedded lesion using 3-D finite-element-model-based forward algorithm, and neural-network-based inversion algorithm. The experimental results showed that the proposed characterization method can be diffierentiate the benign and malignant breast lesions.
Teipel, Stefan J.; Grothe, Michel J.; Metzger, Coraline D.; Grimmer, Timo; Sorg, Christian; Ewers, Michael; Franzmeier, Nicolai; Meisenzahl, Eva; Klöppel, Stefan; Borchardt, Viola; Walter, Martin; Dyrba, Martin
2017-01-01
The large number of multicollinear regional features that are provided by resting state (rs) fMRI data requires robust feature selection to uncover consistent networks of functional disconnection in Alzheimer's disease (AD). Here, we compared elastic net regularized and classical stepwise logistic regression in respect to consistency of feature selection and diagnostic accuracy using rs-fMRI data from four centers of the “German resting-state initiative for diagnostic biomarkers” (psymri.org), comprising 53 AD patients and 118 age and sex matched healthy controls. Using all possible pairs of correlations between the time series of rs-fMRI signal from 84 functionally defined brain regions as the initial set of predictor variables, we calculated accuracy of group discrimination and consistency of feature selection with bootstrap cross-validation. Mean areas under the receiver operating characteristic curves as measure of diagnostic accuracy were 0.70 in unregularized and 0.80 in regularized regression. Elastic net regression was insensitive to scanner effects and recovered a consistent network of functional connectivity decline in AD that encompassed parts of the dorsal default mode as well as brain regions involved in attention, executive control, and language processing. Stepwise logistic regression found no consistent network of AD related functional connectivity decline. Regularized regression has high potential to increase diagnostic accuracy and consistency of feature selection from multicollinear functional neuroimaging data in AD. Our findings suggest an extended network of functional alterations in AD, but the diagnostic accuracy of rs-fMRI in this multicenter setting did not reach the benchmark defined for a useful biomarker of AD. PMID:28101051
Effects of disorder and chain stiffening on the elasticity of flexible polymer networks
NASA Astrophysics Data System (ADS)
Caroli, Christiane; Lemaître, Anaël
2017-03-01
We examine how the distribution of contour lengths and the high-stretch stiffening of individual chain segments affect the macroscopic shear modulus of flexible polymer gels, using a two-dimensional numerical model in which polymer segments form a triangular network and disorder is introduced by varying their contour lengths. We show that, in the relevant parameter range: (i) the nonaffine contribution to the shear modulus is negligible, i.e., the Born approximation is satisfactory, and (ii) the shear modulus is dominated by the contribution originating from equilibrium chain tensions. Moreover, mechanical equilibration at the nodes induces specific correlations between the end-to-end distances and contour lengths of chain segments, which must be properly accounted for to construct reasonable estimates of chain pressure and shear modulus.
Validation of elastic cross section models for space radiation applications
NASA Astrophysics Data System (ADS)
Werneth, C. M.; Xu, X.; Norman, R. B.; Ford, W. P.; Maung, K. M.
2017-02-01
The space radiation field is composed of energetic particles that pose both acute and long-term risks for astronauts in low earth orbit and beyond. In order to estimate radiation risk to crew members, the fluence of particles and biological response to the radiation must be known at tissue sites. Given that the spectral fluence at the boundary of the shielding material is characterized, radiation transport algorithms may be used to find the fluence of particles inside the shield and body, and the radio-biological response is estimated from experiments and models. The fidelity of the radiation spectrum inside the shield and body depends on radiation transport algorithms and the accuracy of the nuclear cross sections. In a recent study, self-consistent nuclear models based on multiple scattering theory that include the option to study relativistic kinematics were developed for the prediction of nuclear cross sections for space radiation applications. The aim of the current work is to use uncertainty quantification to ascertain the validity of the models as compared to a nuclear reaction database and to identify components of the models that can be improved in future efforts.
Modeling of porous elastic viscoplastic material with tensile failure
Glenn, L A; Rubin, M; Vorobiev, O
1998-11-01
This work describes simple but comprehensive constitutive equations that model a number of physical phenomena exhibited by dry porous geological materials and metals. Moreover, formulas have been developed for robust numerical integration of the evolution equations at the element level that can be easily implemented into standard computer programs for dynamic response of materials.
Using the Theory of Elasticity to Model the Structure of DNA Loops
NASA Astrophysics Data System (ADS)
Balaeff, Alexander; Mahadevan, L.; Schulten, Klaus
2000-03-01
A fast computational method to study the conformation and energetics of short DNA loops is presented. The DNA is modeled as an electrically charged elastic rod. The ensemble of equilibrium conformations of the DNA loop, attainable for given boundary conditions, is generated as a set of numerical solutions to the equations of the Kirchhoff-Love theory of elasticity. The equations are augmented by electrostatic and van der Waals force terms. These modifications allow one to account for the DNA self-repulsion and to model the DNA loop interactions with other macromolecules, involved in a biomolecular system. We demonstrate the application of the method to the test system: the looped lac operon promoter of E. coli clamped by the repressor protein and stabilized by the catabolite gene activator protein. The developed coarse-grained modeling method provides the basis for multi-resolution modeling of protein-DNA complexes, e.g., in combination with all-atom molecular dynamics simulations.
NASA Technical Reports Server (NTRS)
Hill, Gary; Du Val, Ronald W.; Green, John A.; Huynh, Loc C.
1990-01-01
A piloted comparison of rigid and aeroelastic blade-element rotor models was conducted at the Crew Station Research and Development Facility (CSRDF) at Ames Research Center. FLIGHTLAB, a new simulation development and analysis tool, was used to implement these models in real time using parallel processing technology. Pilot comments and quantitative analysis performed both on-line and off-line confirmed that elastic degrees of freedom significantly affect perceived handling qualities. Trim comparisons show improved correlation with flight test data when elastic modes are modeled. The results demonstrate the efficiency with which the mathematical modeling sophistication of existing simulation facilities can be upgraded using parallel processing, and the importance of these upgrades to simulation fidelity.
Cheng, Cheng; Cheng, Xiaosheng; Dai, Ning; Sun, Yuchun; Jiang, Xiaotong; Li, Weiwei
2017-02-07
With the development of 3D printing and computer graphics technology, mouth rehabilitation has increasingly adopted digital methods. This research proposes a new method to transform the appearance of facial model after complete denture prosthesis. A feature template with few feature points is first constructed according to the facial muscle anatomy and facial deformation after complete denture prosthesis. Next, the traditional as-rigid-as-possible (ARAP) method is optimised by clustering based on facial muscles. The optimised ARAP method is then used for real-time and interactive simulations. Finally, by classifying the degrees of elasticity in the model with additional weights, the simulation can be customised to the skin of individual patients. Different degrees of elastic deformation and post-operative models are superimposed for match analysis. Compared with our previous study, the error is reduced by 24.05%. Results show that our method can deform facial models accurately and efficiently.
Bayesian Networks for Social Modeling
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.
AeroPropulsoServoElasticity: Dynamic Modeling of the Variable Cycle Propulsion System
NASA Technical Reports Server (NTRS)
Kopasakis, George
2012-01-01
This presentation was made at the 2012 Fundamental Aeronautics Program Technical Conference and it covers research work for the Dynamic Modeling of the Variable cycle Propulsion System that was done under the Supersonics Project, in the area of AeroPropulsoServoElasticity. The presentation covers the objective for the propulsion system dynamic modeling work, followed by the work that has been done so far to model the variable Cycle Engine, modeling of the inlet, the nozzle, the modeling that has been done to model the affects of flow distortion, and finally presenting some concluding remarks and future plans.
Modelling land-fast sea ice using a linear elastic model
NASA Astrophysics Data System (ADS)
Plante, Mathieu; Tremblay, Bruno
2016-04-01
Land-fast ice is an important component of the Arctic system, capping the coastal Arctic waters for most of the year and exerting a large influence on ocean-atmosphere heat exchanges. Yet, the accurate representation of land-fast ice in most large-scale sea ice models remains a challenge, part due to the difficult (and sometimes non-physical) parametrisation of ice fracture. In this study, a linear elastic model is developed to investigate the internal stresses induced by the wind forcing on the land-fast ice, modelled as a 2D elastic plate. The model simulates ice fracture by the implementation of a damage coefficient which causes a local reduction in internal stress. This results in a cascade propagation of damage, simulating the ice fracture that determines the position of the land-fast ice edge. The modelled land-fast ice cover is sensitive to the choice of failure criterion. The parametrised cohesion, tensile and compressive strength and the relationship with the land-fast ice stability is discussed. To estimate the large scale mechanical properties of land-fast ice, these results are compared to a set of land-fast ice break up events and ice bridge formations observed in the Siberian Arctic. These events are identified using brightness temperature imagery from the MODIS (Moderate Resolution Imaging Spectroradiometer) Terra and Aqua satellites, from which the position of the flaw lead is identifiable by the opening of polynyi adjacent to the land-fast ice edge. The shape of the land-fast ice before, during and after these events, along with the characteristic scale of the resulting ice floes, are compared to the model results to extrapolate the stress state that corresponds to these observations. The model setting that best reproduce the scale of the observed break up events is used to provide an estimation of the strength of the ice relative to the wind forcing. These results will then be used to investigate the relationship between the ice thickness and the
NASA Technical Reports Server (NTRS)
Lissenden, Cliff J.; Herakovich, Carl T.
1992-01-01
Results for the predicted effective elastic properties of unidirectional composites are presented for glass/epoxy and graphite/epoxy using eight different models. A brief review of each of the models is given along with the final equations in most cases. It is shown that there is wide variation in some predictions for glass/epoxy and that the upper and lower composite cylinder assemblage bounds do not always fall close together for this material.
A 3D Orthotropic Strain-Rate Dependent Elastic Damage Material Model.
English, Shawn Allen
2014-09-01
A three dimensional orthotropic elastic constitutive model with continuum damage and cohesive based fracture is implemented for a general polymer matrix composite lamina. The formulation assumes the possibility of distributed (continuum) damage followed b y localized damage. The current damage activation functions are simply partially interactive quadratic strain criteria . However, the code structure allows for changes in the functions without extraordinary effort. The material model formulation, implementation, characterization and use cases are presented.
Modelling of nonlinear wave scattering in a delaminated elastic bar
Khusnutdinova, K. R.; Tranter, M. R.
2015-01-01
Integrity of layered structures, extensively used in modern industry, strongly depends on the quality of their interfaces; poor adhesion or delamination can lead to a failure of the structure. Can nonlinear waves help us to control the quality of layered structures? In this paper, we numerically model the dynamics of a long longitudinal strain solitary wave in a split, symmetric layered bar. The recently developed analytical approach, based on matching two asymptotic multiple-scales expansions and the integrability theory of the Korteweg–de Vries equation by the inverse scattering transform, is used to develop an effective semi-analytical numerical approach for these types of problems. We also employ a direct finite-difference method and compare the numerical results with each other, and with the analytical predictions. The numerical modelling confirms that delamination causes fission of an incident solitary wave and, thus, can be used to detect the defect. PMID:26730218
Anisotropic Elastic Resonance Scattering model for the Neutron Transport equation
Mohamed Ouisloumen; Abderrafi M. Ougouag; Shadi Z. Ghrayeb
2014-11-24
The resonance scattering transfer cross-section has been reformulated to account for anisotropic scattering in the center-of-mass of the neutron-nucleus system. The main innovation over previous implementations is the relaxation of the ubiquitous assumption of isotropic scattering in the center-of-mass and the actual effective use of scattering angle distributions from evaluated nuclear data files in the computation of the angular moments of the resonant scattering kernels. The formulas for the high order anisotropic moments in the laboratory system are also derived. A multi-group numerical formulation is derived and implemented into a module incorporated within the NJOY nuclear data processing code. An ultra-fine energy mesh cross section library was generated using these new theoretical models and then was used for fuel assembly calculations with the PARAGON lattice physics code. The results obtained indicate a strong effect of this new model on reactivity, multi-group fluxes and isotopic inventory during depletion.
Determination of Viral Capsid Elastic Properties from Equilibrium Thermal Fluctuations
NASA Astrophysics Data System (ADS)
May, Eric R.; Brooks, Charles L., III
2011-05-01
We apply two-dimensional elasticity theory to viral capsids to develop a framework for calculating elastic properties of viruses from equilibrium thermal fluctuations of the capsid surface in molecular dynamics and elastic network model trajectories. We show that the magnitudes of the long wavelength modes of motion available in a simulation with all atomic degrees of freedom are recapitulated by an elastic network model. For the mode spectra to match, the elastic network model must be scaled appropriately by a factor which can be determined from an icosahedrally constrained all-atom simulation. With this method we calculate the two-dimensional Young’s modulus Y, bending modulus κ, and Föppl-von Kármán number γ, for the T=1 mutant of the Sesbania mosaic virus. The values determined are in the range of previous theoretical estimates.
Colacino, Francesco Maria; Moscato, Francesco; Piedimonte, Fabio; Danieli, Guido; Nicosia, Salvatore; Arabia, Maurizio
2008-01-01
This article describes an elastance-based mock ventricle able to reproduce the correct ventricular pressure-volume relationship and its correct interaction with the hydraulic circuit connected to it. A real-time control of the mock ventricle was obtained by a new left ventricular mathematical model including resistive and inductive terms added to the classical Suga-Sagawa elastance model throughout the whole cardiac cycle. A valved piston pump was used to mimic the left ventricle. The pressure measured into the pump chamber was fed back into the mathematical model and the calculated reference left ventricular volume was used to drive the piston. Results show that the classical model is very sensitive to pressure disturbances, especially during the filling phase, while the modified model is able to filter out the oscillations thus eliminating their detrimental effects. The presented model is thus suitable to control mock ventricles in real-time, where sudden pressure disturbances represent a key issue and are not negligible. This real-time controlled mock ventricle is able to reproduce the elastance mechanism of a natural ventricle by mimicking its preload (mean atrial pressure) and afterload (mean aortic pressure) sensitivity, i.e., the Starling law. Therefore, it can be used for designing and testing cardiovascular prostheses due to its capability to reproduce the correct ventricle-vascular system interaction.
An Elastic-Plastic and Strength Prediction Model for Injection-Molded Long-Fiber Thermoplastics
Nguyen, Ba Nghiep; Kunc, Vlastimil; Phelps, Jay; Tucker III, Charles L.; Bapanapalli, Satish K.
2008-09-01
This paper applies a recently developed model to predict the elastic-plastic stress/strain response and strength of injection-molded long-fiber thermoplastics (LFTs). The model combines a micro-macro constitutive modeling approach with experimental characterization and modeling of the composite microstructure to determine the composite stress/strain response and strength. Specifically, it accounts for elastic fibers embedded in a thermoplastic resin that exhibits the elastic-plastic behavior obeying the Ramberg-Osgood relation and J-2 deformation theory of plasticity. It also accounts for fiber length, orientation and volume fraction distributions in the composite formed by the injection-molding process. Injection-molded-long-glass-fiber/polypropylene (PP) specimens were prepared for mechanical characterization and testing. Fiber length, orientation, and volume fraction distributions were then measured at some selected locations for use in the computation. Fiber orientations in these specimens were also predicted using an anisotropic rotary diffusion model developed for LFTs. The stress-strain response of the as-formed composite was computed by an incremental procedure that uses the Eshelby’s equivalent inclusion method, the Mori-Tanaka assumption and a fiber orientation averaging technique. The model has been validated against the experimental stress-strain results obtained for these long-glass-fiber/PP specimens.
A random interacting network model for complex networks
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
Seismic response modeling of multi-story buildings using neural networks
NASA Astrophysics Data System (ADS)
Conte, Joel P.; Durrani, Ahmad J.; Shelton, Robert O.
1994-05-01
A neural network based approach to model the seismic response of multi-story frame buildings is presented. The seismic response of frames is emulated using multi-layer feedforward neural networks with a backpropagation learning algorithm. Actual earthquake accelerograms and corresponding structural response obtained from analytical models of buildings are used in training the neural networks. The application of the neural network model is demonstrated by studying one to six story high building frames subjected to seismic base excitation. Furthermore, the learning ability of the network is examined for the case of multiple inputs where lateral forces at floor levels are included simultaneously with the base excitation. The effects of the network parameters on learning and accuracy of predictions are discussed. Based on this study, it is found that appropriately configured neural network models can successfully learn and simulate the linear elastic dynamic behavior of multi-story buildings.
Modified fractal model and rheological properties of colloidal networks.
Tang, Dongming; Marangoni, Alejandro G
2008-02-15
The scaling relationship between the storage modulus (G(')) and the volume fraction of solids (Phi) in fat crystal networks has been explained by the fractal model developed by our group. However, many experimental results and simulation studies suggest that the stress distribution within a colloidal network is dramatically heterogeneous, which means that a small part of the network carries most of the stress, while the other part of the network does not contribute much to the elastic properties of the system. This concept was introduced into a modified fractal model. The volume fraction of solids term (Phi) in the original fractal model was replaced by Phi(e), the effective volume fraction of solids, in the modified fractal model, which represents the volume fraction of stress-carrying solids. A proposed expression for Phi(e) is given and a modified expression for the scaling relationship between G(') and Phi is obtained. The modified fractal model fits the experiment data well and successfully explains the sometimes observed nonlinear log-log behavior between the storage modulus of colloidal networks and their volume fraction of solids.
Electro-elastic modeling of a dielectric elastomer diaphragm for a prosthetic blood pump
NASA Astrophysics Data System (ADS)
Goulbourne, Nakhiah C.; Frecker, Mary I.; Mockensturm, Eric
2004-07-01
A dielectric elastomer diaphragm is to be designed for potential use in a prosthetic blood pump. Application of an electric field deforms the membrane such that it moves from an initially flat configuration to an inflated state. This motion creates positive displacement of blood from the cardiac chambers thus mimicking the pump-like behavior of the natural heart. A comprehensive large deformation model accounting for the combined dielectric and elastic effect has been formulated. This paper presents recent developments in the model to further incorporate the entire nonlinear range of material elastic behavior and to more accurately represent the applied electric field by keeping the voltage constant as the membrane thickness decreases. The updated model is used to calculate the effects of varying system parameters such as pressure, voltage, prestretch, material constants, and membrane geometry. Analytical results are obtained for biaxially stretched 3M VHB 4905 polyacrylate films.
Network models. Comment on "Control profiles of complex networks".
Campbell, Colin; Shea, Katriona; Albert, Réka
2014-10-31
Ruths and Ruths (Reports, 21 March 2014, p. 1373) find that existing synthetic random network models fail to generate control profiles that match those found in real network models. Here, we show that a straightforward extension to the Barabási-Albert model allows the control profile to be "tuned" across the control profile space, permitting more meaningful control profile analyses of real networks.
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.
Relation between elastic modulus and glass softening temperature in the delocalized atom model
Sanditov, B. D.; Sangadiev, S. Sh.; Sanditov, D. S.
2012-09-15
The ratio of softening temperature (glass transition temperature) to elastic modulus (T{sub g}/E) is mainly determined by the limiting elastic deformation of an interatomic bond, which characterizes the transition of a structural microregion from an elastic into a viscous-flow state. In silicate glasses, this transition is caused by the limiting deformation of directed ionic-covalent Si-O-Si bonds. In the case of amorphous hydrocarbons, it is related to the relatively weak intermolecular bonds between regions in chain macromolecules, and the T{sub g}/E ratio is significantly higher than in inorganic glasses. In glassy systems of one class, this ratio turns out to be constant (T{sub g}/E Almost-Equal-To const), and a linear correlation is detected between softening temperature and elastic modulus, which can be explained in terms of the delocalized atom model. The values of T{sub g}/E can be used to classify glasses similarly to the well-known Angell classification according to so-called fragility.
Small oscillations of a pressurized, elastic, spherical shell: Model and experiments
NASA Astrophysics Data System (ADS)
Kuo, K. A.; Hunt, H. E. M.; Lister, John R.
2015-12-01
This paper presents a model for the small oscillations of a pressurized, elastic, spherical shell subject to internal and external fluid effects. The shell has three features: a pressure difference across the skin; a thin, tensioned shell; and a double curved interfacial surface. An analytical solution for the natural frequencies and mode shapes, incorporating the inertia both of the shell and the surrounding fluids, is derived. Two key parameters that quantify the effect of pre-stress and fluid inertia on the shell's behaviour are identified. When the skin tension is set to zero and the inertial effects of the fluid are removed, the results converge to the analytical solution for an elastic spherical shell, and when the skin elasticity is neglected, the results converge to the constant-tension solution of a bubble. The analytical solution is used to predict the natural frequencies of a small balloon, based on a value for the elastic modulus that is determined using inflation measurements. These predictions are compared to experimental measurements of balloon vibrations using impact-hammer testing, and good agreement is seen.
Hulthén potential models for α-α and α-He 3 elastic scattering
NASA Astrophysics Data System (ADS)
BHOI, J.; LAHA, U.
2017-03-01
Simple Hulthén-type potential models are proposed to treat the α- α and α {-} {He}3 elastic scattering. The merit of our approach is examined by computing elastic scattering phases through the judicious use of the phase function method. Reasonable agreements in scattering phase shifts are obtained with the standard data.
NASA Astrophysics Data System (ADS)
Rosa, A. N. F.; Wiatr, P.; Cavdar, C.; Carvalho, S. V.; Costa, J. C. W. A.; Wosinska, L.
2015-11-01
In Elastic Optical Network (EON), spectrum fragmentation refers to the existence of non-aligned, small-sized blocks of free subcarrier slots in the optical spectrum. Several metrics have been proposed in order to quantify a level of spectrum fragmentation. Approximation methods might be used for estimating average blocking probability and some fragmentation measures, but are so far unable to accurately evaluate the influence of different sizes of connection requests and do not allow in-depth investigation of blocking events and their relation to fragmentation. The analytical study of the effect of fragmentation on requests' blocking probability is still under-explored. In this work, we introduce new definitions for blocking that differentiate between the reasons for the blocking events. We developed a framework based on Markov modeling to calculate steady-state probabilities for the different blocking events and to analyze fragmentation related problems in elastic optical links under dynamic traffic conditions. This framework can also be used for evaluation of different definitions of fragmentation in terms of their relation to the blocking probability. We investigate how different allocation request sizes contribute to fragmentation and blocking probability. Moreover, we show to which extend blocking events, due to insufficient amount of available resources, become inevitable and, compared to the amount of blocking events due to fragmented spectrum, we draw conclusions on the possible gains one can achieve by system defragmentation. We also show how efficient spectrum allocation policies really are in reducing the part of fragmentation that in particular leads to actual blocking events. Simulation experiments are carried out showing good match with our analytical results for blocking probability in a small scale scenario. Simulated blocking probabilities for the different blocking events are provided for a larger scale elastic optical link.
Random Boolean network models and the yeast transcriptional network
NASA Astrophysics Data System (ADS)
Kauffman, Stuart; Peterson, Carsten; Samuelsson, Björn; Troein, Carl
2003-12-01
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean networks. We find that for ensembles of generated models, those with canalyzing Boolean rules are remarkably stable, whereas those with random Boolean rules are only marginally stable. Furthermore, substantial parts of the generated networks are frozen, in the sense that they reach the same state regardless of initial state. Thus, our ensemble approach suggests that the yeast network shows highly ordered dynamics.
Phase Field Models for Thin Elastic Structures with Topological Constraint
NASA Astrophysics Data System (ADS)
Dondl, Patrick W.; Lemenant, Antoine; Wojtowytsch, Stephan
2017-02-01
This article is concerned with the problem of minimising the Willmore energy in the class of connected surfaces with prescribed area which are confined to a small container. We propose a phase field approximation based on De Giorgi's diffuse Willmore functional to this variational problem. Our main contribution is a penalisation term which ensures connectedness in the sharp interface limit. The penalisation of disconnectedness is based on a geodesic distance chosen to be small between two points that lie on the same connected component of the transition layer of the phase field. We prove that in two dimensions, sequences of phase fields with uniformly bounded diffuse Willmore energy and diffuse area converge uniformly to the zeros of a double-well potential away from the support of a limiting measure. In three dimensions, we show that they converge H^1-almost everywhere on curves. This enables us to show {Γ}-convergence to a sharp interface problem that only allows for connected structures. The results also imply Hausdorff convergence of the level sets in two dimensions and a similar result in three dimensions. Furthermore, we present numerical evidence of the effectiveness of our model. The implementation relies on a coupling of Dijkstra's algorithm in order to compute the topological penalty to a finite element approach for the Willmore term.
Probabilistic logic modeling of network reliability for hybrid network architectures
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.
Paul, Shirshendu; Katiyar, Amit; Sarkar, Kausik; Chatterjee, Dhiman; Shi, William T.; Forsberg, Flemming
2010-01-01
Two nonlinear interfacial elasticity models—interfacial elasticity decreasing linearly and exponentially with area fraction—are developed for the encapsulation of contrast microbubbles. The strain softening (decreasing elasticity) results from the decreasing association between the constitutive molecules of the encapsulation. The models are used to find the characteristic properties (surface tension, interfacial elasticity, interfacial viscosity and nonlinear elasticity parameters) for a commercial contrast agent. Properties are found using the ultrasound attenuation measured through a suspension of contrast agent. Dynamics of the resulting models are simulated, compared with other existing models and discussed. Imposing non-negativity on the effective surface tension (the encapsulation experiences no net compressive stress) shows “compression-only” behavior. The exponential and the quadratic (linearly varying elasticity) models result in similar behaviors. The validity of the models is investigated by comparing their predictions of the scattered nonlinear response for the contrast agent at higher excitations against experimental measurement. All models predict well the scattered fundamental response. The nonlinear strain softening included in the proposed elastic models of the encapsulation improves their ability to predict subharmonic response. They predict the threshold excitation for the initiation of subharmonic response and its subsequent saturation. PMID:20550283
NASA Astrophysics Data System (ADS)
Khatri, Jaidev
This thesis examines themodeling, analysis, and control system design issues for scramjet powered hypersonic vehicles. A nonlinear three degrees of freedom longitudinal model which includes aero-propulsion-elasticity effects was used for all analyses. This model is based upon classical compressible flow and Euler-Bernouli structural concepts. Higher fidelity computational fluid dynamics and finite element methods are needed for more precise intermediate and final evaluations. The methods presented within this thesis were shown to be useful for guiding initial control relevant design. The model was used to examine the vehicle's static and dynamic characteristics over the vehicle's trimmable region. The vehicle has significant longitudinal coupling between the fuel equivalency ratio (FER) and the flight path angle (FPA). For control system design, a two-input two-output plant (FER - elevator to speed-FPA) with 11 states (including 3 flexible modes) was used. Velocity, FPA, and pitch were assumed to be available for feedback. Aerodynamic heat modeling and design for the assumed TPS was incorporated to original Bolender's model to study the change in static and dynamic properties. De-centralized control stability, feasibility and limitations issues were dealt with the change in TPS elasticity, mass and physical dimension. The impact of elasticity due to TPS mass, TPS physical dimension as well as prolonged heating was also analyzed to understand performance limitations of de-centralized control designed for nominal model.
Models for Gas Hydrate-Bearing Sediments Inferred from Hydraulic Permeability and Elastic Velocities
Lee, Myung W.
2008-01-01
Elastic velocities and hydraulic permeability of gas hydrate-bearing sediments strongly depend on how gas hydrate accumulates in pore spaces and various gas hydrate accumulation models are proposed to predict physical property changes due to gas hydrate concentrations. Elastic velocities and permeability predicted from a cementation model differ noticeably from those from a pore-filling model. A nuclear magnetic resonance (NMR) log provides in-situ water-filled porosity and hydraulic permeability of gas hydrate-bearing sediments. To test the two competing models, the NMR log along with conventional logs such as velocity and resistivity logs acquired at the Mallik 5L-38 well, Mackenzie Delta, Canada, were analyzed. When the clay content is less than about 12 percent, the NMR porosity is 'accurate' and the gas hydrate concentrations from the NMR log are comparable to those estimated from an electrical resistivity log. The variation of elastic velocities and relative permeability with respect to the gas hydrate concentration indicates that the dominant effect of gas hydrate in the pore space is the pore-filling characteristic.
A 2D multiring model of blood flow in elastic arteries
NASA Astrophysics Data System (ADS)
Ghigo, Arthur; Lagrée, Pierre-Yves; Fullana, Jose-Maria
2016-11-01
Three-dimensional simulations of blood flow in elastic arteries are difficult and costly due to the complex fluid-structure interactions between the motion of the fluid and the displacement of the wall. We propose a two-dimensional multiring model to overcome those difficulties and obtain at a reasonable computational cost an asymptotically valid description of blood flow in large elastic arteries. The multiring equations are derived by integrating over concentric rings of fluid a simplified system of equations based on a long wave approximation of the axisymmetric Navier-Stokes equations and a thin-cylinder description of the arterial wall. Contrary to classical one-dimensional models, obtained by integrating the same system over a single ring, the multiring model computes the velocity profile as well as the wall shear stress and requires no a priori estimation of model coefficients. We show that by numerically solving the multiring system of equations, we are able to compute a large range of classical blood flow solutions, ranging from the elastic Womersley solution to the rigid tube Poiseuille solution.
NASA Astrophysics Data System (ADS)
Berryman, James G.; Grechka, Vladimir
2006-12-01
A model study on fractured systems was performed using a concept that treats isotropic cracked systems as ensembles of cracked grains by analogy to isotropic polycrystalline elastic media. The approach has two advantages: (a) Averaging performed is ensemble averaging, thus avoiding the criticism legitimately leveled at most effective medium theories of quasistatic elastic behavior for cracked media based on volume concentrations of inclusions. Since crack effects are largely independent of the volume they occupy in the composite, such a non-volume-based method offers an appealingly simple modeling alternative. (b) The second advantage is that both polycrystals and fractured media are stiffer than might otherwise be expected, due to natural bridging effects of the strong components. These same effects have also often been interpreted as crack-crack screening in high-crack-density fractured media, but there is no inherent conflict between these two interpretations of this phenomenon. Results of the study are somewhat mixed. The spread in elastic constants observed in a set of numerical experiments is found to be very comparable to the spread in values contained between the Reuss and Voigt bounds for the polycrystal model. Unfortunately, computed Hashin-Shtrikman bounds are much too tight to be in agreement with the numerical data, showing that polycrystals of cracked grains tend to violate some implicit assumptions of the Hashin-Shtrikman bounding approach. However, the self-consistent estimates obtained for the random polycrystal model are nevertheless very good estimators of the observed average behavior.
Laplace-domain waveform modeling and inversion for the 3D acoustic-elastic coupled media
NASA Astrophysics Data System (ADS)
Shin, Jungkyun; Shin, Changsoo; Calandra, Henri
2016-06-01
Laplace-domain waveform inversion reconstructs long-wavelength subsurface models by using the zero-frequency component of damped seismic signals. Despite the computational advantages of Laplace-domain waveform inversion over conventional frequency-domain waveform inversion, an acoustic assumption and an iterative matrix solver have been used to invert 3D marine datasets to mitigate the intensive computing cost. In this study, we develop a Laplace-domain waveform modeling and inversion algorithm for 3D acoustic-elastic coupled media by using a parallel sparse direct solver library (MUltifrontal Massively Parallel Solver, MUMPS). We precisely simulate a real marine environment by coupling the 3D acoustic and elastic wave equations with the proper boundary condition at the fluid-solid interface. In addition, we can extract the elastic properties of the Earth below the sea bottom from the recorded acoustic pressure datasets. As a matrix solver, the parallel sparse direct solver is used to factorize the non-symmetric impedance matrix in a distributed memory architecture and rapidly solve the wave field for a number of shots by using the lower and upper matrix factors. Using both synthetic datasets and real datasets obtained by a 3D wide azimuth survey, the long-wavelength component of the P-wave and S-wave velocity models is reconstructed and the proposed modeling and inversion algorithm are verified. A cluster of 80 CPU cores is used for this study.
Improved free-surface expression for frequency-domain elastic optimal mixed-grid modeling
NASA Astrophysics Data System (ADS)
Cao, Jian; Chen, Jing-Bo; Dai, Meng-Xue
2016-07-01
An accurate and efficient forward modeling is the foundation of full-waveform inversion (FWI). In elastic wave modeling, one of the key problems is how to deal with the free-surface boundary condition appropriately. For the representation of the free-surface boundary condition, conventional displacement-based approaches and staggered-grid approaches are often used in time-domain. In frequency-domain, considering the saving of storage and CPU time, we integrate the idea of physical parameter-modified staggered-grid approach in time-domain with an elastic optimal mixed-grid modeling scheme to design an improved parameter-modified free-surface expression. Accuracy analysis shows that an elastic optimal mixed-grid modeling scheme using the parameter-modified free-surface expression can provide more accurate solutions with only 4 grid points per smallest shear wavelength than conventional displacement-based approaches and is stable for most Poisson ratios. Besides, it also yields smaller condition number of the resulting impedance matrix than conventional displacement-based approaches in laterally varying complex media. These advantages reveal great potential of this free-surface expression in big-data practical application.
NASA Astrophysics Data System (ADS)
Haddag, Badis; Abed-Meraim, Farid; Balan, Tudor
2007-05-01
In this work, an advanced anisotropic elastic-plasticity model is combined with a damage model and a strain localization criterion in the aim to describe accurately the mechanical behavior of sheet metals. Large strain, fully three-dimensional, implicit time integration algorithms are developed for this model and implemented in the finite element code Abaqus. The resulting code is used to predict the strain localization limits as well as the springback after forming of sheet steels. The impact of strain-path dependent hardening models on the limit strains and on the amount of springback is addressed.
Plate and butt-weld stresses beyond elastic limit, material and structural modeling
NASA Technical Reports Server (NTRS)
Verderaime, V.
1991-01-01
Ultimate safety factors of high performance structures depend on stress behavior beyond the elastic limit, a region not too well understood. An analytical modeling approach was developed to gain fundamental insights into inelastic responses of simple structural elements. Nonlinear material properties were expressed in engineering stresses and strains variables and combined with strength of material stress and strain equations similar to numerical piece-wise linear method. Integrations are continuous which allows for more detailed solutions. Included with interesting results are the classical combined axial tension and bending load model and the strain gauge conversion to stress beyond the elastic limit. Material discontinuity stress factors in butt-welds were derived. This is a working-type document with analytical methods and results applicable to all industries of high reliability structures.
Microscopic cluster model analysis of 14O+p elastic scattering
NASA Astrophysics Data System (ADS)
Baye, D.; Descouvemont, P.; Leo, F.
2005-08-01
The 14O+p elastic scattering is discussed in detail in a fully microscopic cluster model. The 14O cluster is described by a closed p shell for protons and a closed p3/2 subshell for neutrons in the translation-invariant harmonic-oscillator model. The exchange and spin-orbit parameters of the effective forces are tuned on the energy levels of the 15C mirror system. With the generator-coordinate and microscopic R-matrix methods, phase shifts and cross sections are calculated for the 14O+p elastic scattering. An excellent agreement is found with recent experimental data. A comparison is performed with phenomenological R-matrix fits. Resonances properties in 15F are discussed.
Microscopic cluster model analysis of {sup 14}O+p elastic scattering
Baye, D.; Descouvemont, P.; Leo, F.
2005-08-01
The {sup 14}O+p elastic scattering is discussed in detail in a fully microscopic cluster model. The {sup 14}O cluster is described by a closed p shell for protons and a closed p3/2 subshell for neutrons in the translation-invariant harmonic-oscillator model. The exchange and spin-orbit parameters of the effective forces are tuned on the energy levels of the {sup 15}C mirror system. With the generator-coordinate and microscopic R-matrix methods, phase shifts and cross sections are calculated for the {sup 14}O+p elastic scattering. An excellent agreement is found with recent experimental data. A comparison is performed with phenomenological R-matrix fits. Resonances properties in {sup 15}F are discussed.
NASA Technical Reports Server (NTRS)
Rehfield, Lawrence W.; Pickings, Richard D.; Chang, Stephen; Holl, Michael
1991-01-01
Structural tailoring concepts were developed to create wings with elastically produced camber for the purpose of increasing lift during takeoff conditions. Simple models based upon enhancements to the thin walled composite beam theory of Rehfield were developed to investigate prospects for elastic tailoring of the chordwise deformation of wing structures. The purpose here is to provide a comparison of the theoretical results with a finite element model for the bending method of producing camber. Finite element correlation studies were completed for two cases: a bonded unstiffened structural box, and a bolted unstiffened structural box. Results from these studies show an error of less than one percent for the bonded case and less than six percent for the bolted case in predicting camber curvature for the structural box. Examination of the results shows that the theory is very accurate for the cases studied and will provide an excellent basis for conducting further tailoring studies.
Elastic {sup 16}O+{sup 20}Ne scattering from a folding model analysis
Yang Yongxu; Li Qingrun
2011-07-15
A folding potential for elastic {sup 16}O+{sup 20}Ne scattering is constructed based on the four-{alpha}-particle model for the {sup 16}O nucleus and the {alpha}+{sup 16}O model for the {sup 20}Ne nucleus. The elastic scattering angular distributions of the {sup 16}O+{sup 20}Ne system in the energy range of E{sub c.m.}=24.5-35.5 MeV are calculated by use of the {alpha}-folding potential obtained. The calculations show that the experimental data can be reasonably well described. The surface term in the imaginary potential has a significant effect on the calculations of the cross section at large angles for the energies considered.
Modeling the Dynamics of Compromised Networks
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.
NASA Technical Reports Server (NTRS)
Kim, H. Alicia; Hardie, Robert; Yamakov, Vesselin; Park, Cheol
2015-01-01
This paper is the second part of a two-part series where the first part presents a molecular dynamics model of a single Boron Nitride Nanotube (BNNT) and this paper scales up to multiple BNNTs in a polymer matrix. This paper presents finite element (FE) models to investigate the effective elastic and piezoelectric properties of (BNNT) nanocomposites. The nanocomposites studied in this paper are thin films of polymer matrix with aligned co-planar BNNTs. The FE modelling approach provides a computationally efficient way to gain an understanding of the material properties. We examine several FE models to identify the most suitable models and investigate the effective properties with respect to the BNNT volume fraction and the number of nanotube walls. The FE models are constructed to represent aligned and randomly distributed BNNTs in a matrix of resin using 2D and 3D hollow and 3D filled cylinders. The homogenisation approach is employed to determine the overall elastic and piezoelectric constants for a range of volume fractions. These models are compared with an analytical model based on Mori-Tanaka formulation suitable for finite length cylindrical inclusions. The model applies to primarily single-wall BNNTs but is also extended to multi-wall BNNTs, for which preliminary results will be presented. Results from the Part 1 of this series can help to establish a constitutive relationship for input into the finite element model to enable the modeling of multiple BNNTs in a polymer matrix.
Simulation model for flow of neutrophils in pulmonary capillary network.
Shirai, Atsushi; Fujita, Ryo; Hayase, Toshiyuki
2005-01-01
The concentration of neutrophils in the pulmonary microvasculature is higher than in systemic large vessels. It is thought that the high concentration of neutrophils facilitates their effective recruitment to sites of inflammation. Thus, in order to understand the role of neutrophils in the immune system, it is important to clarify their flow characteristics in the pulmonary microvasculature. In previous studies, we numerically investigated the motion of a neutrophil through a single capillary segment modeled by a moderate axisymmetric constriction in a straight pipe, developing a mathematical model for the prediction of the transit time of the cell through the segment. In the present study, this model was extended for application to network simulation of the motion of neutrophils. First, we numerically investigated shape recovery of a neutrophil after expulsion from a narrow capillary segment. This process was modeled in two different phases: elastic recovery and viscous recovery. The resulting model was combined with the previously developed models to simulate motion of the cells and plasma flow in a capillary network. A numerical simulation of the motion of neutrophils and plasma flow in a simple lattice capillary network showed that neutrophils were widely dispersed in the network with an increased concentration.
A highly elastic, capacitive strain gauge based on percolating nanotube networks.
Cohen, Daniel J; Mitra, Debkishore; Peterson, Kevin; Maharbiz, Michel M
2012-04-11
We present a highly elastic strain gauge based on capacitive sensing of parallel, carbon nanotube-based percolation electrodes separated by a dielectric elastomer. The fabrication, relying on vacuum filtration of single-walled carbon nanotubes and hydrophobic patterning of silicone, is both rapid and inexpensive. We demonstrate reliable, linear performance over thousands of cycles at up to 100% strain with less than 3% variability and the highest reported gauge factor for a device of this class (0.99). We further demonstrate use of this sensor in a robotics context to transduce joint angles.
NASA Astrophysics Data System (ADS)
Enakoutsa, Koffi
2015-06-01
Recently, the works by Toupin, Mindlin, Sokolowski and Germain have been developed following two research streams. In the first one, higher-order gradient continuum models were developed based on the Cauchy tetrahedron argument (see, e.g., dell'Isola and Seppecher in Comptes Rendus de l Academie de Sciences 17 Serie IIb: Mecanique, Physique, Chimie, Astronomie 321:303-308, 1995, Meccanica 32:33-52 1997, Zeitschrift fr Angewandte Mathematik und Physik 63(6):1119-1141, 2012). In the second one, the structure of higher-order gradient models is developed with a view to the applications. In particular in the model of linear isotropic solids proposed by Dell'Isola, Sciarra and Vidoli (DSV), the main constitutive equation is obtained for the case of second gradient models. This model introduces in addition to the two well-known Lame's elastic constants five constitutive constants. The practical applications of this model remain in its infancy since the issue of determining the new moduli it introduces is not yet completely addressed. Also, analytical solutions of simple boundary value problems that can be helpful to grasp some of the physical foundations of this model are missing. This paper aims to address these two issues by providing the analytical solutions for two model problems, a spherical shell subjected to axisymmetric loading conditions and the circular bending of a beam in plane strain, both the beam and the shell obeying the DSV second gradient isotropic elastic model. The solution of the circular bending of a beam has served to grasp some of the physical soundness of the model. A framework based on homogenization under inhomogeneous boundary conditions is also suggested to determine the unknown constitutive constants, which are provided in the particular case of elastic porous heterogeneous materials.
Stochastic multiscale modelling of cortical bone elasticity based on high-resolution imaging.
Sansalone, Vittorio; Gagliardi, Davide; Desceliers, Christophe; Bousson, Valérie; Laredo, Jean-Denis; Peyrin, Françoise; Haïat, Guillaume; Naili, Salah
2016-02-01
Accurate and reliable assessment of bone quality requires predictive methods which could probe bone microstructure and provide information on bone mechanical properties. Multiscale modelling and simulation represent a fast and powerful way to predict bone mechanical properties based on experimental information on bone microstructure as obtained through X-ray-based methods. However, technical limitations of experimental devices used to inspect bone microstructure may produce blurry data, especially in in vivo conditions. Uncertainties affecting the experimental data (input) may question the reliability of the results predicted by the model (output). Since input data are uncertain, deterministic approaches are limited and new modelling paradigms are required. In this paper, a novel stochastic multiscale model is developed to estimate the elastic properties of bone while taking into account uncertainties on bone composition. Effective elastic properties of cortical bone tissue were computed using a multiscale model based on continuum micromechanics. Volume fractions of bone components (collagen, mineral, and water) were considered as random variables whose probabilistic description was built using the maximum entropy principle. The relevance of this approach was proved by analysing a human bone sample taken from the inferior femoral neck. The sample was imaged using synchrotron radiation micro-computed tomography. 3-D distributions of Haversian porosity and tissue mineral density extracted from these images supplied the experimental information needed to build the stochastic models of the volume fractions. Thus, the stochastic multiscale model provided reliable statistical information (such as mean values and confidence intervals) on bone elastic properties at the tissue scale. Moreover, the existence of a simpler "nominal model", accounting for the main features of the stochastic model, was investigated. It was shown that such a model does exist, and its relevance
NASA Astrophysics Data System (ADS)
Enakoutsa, Koffi
2014-09-01
Recently, the works by Toupin, Mindlin, Sokolowski and Germain have been developed following two research streams. In the first one, higher-order gradient continuum models were developed based on the Cauchy tetrahedron argument (see, e.g., dell'Isola and Seppecher in Comptes Rendus de l Academie de Sciences 17 Serie IIb: Mecanique, Physique, Chimie, Astronomie 321:303-308, 1995, Meccanica 32:33-52 1997, Zeitschrift fr Angewandte Mathematik und Physik 63(6):1119-1141, 2012). In the second one, the structure of higher-order gradient models is developed with a view to the applications. In particular in the model of linear isotropic solids proposed by Dell'Isola, Sciarra and Vidoli (DSV), the main constitutive equation is obtained for the case of second gradient models. This model introduces in addition to the two well-known Lame's elastic constants five constitutive constants. The practical applications of this model remain in its infancy since the issue of determining the new moduli it introduces is not yet completely addressed. Also, analytical solutions of simple boundary value problems that can be helpful to grasp some of the physical foundations of this model are missing. This paper aims to address these two issues by providing the analytical solutions for two model problems, a spherical shell subjected to axisymmetric loading conditions and the circular bending of a beam in plane strain, both the beam and the shell obeying the DSV second gradient isotropic elastic model. The solution of the circular bending of a beam has served to grasp some of the physical soundness of the model. A framework based on homogenization under inhomogeneous boundary conditions is also suggested to determine the unknown constitutive constants, which are provided in the particular case of elastic porous heterogeneous materials.
NASA Technical Reports Server (NTRS)
Kopasakis, George; Connolly, Joseph W.; Seiel, Jonathan
2016-01-01
A summary of the propulsion system modeling under NASA's High Speed Project (HSP) AeroPropulsoServoElasticity (APSE) task is provided with a focus on the propulsion system for the low-boom supersonic configuration developed by Lockheed Martin and referred to as the N+2 configuration. This summary includes details on the effort to date to develop computational models for the various propulsion system components. The objective of this paper is to summarize the model development effort in this task, while providing more detail in the modeling areas that have not been previously published. The purpose of the propulsion system modeling and the overall APSE effort is to develop an integrated dynamic vehicle model to conduct appropriate unsteady analysis of supersonic vehicle performance. This integrated APSE system model concept includes the propulsion system model, and the vehicle structural aerodynamics model. The development to date of such a preliminary integrated model will also be summarized in this report
NASA Technical Reports Server (NTRS)
Kopasakis, George; Connolly, Joseph W.; Seidel, Jonathan
2014-01-01
A summary of the propulsion system modeling under NASA's High Speed Project (HSP) AeroPropulsoServoElasticity (APSE) task is provided with a focus on the propulsion system for the lowboom supersonic configuration developed by Lockheed Martin and referred to as the N+2 configuration. This summary includes details on the effort to date to develop computational models for the various propulsion system components. The objective of this paper is to summarize the model development effort in this task, while providing more detail in the modeling areas that have not been previously published. The purpose of the propulsion system modeling and the overall APSE effort is to develop an integrated dynamic vehicle model to conduct appropriate unsteady analysis of supersonic vehicle performance. This integrated APSE system model concept includes the propulsion system model, and the vehicle structural-aerodynamics model. The development to date of such a preliminary integrated model will also be summarized in this report.
Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM)
NASA Astrophysics Data System (ADS)
Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei
2015-11-01
Gaussian network model (GNM) and anisotropic network model (ANM) are some of the most popular methods for the study of protein flexibility and related functions. In this work, we propose generalized GNM (gGNM) and ANM methods and show that the GNM Kirchhoff matrix can be built from the ideal low-pass filter, which is a special case of a wide class of correlation functions underpinning the linear scaling flexibility-rigidity index (FRI) method. Based on the mathematical structure of correlation functions, we propose a unified framework to construct generalized Kirchhoff matrices whose matrix inverse leads to gGNMs, whereas, the direct inverse of its diagonal elements gives rise to FRI method. With this connection, we further introduce two multiscale elastic network models, namely, multiscale GNM (mGNM) and multiscale ANM (mANM), which are able to incorporate different scales into the generalized Kirchhoff matrices or generalized Hessian matrices. We validate our new multiscale methods with extensive numerical experiments. We illustrate that gGNMs outperform the original GNM method in the B-factor prediction of a set of 364 proteins. We demonstrate that for a given correlation function, FRI and gGNM methods provide essentially identical B-factor predictions when the scale value in the correlation function is sufficiently large. More importantly, we reveal intrinsic multiscale behavior in protein structures. The proposed mGNM and mANM are able to capture this multiscale behavior and thus give rise to a significant improvement of more than 11% in B-factor predictions over the original GNM and ANM methods. We further demonstrate the benefits of our mGNM through the B-factor predictions of many proteins that fail the original GNM method. We show that the proposed mGNM can also be used to analyze protein domain separations. Finally, we showcase the ability of our mANM for the analysis of protein collective motions.
Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM).
Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei
2015-11-28
Gaussian network model (GNM) and anisotropic network model (ANM) are some of the most popular methods for the study of protein flexibility and related functions. In this work, we propose generalized GNM (gGNM) and ANM methods and show that the GNM Kirchhoff matrix can be built from the ideal low-pass filter, which is a special case of a wide class of correlation functions underpinning the linear scaling flexibility-rigidity index (FRI) method. Based on the mathematical structure of correlation functions, we propose a unified framework to construct generalized Kirchhoff matrices whose matrix inverse leads to gGNMs, whereas, the direct inverse of its diagonal elements gives rise to FRI method. With this connection, we further introduce two multiscale elastic network models, namely, multiscale GNM (mGNM) and multiscale ANM (mANM), which are able to incorporate different scales into the generalized Kirchhoff matrices or generalized Hessian matrices. We validate our new multiscale methods with extensive numerical experiments. We illustrate that gGNMs outperform the original GNM method in the B-factor prediction of a set of 364 proteins. We demonstrate that for a given correlation function, FRI and gGNM methods provide essentially identical B-factor predictions when the scale value in the correlation function is sufficiently large. More importantly, we reveal intrinsic multiscale behavior in protein structures. The proposed mGNM and mANM are able to capture this multiscale behavior and thus give rise to a significant improvement of more than 11% in B-factor predictions over the original GNM and ANM methods. We further demonstrate the benefits of our mGNM through the B-factor predictions of many proteins that fail the original GNM method. We show that the proposed mGNM can also be used to analyze protein domain separations. Finally, we showcase the ability of our mANM for the analysis of protein collective motions.
Berryman, James G.; Grechka, Vladimir
2006-07-08
A model study on fractured systems was performed using aconcept that treats isotropic cracked systems as ensembles of crackedgrains by analogy to isotropic polycrystalline elastic media. Theapproach has two advantages: (a) Averaging performed is ensembleaveraging, thus avoiding the criticism legitimately leveled at mosteffective medium theories of quasistatic elastic behavior for crackedmedia based on volume concentrations of inclusions. Since crack effectsare largely independent of the volume they occupy in the composite, sucha non-volume-based method offers an appealingly simple modelingalternative. (b) The second advantage is that both polycrystals andfractured media are stiffer than might otherwise be expected, due tonatural bridging effects of the strong components. These same effectshave also often been interpreted as crack-crack screening inhigh-crack-density fractured media, but there is no inherent conflictbetween these two interpretations of this phenomenon. Results of thestudy are somewhat mixed. The spread in elastic constants observed in aset of numerical experiments is found to be very comparable to the spreadin values contained between the Reuss and Voigt bounds for thepolycrystal model. However, computed Hashin-Shtrikman bounds are much tootight to be in agreement with the numerical data, showing thatpolycrystals of cracked grains tend to violate some implicit assumptionsof the Hashin-Shtrikman bounding approach. However, the self-consistentestimates obtained for the random polycrystal model are nevertheless verygood estimators of the observed average behavior.
NASA Astrophysics Data System (ADS)
Johnson, Stanley
An increasing adoption of digital signal processing (DSP) in optical fiber telecommunication has brought to the fore several interesting DSP enabled modulation formats. One such format is orthogonal frequency division multiplexing (OFDM), which has seen great success in wireless and wired RF applications, and is being actively investigated by several research groups for use in optical fiber telecom. In this dissertation, I present three implementations of OFDM for elastic optical networking and distributed network control. The first is a field programmable gate array (FPGA) based real-time implementation of a version of OFDM conventionally known as intensity modulation and direct detection (IMDD) OFDM. I experimentally demonstrate the ability of this transmission system to dynamically adjust bandwidth and modulation format to meet networking constraints in an automated manner. To the best of my knowledge, this is the first real-time software defined networking (SDN) based control of an OFDM system. In the second OFDM implementation, I experimentally demonstrate a novel OFDM transmission scheme that supports both direct detection and coherent detection receivers simultaneously using the same OFDM transmitter. This interchangeable receiver solution enables a trade-off between bit rate and equipment cost in network deployment and upgrades. I show that the proposed transmission scheme can provide a receiver sensitivity improvement of up to 1.73 dB as compared to IMDD OFDM. I also present two novel polarization analyzer based detection schemes, and study their performance using experiment and simulation. In the third implementation, I present an OFDM pilot-tone based scheme for distributed network control. The first instance of an SDN-based OFDM elastic optical network with pilot-tone assisted distributed control is demonstrated. An improvement in spectral efficiency and a fast reconfiguration time of 30 ms have been achieved in this experiment. Finally, I
Shouchun Deng; Robert Podgorney; Hai Huang
2011-02-01
Key challenges associated with the EGS reservoir development include the ability to reliably predict hydraulic fracturing and the deformation of natural fractures as well as estimating permeability evolution of the fracture network with time. We have developed a physics-based rock deformation and fracture propagation simulator by coupling a discrete element model (DEM) for fracturing with a network flow model. In DEM model, solid rock is represented by a network of discrete elements (often referred as particles) connected by various types of mechanical bonds such as springs, elastic beams or bonds that have more complex properties (such as stress-dependent elastic constants). Fracturing is represented explicitly as broken bonds (microcracks), which form and coalesce into macroscopic fractures when external and internal load is applied. The natural fractures are represented by a series of connected line segments. Mechanical bonds that intersect with such line segments are removed from the DEM model. A network flow model using conjugate lattice to the DEM network is developed and coupled with the DEM. The fluid pressure gradient exerts forces on individual elements of the DEM network, which therefore deforms the mechanical bonds and breaks them if the deformation reaches a prescribed threshold value. Such deformation/fracturing in turn changes the permeability of the flow network, which again changes the evolution of fluid pressure, intimately coupling the two processes. The intimate coupling between fracturing/deformation of fracture networks and fluid flow makes the meso-scale DEM- network flow simulations necessary in order to accurately evaluate the permeability evolution, as these methods have substantial advantages over conventional continuum mechanical models of elastic rock deformation. The challenges that must be overcome to simulate EGS reservoir stimulation, preliminary results, progress to date and near future research directions and opportunities will be
Dahl, Kris Noel; Kahn, Samuel M; Wilson, Katherine L; Discher, Dennis E
2004-09-15
Mechanical properties of the nuclear envelope have implications for cell and nuclear architecture as well as gene regulation. Using isolated Xenopus oocyte nuclei, we have established swelling conditions that separate the intact nuclear envelope (membranes, pore complexes and underlying lamin filament network) from nucleoplasm and the majority of chromatin. Swelling proves reversible with addition of high molecular mass dextrans. Micropipette aspiration of swollen and unswollen nuclear envelopes is also reversible and yields a network elastic modulus, unaffected by nucleoplasm, that averages 25 mN/m. Compared to plasma membranes of cells, the nuclear envelope is much stiffer and more resilient. Our results suggest that the nuclear lamina forms a compressed network shell of interconnected rods that is extensible but limited in compressibility from the native state, thus acting as a 'molecular shock absorber'. In light of the conservation of B-type lamins in metazoan evolution, the mechanical properties determined in this investigation suggest physical mechanisms by which mutated lamins can either destabilize nuclear architecture or influence nuclear responses to mechanical signals in Emery-Dreifuss muscular dystrophy, cardiomyopathy, progeria syndromes (premature 'aging') and other laminopathies.
A continuum model to study interphase effects on elastic properties of CNT/GS-nanocomposite
NASA Astrophysics Data System (ADS)
Srivastava, Ashish; Kumar, Dinesh
2017-02-01
In the present study, initially a continuum level model of interphase region in a carbon nanotube (CNT)/graphene sheet (GS) based nanocomposite is established. Cohesive zone model through Lennard Jones (i.e. LJ) potential is utilized to model the interphase zone in terms of its thickness and elastic modulus, for different matrix materials containing CNTs of various radii (including graphene—a CNT of infinite radius). Thereafter, a finite element based study is conducted to characterize and compare the CNT- and GS-reinforced nanocomposites with and without interphase, using the method of representative volume element (RVE). Based on the study, it is concluded that the thickness as well as elastic modulus of the interphase zone is significantly affected by the matrix material of nanocomposite which is in contrast to the general assumption, made in the literature, of constant thickness of interphase zone for different matrix materials. In the case of nanocomposite with small radius CNTs, slightly higher, noticeable only at narrow scale, elastic modulus of interphase zone is obtained than the nanocomposite with large radius CNTs, irrespective of matrix materials. For metal nanocomposites, interphase zone results in loss of all stiffness properties of the resulting CNT/GS nanocomposite, and this loss is more prevalent in GS nanocomposite for its out-of-plane stiffness properties. But, on the contrary, in the case of polyethylene (i.e. PE) nanocomposite, the elastic modulus of interphase causes enhanced stiffness properties of the resulting nanocomposite, as compared to the perfectly bonded nanocomposite, for CNT and GS reinforcements.
Modeling static and dynamic thermography of the human breast under elastic deformation.
Jiang, Li; Zhan, Wang; Loew, Murray H
2011-01-07
An abnormal thermogram has been shown to be a reliable indicator of increased risk of breast cancer. Numerical modeling techniques for thermography are proposed to quantify the complex relationships between the breast thermal behaviors and the underlying physiological/pathological conditions. Previous thermal modeling techniques did not account for gravity-induced elastic deformation arising from various body postures, nor did they suggest that a dynamic thermal procedure may be used to enhance clinical diagnosis. In this paper, 3D finite element method (FEM)-based thermal and elastic modeling techniques are developed to characterize comprehensively both the thermal and elastic properties of normal and tumorous breast tissues during static and dynamic thermography. In the steady state, gravity-induced breast deformation is found to cause an upper-lower asymmetric surface temperature contrast for sitting/standing up body posture, even though all the thermal and elastic properties are assumed uniform. Additionally, the tumor-induced surface temperature alterations are found to be caused primarily by shallow tumors and to be less sensitive to tumor size than to tumor depth. In the dynamic state, the breast exhibits distinctive temporal patterns that are associated with distinct thermal events: cold stress and thermal recovery induced by changes in the ambient temperature. Specifically, the tumor-induced thermal contrast shows an opposite initial change and delayed peak as compared with the deformation-induced thermal contrast. These findings are expected to provide a stronger foundation for, and greater specificity and precision in, thermographic diagnosis, and treatment of breast cancer.
NASA Astrophysics Data System (ADS)
Norouzzadeh, A.; Ansari, R.
2017-04-01
Stress-strain relation in Eringen's nonlocal elasticity theory was originally formulated within the framework of an integral model. Due to difficulty of working with that integral model, the differential model of nonlocal constitutive equation is widely used for nanostructures. However, paradoxical results may be obtained by the differential model for some boundary and loading conditions. Presented in this article is a finite element analysis of Timoshenko nano-beams based on the integral model of nonlocal continuum theory without employing any simplification in the model. The entire procedure of deriving equations of motion is carried out in the matrix form of representation, and hence, they can be easily used in the finite element analysis. For comparison purpose, the differential counterparts of equations are also derived. To study the outcome of analysis based on the integral and differential models, some case studies are presented in which the influences of boundary conditions, nonlocal length scale parameter and loading factor are analyzed. It is concluded that, in contrast to the differential model, there is no paradox in the numerical results of developed integral model of nonlocal continuum theory for different situations of problem characteristics. So, resolving the mentioned paradoxes by means of a purely numerical approach based on the original integral form of nonlocal elasticity theory is the major contribution of present study.
Double Folding Potential of Different Interaction Models for 16O + 12C Elastic Scattering
NASA Astrophysics Data System (ADS)
Hamada, Sh.; Bondok, I.; Abdelmoatmed, M.
2016-12-01
The elastic scattering angular distributions for 16O + 12C nuclear system have been analyzed using double folding potential of different interaction models: CDM3Y1, CDM3Y6, DDM3Y1 and BDM3Y1. We have extracted the renormalization factor N r for the different concerned interaction models. Potential created by BDM3Y1 model of interaction has the shallowest depth which reflects the necessity to use higher renormalization factor. The experimental angular distributions for 16O + 12C nuclear system in the energy range 115.9-230 MeV exhibited unmistakable refractive features and rainbow phenomenon.
A better prediction of conformational changes of proteins using minimally connected network models
NASA Astrophysics Data System (ADS)
Ahmadi Toussi, Cyrus; Soheilifard, Reza
2016-12-01
Elastic network models have recently been used for studying low-frequency collective motions of proteins. These models simplify the complexity that arises from normal mode analysis by considering a simplified potential involving a few parameters. Two common parameters in most of the elastic network models are cutoff radius and force constant. Although the latter has been studied extensively and even elaborate new models were introduced, for the former usually an ad-hoc cutoff radius is considered. Moreover, the quality of the network models is usually assessed by evaluating their prediction against experimental B-factors. In this work, we consider various common elastic network models with different cutoff radii and assess them by their ability to predict conformational changes of proteins in complexes from unbound to bound state. This prediction is performed by perturbing the unbound structure using a number of low-frequency normal modes of its network model to optimally fit the bound structure. We evaluated a dataset of 30 proteins with distinct unbound and bound structures using this criterion. The results showed that, opposed to the common calibration process based on B-factors, a meaningful relationship exists between the quality of the prediction and model parameters. It was shown that the cutoff radius has a major role in this prediction and minimally connected network models, which use the shortest cutoff radius for which the network is stable, give the best results. It was also shown that by considering the first ten normal modes, the conformational changes can be predicted by about 25 percent. Hence, the evaluation process was extended to the case of considering the contribution of all normal modes in the prediction. The results indicated that minimally connected network models are superior, despite their simplicity, when any number of modes are considered in the prediction.
Network Bandwidth Utilization Forecast Model on High Bandwidth Network
Yoo, Wucherl; Sim, Alex
2014-07-07
With the increasing number of geographically distributed scientific collaborations and the scale of the data size growth, it has become more challenging for users to achieve the best possible network performance on a shared network. We have developed a forecast model to predict expected bandwidth utilization for high-bandwidth wide area network. The forecast model can improve the efficiency of resource utilization and scheduling data movements on high-bandwidth network to accommodate ever increasing data volume for large-scale scientific data applications. Univariate model is developed with STL and ARIMA on SNMP path utilization data. Compared with traditional approach such as Box-Jenkins methodology, our forecast model reduces computation time by 83.2percent. It also shows resilience against abrupt network usage change. The accuracy of the forecast model is within the standard deviation of the monitored measurements.
Models of the elastic x-ray scattering feature for warm dense aluminum
NASA Astrophysics Data System (ADS)
Starrett, C. E.; Saumon, D.
2015-09-01
The elastic feature of x-ray scattering from warm dense aluminum has recently been measured by Fletcher et al. [Nature Photonics 9, 274 (2015)], 10.1038/nphoton.2015.41 with much higher accuracy than had hitherto been possible. This measurement is a direct test of the ionic structure predicted by models of warm dense matter. We use the method of pseudoatom molecular dynamics to predict this elastic feature for warm dense aluminum with temperatures of 1-100 eV and densities of 2.7 -8.1 g/cm 3 . We compare these predictions to experiments, finding good agreement with Fletcher et al. and corroborating the discrepancy found in analyses of an earlier experiment of Ma et al. [Phys. Rev. Lett. 110, 065001 (2013)], 10.1103/PhysRevLett.110.065001. We also evaluate the validity of the Thomas-Fermi model of the electrons and of the hypernetted chain approximation in computing the elastic feature and find them both wanting in the regime currently probed by experiments.
Models of the elastic x-ray scattering feature for warm dense aluminum
Starrett, Charles Edward; Saumon, Didier
2015-09-03
The elastic feature of x-ray scattering from warm dense aluminum has recently been measured by Fletcher et al. [Nature Photonics 9, 274 (2015)] with much higher accuracy than had hitherto been possible. This measurement is a direct test of the ionic structure predicted by models of warm dense matter. We use the method of pseudoatom molecular dynamics to predict this elastic feature for warm dense aluminum with temperatures of 1–100 eV and densities of 2.7–8.1g/cm3. We compare these predictions to experiments, finding good agreement with Fletcher et al. and corroborating the discrepancy found in analyses of an earlier experiment ofmore » Ma et al. [Phys. Rev. Lett. 110, 065001 (2013)]. Lastly, we also evaluate the validity of the Thomas-Fermi model of the electrons and of the hypernetted chain approximation in computing the elastic feature and find them both wanting in the regime currently probed by experiments.« less
Models of the elastic x-ray scattering feature for warm dense aluminum
Starrett, Charles Edward; Saumon, Didier
2015-09-03
The elastic feature of x-ray scattering from warm dense aluminum has recently been measured by Fletcher et al. [Nature Photonics 9, 274 (2015)] with much higher accuracy than had hitherto been possible. This measurement is a direct test of the ionic structure predicted by models of warm dense matter. We use the method of pseudoatom molecular dynamics to predict this elastic feature for warm dense aluminum with temperatures of 1–100 eV and densities of 2.7–8.1g/cm^{3}. We compare these predictions to experiments, finding good agreement with Fletcher et al. and corroborating the discrepancy found in analyses of an earlier experiment of Ma et al. [Phys. Rev. Lett. 110, 065001 (2013)]. Lastly, we also evaluate the validity of the Thomas-Fermi model of the electrons and of the hypernetted chain approximation in computing the elastic feature and find them both wanting in the regime currently probed by experiments.
Hamed, Elham; Novitskaya, Ekaterina; Li, Jun; Jasiuk, Iwona; McKittrick, Joanna
2015-09-01
The elastic moduli of trabecular bone were modeled using an analytical multiscale approach. Trabecular bone was represented as a porous nanocomposite material with a hierarchical structure spanning from the collagen-mineral level to the trabecular architecture level. In parallel, compression testing was done on bovine femoral trabecular bone samples in two anatomical directions, parallel to the femoral neck axis and perpendicular to it, and the measured elastic moduli were compared with the corresponding theoretical results. To gain insights on the interaction of collagen and minerals at the nanoscale, bone samples were deproteinized or demineralized. After such processing, the treated samples remained as self-standing structures and were tested in compression. Micro-computed tomography was used to characterize the hierarchical structure of these three bone types and to quantify the amount of bone porosity. The obtained experimental data served as inputs to the multiscale model and guided us to represent bone as an interpenetrating composite material. Good agreement was found between the theory and experiments for the elastic moduli of the untreated, deproteinized, and demineralized trabecular bone.
Point defect modeling in materials: Coupling ab initio and elasticity approaches
NASA Astrophysics Data System (ADS)
Varvenne, Céline; Bruneval, Fabien; Marinica, Mihai-Cosmin; Clouet, Emmanuel
2013-10-01
Modeling point defects at an atomic scale requires careful treatment of the long-range atomic relaxations. This elastic field can strongly affect point defect properties calculated in atomistic simulations because of the finite size of the system under study. This is an important restriction for ab initio methods which are limited to a few hundred atoms. We propose an original approach coupling ab initio calculations and linear elasticity theory to obtain the properties of an isolated point defect for reduced supercell sizes. The reliability and benefit of our approach are demonstrated for three problematic cases: the self-interstitial in zirconium, clusters of self-interstitials in iron, and the neutral vacancy in silicon.
Dynamic thermal modeling of the normal and tumorous breast under elastic deformation.
Jiang, Li; Zhan, Wang; Loew, Murray H
2008-01-01
To quantify the complex relationships between (1) the temperature, and temperature differences, on the surface of the breast as recorded by infrared thermal imaging and (2) the underlying physiological and pathological factors, we have developed a dynamic finite element method for comprehensive modeling of both the thermal and elastic properties of normal and tumorous breast tissues. In the steady state, the gravity-induced deformation is found to cause markedly asymmetric surface temperatures even though all thermal-elastic properties are symmetrical. In the dynamic state, the time course of breast thermal imaging in cold-stress and thermal-recovery procedures is found to be useful in characterizing the origins of the thermal contrast on the breast surface. The tumor-induced thermal contrast has slower temporal behavior than the deformation-induced thermal contrast on the breast surface, which may lead to improvements in breast-tumor diagnosis.
Model for natural convective flow of visco-elastic nanofluid past an isothermal vertical plate
NASA Astrophysics Data System (ADS)
Mustafa, M.; Mushtaq, Ammar
2015-09-01
The present article addresses the classical problem of the natural convection flow past a vertical plate by considering visco-elastic nanofluid. The mathematical model is constructed by following the constitutive equations of the upper-convected Maxwell (UCM) fluid. The novel aspects of Brownian motion and thermophoresis are taken into account. The recently proposed condition of passively controlled wall nanoparticle volume fraction is used. The shooting approach combined with the fourth-fifth-order Runge-Kutta integration procedure is utilized for computing the numerical solutions. The results are in agreement with the available studies in limiting sense. Our results indicate that the velocity profile is parabolic and it decreases with an increment in the visco-elastic parameter.
Elastic properties of compressed crystalline Ne in the model of deformable atoms
NASA Astrophysics Data System (ADS)
Troitskaya, E. P.; Chabanenko, V. V.; Zhikharev, I. V.; Gorbenko, Ie. Ie.; Pilipenko, E. A.
2013-02-01
An ab initio version of the model with deformable atoms has been constructed to investigate the elastic properties of compressed crystalline neon. Approximations for the calculating parameters of quadrupole deformation of atomic electron shells have been discussed. It has been shown that the pressure dependence of the deviation from the Cauchy relation δ is the result of two competitive interactions, namely, the many-body and electron-phonon interactions, which manifests itself in the deformation of atomic electron shells during the shift of nuclei. In the case of Ne, contributions of these interactions are compensated to a large degree, which provides a weakly pressure-dependent positive value for δ. The agreement of calculated elastic moduli and deviations from the Cauchy relation for Ne with the experiment is good.
Gao, Wei; Chen, Dongliang; Wang, Xu
2016-01-01
To compute the stability of underground engineering, a constitutive model of surrounding rock must be identified. Many constitutive models for rock mass have been proposed. In this model identification study, a generalized constitutive law for an elastic-plastic constitutive model is applied. Using the generalized constitutive law, the problem of model identification is transformed to a problem of parameter identification, which is a typical and complicated optimization. To improve the efficiency of the traditional optimization method, an immunized genetic algorithm that is proposed by the author is applied in this study. In this new algorithm, the principle of artificial immune algorithm is combined with the genetic algorithm. Therefore, the entire computation efficiency of model identification will be improved. Using this new model identification method, a numerical example and an engineering example are used to verify the computing ability of the algorithm. The results show that this new model identification algorithm can significantly improve the computation efficiency and the computation effect.
Seleson, Pablo; Du, Qiang; Parks, Michael L.
2016-08-16
The peridynamic theory of solid mechanics is a nonlocal reformulation of the classical continuum mechanics theory. At the continuum level, it has been demonstrated that classical (local) elasticity is a special case of peridynamics. Such a connection between these theories has not been extensively explored at the discrete level. This paper investigates the consistency between nearest-neighbor discretizations of linear elastic peridynamic models and finite difference discretizations of the Navier–Cauchy equation of classical elasticity. While nearest-neighbor discretizations in peridynamics have been numerically observed to present grid-dependent crack paths or spurious microcracks, this paper focuses on a different, analytical aspect of such discretizations. We demonstrate that, even in the absence of cracks, such discretizations may be problematic unless a proper selection of weights is used. Specifically, we demonstrate that using the standard meshfree approach in peridynamics, nearest-neighbor discretizations do not reduce, in general, to discretizations of corresponding classical models. We study nodal-based quadratures for the discretization of peridynamic models, and we derive quadrature weights that result in consistency between nearest-neighbor discretizations of peridynamic models and discretized classical models. The quadrature weights that lead to such consistency are, however, model-/discretization-dependent. We motivate the choice of those quadrature weights through a quadratic approximation of displacement fields. The stability of nearest-neighbor peridynamic schemes is demonstrated through a Fourier mode analysis. Finally, an approach based on a normalization of peridynamic constitutive constants at the discrete level is explored. This approach results in the desired consistency for one-dimensional models, but does not work in higher dimensions. The results of the work presented in this paper suggest that even though nearest
A system dynamics model for communications networks
NASA Astrophysics Data System (ADS)
Awcock, A. J.; King, T. E. G.
1985-09-01
An abstract model of a communications network in system dynamics terminology is developed as implementation of this model by a FORTRAN program package developed at RSRE is discussed. The result of this work is a high-level simulation package in which the performance of adaptive routing algorithms and other network controls may be assessed for a network of arbitrary topology.
A nonaffine network model for elastomers undergoing finite deformations
NASA Astrophysics Data System (ADS)
Davidson, Jacob D.; Goulbourne, N. C.
2013-08-01
In this work, we construct a new physics-based model of rubber elasticity to capture the strain softening, strain hardening, and deformation-state dependent response of rubber materials undergoing finite deformations. This model is unique in its ability to capture large-stretch mechanical behavior with parameters that are connected to the polymer chemistry and can also be easily identified with the important characteristics of the macroscopic stress-stretch response. The microscopic picture consists of two components: a crosslinked network of Langevin chains and an entangled network with chains confined to a nonaffine tube. These represent, respectively, changes in entropy due to thermally averaged chain conformations and changes in entropy due to the magnitude of these conformational fluctuations. A simple analytical form for the strain energy density is obtained using Rubinstein and Panyukov's single-chain description of network behavior. The model only depends on three parameters that together define the initial modulus, extent of strain softening, and the onset of strain hardening. Fits to large stretch data for natural rubber, silicone rubber, VHB 4905 (polyacrylate rubber), and b186 rubber (a carbon black-filled rubber) are presented, and a comparison is made with other similar constitutive models of large-stretch rubber elasticity. We demonstrate that the proposed model provides a complete description of elastomers undergoing large deformations for different applied loading configurations. Moreover, since the strain energy is obtained using a clear set of physical assumptions, this model may be tested and used to interpret the results of computer simulation and experiments on polymers of known microscopic structure.
An Adaptive Complex Network Model for Brain Functional Networks
Gomez Portillo, Ignacio J.; Gleiser, Pablo M.
2009-01-01
Brain functional networks are graph representations of activity in the brain, where the vertices represent anatomical regions and the edges their functional connectivity. These networks present a robust small world topological structure, characterized by highly integrated modules connected sparsely by long range links. Recent studies showed that other topological properties such as the degree distribution and the presence (or absence) of a hierarchical structure are not robust, and show different intriguing behaviors. In order to understand the basic ingredients necessary for the emergence of these complex network structures we present an adaptive complex network model for human brain functional networks. The microscopic units of the model are dynamical nodes that represent active regions of the brain, whose interaction gives rise to complex network structures. The links between the nodes are chosen following an adaptive algorithm that establishes connections between dynamical elements with similar internal states. We show that the model is able to describe topological characteristics of human brain networks obtained from functional magnetic resonance imaging studies. In particular, when the dynamical rules of the model allow for integrated processing over the entire network scale-free non-hierarchical networks with well defined communities emerge. On the other hand, when the dynamical rules restrict the information to a local neighborhood, communities cluster together into larger ones, giving rise to a hierarchical structure, with a truncated power law degree distribution. PMID:19738902
Yang, Hui; Zhang, Jie; Ji, Yuefeng; Tian, Rui; Han, Jianrui; Lee, Young
2015-11-30
Data center interconnect 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 multi-stratum resilience between IP and elastic optical networks that allows to accommodate data center services. In view of this, this study extends to consider the resource integration by breaking the limit of network device, which can enhance the resource utilization. We propose a novel multi-stratum resources integration (MSRI) architecture based on network function virtualization in software defined elastic data center optical interconnect. A resource integrated mapping (RIM) scheme for MSRI is introduced in the proposed architecture. The MSRI can accommodate the data center services with resources integration when the single function or resource is relatively scarce to provision the services, and enhance globally integrated optimization of optical network and application resources. The overall feasibility and efficiency of the proposed architecture are experimentally verified on the control plane of OpenFlow-based enhanced software defined networking (eSDN) testbed. The performance of RIM scheme under heavy traffic load scenario is also quantitatively evaluated based on MSRI architecture in terms of path blocking probability, provisioning latency and resource utilization, compared with other provisioning schemes.
Modeling gene regulatory networks: A network simplification algorithm
NASA Astrophysics Data System (ADS)
Ferreira, Luiz Henrique O.; de Castro, Maria Clicia S.; da Silva, Fabricio A. B.
2016-12-01
Boolean networks have been used for some time to model Gene Regulatory Networks (GRNs), which describe cell functions. Those models can help biologists to make predictions, prognosis and even specialized treatment when some disturb on the GRN lead to a sick condition. However, the amount of information related to a GRN can be huge, making the task of inferring its boolean network representation quite a challenge. The method shown here takes into account information about the interactome to build a network, where each node represents a protein, and uses the entropy of each node as a key to reduce the size of the network, allowing the further inferring process to focus only on the main protein hubs, the ones with most potential to interfere in overall network behavior.
2007-05-04
amplitude of oscillation, 01 0, kF ox <<−=− and A kF ox <<−=+ 02 , , where 12 kk < . If 02 =k , the elastoplastic case of Iwan’s model for...curve identifies the system as potentially mesoscopic elastic. The elasto-slip model of elastoplastic hysteresis presented by Iwan exhibits linear...in damaged concrete: Quantitative analysis of slow and fast dynamics,” Phys. Rev. B, 73, 014116 (2006). Bolton, M.D., and Wilson, J.M.R, “An
Coexistence of ordinary elasticity and superfluidity in a model of a defect-free supersolid.
Josserand, Christophe; Pomeau, Yves; Rica, Sergio
2007-05-11
The mechanical behavior of a supersolid is studied in the framework of a fully explicit model derived from the Gross-Pitaevskii equation without assuming any defect or vacancy. A set of coupled nonlinear partial differential equations plus boundary conditions is derived. The conditions of mechanical equilibrium are studied under external constraints such as steady rotation and external stress. Our model explains the experimentally observed paradoxical behavior: a nonclassical rotational inertia fraction in the limit of small rotation speed but a solidlike elastic response to small stress or an external force field.
Rough surface scattering from an elastic scale model of an ocean bottom
NASA Astrophysics Data System (ADS)
Soukup, Raymond J.; Gragg, Robert F.; Wiley, Robert W.; Inanli, Burcin
2003-10-01
Monostatic and bistatic scattering strength measurements with a rough PVC surface were collected during two experiments in an acoustic tank facility at the Allied Geophysical Laboratories in the University of Houston. The PVC surface was analogous to limestone ocean bottoms in its two-dimensional power-law roughness spectrum and its large dependence of scattering strength on the roughness parameters. The experiments represent an initial effort to use physical models with ground-truth measurements of roughness and compressional/shear speeds and attenuations to verify the predicted effects of interface scattering models, e.g., the small-slope model developed at the Naval Research Laboratory for elastic bottoms. Comparisons between the small-slope model, perturbation theory, and the observed data are shown for the various geometries using acoustic transmissions in the 100-400 kHz band. The success in obtaining a good model-data fit is shown to be directly related to the ensonification of an area that represents a sufficient statistical sample of the roughness. Plans for a series of tank experiments with physical models for verifying predictions of rough surface scattering theories and elastic PE are described. [Work supported by ONR.
Finite-element modelling of elastic wave propagation and scattering within heterogeneous media
NASA Astrophysics Data System (ADS)
Van Pamel, A.; Sha, G.; Rokhlin, S. I.; Lowe, M. J. S.
2017-01-01
The scattering treated here arises when elastic waves propagate within a heterogeneous medium defined by random spatial fluctuation of its elastic properties. Whereas classical analytical studies are based on lower-order scattering assumptions, numerical methods conversely present no such limitations by inherently incorporating multiple scattering. Until now, studies have typically been limited to two or one dimension, however, owing to computational constraints. This article seizes recent advances to realize a finite-element formulation that solves the three-dimensional elastodynamic scattering problem. The developed methodology enables the fundamental behaviour of scattering in terms of attenuation and dispersion to be studied. In particular, the example of elastic waves propagating within polycrystalline materials is adopted, using Voronoi tessellations to randomly generate representative models. The numerically observed scattering is compared against entirely independent but well-established analytical scattering theory. The quantitative agreement is found to be excellent across previously unvisited scattering regimes; it is believed that this is the first quantitative validation of its kind which provides significant support towards the existence of the transitional scattering regime and facilitates future deployment of numerical methods for these problems.
Micro-CT based finite element models for elastic properties of glass-ceramic scaffolds.
Tagliabue, Stefano; Rossi, Erica; Baino, Francesco; Vitale-Brovarone, Chiara; Gastaldi, Dario; Vena, Pasquale
2017-01-01
In this study, the mechanical properties of porous glass-ceramic scaffolds are investigated by means of three-dimensional finite element models based on micro-computed tomography (micro-CT) scan data. In particular, the quantitative relationship between the morpho-architectural features of the obtained scaffolds, such as macroscopic porosity and strut thickness, and elastic properties, is sought. The macroscopic elastic properties of the scaffolds have been obtained through numerical homogenization approaches using the mechanical characteristics of the solid walls of the scaffolds (assessed through nanoindentation) as input parameters for the numerical simulations. Anisotropic mechanical properties of the produced scaffolds have also been investigated by defining a suitable anisotropy index. A comparison with morphological data obtained through the micro-CT scans is also presented. The proposed study shows that the produced glass-ceramic scaffolds exhibited a macroscopic porosity ranging between 29% and 97% which corresponds to an average stiffness ranging between 42.4GPa and 36MPa. A quantitative estimation of the isotropy of the macroscopic elastic properties has been performed showing that the samples with higher solid fractions were those closest to an isotropic material.
A mechanical model to compute elastic modulus of tissues for harmonic motion imaging.
Shan, Baoxiang; Pelegri, Assimina A; Maleke, Caroline; Konofagou, Elisa E
2008-07-19
Numerous experimental and computational methods have been developed to estimate tissue elasticity. The existing testing techniques are generally classified into in vitro, invasive in vivo and non-invasive in vivo. For each experimental method, a computational scheme is accordingly proposed to calculate mechanical properties of soft biological tissues. Harmonic motion imaging (HMI) is a new technique that performs radio frequency (RF) signal tracking to estimate the localized oscillatory motion resulting from a radiation force produced by focused ultrasound. A mechanical model and computational scheme based on the superposition principle are developed in this paper to estimate the Young's modulus of a tissue mimicking phantom and bovine liver in vitro tissue from the harmonic displacement measured by HMI. The simulation results are verified by two groups of measurement data, and good agreement is shown in each comparison. Furthermore, an inverse function is observed to correlate the elastic modulus of uniform phantoms with amplitude of displacement measured in HMI. The computational scheme is also implemented to estimate 3D elastic modulus of bovine liver in vitro.
Finite-element modelling of elastic wave propagation and scattering within heterogeneous media
Sha, G.; Rokhlin, S. I.; Lowe, M. J. S.
2017-01-01
The scattering treated here arises when elastic waves propagate within a heterogeneous medium defined by random spatial fluctuation of its elastic properties. Whereas classical analytical studies are based on lower-order scattering assumptions, numerical methods conversely present no such limitations by inherently incorporating multiple scattering. Until now, studies have typically been limited to two or one dimension, however, owing to computational constraints. This article seizes recent advances to realize a finite-element formulation that solves the three-dimensional elastodynamic scattering problem. The developed methodology enables the fundamental behaviour of scattering in terms of attenuation and dispersion to be studied. In particular, the example of elastic waves propagating within polycrystalline materials is adopted, using Voronoi tessellations to randomly generate representative models. The numerically observed scattering is compared against entirely independent but well-established analytical scattering theory. The quantitative agreement is found to be excellent across previously unvisited scattering regimes; it is believed that this is the first quantitative validation of its kind which provides significant support towards the existence of the transitional scattering regime and facilitates future deployment of numerical methods for these problems. PMID:28265198
Radius exponent in elastic and rigid arterial models optimized by the least energy principle
Nakamura, Yoshihiro; Awa, Shoichi
2014-01-01
Abstract It was analyzed in normal physiological arteries whether the least energy principle would suffice to account for the radius exponent x. The mammalian arterial system was modeled as two types, the elastic or the rigid, to which Bernoulli's and Hagen‐Poiseuille's equations were applied, respectively. We minimized the total energy function E, which was defined as the sum of kinetic, pressure, metabolic and thermal energies, and loss of each per unit time in a single artery transporting viscous incompressible blood. Assuming a scaling exponent α between the vessel radius (r) and length (l) to be 1.0, x resulted in 2.33 in the elastic model. The rigid model provided a continuously changing x from 2.33 to 3.0, which corresponded to Uylings’ and Murray's theories, respectively, through a function combining Reynolds number with a proportional coefficient of the l − r relationship. These results were expanded to an asymmetric arterial fractal tree with the blood flow preservation rule. While x in the optimal elastic model accounted for around 2.3 in proximal systemic (r >1 mm) and whole pulmonary arteries (r ≥0.004 mm), optimal x in the rigid model explained 2.7 in elastic‐muscular (0.1 < r ≤1 mm) and 3.0 in peripheral resistive systemic arteries (0.004 ≤ r ≤0.1 mm), in agreement with data obtained from angiographic, cast‐morphometric, and in vivo experimental studies in the literature. The least energy principle on the total energy basis provides an alternate concept of optimality relating to mammalian arterial fractal dimensions under α = 1.0. PMID:24744905
NASA Astrophysics Data System (ADS)
Breuer, S.; Schilling, F. R.; Mueller, B.; Scheffzuek, C.
2015-12-01
Mechanical properties of sedimentary rocks such as stress-strain-relations are essential for understanding dynamic processes within the Earth's crust. The measurement of in-situ lattice strain in bulk samples is possible with diffraction methods, e.g. with neutrons. The advantage of neutron diffraction is their high penetration depth, which enables to gather a statistically relevant number of grains by diffraction. The neutron time-of-flight diffraction at the strain diffractometer EPSILON which is located at the pulsed neutron source IBR-2M (JINR Dubna, RUS) enables the detection of the complete diffraction pattern up to λ = 7.1 Å (d = 5.1 Å). Uniaxial cyclic deformation experiments were carried out up to 50 MPa (three steps) on a macroscopically isotropic sandstone from Kuhbach / Lahr (Germany). The aim of the present study is to model diffraction patterns for different applied stress-levels, based on the zero-stress diffraction pattern and known elastic properties of Quartz single crystals. The as received model-predictions are compared to observations, both, in the direction of maximum stress (along the cylindric axis) and perpendicular to it. The results show that the shape of the grains has an influence on the macroscopic elastic behavior of the rock whereas the microscopic strain is affected in a different manner. The model is based on spherical quartz grains. The spheres are divided into slices. By removing some slices, the shape of sand grains is approximated. The reaction of each slice through the applied stress is modelled. Together with the relative volume of each slice and it´s elastic behavior, the diffraction pattern is predicted for different applied loads. Measured and modelled diffraction-patterns at different applied loads are in good agreement.
Modeling Diagnostic Assessments with Bayesian Networks
ERIC Educational Resources Information Center
Almond, Russell G.; DiBello, Louis V.; Moulder, Brad; Zapata-Rivera, Juan-Diego
2007-01-01
This paper defines Bayesian network models and examines their applications to IRT-based cognitive diagnostic modeling. These models are especially suited to building inference engines designed to be synchronous with the finer grained student models that arise in skills diagnostic assessment. Aspects of the theory and use of Bayesian network models…
Elastic model-based segmentation of 3-D neuroradiological data sets.
Kelemen, A; Székely, G; Gerig, G
1999-10-01
This paper presents a new technique for the automatic model-based segmentation of three-dimensional (3-D) objects from volumetric image data. The development closely follows the seminal work of Taylor and Cootes on active shape models, but is based on a hierarchical parametric object description rather than a point distribution model. The segmentation system includes both the building of statistical models and the automatic segmentation of new image data sets via a restricted elastic deformation of shape models. Geometric models are derived from a sample set of image data which have been segmented by experts. The surfaces of these binary objects are converted into parametric surface representations, which are normalized to get an invariant object-centered coordinate system. Surface representations are expanded into series of spherical harmonics which provide parametric descriptions of object shapes. It is shown that invariant object surface parametrization provides a good approximation to automatically determine object homology in terms of sets of corresponding sets of surface points. Gray-level information near object boundaries is represented by 1-D intensity profiles normal to the surface. Considering automatic segmentation of brain structures as our driving application, our choice of coordinates for object alignment was the well-accepted stereotactic coordinate system. Major variation of object shapes around the mean shape, also referred to as shape eigenmodes, are calculated in shape parameter space rather than the feature space of point coordinates. Segmentation makes use of the object shape statistics by restricting possible elastic deformations into the range of the training shapes. The mean shapes are initialized in a new data set by specifying the landmarks of the stereotactic coordinate system. The model elastically deforms, driven by the displacement forces across the object's surface, which are generated by matching local intensity profiles. Elastic
A dynamic network model for interbank market
NASA Astrophysics Data System (ADS)
Xu, Tao; He, Jianmin; Li, Shouwei
2016-12-01
In this paper, a dynamic network model based on agent behavior is introduced to explain the formation mechanism of interbank market network. We investigate the impact of credit lending preference on interbank market network topology, the evolution of interbank market network and stability of interbank market. Experimental results demonstrate that interbank market network is a small-world network and cumulative degree follows the power-law distribution. We find that the interbank network structure keeps dynamic stability in the network evolution process. With the increase of bank credit lending preference, network clustering coefficient increases and average shortest path length decreases monotonously, which improves the stability of the network structure. External shocks are main threats for the interbank market and the reduction of bank external investment yield rate and deposits fluctuations contribute to improve the resilience of the banking system.
A Biologically Inspired Network Design Model
Zhang, Xiaoge; Adamatzky, Andrew; Chan, Felix T.S.; Deng, Yong; Yang, Hai; Yang, Xin-She; Tsompanas, Michail-Antisthenis I.; Sirakoulis, Georgios Ch.; Mahadevan, Sankaran
2015-01-01
A network design problem is to select a subset of links in a transport network that satisfy passengers or cargo transportation demands while minimizing the overall costs of the transportation. We propose a mathematical model of the foraging behaviour of slime mould P. polycephalum to solve the network design problem and construct optimal transport networks. In our algorithm, a traffic flow between any two cities is estimated using a gravity model. The flow is imitated by the model of the slime mould. The algorithm model converges to a steady state, which represents a solution of the problem. We validate our approach on examples of major transport networks in Mexico and China. By comparing networks developed in our approach with the man-made highways, networks developed by the slime mould, and a cellular automata model inspired by slime mould, we demonstrate the flexibility and efficiency of our approach. PMID:26041508
Al-Mutairi, N.H.; Eltony, M.N.
1995-12-31
This paper estimates the demand for energy in Kuwait for the period 1965-1989 using two econometric models: a cointegration and error correction model (ECM) and a simultaneous-equation model (SEM). The results obtained from both models are similar. It is found that the energy demand is inelastic with respect to price in the short and long run, and while it is elastic in the long run, the energy demand is inelastic with respect to income in the short run. Both models` validation shows that the ECM performed better in replicating the past than the simultaneous model, suggesting the need to use the ECM to identify future prospects for energy demand in Kuwait.
NASA Astrophysics Data System (ADS)
Feldman, J. L.; Broughton, J. Q.; Wooten, F.
1991-01-01
Calculations, based on the Stillinger-Weber (SW) interatomic-potential model and the method of long waves, are presented for the elastic properties of amorphous Si (a-Si) and for pressure derivatives of the elastic constants of crystalline Si. Several models of a-Si, relaxed on the basis of the SW potential, are considered, and the external stresses that are associated with these models are evaluated using the Born-Huang relations. The elastic constants appear to obey the isotropy conditions to within a reasonable accuracy and are also consistent with other predictions based on the SW potential at finite temperature obtained by Kluge and Ray. Estimates of the pressure dependence of the elastic constants, Debye temperature, and Grüeisen parameter for a-Si are also provided on the basis of these calculations.
Auxins and Cytokinins as Antipodal Modulators of Elasticity within the Actin Network of Plant Cells.
Grabski, S.; Schindler, M.
1996-01-01
The cytoskeleton of plant and animal cells serves as a transmitter, transducer, and effector of cell signaling mechanisms. In plants, pathways for proliferation, differentiation, intracellular vesicular transport, cell-wall biosynthesis, symbiosis, secretion, and membrane recycling depend on the organization and dynamic properties of actin- and tubulin-based structures that are either associated with the plasma membrane or traverse the cytoplasm. Recently, a new in vivo cytoskeletal assay (cell optical displacement assay) was introduced to measure the tension within subdomains (cortical, transvacuolar, and perinuclear) of the actin network in living plant cells. Cell optical displacement assay measurements within soybean (Glycine max [L.]) root cells previously demonstrated that lipophilic signals, e.g. linoleic acid and arachidonic acid or changes in cytoplasmic pH gradients, could induce significant reductions in the tension within the actin network of transvacuolar strands. In contrast, enhancement of cytoplasmic free Ca2+ resulted in an increase in tension. In the present communication we have used these measurements to show that a similar antipodal pattern of activity exists for auxins and cytokinins (in their ability to modify the tension within the actin network of plant cells). It is suggested that these growth substances exert their effect on the cytoskeleton through the activation of signaling cascades, which result in the production of lipophilic and ionic second messengers, both of which have been demonstrated to directly effect the tension within the actin network of soybean root cells. PMID:12226233
Proietti, Roberto; Qin, Chuan; Guan, Binbin; Yin, Yawei; Scott, Ryan P; Yu, Runxiang; Yoo, S J B
2012-11-19
This paper demonstrates a rapid and full hitless defragmentation method in elastic optical networks exploiting a new technique for fast wavelength tracking in coherent receivers. This technique can be applied to a single-carrier connection or each of the subcarriers forming a super-channel. A proof-of-concept demonstration shows hitless defragmentation of a 10 Gb/s QPSK single-carrier connection from 1547.75 nm to 1550.1 nm in less than 1 µs. This was obtained using a small (0.625 kB) link-layer transmitter buffer without the need for any additional transponder. We also demonstrated that the proposed defragmentation technique is capable of hopping over an existing connection, i.e. 10 Gb/s OOK at 1548.5 nm, without causing any degradation of its real-time Bit Error Rate (BER) value. The proposed scheme gives advantages in terms of overall network blocking probability reduction up to a factor of 40.
Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes.
Różycki, Bartosz; Boura, Evzen; Hurley, James H; Hummer, Gerhard
2012-01-01
The formation of vesicles is essential for many biological processes, in particular for the trafficking of membrane proteins within cells. The Endosomal Sorting Complex Required for Transport (ESCRT) directs membrane budding away from the cytosol. Unlike other vesicle formation pathways, the ESCRT-mediated budding occurs without a protein coat. Here, we propose a minimal model of ESCRT-induced vesicle budding. Our model is based on recent experimental observations from direct fluorescence microscopy imaging that show ESCRT proteins colocalized only in the neck region of membrane buds. The model, cast in the framework of membrane elasticity theory, reproduces the experimentally observed vesicle morphologies with physically meaningful parameters. In this parameter range, the minimum energy configurations of the membrane are coatless buds with ESCRTs localized in the bud neck, consistent with experiment. The minimum energy configurations agree with those seen in the fluorescence images, with respect to both bud shapes and ESCRT protein localization. On the basis of our model, we identify distinct mechanistic pathways for the ESCRT-mediated budding process. The bud size is determined by membrane material parameters, explaining the narrow yet different bud size distributions in vitro and in vivo. Our membrane elasticity model thus sheds light on the energetics and possible mechanisms of ESCRT-induced membrane budding.
Lucchinetti, E; Stüssi, E
2004-01-01
Measuring the elasticity constants of biological materials often sets important constraints, such as the limited size or the irregular geometry of the samples. In this paper, the identification approach as applied to the specific problem of accurately retrieving the material properties of small bone samples from a measured displacement field is discussed. The identification procedure can be formulated as an optimization problem with the goal of minimizing the difference between computed and measured displacements by searching for an appropriate set of material parameters using dedicated algorithms. Alternatively, the backcalculation of the material properties from displacement maps can be implemented using artificial neural networks. In a practical situation, however, measurement errors strongly affect the identification results, calling for robust optimization approaches in order accurately to retrieve the material properties from error-polluted sample deformation maps. Using a simple model problem, the performances of both classical and neural network driven optimization are compared. When performed before the collection of experimental data, this evaluation can be very helpful in pinpointing potential problems with the envisaged experiments such as the need for a sufficient signal-to-noise ratio, particularly important when working with small tissue samples such as specimens cut from rodent bones or single bone trabeculae.
Modeling the Elastic Modulus of 2D Woven CVI SiC Composites
NASA Technical Reports Server (NTRS)
Morscher, Gregory N.
2006-01-01
The use of fiber, interphase, CVI SiC minicomposites as structural elements for 2D-woven SiC fiber reinforced chemically vapor infiltrated (CVI) SiC matrix composites is demonstrated to be a viable approach to model the elastic modulus of these composite systems when tensile loaded in an orthogonal direction. The 0deg (loading direction) and 90deg (perpendicular to loading direction) oriented minicomposites as well as the open porosity and excess SiC associated with CVI SiC composites were all modeled as parallel elements using simple Rule of Mixtures techniques. Excellent agreement for a variety of 2D woven Hi-Nicalon(TradeMark) fiber-reinforced and Sylramic-iBN reinforced CVI SiC matrix composites that differed in numbers of plies, constituent content, thickness, density, and number of woven tows in either direction (i.e, balanced weaves versus unbalanced weaves) was achieved. It was found that elastic modulus was not only dependent on constituent content, but also the degree to which 90deg minicomposites carried load. This depended on the degree of interaction between 90deg and 0deg minicomposites which was quantified to some extent by composite density. The relationships developed here for elastic modulus only necessitated the knowledge of the fractional contents of fiber, interphase and CVI SiC as well as the tow size and shape. It was concluded that such relationships are fairly robust for orthogonally loaded 2D woven CVI SiC composite system and can be implemented by ceramic matrix composite component modelers and designers for modeling the local stiffness in simple or complex parts fabricated with variable constituent contents.
2012-01-01
Background Genomic selection (GS) is emerging as an efficient and cost-effective method for estimating breeding values using molecular markers distributed over the entire genome. In essence, it involves estimating the simultaneous effects of all genes or chromosomal segments and combining the estimates to predict the total genomic breeding value (GEBV). Accurate prediction of GEBVs is a central and recurring challenge in plant and animal breeding. The existence of a bewildering array of approaches for predicting breeding values using markers underscores the importance of identifying approaches able to efficiently and accurately predict breeding values. Here, we comparatively evaluate the predictive performance of six regularized linear regression methods-- ridge regression, ridge regression BLUP, lasso, adaptive lasso, elastic net and adaptive elastic net-- for predicting GEBV using dense SNP markers. Methods We predicted GEBVs for a quantitative trait using a dataset on 3000 progenies of 20 sires and 200 dams and an accompanying genome consisting of five chromosomes with 9990 biallelic SNP-marker loci simulated for the QTL-MAS 2011 workshop. We applied all the six methods that use penalty-based (regularization) shrinkage to handle datasets with far more predictors than observations. The lasso, elastic net and their adaptive extensions further possess the desirable property that they simultaneously select relevant predictive markers and optimally estimate their effects. The regression models were trained with a subset of 2000 phenotyped and genotyped individuals and used to predict GEBVs for the remaining 1000 progenies without phenotypes. Predictive accuracy was assessed using the root mean squared error, the Pearson correlation between predicted GEBVs and (1) the true genomic value (TGV), (2) the true breeding value (TBV) and (3) the simulated phenotypic values based on fivefold cross-validation (CV). Results The elastic net, lasso, adaptive lasso and the
Network model of bilateral power markets based on complex networks
NASA Astrophysics Data System (ADS)
Wu, Yang; Liu, Junyong; Li, Furong; Yan, Zhanxin; Zhang, Li
2014-06-01
The bilateral power transaction (BPT) mode becomes a typical market organization with the restructuring of electric power industry, the proper model which could capture its characteristics is in urgent need. However, the model is lacking because of this market organization's complexity. As a promising approach to modeling complex systems, complex networks could provide a sound theoretical framework for developing proper simulation model. In this paper, a complex network model of the BPT market is proposed. In this model, price advantage mechanism is a precondition. Unlike other general commodity transactions, both of the financial layer and the physical layer are considered in the model. Through simulation analysis, the feasibility and validity of the model are verified. At same time, some typical statistical features of BPT network are identified. Namely, the degree distribution follows the power law, the clustering coefficient is low and the average path length is a bit long. Moreover, the topological stability of the BPT network is tested. The results show that the network displays a topological robustness to random market member's failures while it is fragile against deliberate attacks, and the network could resist cascading failure to some extent. These features are helpful for making decisions and risk management in BPT markets.
Elastic Properties of 3D-Printed Rock Models: Dry and Saturated Cracks
NASA Astrophysics Data System (ADS)
Huang, L.; Stewart, R.; Dyaur, N.
2014-12-01
Many regions of subsurface interest are, or will be, fractured. In addition, these zones many be subject to varying saturations and stresses. New 3D printing techniques using different materials and structures, provide opportunities to understand porous or fractured materials and fluid effects on their elastic properties. We use a 3D printer (Stratasys Dimension SST 768) to print two rock models: a solid octahedral prism and a porous cube with thousands of penny-shaped cracks. The printing material is ABS thermal plastic with a density of 1.04 g/cm3. After printing, we measure the elastic properties of the models, both dry and 100% saturated with water. Both models exhibit VTI (Vertical Transverse Isotropic) symmetry due to laying (about 0.25 mm thick) of the printing process. The prism has a density of 0.96 g/cm3 before saturation and 1.00 g/cm3 after saturation. Its effective porosity is calculated to be 4 %. We use ultrasonic transducers (500 kHz) to measure both P- and shear-wave velocities, and the raw material has a P-wave velocity of 1.89 km/s and a shear-wave velocity of 0.91 km/s. P-wave velocity in the un-saturated prism increases from 1.81 km/s to 1.84 km/s after saturation in the direction parallel to layering and from 1.73 km/s to 1.81 km/s in the direction perpendicular to layering. The fast shear-wave velocity decreases from 0.88 km/s to 0.87 km/s and the slow shear-wave velocity decreases from 0.82 km/s to 0.81 km/s. The cube, printed with penny-shaped cracks, gives a density of 0.79 g/cm3 and a porosity of 24 %. We measure its P-wave velocity as 1.78 km/s and 1.68 km/s in the direction parallel and perpendicular to the layering, respectively. Its fast shear-wave velocity is 0.88 km/s and slow shear-wave velocity is 0.70 km/s. The penny-shaped cracks have significant influence on the elastic properties of the 3D-printed rock models. To better understand and explain the fluid effects on the elastic properties of the models, we apply the extended
A Modeling Approach for Burn Scar Assessment Using Natural Features and Elastic Property
Tsap, L V; Zhang, Y; Goldgof, D B; Sarkar, S
2004-04-02
A modeling approach is presented for quantitative burn scar assessment. Emphases are given to: (1) constructing a finite element model from natural image features with an adaptive mesh, and (2) quantifying the Young's modulus of scars using the finite element model and the regularization method. A set of natural point features is extracted from the images of burn patients. A Delaunay triangle mesh is then generated that adapts to the point features. A 3D finite element model is built on top of the mesh with the aid of range images providing the depth information. The Young's modulus of scars is quantified with a simplified regularization functional, assuming that the knowledge of scar's geometry is available. The consistency between the Relative Elasticity Index and the physician's rating based on the Vancouver Scale (a relative scale used to rate burn scars) indicates that the proposed modeling approach has high potentials for image-based quantitative burn scar assessment.
Form-Finding Model Shows How Cytoskeleton Network Stiffness Is Realized
Gong, Jinghai; Zhang, Daxu; Tseng, Yiider; Li, Baolong; Wirtz, Denis; Schafer, Benjamin William
2013-01-01
In eukaryotic cells the actin-cytoskeletal network provides stiffness and the driving force that contributes to changes in cell shape and cell motility, but the elastic behavior of this network is not well understood. In this paper a two dimensional form-finding model is proposed to investigate the elasticity of the actin filament network. Utilizing an initially random array of actin filaments and actin-cross-linking proteins the form-finding model iterates until the random array is brought into a stable equilibrium configuration. With some care given to actin filament density and length, distance between host sites for cross-linkers, and overall domain size the resulting configurations from the form-finding model are found to be topologically similar to cytoskeletal networks in real cells. The resulting network may then be mechanically exercised to explore how the actin filaments deform and align under load and the sensitivity of the network’s stiffness to actin filament density, length, etc. Results of the model are consistent with the experimental literature, e.g. actin filaments tend to re-orient in the direction of stretching; and the filament relative density, filament length, and actin-cross-linking protein’s relative density, control the actin-network stiffness. The model provides a ready means of extension to more complicated domains and a three-dimensional form-finding model is under development as well as models studying the formation of actin bundles. PMID:24146992
Validation of linear elastic model for soft tissue simulation in craniofacial surgery
NASA Astrophysics Data System (ADS)
Gladilin, Evgeny; Zachow, Stefan; Deuflhard, Peter; Hege, Hans-Christian
2001-05-01
Physically based soft tissue modeling is a state of the art in computer assisted surgery (CAS). But even such a sophisticated approach has its limits. The biomechanic behavior of soft tissue is highly complex, so that simplified models have to be applied. Under assumption of small deformations, usually applied in soft tissue modeling, soft tissue can be approximately described as a linear elastic continuum. Since there exist efficient techniques for solving linear partial differential equations, the linear elastic model allows comparatively fast calculation of soft tissue deformation and consequently the prediction of a patient's postoperative appearance. However, for the calculation of large deformations, which are not unusual in craniofacial surgery, this approach can implicate substantial error depending on the intensity of the deformation. The monitoring of the linearization error could help to estimate the scope of validity of calculations upon user defined precision. In order to quantify this error one even do not need to know the correct solution, since the linear theory implies the appropriate instruments for error detection in itself.
NASA Astrophysics Data System (ADS)
Andreaus, Ugo; Giorgio, Ivan; Madeo, Angela
2015-02-01
In this paper, a continuum mixture model with evolving mass densities and porosity is proposed to describe the process of bone remodeling in the presence of bio-resorbable materials as driven by externally applied loads. From a mechanical point of view, both bone tissue and biomaterial are modeled as linear elastic media with voids in the sense of Cowin and Nunziato (J Elast 13:125-147, 1983). In the proposed continuum model, the change of volume fraction related to the void volume is directly accounted for by considering porosity as an independent kinematical field. The bio-mechanical coupling is ensured by the introduction of a suitable stimulus which allows for discriminating between resorption (of both bone and biomaterial) and synthesis (of the sole natural bone) depending on the level of externally applied loads. The presence of a `lazy zone' associated with intermediate deformation levels is also considered in which neither resorption nor synthesis occur. Some numerical solutions of the integro-differential equations associated with the proposed model are provided for the two-dimensional case. Ranges of values of the parameters for which different percentages of biomaterial substitution occur are proposed, namely parameters characterizing initial and maximum values of mass densities of bone tissue and of the bio-resorbable material.
Modeling and optimization of an elastic arthroplastic disc for a degenerated disc
NASA Astrophysics Data System (ADS)
Ghouchani, Azadeh; Ravari, Mohammad; Mahmoudi, Farid
2011-10-01
A three-dimensional finite element model (FEM) of the L3-L4 motion segment using ABAQUS v 6.9 has been developed. The model took into account the material nonlinearities and is imposed different loading conditions. In this study, we validated the model by comparison of its predictions with several sets of experimental data. Disc deformation under compression and segmental rotational motions under moment loads for the normal disc model agreed well with the corresponding in vivo studies. By linking ABAQUS with MATLAB 2010.a, we determined the optimal Young s modulus as well as the Poisson's ratio for the artificial disc under different physiologic loading conditions. The results of the present study confirmed that a well-designed elastic arthroplastic disc preferably has an annulus modulus of 19.1 MPa and 1.24 MPa for nucleus section and Poisson ratio of 0.41 and 0.47 respectively. Elastic artificial disc with such properties can then achieve the goal of restoring the disc height and mechanical function of intact disc under different loading conditions and so can reduce low back pain which is mostly caused due to disc degeneration.
Model Of Neural Network With Creative Dynamics
NASA Technical Reports Server (NTRS)
Zak, Michail; Barhen, Jacob
1993-01-01
Paper presents analysis of mathematical model of one-neuron/one-synapse neural network featuring coupled activation and learning dynamics and parametrical periodic excitation. Demonstrates self-programming, partly random behavior of suitable designed neural network; believed to be related to spontaneity and creativity of biological neural networks.
Doyle, Heather; Lohfeld, Stefan; McHugh, Peter
2014-03-01
This study assesses the ability of finite element (FE) models to capture the mechanical behaviour of sintered orthopaedic scaffold materials. Individual scaffold struts were fabricated from a 50:50 wt% poly-ε-caprolactone (PCL)/β-tricalcium phosphate (β-TCP) blend, using selective laser sintering. The tensile elastic modulus of single struts was determined experimentally. High resolution FE models of single struts were generated from micro-CT scans (28.8 μm resolution) and an effective strut elastic modulus was calculated from tensile loading simulations. Three material assignment methods were employed: (1) homogeneous PCL elastic constants, (2) composite PCL/β-TCP elastic constants based on rule of mixtures, and (3) heterogeneous distribution of micromechanically-determined elastic constants. In comparison with experimental results, the use of homogeneous PCL properties gave a good estimate of strut modulus; however it is not sufficiently representative of the real material as it neglects the β-TCP phase. The rule of mixtures method significantly overestimated strut modulus, while there was no significant difference between strut modulus evaluated using the micromechanically-determined elastic constants and experimentally evaluated strut modulus. These results indicate that the multi-scale approach of linking micromechanical modelling of the sintered scaffold material with macroscale modelling gives an accurate prediction of the mechanical behaviour of the sintered structure.
Single-molecule elasticity of single-stranded DNA, a model flexible polyelectrolyte
NASA Astrophysics Data System (ADS)
McIntosh, Dustin B.
Understanding the structure of unfolded, flexible polyelectrolytes is important for our comprehension of basic processes in molecular biology (e.g., RNA and protein folding) and our ability to exploit the polymers in technology (e.g., in self-assembled nanostructures). Here, we investigate the structure of single single-stranded DNA molecules and their interactions with ions using magnetic tweezers. Our data reveal that single-stranded DNA is not well-described by ideal polymer models such as the Worm-Like Chain. At low force, we report the first experimental observation of a nonlinear elastic regime revealing the relevance of long-range excluded volume effects. At high force, the extension scales as a logarithm in monovalent salt. Molecular dynamics simulations indicate that this logarithmic regime is the result of ion-stabilized wrinkles at short-length scales along the polymer backbone. Addition of divalent salt to the buffer results in enhanced elasticity indicating increased wrinkling or polymer ''wrapping" around the divalent ions. Using a thermodynamic identity, we are able to count ions as they are released into the bulk upon polymer elongation. We find that ssDNA releases significantly more ions than dsDNA. We posit that the recently termed ''Snake-Like Chain" model (Ullner, J. Phys. Chem B (2003)) for flexible polyelectrolytes may explain these observations. As a first step towards characterizing biologically relevant nucleic acid structures, we measure the effects of base-stacking on ssDNA elasticity. We find that base-stacking in poly(dA) significantly enhances the rigidity of the polymer as evidenced by the low-force elasticity. The unstacking transition of poly(dA) at high force reveals that the intrinsic electrostatic tension on the molecule varies significantly more weakly on salt concentration than predictions from mean-field models. Further, we provide a model-independent estimate of the free energy difference between stacked and unstacked nucleic
Application of an Uncoupled Elastic-plastic-creep Constitutive Model to Metals at High Temperature
NASA Technical Reports Server (NTRS)
Haisler, W. E.
1983-01-01
A uniaxial, uncoupled constitutive model to predict the response of thermal and rate dependent elastic-plastic material behavior is presented. The model is based on an incremental classicial plasticity theory extended to account for thermal, creep, and transient temperature conditions. Revisions to he combined hardening rule of the theory allow for better representation of cyclic phenomenon including the high rate of strain hardening upon cyclic reyield and cyclic saturation. An alternative approach is taken to model the rate dependent inelastic deformation which utilizes hysteresis loops and stress relaxation test data at various temperatures. The model is evaluated and compared to experiments which involve various thermal and mechanical load histories on 5086 aluminum alloy, 304 stainless steel and Hastelloy-X.
Salguero, Laura; Saadat, Fatemeh; Sevostianov, Igor
2014-10-17
The paper analyzes the connection between microstructure of the osteonal cortical bone and its overall elastic properties. The existing models either neglect anisotropy of the dense tissue or simplify cortical bone microstructure (accounting for Haversian canals only). These simplifications (related mostly to insufficient mathematical apparatus) complicate quantitative analysis of the effect of microstructural changes - produced by age, microgravity, or some diseases - on the overall mechanical performance of cortical bone. The present analysis fills this gap; it accounts for anisotropy of the dense tissue and uses realistic model of the porous microstructure. The approach is based on recent results of Sevostianov et al. (2005) and Saadat et al. (2012) on inhomogeneities in a transversely-isotropic material. Bone's microstructure is modeled according to books of Martin and Burr (1989), Currey (2002), and Fung (1993) and includes four main families of pores. The calculated elastic constants for porous cortical bone are in agreement with available experimental data. The influence of each of the pore types on the overall moduli is examined.
Elastic wave modelling in 3D heterogeneous media: 3D grid method
NASA Astrophysics Data System (ADS)
Jianfeng, Zhang; Tielin, Liu
2002-09-01
We present a new numerical technique for elastic wave modelling in 3D heterogeneous media with surface topography, which is called the 3D grid method in this paper. This work is an extension of the 2D grid method that models P-SV wave propagation in 2D heterogeneous media. Similar to the finite-element method in the discretization of a numerical mesh, the proposed scheme is flexible in incorporating surface topography and curved interfaces; moreover it satisfies the free-surface boundary conditions of 3D topography naturally. The algorithm, developed from a parsimonious staggered-grid scheme, solves the problem using integral equilibrium around each node, instead of satisfying elastodynamic differential equations at each node as in the conventional finite-difference method. The computational cost and memory requirements for the proposed scheme are approximately the same as those used by the same order finite-difference method. In this paper, a mixed tetrahedral and parallelepiped grid method is presented; and the numerical dispersion and stability criteria on the tetrahedral grid method and parallelepiped grid method are discussed in detail. The proposed scheme is successfully tested against an analytical solution for the 3D Lamb problem and a solution of the boundary method for the diffraction of a hemispherical crater. Moreover, examples of surface-wave propagation in an elastic half-space with a semi-cylindrical trench on the surface and 3D plane-layered model are presented.
Shen, Hui-Shen
2010-06-01
Buckling and postbuckling analysis is presented for axially compressed microtubules (MTs) embedded in an elastic matrix of cytoplasm. The microtubule is modeled as a nonlocal shear deformable cylindrical shell which contains small scale effects. The surrounding elastic medium is modeled as a Pasternak foundation. The governing equations are based on higher order shear deformation shell theory with a von Kármán-Donnell-type of kinematic nonlinearity and include the extension-twist and flexural-twist couplings. The thermal effects are also included and the material properties are assumed to be temperature-dependent. The small scale parameter e (0) a is estimated by matching the buckling load from their vibrational behavior of MTs with the numerical results obtained from the nonlocal shear deformable shell model. The numerical results show that buckling load and postbuckling behavior of MTs are very sensitive to the small scale parameter e (0) a. The results reveal that the MTs under axial compressive loading condition have an unstable postbuckling path, and the lateral constraint has a significant effect on the postbuckling response of a microtubule when the foundation stiffness is sufficiently large.
Nonlocal-integro-differential modeling of vibration of elastically supported nanorods
NASA Astrophysics Data System (ADS)
Kiani, Keivan
2016-09-01
In the previously established nonlocal continuum-based models, small characteristic length was commonly incorporated into the mass matrix and the driving force vector which is a bit in contradiction with our sense regarding these factors. Herein, a nonlocal-integro-differential version of the constitutive relations is employed for the bulk and the surface layer of the nanorod. By adopting Hamilton's principle, integro-partial differential equations of motion of elastically supported nanorods are established accounting for both nonlocality and surface energy effects. Then, these are solved by an efficient meshless methodology. For fixed-fixed and fixed-free nanorods, modal analysis of the problem is also performed and the explicit expressions of the mass and stiffness matrices are derived. For these special cases, the obtained results by the meshless technique are successfully verified with those of the modal solution. In the newly developed numerical model, the small-scale parameter is only incorporated into the stiffness matrix which gives us a more realistic sense about the nonlocality effect. Subsequently, the roles of the surface energy, small-scale parameter, elastic supports, and kernel function on natural frequencies of the nanostructure are discussed and explained. This work can be considered as a pivotal step towards a more reasonable nonlocal modeling of vibration of nanoscale structures.
Evolutionary Phylogenetic Networks: Models and Issues
NASA Astrophysics Data System (ADS)
Nakhleh, Luay
Phylogenetic networks are special graphs that generalize phylogenetic trees to allow for modeling of non-treelike evolutionary histories. The ability to sequence multiple genetic markers from a set of organisms and the conflicting evolutionary signals that these markers provide in many cases, have propelled research and interest in phylogenetic networks to the forefront in computational phylogenetics. Nonetheless, the term 'phylogenetic network' has been generically used to refer to a class of models whose core shared property is tree generalization. Several excellent surveys of the different flavors of phylogenetic networks and methods for their reconstruction have been written recently. However, unlike these surveys, this chapte focuses specifically on one type of phylogenetic networks, namely evolutionary phylogenetic networks, which explicitly model reticulate evolutionary events. Further, this chapter focuses less on surveying existing tools, and addresses in more detail issues that are central to the accurate reconstruction of phylogenetic networks.
Queuing theory models for computer networks
NASA Technical Reports Server (NTRS)
Galant, David C.
1989-01-01
A set of simple queuing theory models which can model the average response of a network of computers to a given traffic load has been implemented using a spreadsheet. The impact of variations in traffic patterns and intensities, channel capacities, and message protocols can be assessed using them because of the lack of fine detail in the network traffic rates, traffic patterns, and the hardware used to implement the networks. A sample use of the models applied to a realistic problem is included in appendix A. Appendix B provides a glossary of terms used in this paper. This Ames Research Center computer communication network is an evolving network of local area networks (LANs) connected via gateways and high-speed backbone communication channels. Intelligent planning of expansion and improvement requires understanding the behavior of the individual LANs as well as the collection of networks as a whole.
A Multi-Backup Path Protection scheme for survivability in Elastic Optical Networks
NASA Astrophysics Data System (ADS)
Yadav, Dharmendra Singh; Chakraborty, Abhishek; Manoj, B. S.
2016-07-01
Two important challenges in designing a survivable optical network are minimizing backup spectrum allocation and ensuring spectrum assignment constraints. Allocating backup spectrum is one important approach for survivable optical network design. Connection requests which are rejected due to the unavailability of a single backup path can be survived using multiple backup routes. Multiple backup routes not only increase connection acceptance rate, but also improve backup resource sharing. In this paper, we present a strategy for survivability which optimizes primary and backup spectrum allocations and multiple backup route assignments for surviving a connection request. In our strategy, named as Backup Spectrum Reservation with MultiPath Protection (BSR-MPP), multiple backup routes are searched over advance reserved backup resources when an optical connection is concerned. Simulation results show that confinement of backup resources result in higher resource sharing and assignment of multiple backup lightpaths. It can also be observed that BSR-MPP has lower Bandwidth Blocking Probability and higher spectrum efficiency as compared to conventional Shared Path Protection (SPP) and MultiPath Protection (MPP) strategies.
Modeling Unreliable Observations in Bayesian Networks by Credal Networks
NASA Astrophysics Data System (ADS)
Antonucci, Alessandro; Piatti, Alberto
Bayesian networks are probabilistic graphical models widely employed in AI for the implementation of knowledge-based systems. Standard inference algorithms can update the beliefs about a variable of interest in the network after the observation of some other variables. This is usually achieved under the assumption that the observations could reveal the actual states of the variables in a fully reliable way. We propose a procedure for a more general modeling of the observations, which allows for updating beliefs in different situations, including various cases of unreliable, incomplete, uncertain and also missing observations. This is achieved by augmenting the original Bayesian network with a number of auxiliary variables corresponding to the observations. For a flexible modeling of the observational process, the quantification of the relations between these auxiliary variables and those of the original Bayesian network is done by credal sets, i.e., convex sets of probability mass functions. Without any lack of generality, we show how this can be done by simply estimating the bounds of likelihoods of the observations for the different values of the observed variables. Overall, the Bayesian network is transformed into a credal network, for which a standard updating problem has to be solved. Finally, a number of transformations that might simplify the updating of the resulting credal network is provided.
Seleson, Pablo; Du, Qiang; Parks, Michael L.
2016-08-16
The peridynamic theory of solid mechanics is a nonlocal reformulation of the classical continuum mechanics theory. At the continuum level, it has been demonstrated that classical (local) elasticity is a special case of peridynamics. Such a connection between these theories has not been extensively explored at the discrete level. This paper investigates the consistency between nearest-neighbor discretizations of linear elastic peridynamic models and finite difference discretizations of the Navier–Cauchy equation of classical elasticity. While nearest-neighbor discretizations in peridynamics have been numerically observed to present grid-dependent crack paths or spurious microcracks, this paper focuses on a different, analytical aspect of suchmore » discretizations. We demonstrate that, even in the absence of cracks, such discretizations may be problematic unless a proper selection of weights is used. Specifically, we demonstrate that using the standard meshfree approach in peridynamics, nearest-neighbor discretizations do not reduce, in general, to discretizations of corresponding classical models. We study nodal-based quadratures for the discretization of peridynamic models, and we derive quadrature weights that result in consistency between nearest-neighbor discretizations of peridynamic models and discretized classical models. The quadrature weights that lead to such consistency are, however, model-/discretization-dependent. We motivate the choice of those quadrature weights through a quadratic approximation of displacement fields. The stability of nearest-neighbor peridynamic schemes is demonstrated through a Fourier mode analysis. Finally, an approach based on a normalization of peridynamic constitutive constants at the discrete level is explored. This approach results in the desired consistency for one-dimensional models, but does not work in higher dimensions. The results of the work presented in this paper suggest that even though nearest
3D Discontinuous Galerkin elastic seismic wave modeling based upon a grid injection method
NASA Astrophysics Data System (ADS)
Monteiller, V.
2015-12-01
Full waveform inversion (FWI) is a seismic imaging method that estimates thesub-surface physical properties with a spatial resolution of the order of thewavelength. FWI is generally recast as the iterative optimization of anobjective function that measures the distance between modeled and recordeddata. In the framework of local descent methods, FWI requires to perform atleast two seismic modelings per source and per FWI iteration.Due to the resulting computational burden, applications of elastic FWI have been usuallyrestricted to 2D geometries. Despite the continuous growth of high-performancecomputing facilities, application of 3D elastic FWI to real-scale problemsremain computationally too expensive. To perform elastic seismic modeling with a reasonable amount of time, weconsider a reduced computational domain embedded in a larger background modelin which seismic sources are located. Our aim is to compute repeatedly thefull wavefield in the targeted domain after model alteration, once theincident wavefield has been computed once for all in the background model. Toachieve this goal, we use a grid injection method referred to as the Total-Field/Scattered-Field (TF/SF) technique in theelectromagnetic community. We implemented the Total-Field/Scattered-Field approach in theDiscontinuous Galerkin Finite Element method (DG-FEM) that is used to performmodeling in the local domain. We show how to interface the DG-FEM with any modeling engine (analytical solution, finite difference or finite elements methods) that is suitable for the background simulation. One advantage of the Total-Field/Scattered-Field approach is related to thefact that the scattered wavefield instead of the full wavefield enter thePMLs, hence making more efficient the absorption of the outgoing waves at theouter edges of the computational domain. The domain reduction in which theDG-FEM is applied allows us to use modest computational resources opening theway for high-resolution imaging by full
Hunke, E.C.; Zhang, Y.
1997-12-31
A nonlinear viscous-plastic (VP) rheology proposed by Hibler (1979) has been demonstrated to be the most suitable of the rheologies commonly used for modeling sea ice dynamics. However, the presence of a huge range of effective viscosities hinders numerical implementations of this model, particularly on high resolution grids or when the ice model is coupled to an ocean or atmosphere model. Hunke and Dukowicz (1997) have modified the VP model by including elastic waves as a numerical regularization in the case of zero strain rate. This modification (EVP) allows an efficient, fully explicit discretization that adapts well to parallel architectures. The authors present a comparison of EVP and VP dynamics model results from two 5-year simulations of Arctic sea ice, obtained with a high resolution sea ice model. The purpose of the comparison is to determine how differently the two dynamics models behave, and to decide whether the elastic-viscous-plastic model is preferable for high resolution climate simulations, considering its high efficiency in parallel computation. Results from the first year of this experiment (1990) are discussed in detail in Hunke and Zhang (1997).
[Pulsatile flow model with elastic blood vessels for duplex ultrasound studies].
Petrick, J; Schlief, R; Zomack, M; Langholz, J; Urbank, A
1992-12-01
Using ultrasound duplex technique flow phenomena in patients' circulation can be examined. For the interpretation of these examinations it is necessary to have extensive knowledge on flow influencing parameters. This can be easily obtained from simplified flow models. This article describes the components of a flow model that allows examination of ultrasonic contrast media flowing through an artificial heart and vessel mimicking tubes. The artificial heart is the drive which pumps a water glycerol cellulose mixture through the circulation in a pulsatile manner. The shape of the ventricle, the compliance of the aorta, the viscosity of the flow medium and the wall elasticity of the examination vessel were taken into account. The attenuation caused by the surrounding tissue is simulated by a variable layer of castor oil. The flow model is suitable to produce flow profiles that are very similar to physiological profiles.
NASA Astrophysics Data System (ADS)
Harne, R. L.
2013-07-01
Several past works have considered a passive vibration absorber device utilizing distributed mass and spring layers. The thickness of the poroelastic foam spring and the area density of the mass layer are modified to achieve a target natural frequency of the device while the foam itself provides adequate dissipation of energy as the mass dynamically compresses it at resonance. A model of the device earlier developed is briefly reviewed and validated by new experiments. The dependence of the absorber natural frequency and damping on the poroelastic spring thickness is observed in detail and is found to be consistent with past work on poroelastic material elastic characteristics outside of the linear dynamic regime. The results set a practical limit on the applicability of linearity assumptions in the present modeling of the distributed poroelastic vibration absorbers and thus determine a design parameter range for which the computationally efficient model is accurate.
History-Dependent Problems with Applications to Contact Models for Elastic Beams
Bartosz, Krzysztof; Kalita, Piotr; Migórski, Stanisław; Ochal, Anna; Sofonea, Mircea
2016-02-15
We prove an existence and uniqueness result for a class of subdifferential inclusions which involve a history-dependent operator. Then we specialize this result in the study of a class of history-dependent hemivariational inequalities. Problems of such kind arise in a large number of mathematical models which describe quasistatic processes of contact. To provide an example we consider an elastic beam in contact with a reactive obstacle. The contact is modeled with a new and nonstandard condition which involves both the subdifferential of a nonconvex and nonsmooth function and a Volterra-type integral term. We derive a variational formulation of the problem which is in the form of a history-dependent hemivariational inequality for the displacement field. Then, we use our abstract result to prove its unique weak solvability. Finally, we consider a numerical approximation of the model, solve effectively the approximate problems and provide numerical simulations.
Experimental validation of opto-thermo-elastic modeling in OOFELIE multiphysics
NASA Astrophysics Data System (ADS)
Mazzoli, Alexandra; Saint-Georges, Philippe; Orban, Anne; Ruess, Jean-Sébastien; Loicq, Jérôme; Barbier, Christian; Stockman, Yvan; Georges, Marc; Nachtergaele, Philippe; Paquay, Stéphane; De Vincenzo, Pascal
2011-10-01
The objective of this work is to demonstrate the correlation between a simple laboratory test bench case and the predictions of the OOFELIE Multiphysics software in order to deduce modeling guidelines and improvements. For that purpose two optical systems have been analyzed. The first one is a spherical lens fixed in an aluminium barrel, which is the simplest structure found in an opto-mechanical system. In this study, material characteristics are assumed to be well known: BK7 and aluminium have been retained. Temperature variations between 0 and +60°C from ambient have been applied to the samples. The second system is a YAG laser bar heated by means of a dedicated oven. For the two test benches thermo-elastic distortions have been measured using a Fizeau interferometer. This sensor measures wavefront error in the range of 20 nm to 1 μm without physical contact with the opto-mechanical system. For the YAG bar, birefringence and polarization measurements have also been performed using a polarimetric bench. The tests results have been compared to the predictions obtained by OOFELIE Multiphysics which is a simulation software dedicated to multiphysics coupled problems involving optics, mechanics, thermal physics, electricity, electromagnetism, acoustics and hydrodynamics. From this comparison modeling guidelines have been issued with the aim of improving the accuracy of computed thermo-elastic distortions and their impact on the optical performances.
Bitzén, Ulrika; Niklason, Lisbet; Göransson, Ingegerd; Jonson, Björn
2010-11-01
Elastic pressure/volume (P(el) /V) and elastic pressure/resistance (P(el) /R) diagrams reflect parenchymal and bronchial properties, respectively. The objective was to develop a method for determination and mathematical characterization of P(el) /V and P(el) /R relationships, simultaneously studied at sinusoidal flow-modulated vital capacity expirations in a body plethysmograph. Analysis was carried out by iterative parameter estimation based on a composite mathematical model describing a three-segment P(el) /V curve and a hyperbolic P(el) /R curve. The hypothesis was tested that the sigmoid P(el) /V curve is non-symmetric. Thirty healthy subjects were studied. The hypothesis of a non-symmetric P(el) /V curve was verified. Its upper volume asymptote was nearly equal to total lung capacity (TLC), indicating lung stiffness increasing at high lung volume as the main factor limiting TLC at health. The asymptotic minimal resistance of the hyperbolic P(el) /R relationship reflected lung size. A detailed description of both P(el) /V and P(el) /R relationships was simultaneously derived from sinusoidal flow-modulated vital capacity expirations. The nature of the P(el) /V curve merits the use of a non-symmetric P(el) /V model.
Quantitative description and modeling of real networks
NASA Astrophysics Data System (ADS)
Capocci, Andrea; Caldarelli, Guido; de Los Rios, Paolo
2003-10-01
We present data analysis and modeling of two particular cases of study in the field of growing networks. We analyze World Wide Web data set and authorship collaboration networks in order to check the presence of correlation in the data. The results are reproduced with good agreement through a suitable modification of the standard Albert-Barabási model of network growth. In particular, intrinsic relevance of sites plays a role in determining the future degree of the vertex.
Creating, documenting and sharing network models.
Crook, Sharon M; Bednar, James A; Berger, Sandra; Cannon, Robert; Davison, Andrew P; Djurfeldt, Mikael; Eppler, Jochen; Kriener, Birgit; Furber, Steve; Graham, Bruce; Plesser, Hans E; Schwabe, Lars; Smith, Leslie; Steuber, Volker; van Albada, Sacha
2012-01-01
As computational neuroscience matures, many simulation environments are available that are useful for neuronal network modeling. However, methods for successfully documenting models for publication and for exchanging models and model components among these projects are still under development. Here we briefly review existing software and applications for network model creation, documentation and exchange. Then we discuss a few of the larger issues facing the field of computational neuroscience regarding network modeling and suggest solutions to some of these problems, concentrating in particular on standardized network model terminology, notation, and descriptions and explicit documentation of model scaling. We hope this will enable and encourage computational neuroscientists to share their models more systematically in the future.
Biodiversity: modelling angiosperms as networks.
Gottlieb, O R; Borin, M R
2000-11-01
In the neotropics, one of the last biological frontiers, the major ecological concern should not involve local strategies, but global effects often responsible for irreparable damage. For a holistic approach, angiosperms are ideal model systems dominating most land areas of the present world in an astonishing variety of form and function. Recognition of biogeographical patterns requires new methodologies and entails several questions, such as their nature, dynamics and mechanism. Demographical patterns of families, modelled via species dominance, reveal the existence of South American angiosperm networks converging at the central Brazilian plateau. Biodiversity of habitats, measured via taxonomic uniqueness, reveal higher creative power at this point of convergence than in more peripheral regions. Compositional affinities of habitats, measured via bioconnectivity, reveal the decisive role of ecotones in the exchange or redistribution of information, energy and organisms among the ecosystems. Forming dynamic boundaries, ecotones generate and relay evolutionary novelty, and integrate all neotropical ecosystems into a single vegetation net. Connectivity in such plant webs may depend on mycorrhizal links. If sufficiently general such means of metabolic transfer will require revision of the chemical composition of many plants.
Modeling Injection Induced Seismicity with Poro-Elasticity and Time-Dependent Earthquake Nucleation
NASA Astrophysics Data System (ADS)
Lu, S.; Segall, P.
2014-12-01
The standard approach to modeling injection-induced seismicity (IIS) considers Coulomb failure stress changes accounting only for pore-pressure changes, which are solved by the diffusion equation. However, this "diffusion" triggering mechanism is not comprehensive. Lab experiments indicate earthquake nucleation also depends on stress history. Here we add two effects in modeling IIS: 1) poro-elastic coupling between solid stresses and pore-pressure, and 2) time dependent earthquake nucleation under applied stresses. In this model, we compute stress and pore-pressure changes due to a point source injecting in a homogeneous, poro-elastic full space (Rudnicki, 1986). The Coulomb stress history is used to compute seismicity rate changes based on the time-dependent nucleation model of Dieterich (1994). Our new model reveals: 1) poro-elastic coupling breaks the radial symmetry in seismicity, 2) nucleation introduces a characteristic nucleation time ta, which affects the temporal evolution of seismicity rates, and 3) for some fault geometries, the seismicity rate may increase following shut in. For constant injection flux, the log of seismicity rate scales with the change in Coulomb stress at short time, consistent with diffusion profiles. At longer time, the model predicts seismicity rates decaying with time, consistent with some observations. The contour shape and decay time are characterized by ta. For finite injection with box-car flux history, seismicity rates plummet near the injector, but may continue for some time at greater distance. Depending on fault orientations, seismicity rates may increase after shut-in due to coupling effects. It has been observed in some cases that the maximum magnitude of induced quakes occurs after shut-in. This may be understood by the fact that the volume of perturbed crust increases with injection time, which influences probability of triggering an event of a given magnitude. Whether coupling effects are important in post shut
NASA Technical Reports Server (NTRS)
Kopasakis, George; Connolly, Joseph; Seidel, Jonathan
2014-01-01
A summary of the propulsion system modeling under NASA's High Speed Project (HSP) AeroPropulsoServoElasticity (APSE) task is provided with a focus on the propulsion system for the low-boom supersonic configuration developed by Lockheed Martin and referred to as the N+2 configuration. This summary includes details on the effort to date to develop computational models for the various propulsion system components. The objective of this paper is to summarize the model development effort in this task, while providing more detail in the modeling areas that have not been previously published. The purpose of the propulsion system modeling and the overall APSE effort is to develop an integrated dynamic vehicle model to conduct appropriate unsteady analysis of supersonic vehicle performance. This integrated APSE system model concept includes the propulsion system model, and the vehicle structural-aerodynamics model. The development to date of such a preliminary integrated model will also be summarized in this report.propulsion system dynamics, the structural dynamics, and aerodynamics.
Modeling of hysteresis in gene regulatory networks.
Hu, J; Qin, K R; Xiang, C; Lee, T H
2012-08-01
Hysteresis, observed in many gene regulatory networks, has a pivotal impact on biological systems, which enhances the robustness of cell functions. In this paper, a general model is proposed to describe the hysteretic gene regulatory network by combining the hysteresis component and the transient dynamics. The Bouc-Wen hysteresis model is modified to describe the hysteresis component in the mammalian gene regulatory networks. Rigorous mathematical analysis on the dynamical properties of the model is presented to ensure the bounded-input-bounded-output (BIBO) stability and demonstrates that the original Bouc-Wen model can only generate a clockwise hysteresis loop while the modified model can describe both clockwise and counter clockwise hysteresis loops. Simulation studies have shown that the hysteresis loops from our model are consistent with the experimental observations in three mammalian gene regulatory networks and two E.coli gene regulatory networks, which demonstrate the ability and accuracy of the mathematical model to emulate natural gene expression behavior with hysteresis. A comparison study has also been conducted to show that this model fits the experiment data significantly better than previous ones in the literature. The successful modeling of the hysteresis in all the five hysteretic gene regulatory networks suggests that the new model has the potential to be a unified framework for modeling hysteresis in gene regulatory networks and provide better understanding of the general mechanism that drives the hysteretic function.
A Simple ``Sticky Disc'' Model for Crystalline and Amorphous Networks
NASA Astrophysics Data System (ADS)
Huerta, Adrian; Chubynsky, Nikita; Naumis, Gerardo; Thorpe, Michael
2005-03-01
Using Monte Carlo simulations, we study the structural and thermodynamic behavior of a simple one component network forming model made up of ``sticky discs.'' Central and bond bending forces was included, modeling such interactions as a simple square well radial and angular three body term in the potential respectively. The main feature of this model is the ability to form crystalline and amorphous networks upon cooling, similar to that obtained using the so called WWW methodology to describe the network of some vitreous structures [1]. With the ``pebble game'' algorithm [2], we evaluate the number of degrees of freedom and the amount of stress in both the amorphous and crystalline structures. We discuss the connection between the configurational entropy (associated with the topology) and the degrees of freedom. Other effects such as elasticity of these structures are also discussed. 1. Wooten, F., Winer, K. and Weaire, D., Phys. Rev. Lett., 54 1392- 1395 (1985). 2. Jacobs, D.J. and Thorpe, M.F., Phys. Rev. Lett., 75 4051- 4054 (1995).
Modelling dendritic ecological networks in space: anintegrated network perspective
Peterson, Erin E.; Ver Hoef, Jay M.; Isaak, Dan J.; Falke, Jeffrey A.; Fortin, Marie-Josée; Jordon, Chris E.; McNyset, Kristina; Monestiez, Pascal; Ruesch, Aaron S.; Sengupta, Aritra; Som, Nicholas; Steel, E. Ashley; Theobald, David M.; Torgersen, Christian E.; Wenger, Seth J.
2013-01-01
the context of stream ecology. Within this context, we summarise the key innovations of a new family of spatial statistical models that describe spatial relationships in DENs. Finally, we discuss how different network analyses may be combined to address more complex and novel research questions. While our main focus is streams, the taxonomy of network analyses is also relevant anywhere spatial patterns in both network and 2-D space can be used to explore the influence of multi-scale processes on biota and their habitat (e.g. plant morphology and pest infestation, or preferential migration along stream or road corridors).
Autonomous Boolean modeling of gene regulatory networks
NASA Astrophysics Data System (ADS)
Socolar, Joshua; Sun, Mengyang; Cheng, Xianrui
2014-03-01
In cases where the dynamical properties of gene regulatory networks are important, a faithful model must include three key features: a network topology; a functional response of each element to its inputs; and timing information about the transmission of signals across network links. Autonomous Boolean network (ABN) models are efficient representations of these elements and are amenable to analysis. We present an ABN model of the gene regulatory network governing cell fate specification in the early sea urchin embryo, which must generate three bands of distinct tissue types after several cell divisions, beginning from an initial condition with only two distinct cell types. Analysis of the spatial patterning problem and the dynamics of a network constructed from available experimental results reveals that a simple mechanism is at work in this case. Supported by NSF Grant DMS-10-68602
Modeling information flow in biological networks.
Kim, Yoo-Ah; Przytycki, Jozef H; Wuchty, Stefan; Przytycka, Teresa M
2011-06-01
Large-scale molecular interaction networks are being increasingly used to provide a system level view of cellular processes. Modeling communications between nodes in such huge networks as information flows is useful for dissecting dynamical dependences between individual network components. In the information flow model, individual nodes are assumed to communicate with each other by propagating the signals through intermediate nodes in the network. In this paper, we first provide an overview of the state of the art of research in the network analysis based on information flow models. In the second part, we describe our computational method underlying our recent work on discovering dysregulated pathways in glioma. Motivated by applications to inferring information flow from genotype to phenotype in a very large human interaction network, we generalized previous approaches to compute information flows for a large number of instances and also provided a formal proof for the method.
Reduced-Order Modeling for Flutter/LCO Using Recurrent Artificial Neural Network
NASA Technical Reports Server (NTRS)
Yao, Weigang; Liou, Meng-Sing
2012-01-01
The present study demonstrates the efficacy of a recurrent artificial neural network to provide a high fidelity time-dependent nonlinear reduced-order model (ROM) for flutter/limit-cycle oscillation (LCO) modeling. An artificial neural network is a relatively straightforward nonlinear method for modeling an input-output relationship from a set of known data, for which we use the radial basis function (RBF) with its parameters determined through a training process. The resulting RBF neural network, however, is only static and is not yet adequate for an application to problems of dynamic nature. The recurrent neural network method [1] is applied to construct a reduced order model resulting from a series of high-fidelity time-dependent data of aero-elastic simulations. Once the RBF neural network ROM is constructed properly, an accurate approximate solution can be obtained at a fraction of the cost of a full-order computation. The method derived during the study has been validated for predicting nonlinear aerodynamic forces in transonic flow and is capable of accurate flutter/LCO simulations. The obtained results indicate that the present recurrent RBF neural network is accurate and efficient for nonlinear aero-elastic system analysis
Process modeling with the regression network.
van der Walt, T; Barnard, E; van Deventer, J
1995-01-01
A new connectionist network topology called the regression network is proposed. The structural and underlying mathematical features of the regression network are investigated. Emphasis is placed on the intricacies of the optimization process for the regression network and some measures to alleviate these difficulties of optimization are proposed and investigated. The ability of the regression network algorithm to perform either nonparametric or parametric optimization, as well as a combination of both, is also highlighted. It is further shown how the regression network can be used to model systems which are poorly understood on the basis of sparse data. A semi-empirical regression network model is developed for a metallurgical processing operation (a hydrocyclone classifier) by building mechanistic knowledge into the connectionist structure of the regression network model. Poorly understood aspects of the process are provided for by use of nonparametric regions within the structure of the semi-empirical connectionist model. The performance of the regression network model is compared to the corresponding generalization performance results obtained by some other nonparametric regression techniques.
Gossip spread in social network Models
NASA Astrophysics Data System (ADS)
Johansson, Tobias
2017-04-01
Gossip almost inevitably arises in real social networks. In this article we investigate the relationship between the number of friends of a person and limits on how far gossip about that person can spread in the network. How far gossip travels in a network depends on two sets of factors: (a) factors determining gossip transmission from one person to the next and (b) factors determining network topology. For a simple model where gossip is spread among people who know the victim it is known that a standard scale-free network model produces a non-monotonic relationship between number of friends and expected relative spread of gossip, a pattern that is also observed in real networks (Lind et al., 2007). Here, we study gossip spread in two social network models (Toivonen et al., 2006; Vázquez, 2003) by exploring the parameter space of both models and fitting them to a real Facebook data set. Both models can produce the non-monotonic relationship of real networks more accurately than a standard scale-free model while also exhibiting more realistic variability in gossip spread. Of the two models, the one given in Vázquez (2003) best captures both the expected values and variability of gossip spread.
Wave propagation in magneto-electro-elastic nanobeams via two nonlocal beam models
NASA Astrophysics Data System (ADS)
Ma, Li-Hong; Ke, Liao-Liang; Wang, Yi-Ze; Wang, Yue-Sheng
2017-02-01
This paper makes the first attempt to investigate the dispersion behavior of waves in magneto-electro-elastic (MEE) nanobeams. The Euler nanobeam model and Timoshenko nanobeam model are developed in the formulation based on the nonlocal theory. By using the Hamilton's principle, we derive the governing equations which are then solved analytically to obtain the dispersion relations of MEE nanobeams. Results are presented to highlight the influences of the thermo-electro-magnetic loadings and nonlocal parameter on the wave propagation characteristics of MEE nanobeams. It is found that the thermo-electro-magnetic loadings can lead to the occurrence of the cut-off wave number below which the wave can't propagate in MEE nanobeams.
Analysis of Signal Propagation in an Elastic-Tube Flow Model
NASA Astrophysics Data System (ADS)
Waggy, Scott; Akman, Ozgur; Biringen, Sedat
2009-11-01
We combine linear and nonlinear signal analysis techniques to investigate the transmission of pressure signals along a one-dimensional model of fluid flow in an elastic tube. We derive a simple measure for the robustness of a simulated vessel against in vivo fluctuations in the pressure, based on quantifying the degree of synchronization between proximal and distal pressure pulses. The practical use of this measure will be in its application to simulated pulses generated in response to a stochastic forcing term mimicking biological variations of root pressure in arterial blood flow. Using spectral analysis methods based on synchronization theory, we introduce a novel nonlinear index for measuring the robustness of the model against fluctuations in the forcing signal, based on a general scheme for deriving low-dimensional measures of (biological) performance from higher-dimensional systems of equations.
Elastic-plastic cube model for ultrasonic friction reduction via Poisson's effect.
Dong, Sheng; Dapino, Marcelo J
2014-01-01
Ultrasonic friction reduction has been studied experimentally and theoretically. This paper presents a new elastic-plastic cube model which can be applied to various ultrasonic lubrication cases. A cube is used to represent all the contacting asperities of two surfaces. Friction force is considered as the product of the tangential contact stiffness and the deformation of the cube. Ultrasonic vibrations are projected onto three orthogonal directions, separately changing contact parameters and deformations. Hence, the overall change of friction forces. Experiments are conducted to examine ultrasonic friction reduction using different materials under normal loads that vary from 40 N to 240 N. Ultrasonic vibrations are generated both in longitudinal and vertical (out-of-plane) directions by way of the Poisson effect. The tests show up to 60% friction reduction; model simulations describe the trends observed experimentally.
An existence result for a model of complete damage in elastic materials with reversible evolution
NASA Astrophysics Data System (ADS)
Bonetti, Elena; Freddi, Francesco; Segatti, Antonio
2017-01-01
In this paper, we consider a model describing evolution of damage in elastic materials, in which stiffness completely degenerates once the material is fully damaged. The model is written by using a phase transition approach, with respect to the damage parameter. In particular, a source of damage is represented by a quadratic form involving deformations, which vanishes in the case of complete damage. Hence, an internal constraint is ensured by a maximal monotone operator. The evolution of damage is considered "reversible", in the sense that the material may repair itself. We can prove an existence result for a suitable weak formulation of the problem, rewritten in terms of a new variable (an internal stress). Some numerical simulations are presented in agreement with the mathematical analysis of the system.
Test of 600 and 750 MeV NN matrix on elastic scattering Glauber model calculations
NASA Astrophysics Data System (ADS)
Brissaud, I.
1980-09-01
The 600 and 750 MeV proton nucleus elastic scattering cross section and polarization calculations have been performed in the framework of the Glauber model to test the pp and pn scattering amplitudes deduced from a phase shift analysis by Bystricky, Lechanoine and Lehar. It is well known that up to now we do not possess a non-phenomenological NN scattering matrix at intermediate energies. However proton-nucleus scattering analyses are used to extract information about short range correlations1), Δ resonance2) or pion condensation presences)... etc. Most scattering calculations made at these energies have been done with phenomenological NN amplitudes having a gaussian q-dependence 10050_2005_Article_BF01438168_TeX2GIFE1.gif A(q) = {kσ }/{4π }(α + i) e^{ - β ^2 q^2 /2} and 10050_2005_Article_BF01438168_TeX2GIFE2.gif C(q) = {kσ }/{4π }iq(α + i) D_e - β ^2 q^2 /2 K and σ being respectively the projectile momentum and the total pN total cross section. The parameters α, β and D are badly known and are adjusted by fitting some specific reactions as p+4He elastic scattering4). Even when these amplitudes provide good fits to the data, our understanding of the dynamics of the scattering remains obscure.
Anisotropic Elastic-Waveform Modeling for Fracture Characterization in EGS Reservoirs
Gao, Kai; Huang, Lianjie
2015-01-28
Enhanced geothermal systems (EGS) contain newly created fractures in addition to possible existing fractures. Accurate characterization and monitoring of EGS reservoirs are crucial for optimal placement of new wells and effective extraction of geothermal heat. The fractured reservoirs behave as anisotropic media where seismic waves propagate with different velocities along different directions. In addition, the anisotropic properties of fluid-filled fracture zones could be different from those of dry fracture zones. We develop an optimized rotated staggered-grid elastic-wave finite-difference method for simulating seismic-wave propagation in heterogeneous, anisotropic media. Our new method uses a few extra grid points and optimized finite-difference coefficients based on the space-time dispersion relation, and reduce numerical dispersion of the conventional rotated staggered-grid finite-difference scheme. We validate our new method using synthetic vertical-seismic-profiling (VSP) data for an anisotropic geophysical model built with geologic features found at the Raft River EGS reservoir. This improved and optimized rotated staggered-grid finite-difference method provides an essential tool for analyzing VSP data, reverse-time migration, and elastic-waveform inversion in anisotropic, fractured reservoirs.
Elastic thickness of the lithosphere and tectonic evolution: implications for GIA models
NASA Astrophysics Data System (ADS)
Amantov, Aleksey; Fjeldskaar, Willy
2015-04-01
Rheological properties used in GIA models require independent verifications and possible modifications. To estimate the flexural rigidity of the lithosphere in simple platform areas we use peneplain distortion, which enable us to compute isostatic response from sediment load and compare the results with observed changes in geometry. This was done for several different platform regions: - Baltic (Fennoscandian) Shield, including structural elements of the Russian Platform - Barents Sea platform areas - Kara and Western Siberian domain - Eastern Siberian Platform In the East European and East Siberian old cratons we modeled isostatic distortion of Neoproterozoic Ediacaran peneplain and some other relevant surfaces. For the Arctic we used Mid-Late Jurassic surface (JP) as a distinct unconformity and well-traced (by seismic and well data) surface in the Arctic region. The isostatic distortion of peneplains under sediment load / erosion for the old Archean - Proterozoic cratons in general confirms earlier rheology model with the flexural rigidity of the lithosphere around 5x10**23 Nm (effective elastic thickness of 30-40 km), but could be slightly lower in the Barents basins. Deviations are generally relatively small and could be explained by e.g. by averaging over fault-zones, tectonic events, compaction structures and density variations. However, the situation for the Kara-Western Siberian domain is very different, with large deviations between observations and calculations. With a slight reduction of the effective elastic thickness in the Kara Sea to 10-20 km the fit is much better. Based on the results we suggest two different major types of lithosphere rigidity in the area. This seems reasonable because they typify domains with different crustal age. Western Siberian platform, with Kara continuation has much younger basement, in addition to significant magmatic activity and Early Mesosoic extension. The lithosphere rigidity is a function of age and temperature; as
A Permeability Model for Coal and Other Fractured, Sorptive-Elastic Media
Eric P. Robertson; Richard L. Christiansen
2006-10-01
This paper describes the derivation of a new equation that can be used to model the permeability behavior of a fractured, sorptive-elastic media, such as coal, under variable stress conditions commonly used during measurement of permeability data in the laboratory. The model is derived for cubic geometry under biaxial or hydrostatic confining pressures. The model is also designed to handle changes in permeability caused by adsorption and desorption of gases from the matrix blocks. The model equations can be used to calculate permeability changes caused by the production of methane from coal as well as the injection of gases, such as carbon dioxide, for sequestration in coal. Sensitivity analysis of the model found that each of the input variables can have a significant impact on the outcome of the permeability forecast as a function of changing pore pressure; thus, accurate input data are essential. The permeability model can also be used as a tool to determine input parameters for field simulations by curve-fitting laboratory-generated permeability data. The new model is compared to two other widely used coal permeability models using a hypothetical coal with average properties.
A permeability model for coal and other fractured, sorptive-elastic media
Robertson, E.P.; Christiansen, R.L.
2008-09-15
This paper describes the derivation of a new equation that can be used to model the permeability behavior of a fractured, sorptive-elastic medium, such as coal, under variable stress conditions. The equation is applicable to confinement pressure schemes commonly used during the collection of permeability data in the laboratory. The model is derived for cubic geometry under biaxial or hydrostatic confining pressures. The model is designed to handle changes in permeability caused by adsorption and desorption of gases onto and from the matrix blocks in fractured media. The model equations can be used to calculate permeability changes caused by the production of methane (CH{sub 4}) from coal as well as the injection of gases, such as carbon dioxide, for sequestration in coal. Sensitivity analysis of the model found that each of the input variables can have a significant impact on the outcome of the permeability forecast as a function of changing pore pressure, thus, accurate input data are essential. The permeability model also can be used as a tool to determine input parameters for field simulations by curve fitting laboratory-generated permeability data. The new model is compared to two other widely used coal-permeability models using a hypothetical coal with average properties.
Amaya, N; Irfan, M; Zervas, G; Nejabati, R; Simeonidou, D; Sakaguchi, J; Klaus, W; Puttnam, B J; Miyazawa, T; Awaji, Y; Wada, N; Henning, I
2013-04-08
We present the first elastic, space division multiplexing, and multi-granular network based on two 7-core MCF links and four programmable optical nodes able to switch traffic utilising the space, frequency and time dimensions with over 6000-fold bandwidth granularity. Results show good end-to-end performance on all channels with power penalties between 0.75 dB and 3.7 dB.
Towards Reproducible Descriptions of Neuronal Network Models
Nordlie, Eilen; Gewaltig, Marc-Oliver; Plesser, Hans Ekkehard
2009-01-01
Progress in science depends on the effective exchange of ideas among scientists. New ideas can be assessed and criticized in a meaningful manner only if they are formulated precisely. This applies to simulation studies as well as to experiments and theories. But after more than 50 years of neuronal network simulations, we still lack a clear and common understanding of the role of computational models in neuroscience as well as established practices for describing network models in publications. This hinders the critical evaluation of network models as well as their re-use. We analyze here 14 research papers proposing neuronal network models of different complexity and find widely varying approaches to model descriptions, with regard to both the means of description and the ordering and placement of material. We further observe great variation in the graphical representation of networks and the notation used in equations. Based on our observations, we propose a good model description practice, composed of guidelines for the organization of publications, a checklist for model descriptions, templates for tables presenting model structure, and guidelines for diagrams of networks. The main purpose of this good practice is to trigger a debate about the communication of neuronal network models in a manner comprehensible to humans, as opposed to machine-readable model description languages. We believe that the good model description practice proposed here, together with a number of other recent initiatives on data-, model-, and software-sharing, may lead to a deeper and more fruitful exchange of ideas among computational neuroscientists in years to come. We further hope that work on standardized ways of describing—and thinking about—complex neuronal networks will lead the scientific community to a clearer understanding of high-level concepts in network dynamics, and will thus lead to deeper insights into the function of the brain. PMID:19662159
ERIC Educational Resources Information Center
Nunn, Robin
2008-01-01
In this article, the author proposes a dynamic, interdisciplinary, network conception of expertise that differs from conventional static, linear conceptions. Using a range of graphic images, the author propose specific visualizations of this network conception of expertise. First, he discusses attempts to pin expertise down in a definition. Then…
NASA Astrophysics Data System (ADS)
Han, Tongcheng; Gurevich, Boris; Pervukhina, Marina; Clennell, Michael Ben; Zhang, Junfang
2016-04-01
Knowledge about the pressure dependency of elastic and electrical properties is important for a variety of geophysical applications. We present a technique to invert for the stiff and compliant porosity from velocity measurements made as a function of differential pressure on saturated sandstones. A dual porosity concept is used for dry rock compressibility and a squirt model is employed for the pressure and frequency dependent elastic properties of the rocks when saturated. The total porosity obtained from inversion shows satisfactory agreement with experimental results. The electrical cementation factor was determined using the inverted porosity in combination with measured electrical conductivity. It was found that cementation factor increased exponentially with increasing differential pressure during isostatic loading. Elastic compressibility, electrical cementation factor and electrical conductivity of the saturated rocks correlate linearly with compliant porosity, and electrical cementation factor and electrical conductivity exhibit linear correlations with elastic compressibility of the saturated rocks under loading. The results show that the dual porosity concept is sufficient to explain the pressure dependency of elastic, electrical and joint elastic-electrical properties of saturated porous sandstones.
Grebenstein, Patricia E.; Burroughs, Danielle; Roiko, Samuel A.; Pentel, Paul R.; LeSage, Mark G.
2015-01-01
Background The FDA is considering reducing the nicotine content in tobacco products as a population-based strategy to reduce tobacco addiction. Research is needed to determine the threshold level of nicotine needed to maintain smoking and the extent of compensatory smoking that could occur during nicotine reduction. Sources of variability in these measures across sub-populations also need to be identified so that policies can take into account the risks and benefits of nicotine reduction in vulnerable populations. Methods The present study examined these issues in a rodent nicotine self- administration model of nicotine reduction policy to characterize individual differences in nicotine reinforcement thresholds, degree of compensation, and elasticity of demand during progressive reduction of the unit nicotine dose. The ability of individual differences in baseline nicotine intake and nicotine pharmacokinetics to predict responses to dose reduction was also examined. Results Considerable variability in the reinforcement threshold, compensation, and elasticity of demand was evident. High baseline nicotine intake was not correlated with the reinforcement threshold, but predicted less compensation and less elastic demand. Higher nicotine clearance predicted low reinforcement thresholds, greater compensation, and less elastic demand. Less elastic demand also predicted lower reinforcement thresholds. Conclusions These findings suggest that baseline nicotine intake, nicotine clearance, and the essential value of nicotine (i.e. elasticity of demand) moderate the effects of progressive nicotine reduction in rats and warrant further study in humans. They also suggest that smokers with fast nicotine metabolism may be more vulnerable to the risks of nicotine reduction. PMID:25891231
Lähdesmäki, Harri; Hautaniemi, Sampsa; Shmulevich, Ilya; Yli-Harja, Olli
2006-01-01
A significant amount of attention has recently been focused on modeling of gene regulatory networks. Two frequently used large-scale modeling frameworks are Bayesian networks (BNs) and Boolean networks, the latter one being a special case of its recent stochastic extension, probabilistic Boolean networks (PBNs). PBN is a promising model class that generalizes the standard rule-based interactions of Boolean networks into the stochastic setting. Dynamic Bayesian networks (DBNs) is a general and versatile model class that is able to represent complex temporal stochastic processes and has also been proposed as a model for gene regulatory systems. In this paper, we concentrate on these two model classes and demonstrate that PBNs and a certain subclass of DBNs can represent the same joint probability distribution over their common variables. The major benefit of introducing the relationships between the models is that it opens up the possibility of applying the standard tools of DBNs to PBNs and vice versa. Hence, the standard learning tools of DBNs can be applied in the context of PBNs, and the inference methods give a natural way of handling the missing values in PBNs which are often present in gene expression measurements. Conversely, the tools for controlling the stationary behavior of the networks, tools for projecting networks onto sub-networks, and efficient learning schemes can be used for DBNs. In other words, the introduced relationships between the models extend the collection of analysis tools for both model classes. PMID:17415411
Perrin, Christian L; Tardy, Philippe M J; Sorbie, Ken S; Crawshaw, John C
2006-03-15
The in situ rheology of polymeric solutions has been studied experimentally in etched silicon micromodels which are idealizations of porous media. The rectangular channels in these etched networks have dimensions typical of pore sizes in sandstone rocks. Pressure drop/flow rate relations have been measured for water and non-Newtonian hydrolyzed-polyacrylamide (HPAM) solutions in both individual straight rectangular capillaries and in networks of such capillaries. Results from these experiments have been analyzed using pore-scale network modeling incorporating the non-Newtonian fluid mechanics of a Carreau fluid. Quantitative agreement is seen between the experiments and the network calculations in the Newtonian and shear-thinning flow regions demonstrating that the 'shift factor,'alpha, can be calculated a priori. Shear-thickening behavior was observed at higher flow rates in the micromodel experiments as a result of elastic effects becoming important and this remains to be incorporated in the network model.
NASA Technical Reports Server (NTRS)
Chen, Chaing
1991-01-01
This study presents a nested-grid nonhydrostatic and elastic model using a terrain-following coordinate transformation as well as a unique application of grid-nesting techniques to the time-splitting elastic model. A simulation of the 10-m-high Witch of Agnesi Mountain provides the control to test this new model. The results show that the model produces the same solution as that derived from a simple linear analytic model. It is demonstrated that the new nested-grid model improves model resolution without resorting to the costly method of placing a fine-resolution grid over the entire domain. Since the wave reflection from the boundaries of the fine-grid model is well controlled, the boundary of the nested fine-grid model can be located even at the wave-active region. The model can be used to simulate various weather systems in which scale interactions are important.
Estimating standard errors in feature network models.
Frank, Laurence E; Heiser, Willem J
2007-05-01
Feature network models are graphical structures that represent proximity data in a discrete space while using the same formalism that is the basis of least squares methods employed in multidimensional scaling. Existing methods to derive a network model from empirical data only give the best-fitting network and yield no standard errors for the parameter estimates. The additivity properties of networks make it possible to consider the model as a univariate (multiple) linear regression problem with positivity restrictions on the parameters. In the present study, both theoretical and empirical standard errors are obtained for the constrained regression parameters of a network model with known features. The performance of both types of standard error is evaluated using Monte Carlo techniques.
Computational Statistical Methods for Social Network Models
Hunter, David R.; Krivitsky, Pavel N.; Schweinberger, Michael
2013-01-01
We review the broad range of recent statistical work in social network models, with emphasis on computational aspects of these methods. Particular focus is applied to exponential-family random graph models (ERGM) and latent variable models for data on complete networks observed at a single time point, though we also briefly review many methods for incompletely observed networks and networks observed at multiple time points. Although we mention far more modeling techniques than we can possibly cover in depth, we provide numerous citations to current literature. We illustrate several of the methods on a small, well-known network dataset, Sampson’s monks, providing code where possible so that these analyses may be duplicated. PMID:23828720
Campelo, Felix; Arnarez, Clement; Marrink, Siewert J; Kozlov, Michael M
2014-06-01
Helfrich model of membrane bending elasticity has been most influential in establishment and development of Soft-Matter Physics of lipid bilayers and biological membranes. Recently, Helfrich theory has been extensively used in Cell Biology to understand the phenomena of shaping, fusion and fission of cellular membranes. The general background of Helfrich theory on the one hand, and the ways of specifying the model parameters on the other, are important for quantitative treatment of particular biologically relevant membrane phenomena. Here we present the origin of Helfrich model within the context of the general Gibbs theory of capillary interfaces, and review the strategies of computing the membrane elastic moduli based on considering a lipid monolayer as a three-dimensional thick layer characterized by trans-monolayer profiles of elastic parameters. We present the results of original computations of these profiles by a state-of-the-art numerical approach.
Modeling the Topology of Sdh Networks
NASA Astrophysics Data System (ADS)
Santiago, A.; Cárdenas, J. P.; Mouronte, M. L.; Feliu, V.; Benito, R. M.
SDH (Synchronous Digital Hierarchy) is the standard technology for the information transmission in broadband optical networks. Unlike the Internet, SDH networks are strictly planned; rings, meshes, stars, or tree-branches topologies are designed to connect their basic elements. In spite of that, we have found that the SDH network operated by Telefónica in Spain shares remarkable topological properties with other real complex networks empirically analyzed, such as the worldwide web network. In particular, we have found power-law scaling in the degree distribution (P(k) ~ k-γ) and properties of small world networks. Considering real planning directives that take into account geographical and technological variables, we propose an ad hoc computational model that reproduces the aforementioned topological traits observed in the Spanish SDH network.
Sequential state generation by model neural networks.
Kleinfeld, D
1986-01-01
Sequential patterns of neural output activity form the basis of many biological processes, such as the cyclic pattern of outputs that control locomotion. I show how such sequences can be generated by a class of model neural networks that make defined sets of transitions between selected memory states. Sequence-generating networks depend upon the interplay between two sets of synaptic connections. One set acts to stabilize the network in its current memory state, while the second set, whose action is delayed in time, causes the network to make specified transitions between the memories. The dynamic properties of these networks are described in terms of motion along an energy surface. The performance of the networks, both with intact connections and with noisy or missing connections, is illustrated by numerical examples. In addition, I present a scheme for the recognition of externally generated sequences by these networks. PMID:3467316
A network model of the interbank market
NASA Astrophysics Data System (ADS)
Li, Shouwei; He, Jianmin; Zhuang, Yaming
2010-12-01
This work introduces a network model of an interbank market based on interbank credit lending relationships. It generates some network features identified through empirical analysis. The critical issue to construct an interbank network is to decide the edges among banks, which is realized in this paper based on the interbank’s degree of trust. Through simulation analysis of the interbank network model, some typical structural features are identified in our interbank network, which are also proved to exist in real interbank networks. They are namely, a low clustering coefficient and a relatively short average path length, community structures, and a two-power-law distribution of out-degree and in-degree.
Super-Grid Modeling of the Elastic Wave Equation in Semi-Bounded Domains
Petersson, N. Anders; Sjögreen, Björn
2014-10-01
We develop a super-grid modeling technique for solving the elastic wave equation in semi-bounded two- and three-dimensional spatial domains. In this method, waves are slowed down and dissipated in sponge layers near the far-field boundaries. Mathematically, this is equivalent to a coordinate mapping that transforms a very large physical domain to a significantly smaller computational domain, where the elastic wave equation is solved numerically on a regular grid. To damp out waves that become poorly resolved because of the coordinate mapping, a high order artificial dissipation operator is added in layers near the boundaries of the computational domain. We prove by energy estimates that the super-grid modeling leads to a stable numerical method with decreasing energy, which is valid for heterogeneous material properties and a free surface boundary condition on one side of the domain. Our spatial discretization is based on a fourth order accurate finite difference method, which satisfies the principle of summation by parts. We show that the discrete energy estimate holds also when a centered finite difference stencil is combined with homogeneous Dirichlet conditions at several ghost points outside of the far-field boundaries. Therefore, the coefficients in the finite difference stencils need only be boundary modified near the free surface. This allows for improved computational efficiency and significant simplifications of the implementation of the proposed method in multi-dimensional domains. Numerical experiments in three space dimensions show that the modeling error from truncating the domain can be made very small by choosing a sufficiently wide super-grid damping layer. The numerical accuracy is first evaluated against analytical solutions of Lamb’s problem, where fourth order accuracy is observed with a sixth order artificial dissipation. We then use successive grid refinements to study the numerical accuracy in the more
Complex Network Modeling with an Emulab HPC
2012-09-01
field. Actual Joint Tactical Radio System (JTRS) radios, Operations Network ( OPNET ) emulations, and GNU (recursive definition for GNU is Not Unix...open-source software-defined-radio software/ firmware/ hardware emulations can be accommodated. Index Terms—network emulation, Emulab, OPNET I...other hand, simulation tools such as MATLAB, Optimized Network Engineering Tools ( OPNET ), NS2, and CORE (a modeling environment from Vitech
Neural Network Retinal Model Real Time Implementation
1992-09-02
addresses the specific needs of vision processing. The goal of this SBIR Phase I project has been to take a significant neural network vision...application and to map it onto dedicated hardware for real time implementation. The neural network was already demonstrated using software simulation on a...general purpose computer. During Phase 1, HNC took a neural network model of the retina and, using HNC’s Vision Processor (ViP) prototype hardware
Modeling Evolution of Weighted Clique Networks
NASA Astrophysics Data System (ADS)
Yang, Xu-Hua; Jiang, Feng-Ling; Chen, Sheng-Yong; Wang, Wan-Liang
2011-11-01
We propose a weighted clique network evolution model, which expands continuously by the addition of a new clique (maximal complete sub-graph) at each time step. And the cliques in the network overlap with each other. The structural expansion of the weighted clique network is combined with the edges' weight and vertices' strengths dynamical evolution. The model is based on a weight-driven dynamics and a weights' enhancement mechanism combining with the network growth. We study the network properties, which include the distribution of vertices' strength and the distribution of edges' weight, and find that both the distributions follow the scale-free distribution. At the same time, we also find that the relationship between strength and degree of a vertex are linear correlation during the growth of the network. On the basis of mean-field theory, we study the weighted network model and prove that both vertices' strength and edges' weight of this model follow the scale-free distribution. And we exploit an algorithm to forecast the network dynamics, which can be used to reckon the distributions and the corresponding scaling exponents. Furthermore, we observe that mean-field based theoretic results are consistent with the statistical data of the model, which denotes the theoretical result in this paper is effective.
Walcott, Sam; Sun, Sean X
2010-04-27
Tissue cells sense and respond to the stiffness of the surface on which they adhere. Precisely how cells sense surface stiffness remains an open question, though various biochemical pathways are critical for a proper stiffness response. Here, based on a simple mechanochemical model of biological friction, we propose a model for cell mechanosensation as opposed to previous more biochemically based models. Our model of adhesion complexes predicts that these cell-surface interactions provide a viscous drag that increases with the elastic modulus of the surface. The force-velocity relation of myosin II implies that myosin generates greater force when the adhesion complexes slide slowly. Then, using a simple cytoskeleton model, we show that an external force applied to the cytoskeleton causes actin filaments to aggregate and orient parallel to the direction of force application. The greater the external force, the faster this aggregation occurs. As the steady-state probability of forming these bundles reflects a balance between the time scale of bundle formation and destruction (because of actin turnover), more bundles are formed when the cytoskeleton time-scale is small (i.e., on stiff surfaces), in agreement with experiment. As these large bundles of actin, called stress fibers, appear preferentially on stiff surfaces, our mechanical model provides a mechanism for stress fiber formation and stiffness sensing in cells adhered to a compliant surface.
NASA Technical Reports Server (NTRS)
Jurenko, Robert J.; Bush, T. Jason; Ottander, John A.
2014-01-01
A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes both quadratically constrained least squares (LSQI) and Direct Shape Mapping (DSM) algorithms to determine physical displacements. This approach is applicable to the simulation of the elastic behavior of launch vehicles and other structures that utilize multiple LTI finite element model (FEM) derived mode sets that are propagated throughout time. The time invariant nature of the elastic data for discrete segments of the launch vehicle trajectory presents a problem of how to properly transition between models while preserving motion across the transition. In addition, energy may vary between flex models when using a truncated mode set. The LSQI-DSM algorithm can accommodate significant changes in energy between FEM models and carries elastic motion across FEM model transitions. Compared with previous approaches, the LSQI-DSM algorithm shows improvements ranging from a significant reduction to a complete removal of transients across FEM model transitions as well as maintaining elastic motion from the prior state.
Frey, Martin; Riener, Robert; Michas, Christian; Regenfelder, Felix; Burgkart, Rainer
2006-01-01
An analytical, dynamic model of the human knee joint has been developed to simulate the unloaded knee joint behaviour in 6 degrees of freedom. It is based on extensive robot-based measurements of the elastic properties of a human cadaver knee joint. The measured data are compared with data from the literature to ensure that a proper database for modelling is used. The analytical modelling of the passive elastic joint properties is done with Local Linear Model Trees. The deduced knee joint model incorporates passive elastic properties of the internal knee joint structures, passive elastic muscle forces, damping forces, gravitational forces, and external forces. There are two sets of parameters, one simulating the movement of the intact knee joint, and a second simulating the knee joint with ruptured anterior cruciate ligament. The dynamic model can be easily processed in real-time. It is implemented in the haptic display of the Munich Knee Joint Simulator (MKS), which enables a person to move a plastic leg driven by a robot manipulator and feel the simulated knee joint force. Orthopaedic physicians judged the performance of the dynamic knee joint model by executing physical knee joint tests at the MKS.
Homophyly/Kinship Model: Naturally Evolving Networks
NASA Astrophysics Data System (ADS)
Li, Angsheng; Li, Jiankou; Pan, Yicheng; Yin, Xianchen; Yong, Xi
2015-10-01
It has been a challenge to understand the formation and roles of social groups or natural communities in the evolution of species, societies and real world networks. Here, we propose the hypothesis that homophyly/kinship is the intrinsic mechanism of natural communities, introduce the notion of the affinity exponent and propose the homophyly/kinship model of networks. We demonstrate that the networks of our model satisfy a number of topological, probabilistic and combinatorial properties and, in particular, that the robustness and stability of natural communities increase as the affinity exponent increases and that the reciprocity of the networks in our model decreases as the affinity exponent increases. We show that both homophyly/kinship and reciprocity are essential to the emergence of cooperation in evolutionary games and that the homophyly/kinship and reciprocity determined by the appropriate affinity exponent guarantee the emergence of cooperation in evolutionary games, verifying Darwin’s proposal that kinship and reciprocity are the means of individual fitness. We propose the new principle of structure entropy minimisation for detecting natural communities of networks and verify the functional module property and characteristic properties by a healthy tissue cell network, a citation network, some metabolic networks and a protein interaction network.
Homophyly/Kinship Model: Naturally Evolving Networks.
Li, Angsheng; Li, Jiankou; Pan, Yicheng; Yin, Xianchen; Yong, Xi
2015-10-19
It has been a challenge to understand the formation and roles of social groups or natural communities in the evolution of species, societies and real world networks. Here, we propose the hypothesis that homophyly/kinship is the intrinsic mechanism of natural communities, introduce the notion of the affinity exponent and propose the homophyly/kinship model of networks. We demonstrate that the networks of our model satisfy a number of topological, probabilistic and combinatorial properties and, in particular, that the robustness and stability of natural communities increase as the affinity exponent increases and that the reciprocity of the networks in our model decreases as the affinity exponent increases. We show that both homophyly/kinship and reciprocity are essential to the emergence of cooperation in evolutionary games and that the homophyly/kinship and reciprocity determined by the appropriate affinity exponent guarantee the emergence of cooperation in evolutionary games, verifying Darwin's proposal that kinship and reciprocity are the means of individual fitness. We propose the new principle of structure entropy minimisation for detecting natural communities of networks and verify the functional module property and characteristic properties by a healthy tissue cell network, a citation network, some metabolic networks and a protein interaction network.
Matrix Pseudospectral Method for (Visco)Elastic Tides Modeling of Planetary Bodies
NASA Astrophysics Data System (ADS)
Zabranova, Eliska; Hanyk, Ladidslav; Matyska, Ctirad
2010-05-01
We deal with the equations and boundary conditions describing deformation and gravitational potential of prestressed spherically symmetric elastic bodies by decomposing governing equations into a series of boundary value problems (BVP) for ordinary differential equations (ODE) of the second order. In contrast to traditional Runge-Kutta integration techniques, highly accurate pseudospectral schemes are employed to directly discretize the BVP on Chebyshev grids and a set of linear algebraic equations with an almost block diagonal matrix is derived. As a consequence of keeping the governing ODEs of the second order instead of the usual first-order equations, the resulting algebraic system is half-sized but derivatives of the model parameters are required. Moreover, they can be easily evaluated for models, where structural parametres are piecewise polynomially dependent. Both accuracy and efficiency of the method are tested by evaluating the tidal Love numbers for the Earth's model PREM. Finally, we also derive complex Love numbers for models with the Maxwell viscoelastic rheology, where viscosity is a depth-dependent function. The method is applied to evaluation of the tidal Love numbers for models of Mars and Venus. The Love numbers of the two Martian models - the former optimized to cosmochemical data and the latter to the moment of inertia (Sohl and Spohn, 1997) - are h2=0.172 (0.212) and k2=0.093 (0.113). For Venus, the value of k2=0.295 (Konopliv and Yoder, 1996), obtained from the gravity-field analysis, is consistent with the results for our model with the liquid-core radius of 3110 km (Zábranová et al., 2009). Together with rapid evaluation of free oscillation periods by an analogous method, this combined matrix approach could by employed as an efficient numerical tool in structural studies of planetary bodies. REFERENCES Konopliv, A. S. and Yoder, C. F., 1996. Venusian k2 tidal Love number from Magellan and PVO tracking data, Geophys. Res. Lett., 23, 1857
NASA Astrophysics Data System (ADS)
Hieber, Simone E.; Koumoutsakos, Petros
2008-11-01
We present a novel Lagrangian particle method for the simulation of linear and nonlinear elastic models of soft tissue. Linear solids are represented by the Lagrangian formulation of the stress-strain relationship that is extended to nonlinear solids by using the Lagrangian evolution of the deformation gradient described in a moving framework. The present method introduces a level set description, along with the particles, to capture the body deformations and to enforce the boundary conditions. Furthermore, the accuracy of the method in cases of large deformations is ensured by implementing a particle remeshing procedure. The method is validated in several benchmark problems, in two and three dimensions and the results compare well with the results of respective finite elements simulations. In simulations of large solid deformation under plane strain compression, the finite element solver exhibits spurious structures that are not present in the Lagrangian particle simulations. The particle simulations are compared with experimental results in an aspiration test of liver tissue.
Daneshmand, Farhang; Ghavanloo, Esmaeal; Amabili, Marco
2011-07-07
Wave propagation along the microtubules is one of the issues of major concern in various microtubule cellular functions. In this study, the general wave propagation behavior in protein microtubules is investigated based on a first-order shear deformation shell theory for orthotropic materials, with particular emphasis on the role of strongly anisotropic elastic properties of microtubules. According to experimental observation, the first-order shear deformation theory is used for the modeling of microtubule walls. A general displacement representation is introduced and a type of coupled polynomial eigenvalue problem is developed. Numerical examples describe the effects of shear deformation and rotary inertia on wave velocities in orthotropic microtubules. Finally, the influences of the microtubule shear modulus, axial external force, effective thickness and material temperature dependency on wave velocities along the microtubule protofilaments, helical pathway and radial directions are elucidated. Most results presented in the present investigation have been absent from the literature for the wave propagation in microtubules.
NASA Technical Reports Server (NTRS)
Kishoni, Doron; Taasan, Shlomo
1994-01-01
Solution of the wave equation using techniques such as finite difference or finite element methods can model elastic wave propagation in solids. This requires mapping the physical geometry into a computational domain whose size is governed by the size of the physical domain of interest and by the required resolution. This computational domain, in turn, dictates the computer memory requirements as well as the calculation time. Quite often, the physical region of interest is only a part of the whole physical body, and does not necessarily include all the physical boundaries. Reduction of the calculation domain requires positioning an artificial boundary or region where a physical boundary does not exist. It is important however that such a boundary, or region, will not affect the internal domain, i.e., it should not cause reflections that propagate back into the material. This paper concentrates on the issue of constructing such a boundary region.
Tracer particles in two-dimensional elastic networks diffuse logarithmically slow
NASA Astrophysics Data System (ADS)
Lizana, Ludvig; Ambjörnsson, Tobias; Lomholt, Michael A.
2017-01-01
Several experiments on tagged molecules or particles in living systems suggest that they move anomalously slow—their mean squared displacement (MSD) increase slower than linearly with time. Leading models aimed at understanding these experiments predict that the MSD grows as a power law with a growth exponent that is smaller than unity. However, in some experiments the growth is so slow (fitted exponent ˜0.1-0.2) that they hint towards other mechanisms at play. In this paper, we theoretically demonstrate how in-plane collective modes excited by thermal fluctuations in a two dimensional membrane lead to logarithmic time dependence for the the tracer particle’s MSD.
Role models for complex networks
NASA Astrophysics Data System (ADS)
Reichardt, J.; White, D. R.
2007-11-01
We present a framework for automatically decomposing (“block-modeling”) the functional classes of agents within a complex network. These classes are represented by the nodes of an image graph (“block model”) depicting the main patterns of connectivity and thus functional roles in the network. Using a first principles approach, we derive a measure for the fit of a network to any given image graph allowing objective hypothesis testing. From the properties of an optimal fit, we derive how to find the best fitting image graph directly from the network and present a criterion to avoid overfitting. The method can handle both two-mode and one-mode data, directed and undirected as well as weighted networks and allows for different types of links to be dealt with simultaneously. It is non-parametric and computationally efficient. The concepts of structural equivalence and modularity are found as special cases of our approach. We apply our method to the world trade network and analyze the roles individual countries play in the global economy.
A poroelastic model coupled to a fluid network with applications in lung modelling.
Berger, Lorenz; Bordas, Rafel; Burrowes, Kelly; Grau, Vicente; Tavener, Simon; Kay, David
2016-01-01
We develop a lung ventilation model based on a continuum poroelastic representation of lung parenchyma that is strongly coupled to a pipe network representation of the airway tree. The continuous system of equations is discretized using a low-order stabilised finite element method. The framework is applied to a realistic lung anatomical model derived from computed tomography data and an artificially generated airway tree to model the conducting airway region. Numerical simulations produce physiologically realistic solutions and demonstrate the effect of airway constriction and reduced tissue elasticity on ventilation, tissue stress and alveolar pressure distribution. The key advantage of the model is the ability to provide insight into the mutual dependence between ventilation and deformation. This is essential when studying lung diseases, such as chronic obstructive pulmonary disease and pulmonary fibrosis. Thus the model can be used to form a better understanding of integrated lung mechanics in both the healthy and diseased states. Copyright © 2015 John Wiley & Sons, Ltd.
Simple model for river network evolution
NASA Astrophysics Data System (ADS)
Leheny, Robert L.
1995-11-01
We simulate the evolution of a drainage basin by erosion from precipitation and avalanching on hillslopes. The avalanches create a competition in growth between neighboring basins and play the central role in driving the evolution. The simulated landscapes form drainage systems that share many qualitative features with Glock's model for natural network evolution and maintain statistical properties that characterize real river networks. We also present results from a second model with a modified, mass conserving avalanche scheme. Although the terrains from these two models are qualitatively dissimilar, their drainage networks share the same general evolution and statistical features.
An endogenous model of the credit network
NASA Astrophysics Data System (ADS)
He, Jianmin; Sui, Xin; Li, Shouwei
2016-01-01
In this paper, an endogenous credit network model of firm-bank agents is constructed. The model describes the endogenous formation of firm-firm, firm-bank and bank-bank credit relationships. By means of simulations, the model is capable of showing some obvious similarities with empirical evidence found by other scholars: the upper-tail of firm size distribution can be well fitted with a power-law; the bank size distribution can be lognormally distributed with a power-law tail; the bank in-degrees of the interbank credit network as well as the firm-bank credit network fall into two-power-law distributions.
Cyber threat model for tactical radio networks
NASA Astrophysics Data System (ADS)
Kurdziel, Michael T.
2014-05-01
The shift to a full information-centric paradigm in the battlefield has allowed ConOps to be developed that are only possible using modern network communications systems. Securing these Tactical Networks without impacting their capabilities has been a challenge. Tactical networks with fixed infrastructure have similar vulnerabilities to their commercial counterparts (although they need to be secure against adversaries with greater capabilities, resources and motivation). However, networks with mobile infrastructure components and Mobile Ad hoc Networks (MANets) have additional unique vulnerabilities that must be considered. It is useful to examine Tactical Network based ConOps and use them to construct a threat model and baseline cyber security requirements for Tactical Networks with fixed infrastructure, mobile infrastructure and/or ad hoc modes of operation. This paper will present an introduction to threat model assessment. A definition and detailed discussion of a Tactical Network threat model is also presented. Finally, the model is used to derive baseline requirements that can be used to design or evaluate a cyber security solution that can be scaled and adapted to the needs of specific deployments.
Kwansa, Albert L; Freeman, Joseph W
2010-02-21
Collagen type I is a structural protein that provides tensile strength to tendons and ligaments. Type I collagen molecules form collagen fibers, which are viscoelastic and can therefore store energy elastically via molecular elongation and dissipate viscous energy through molecular rearrangement and fibrillar slippage. The ability to store elastic energy is important for the resiliency of tendons and ligaments, which must be able to deform and revert to their initial lengths with changes in load. In an earlier paper by one of the present authors, molecular modeling was used to investigate the role of mineralization upon elastic energy storage in collagen type I. Their collagen model showed a similar trend to their experimental data but with an over-estimation of elastic energy storage. Their simulations were conducted in vacuum and employed a distance-dependent dielectric function. In this study, we performed a re-evaluation of Freeman and Silver's model data incorporating the effects of explicit solvation and water infiltration, in order to determine whether the model data could be improved with a more accurate representation of the solvent and osmotic effects. We observed an average decrease in the model's elastic energy storage of 45.1%+/-6.9% in closer proximity to Freeman and Silver's experimental data. This suggests that although the distance-dependent dielectric implicit solvation approach was favored for its increased speed and decreased computational requirements, an explicit representation of water may be necessary to more accurately model solvent interactions in this particular system. In this paper, we discuss the collagen model described by Freeman and Silver, the present model building approach, the application of the present model to that of Freeman and Silver, and additional assumptions and limitations.
Freed, Alan D.; Einstein, Daniel R.
2011-04-14
An isotropic constitutive model for the parenchyma of lung has been derived from the theory of hypo-elasticity. The intent is to use it to represent the mechanical response of this soft tissue in sophisticated, computational, fluid-dynamic models of the lung. This demands that the continuum model be accurate, yet simple and effcient. An objective algorithm for its numeric integration is provided. The response of the model is determined for several boundary-value problems whose experiments are used for material characterization. The effective elastic, bulk, and shear moduli, and Poisson’s ratio, as tangent functions, are also derived. The model is characterized against published experimental data for lung. A bridge between this continuum model and a dodecahedral model of alveolar geometry is investigated, with preliminary findings being reported.
NASA Astrophysics Data System (ADS)
Feuillet, N.; Nostro, C.; Chiarabba, C.; Cocco, M.
2004-02-01
We study a seismic swarm that occurred in 1989-1990 at the Alban Hills volcano and interpret the seismicity pattern in terms of Coulomb stress changes caused by magma intrusion in a local volcanic source and the extensional tectonic stress field. We first image the three-dimensional (3-D) structure of the volcano through a tomographic inversion of P waves and S-P arrival times recorded by a temporary local network. A high Vp and Vp/Vs body exists beneath the area of most recent volcanic activity, which we interpret as a solidified magma body delimiting the position of the volcanic source. We have relocated 661 events (M ≤ 4.0) using this 3-D velocity model and we have computed 64 fault plane solutions. Elevation changes, measured between 1951 and 1994 along a 33-km-long line crossing the western part of the volcano, reveal an uplift of 0.3 m. We model these data to constrain the position and geometry of the volcanic source. We compute the vertical deformation in a homogeneous half-space, testing different volcanic sources (spherical magma chamber, sill and dike). We model the Coulomb stress changes caused by the local volcanic source and the regional tectonic stress field. The inflation of magma generates an increase of Coulomb stress larger than 0.5 MPa in the area where the seismicity is located. More than 85% of fault plane solutions are consistent with the stress perturbations induced by the volcanic source. We conclude that microearthquakes at the Alban Hills are promoted by elastic stress changes caused by volcanic unrest episodes.
Elastically Decoupling Dark Matter.
Kuflik, Eric; Perelstein, Maxim; Lorier, Nicolas Rey-Le; Tsai, Yu-Dai
2016-06-03
We present a novel dark matter candidate, an elastically decoupling relic, which is a cold thermal relic whose present abundance is determined by the cross section of its elastic scattering on standard model particles. The dark matter candidate is predicted to have a mass ranging from a few to a few hundred MeV, and an elastic scattering cross section with electrons, photons and/or neutrinos in the 10^{-3}-1 fb range.
Modeling Social Network Topologies in Elementary Schools
Huerta-Quintanilla, Rodrigo; Canto-Lugo, Efrain; Viga-de Alva, Dolores
2013-01-01
Complex networks are used to describe interactions in many real world systems, including economic, biological and social systems. An analysis was done of inter-student friendship, enmity and kinship relationships at three elementary schools by building social networks of these relationships and studying their properties. Friendship network measurements were similar between schools and produced a Poisson topology with a high clustering index. Enmity network measurements were also similar between schools and produced a power law topology. Spatial confinement and the sense of belonging to a social group played vital roles in shaping these networks. Two models were developed which generate complex friendship and enmity networks that reproduce the properties observed at the three studied elementary schools. PMID:23408976
Modeling social network topologies in elementary schools.
Huerta-Quintanilla, Rodrigo; Canto-Lugo, Efrain; Viga-de Alva, Dolores
2013-01-01
Complex networks are used to describe interactions in many real world systems, including economic, biological and social systems. An analysis was done of inter-student friendship, enmity and kinship relationships at three elementary schools by building social networks of these relationships and studying their properties. Friendship network measurements were similar between schools and produced a Poisson topology with a high clustering index. Enmity network measurements were also similar between schools and produced a power law topology. Spatial confinement and the sense of belonging to a social group played vital roles in shaping these networks. Two models were developed which generate complex friendship and enmity networks that reproduce the properties observed at the three studied elementary schools.
Measuring and modeling correlations in multiplex networks
NASA Astrophysics Data System (ADS)
Nicosia, Vincenzo; Latora, Vito
2015-09-01
The interactions among the elementary components of many complex systems can be qualitatively different. Such systems are therefore naturally described in terms of multiplex or multilayer networks, i.e., networks where each layer stands for a different type of interaction between the same set of nodes. There is today a growing interest in understanding when and why a description in terms of a multiplex network is necessary and more informative than a single-layer projection. Here we contribute to this debate by presenting a comprehensive study of correlations in multiplex networks. Correlations in node properties, especially degree-degree correlations, have been thoroughly studied in single-layer networks. Here we extend this idea to investigate and characterize correlations between the different layers of a multiplex network. Such correlations are intrinsically multiplex, and we first study them empirically by constructing and analyzing several multiplex networks from the real world. In particular, we introduce various measures to characterize correlations in the activity of the nodes and in their degree at the different layers and between activities and degrees. We show that real-world networks exhibit indeed nontrivial multiplex correlations. For instance, we find cases where two layers of the same multiplex network are positively correlated in terms of node degrees, while other two layers are negatively correlated. We then focus on constructing synthetic multiplex networks, proposing a series of models to reproduce the correlations observed empirically and/or to assess their relevance.
A new paradigm for the molecular basis of rubber elasticity
Hanson, David E.; Barber, John L.
2015-02-19
The molecular basis for rubber elasticity is arguably the oldest and one of the most important questions in the field of polymer physics. The theoretical investigation of rubber elasticity began in earnest almost a century ago with the development of analytic thermodynamic models, based on simple, highly-symmetric configurations of so-called Gaussian chains, i.e. polymer chains that obey Markov statistics. Numerous theories have been proposed over the past 90 years based on the ansatz that the elastic force for individual network chains arises from the entropy change associated with the distribution of end-to-end distances of a free polymer chain. There are serious philosophical objections to this assumption and others, such as the assumption that all network nodes undergo affine motion and that all of the network chains have the same length. Recently, a new paradigm for elasticity in rubber networks has been proposed that is based on mechanisms that originate at the molecular level. Using conventional statistical mechanics analyses, quantum chemistry, and molecular dynamics simulations, the fundamental entropic and enthalpic chain extension forces for polyisoprene (natural rubber) have been determined, along with estimates for the basic force constants. Concurrently, the complex morphology of natural rubber networks (the joint probability density distributions that relate the chain end-to-end distance to its contour length) has also been captured in a numerical model. When molecular chain forces are merged with the network structure in this model, it is possible to study the mechanical response to tensile and compressive strains of a representative volume element of a polymer network. As strain is imposed on a network, pathways of connected taut chains, that completely span the network along strain axis, emerge. Although these chains represent only a few percent of the total, they account for nearly all of the elastic stress at high strain. Here we provide a brief
NASA Astrophysics Data System (ADS)
Wang, Neng; Xia, Shuman
2017-01-01
A combined modeling and experimental effort is made in this work to examine the cohesive fracture mechanisms of heterogeneous elastic solids. A two-phase laminated composite, which mimics the key microstructural features of many tough engineering and biological materials, is selected as a model material system. Theoretical and finite element analyses with cohesive zone modeling are performed to study the effective fracture resistance of the heterogeneous material associated with unstable crack propagation and arrest. A crack-tip-position controlled algorithm is implemented in the finite element analysis to overcome the inherent instability issues resulting from crack pinning and depinning at local heterogeneities. Systematic parametric studies are carried out to investigate the effects of various material and geometrical parameters, including the modulus mismatch ratio, phase volume fraction, cohesive zone size, and cohesive law shape. Concurrently, a novel stereolithography-based three-dimensional (3D) printing system is developed and used for fabricating heterogeneous test specimens with well-controlled structural and material properties. Fracture testing of the specimens is performed using the tapered double-cantilever beam (TDCB) test method. With optimal material and geometrical parameters, heterogeneous TDCB specimens are shown to exhibit enhanced effective fracture energy and effective fracture toughness than their homogeneous counterparts, which is in good agreement with the modeling predictions. The integrative computational and experimental study presented here provides a fundamental mechanistic understanding of the fracture mechanisms in brittle heterogeneous materials and sheds light on the rational design of tough materials through patterned heterogeneities.
Elastic plastic self-consistent (EPSC) modeling of plastic deformation in fayalite olivine
Burnley, Pamela C
2015-07-01
Elastic plastic self-consistent (EPSC) simulations are used to model synchrotron X-ray diffraction observations from deformation experiments on fayalite olivine using the deformation DIA apparatus. Consistent with results from other in situ diffraction studies of monomineralic polycrystals, the results show substantial variations in stress levels among grain populations. Rather than averaging the lattice reflection stresses or choosing a single reflection to determine the macroscopic stress supported by the specimen, an EPSC simulation is used to forward model diffraction data and determine a macroscopic stress that is consistent with lattice strains of all measured diffraction lines. The EPSC simulation presented here includesmore » kink band formation among the plastic deformation mechanisms in the simulation. The inclusion of kink band formation is critical to the success of the models. This study demonstrates the importance of kink band formation as an accommodation mechanism during plastic deformation of olivine as well as the utility of using EPSC models to interpret diffraction from in situ deformation experiments.« less
Elastic plastic self-consistent (EPSC) modeling of plastic deformation in fayalite olivine
Burnley, Pamela C
2015-07-01
Elastic plastic self-consistent (EPSC) simulations are used to model synchrotron X-ray diffraction observations from deformation experiments on fayalite olivine using the deformation DIA apparatus. Consistent with results from other in situ diffraction studies of monomineralic polycrystals, the results show substantial variations in stress levels among grain populations. Rather than averaging the lattice reflection stresses or choosing a single reflection to determine the macroscopic stress supported by the specimen, an EPSC simulation is used to forward model diffraction data and determine a macroscopic stress that is consistent with lattice strains of all measured diffraction lines. The EPSC simulation presented here includes kink band formation among the plastic deformation mechanisms in the simulation. The inclusion of kink band formation is critical to the success of the models. This study demonstrates the importance of kink band formation as an accommodation mechanism during plastic deformation of olivine as well as the utility of using EPSC models to interpret diffraction from in situ deformation experiments.
Lester, Brian; Scherzinger, William
2017-01-19
Here, a new method for the solution of the non-linear equations forming the core of constitutive model integration is proposed. Specifically, the trust-region method that has been developed in the numerical optimization community is successfully modified for use in implicit integration of elastic-plastic models. Although attention here is restricted to these rate-independent formulations, the proposed approach holds substantial promise for adoption with models incorporating complex physics, multiple inelastic mechanisms, and/or multiphysics. As a first step, the non-quadratic Hosford yield surface is used as a representative case to investigate computationally challenging constitutive models. The theory and implementation are presented, discussed, andmore » compared to other common integration schemes. Multiple boundary value problems are studied and used to verify the proposed algorithm and demonstrate the capabilities of this approach over more common methodologies. Robustness and speed are then investigated and compared to existing algorithms. Through these efforts, it is shown that the utilization of a trust-region approach leads to superior performance versus a traditional closest-point projection Newton-Raphson method and comparable speed and robustness to a line search augmented scheme.« less
Symbolic regression of generative network models
Menezes, Telmo; Roth, Camille
2014-01-01
Networks are a powerful abstraction with applicability to a variety of scientific fields. Models explaining their morphology and growth processes permit a wide range of phenomena to be more systematically analysed and understood. At the same time, creating such models is often challenging and requires insights that may be counter-intuitive. Yet there currently exists no general method to arrive at better models. We have developed an approach to automatically detect realistic decentralised network growth models from empirical data, employing a machine learning technique inspired by natural selection and defining a unified formalism to describe such models as computer programs. As the proposed method is completely general and does not assume any pre-existing models, it can be applied “out of the box” to any given network. To validate our approach empirically, we systematically rediscover pre-defined growth laws underlying several canonical network generation models and credible laws for diverse real-world networks. We were able to find programs that are simple enough to lead to an actual understanding of the mechanisms proposed, namely for a simple brain and a social network. PMID:25190000
Gene Regulation Networks for Modeling Drosophila Development
NASA Technical Reports Server (NTRS)
Mjolsness, E.
1999-01-01
This chapter will very briefly introduce and review some computational experiments in using trainable gene regulation network models to simulate and understand selected episodes in the development of the fruit fly, Drosophila Melanogaster.
Graphical Model Theory for Wireless Sensor Networks
Davis, William B.
2002-12-08
Information processing in sensor networks, with many small processors, demands a theory of computation that allows the minimization of processing effort, and the distribution of this effort throughout the network. Graphical model theory provides a probabilistic theory of computation that explicitly addresses complexity and decentralization for optimizing network computation. The junction tree algorithm, for decentralized inference on graphical probability models, can be instantiated in a variety of applications useful for wireless sensor networks, including: sensor validation and fusion; data compression and channel coding; expert systems, with decentralized data structures, and efficient local queries; pattern classification, and machine learning. Graphical models for these applications are sketched, and a model of dynamic sensor validation and fusion is presented in more depth, to illustrate the junction tree algorithm.
Brake, M. R. W.
2015-02-17
Impact between metallic surfaces is a phenomenon that is ubiquitous in the design and analysis of mechanical systems. We found that to model this phenomenon, a new formulation for frictional elastic–plastic contact between two surfaces is developed. The formulation is developed to consider both frictional, oblique contact (of which normal, frictionless contact is a limiting case) and strain hardening effects. The constitutive model for normal contact is developed as two contiguous loading domains: the elastic regime and a transitionary region in which the plastic response of the materials develops and the elastic response abates. For unloading, the constitutive model is based on an elastic process. Moreover, the normal contact model is assumed to only couple one-way with the frictional/tangential contact model, which results in the normal contact model being independent of the frictional effects. Frictional, tangential contact is modeled using a microslip model that is developed to consider the pressure distribution that develops from the elastic–plastic normal contact. This model is validated through comparisons with experimental results reported in the literature, and is demonstrated to be significantly more accurate than 10 other normal contact models and three other tangential contact models found in the literature.
Brake, M. R. W.
2015-02-17
Impact between metallic surfaces is a phenomenon that is ubiquitous in the design and analysis of mechanical systems. We found that to model this phenomenon, a new formulation for frictional elastic–plastic contact between two surfaces is developed. The formulation is developed to consider both frictional, oblique contact (of which normal, frictionless contact is a limiting case) and strain hardening effects. The constitutive model for normal contact is developed as two contiguous loading domains: the elastic regime and a transitionary region in which the plastic response of the materials develops and the elastic response abates. For unloading, the constitutive model ismore » based on an elastic process. Moreover, the normal contact model is assumed to only couple one-way with the frictional/tangential contact model, which results in the normal contact model being independent of the frictional effects. Frictional, tangential contact is modeled using a microslip model that is developed to consider the pressure distribution that develops from the elastic–plastic normal contact. This model is validated through comparisons with experimental results reported in the literature, and is demonstrated to be significantly more accurate than 10 other normal contact models and three other tangential contact models found in the literature.« less
Using neural networks to model chaos
Upadhyay, M.D.
1996-12-31
Two types of neural networks -- backpropagation and radial basis function -- are presented for modeling dynamical systems. They were trained to model the Henon, Ikeda and Tinkerbell dynamical systems by providing a set of points randomly chosen from orbits under the functions. After training, the networks were used to simulate the functions to determine the extent to which they could generate the chaotic attractors associated with these systems.
NASA Astrophysics Data System (ADS)
McLaskey, Gregory C.; Glaser, Steven D.
2009-03-01
Experimental studies were performed using high-fidelity broadband Glaser-NIST conical transducers to quantify stress waves produced by the elastic collision of a tiny ball and a massive plate. These sensors are sensitive to surface-normal displacements down to picometers in amplitude, in a frequency range of 20 kHz to over 1 MHz. Both the collision and the resulting transient elastic waves are modeled with the finite element program ABAQUS and described theoretically through a marriage of the Hertz theory of contact and a full elastodynamic Green's function found using generalized ray theory. The calculated displacements were compared to those measured through the Glaser-NIST sensors.
Network Modeling and Simulation (NEMSE)
2013-07-01
this figure, tunnels through the Internet using a Virtual Private Network (VPN) technique to one of the front end “ Condor “ computers. The VPN...connections are shown as heavy lines. Information Assurance (IA) considerations are handled between the Condor machines and “Ops”, “Tips”, and "Boss
Telestroke network business model strategies.
Fanale, Christopher V; Demaerschalk, Bart M
2012-10-01
Our objective is to summarize the evidence that supports the reliability of telemedicine for diagnosis and efficacy in acute stroke treatment, identify strategies for funding the development of a telestroke network, and to present issues with respect to economic sustainability, cost effectiveness, and the status of reimbursement for telestroke.
Wang Weihua
2011-09-01
We study the similarity and correlations between relaxations and plastic deformation in metallic glasses (MGs) and MG-forming liquids. It is shown that the microscope plastic events, the initiation and formation of shear bands, and the mechanical yield in MGs where the atomic sites are topologically unstable induced by applied stress, can be treated as the glass to supercooled liquid state transition induced by external shear stress. On the other hand, the glass transition, the primary and secondary relaxations, plastic deformation and yield can be attributed to the free volume increase induced flow, and the flow can be modeled as the activated hopping between the inherent states in the potential energy landscape. We then propose an extended elastic model to describe the flow based on the energy landscape theory. That is, the flow activation energy density is linear proportional to the instantaneous elastic moduli, and the activation energy density {rho}{sub E} is determined to be a simple expression of {rho}{sub E}=(10/11)G+(1/11)K. The model indicates that both shear and bulk moduli are critical parameters accounting for both the homogeneous and inhomogeneous flows in MGs and MG-forming liquids. The elastic model is experimentally certified. We show that the elastic perspectives offers a simple scenario for the flow in MGs and MG-forming liquids and are suggestive for understanding the glass transition, plastic deformation, and nature and characteristics of MGs.
Mitsak, Anna G; Dunn, Andrew M; Hollister, Scott J
2012-07-01
Scaffold tissue engineering strategies for repairing and replacing soft tissue aim to improve reconstructive and corrective surgical techniques whose limitations include suboptimal mechanical properties, fibrous capsule formation and volume loss due to graft resorption. An effective tissue engineering strategy requires a scaffolding material with low elastic modulus that behaves similarly to soft tissue, which has been characterized as a nonlinear elastic material. The material must also have the ability to be manufactured into specifically designed architectures. Poly(glycerol sebacate) (PGS) is a thermoset elastomer that meets these criteria. We hypothesize that the mechanical properties of PGS can be modulated through curing condition and architecture to produce materials with a range of stiffnesses. To evaluate this hypothesis, we manufactured PGS constructs cured under various conditions and having one of two architectures (solid or porous). Specimens were then tensile tested according to ASTM standards and the data were modeled using a nonlinear elastic Neo-Hookean model. Architecture and testing conditions, including elongation rate and wet versus dry conditions, affected the mechanical properties. Increasing curing time and temperature led to increased tangent modulus and decreased maximum strain for solid constructs. Porous constructs had lower nonlinear elastic properties, as did constructs of both architectures tested under simulated physiological conditions (wetted at 37 °C). Both solid and porous PGS specimens could be modeled well with the Neo-Hookean model. Future studies include comparing PGS properties to other biological tissue types and designing and characterizing PGS scaffolds for regenerating these tissues.
Hay, Todd A.; Ilinskii, Yurii A.; Zabolotskaya, Evgenia A.; Hamilton, Mark F.
2013-01-01
A model is developed for a pulsating and translating gas bubble immersed in liquid in a channel formed by two soft, thin elastic parallel layers having densities equal to that of the surrounding liquid and small, but finite, shear moduli. The bubble is nominally spherical but free to undergo small shape deformations. Shear strain in the elastic layers is estimated in a way which is valid for short, transient excitations of the system. Coupled nonlinear second-order differential equations are obtained for the shape and position of the bubble, and numerical integration of an expression for the liquid velocity at the layer interfaces yields an estimate of the elastic layer displacement. Numerical integration of the dynamical equations reveals behavior consistent with laboratory observations of acoustically excited bubbles in ex vivo vessels reported by Chen et al. [Phys. Rev. Lett. 106, 034301 (2011) and Ultrasound Med. Biol. 37, 2139–2148 (2011)]. PMID:23927185
Anisotropic micro-sphere-based finite elasticity applied to blood vessel modelling
NASA Astrophysics Data System (ADS)
Alastrué, V.; Martínez, M. A.; Doblaré, M.; Menzel, A.
2009-01-01
A fully three-dimensional anisotropic elastic model for vascular tissue modelling is presented here. The underlying strain energy density function is assumed to additively decouple into volumetric and deviatoric contributions. A straightforward isotropic neo-Hooke-type law is used to model the deviatoric response of the ground substance, whereas a micro-structurally or rather micro-sphere-based approach will be employed to model the contribution and distribution of fibres within the biological tissue of interest. Anisotropy was introduced by means of the use of von Mises orientation distribution functions. Two different micro-mechanical approaches—a, say phenomenological, exponential ansatz, and a worm-like-chain-based formulation—are applied to the micro-fibres and illustratively compared. The passage from micro-structural contributions to the macroscopic response is obtained by a computational homogenisation scheme, namely numerical integration over the surface of the individual micro-spheres. The algorithmic treatment of this integration is discussed in detail for the anisotropic problem at hand, so that several cubatures of the micro-sphere are tested in order to optimise the accuracy at reasonable computational cost. Moreover, the introduced material parameters are identified from simple tension tests on human coronary arterial tissue for the two micro-mechanical models investigated. Both approaches are able to recapture the experimental data. Based on the identified sets of parameters, we first discuss a homogeneous deformation in simple shear to evaluate the models' response at the micro-structural level. Later on, an artery-like two-layered tube subjected to internal pressure is simulated by making use of a non-linear finite element setting. This enables to obtain the micro- and macroscopic responses in an inhomogeneous deformation problem, namely a blood vessel representative boundary value problem. The effect of residual stresses is additionally
NASA Astrophysics Data System (ADS)
Jian, Wang; Xiaohong, Meng; Hong, Liu; Wanqiu, Zheng; Yaning, Liu; Sheng, Gui; Zhiyang, Wang
2017-03-01
Full waveform inversion and reverse time migration are active research areas for seismic exploration. Forward modeling in the time domain determines the precision of the results, and numerical solutions of finite difference have been widely adopted as an important mathematical tool for forward modeling. In this article, the optimum combined of window functions was designed based on the finite difference operator using a truncated approximation of the spatial convolution series in pseudo-spectrum space, to normalize the outcomes of existing window functions for different orders. The proposed combined window functions not only inherit the characteristics of the various window functions, to provide better truncation results, but also control the truncation error of the finite difference operator manually and visually by adjusting the combinations and analyzing the characteristics of the main and side lobes of the amplitude response. Error level and elastic forward modeling under the proposed combined system were compared with outcomes from conventional window functions and modified binomial windows. Numerical dispersion is significantly suppressed, which is compared with modified binomial window function finite-difference and conventional finite-difference. Numerical simulation verifies the reliability of the proposed method.
Chemo-mechanical modeling of tumor growth in elastic epithelial tissue
NASA Astrophysics Data System (ADS)
Bratsun, Dmitry A.; Zakharov, Andrey P.; Pismen, Len
2016-08-01
We propose a multiscale chemo-mechanical model of the cancer tumor development in the epithelial tissue. The epithelium is represented by an elastic 2D array of polygonal cells with its own gene regulation dynamics. The model allows the simulation of the evolution of multiple cells interacting via the chemical signaling or mechanically induced strain. The algorithm includes the division and intercalation of cells as well as the transformation of normal cells into a cancerous state triggered by a local failure of the spatial synchronization of the cellular rhythms driven by transcription/translation processes. Both deterministic and stochastic descriptions of the system are given for chemical signaling. The transformation of cells means the modification of their respective parameters responsible for chemo-mechanical interactions. The simulations reproduce a distinct behavior of invasive and localized carcinoma. Generally, the model is designed in such a way that it can be readily modified to take account of any newly understood gene regulation processes and feedback mechanisms affecting chemo-mechanical properties of cells.
An application of multigrid methods for a discrete elastic model for epitaxial systems
Caflisch, R.E. . E-mail: caflisch@math.ucla.edu; Lee, Y.-J. . E-mail: yjlee@math.ucla.edu; Shu, S. . E-mail: shushi@xtu.edu.cn; Xiao, Y.-X. . E-mail: xyx610xyx@yahoo.com.cn; Xu, J. . E-mail: xu@math.psu.edu
2006-12-10
We apply an efficient and fast algorithm to simulate the atomistic strain model for epitaxial systems, recently introduced by Schindler et al. [Phys. Rev. B 67, 075316 (2003)]. The discrete effects in this lattice statics model are crucial for proper simulation of the influence of strain for thin film epitaxial growth, but the size of the atomistic systems of interest is in general quite large and hence the solution of the discrete elastic equations is a considerable numerical challenge. In this paper, we construct an algebraic multigrid method suitable for efficient solution of the large scale discrete strain model. Using this method, simulations are performed for several representative physical problems, including an infinite periodic step train, a layered nanocrystal, and a system of quantum dots. The results demonstrate the effectiveness and robustness of the method and show that the method attains optimal convergence properties, regardless of the problem size, the geometry and the physical parameters. The effects of substrate depth and of invariance due to traction-free boundary conditions are assessed. For a system of quantum dots, the simulated strain energy density supports the observations that trench formation near the dots provides strain relief.
Perfectly matched layer for an elastic parabolic equation model in ocean acoustics
NASA Astrophysics Data System (ADS)
Xu, Chuanxiu; Zhang, Haigang; Piao, Shengchun; Yang, Shi'e.; Sun, Sipeng; Tang, Jun
2017-02-01
The perfectly matched layer (PML) is an effective technique for truncating unbounded domains with minimal spurious reflections. A fluid parabolic equation (PE) model applying PML technique was previously used to analyze the sound propagation problem in a range-dependent waveguide (Lu and Zhu, 2007). However, Lu and Zhu only considered a standard fluid PE to demonstrate the capability of the PML and did not take improved one-way models into consideration. They applied a [1/1] Padé approximant to the parabolic equation. The higher-order PEs are more accurate than standard ones when a very large angle propagation is considered. As for range-dependent problems, the techniques to handle the vertical interface between adjacent regions are mainly energy conserving and single-scattering. In this paper, the PML technique is generalized to the higher order elastic PE, as is to the higher order fluid PE. The correction of energy conserving is used in range-dependent waveguides. Simulation is made in both acoustic cases and seismo-acoustic cases. Range-independent and range-dependent waveguides are both adopted to test the accuracy and efficiency of this method. The numerical results illustrate that a PML is much more effective than an artificial absorbing layer (ABL) both in acoustic and seismo-acoustic sound propagation modeling.
Posterior Predictive Model Checking in Bayesian Networks
ERIC Educational Resources Information Center
Crawford, Aaron
2014-01-01
This simulation study compared the utility of various discrepancy measures within a posterior predictive model checking (PPMC) framework for detecting different types of data-model misfit in multidimensional Bayesian network (BN) models. The investigated conditions were motivated by an applied research program utilizing an operational complex…
Network Reconstruction Using Nonparametric Additive ODE Models
Henderson, James; Michailidis, George
2014-01-01
Network representations of biological systems are widespread and reconstructing unknown networks from data is a focal problem for computational biologists. For example, the series of biochemical reactions in a metabolic pathway can be represented as a network, with nodes corresponding to metabolites and edges linking reactants to products. In a different context, regulatory relationships among genes are commonly represented as directed networks with edges pointing from influential genes to their targets. Reconstructing such networks from data is a challenging problem receiving much attention in the literature. There is a particular need for approaches tailored to time-series data and not reliant on direct intervention experiments, as the former are often more readily available. In this paper, we introduce an approach to reconstructing directed networks based on dynamic systems models. Our approach generalizes commonly used ODE models based on linear or nonlinear dynamics by extending the functional class for the functions involved from parametric to nonparametric models. Concomitantly we limit the complexity by imposing an additive structure on the estimated slope functions. Thus the submodel associated with each node is a sum of univariate functions. These univariate component functions form the basis for a novel coupling metric that we define in order to quantify the strength of proposed relationships and hence rank potential edges. We show the utility of the method by reconstructing networks using simulated data from computational models for the glycolytic pathway of Lactocaccus Lactis and a gene network regulating the pluripotency of mouse embryonic stem cells. For purposes of comparison, we also assess reconstruction performance using gene networks from the DREAM challenges. We compare our method to those that similarly rely on dynamic systems models and use the results to attempt to disentangle the distinct roles of linearity, sparsity, and derivative
A simple model for studying interacting networks
NASA Astrophysics Data System (ADS)
Liu, Wenjia; Jolad, Shivakumar; Schmittmann, Beate; Zia, R. K. P.
2011-03-01
Many specific physical networks (e.g., internet, power grid, interstates), have been characterized in considerable detail, but in isolation from each other. Yet, each of these networks supports the functions of the others, and so far, little is known about how their interactions affect their structure and functionality. To address this issue, we consider two coupled model networks. Each network is relatively simple, with a fixed set of nodes, but dynamically generated set of links which has a preferred degree, κ . In the stationary state, the degree distribution has exponential tails (far from κ), an attribute which we can explain. Next, we consider two such networks with different κ 's, reminiscent of two social groups, e.g., extroverts and introverts. Finally, we let these networks interact by establishing a controllable fraction of cross links. The resulting distribution of links, both within and across the two model networks, is investigated and discussed, along with some potential consequences for real networks. Supported in part by NSF-DMR-0705152 and 1005417.
Fractal modeling of natural fracture networks
Ferer, M.; Dean, B.; Mick, C.
1995-06-01
West Virginia University will implement procedures for a fractal analysis of fractures in reservoirs. This procedure will be applied to fracture networks in outcrops and to fractures intersecting horizontal boreholes. The parameters resulting from this analysis will be used to generate synthetic fracture networks with the same fractal characteristics as the real networks. Recovery from naturally fractured, tight-gas reservoirs is controlled by the fracture network. Reliable characterization of the actual fracture network in the reservoir is severely limited. The location and orientation of fractures intersecting the borehole can be determined, but the length of these fractures cannot be unambiguously determined. Because of the lack of detailed information about the actual fracture network, modeling methods must represent the porosity and permeability associated with the fracture network, as accurately as possible with very little a priori information. In the sections following, the authors will (1) present fractal analysis of the MWX site, using the box-counting procedure; (2) review evidence testing the fractal nature of fracture distributions and discuss the advantages of using the fractal analysis over a stochastic analysis; and (3) present an efficient algorithm for producing a self-similar fracture networks which mimic the real MWX outcrop fracture network.
NASA Technical Reports Server (NTRS)
Moore, W.; Schubert, Gerald; Sandwell, David T.
1992-01-01
Magellan altimetry has revealed that many coronae on Venus have trenches or moats around their peripheries and rises outboard of the trenches. This trench/outer rise topographic signature is generally associated with the tectonic annulus of the corona. Sandwell and Schubert have interpreted the trench/outer rise topography and the associated tectonic annulus around coronae to be the result of elastic bending of the Venus lithosphere (though the tectonic structures are consequences of inelastic deformation of the lithosphere). They used two-dimensional elastic plate flexure theory to fit topographic profiles across a number of large coronae and inferred elastic lithosphere thicknesses between about 15 and 40 km, similar to inferred values of elastic thickness for the Earth's lithosphere at subduction zones around the Pacific Ocean. Here, we report the results of using axisymmetric elastic flexure theory for the deformation of thin spherical shell plates to interpret the trench/outer rise topography of the large coronae modeled by Sandwell and Schubert and of coronae as small as 250 km in diameter. In the case of a corona only a few hundred kilometers in diameter, the model accounts for the small planform radius of the moat and the nonradial orientation of altimetric traces across the corona. By fitting the flexural topography of coronae we determine the elastic thickness and loading necessary to account for the observed flexure. We calculate the associated bending moment and determine whether the corona interior topographic load can provide the required moment. We also calculate surface stresses and compare the stress distribution with the location of annular tectonic features.
Modeling gene regulatory network motifs using statecharts
2012-01-01
Background Gene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. Recently, a great effort has been devoted to give gene regulatory networks a formal semantics based on existing computational frameworks. For this purpose, we consider Statecharts, which are a modular, hierarchical and executable formal model widely used to represent software systems. We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs. Results We present an improved method for modeling gene regulatory network motifs using Statecharts and we describe the successful modeling of several motifs, including those which could not be modeled or whose models could not be distinguished using the method of a previous proposal. We model motifs in an easy and intuitive way by taking advantage of the visual features of Statecharts. Our modeling approach is able to simulate some interesting temporal properties of gene regulatory network motifs: the delay in the activation and the deactivation of the "output" gene in the coherent type-1 feedforward loop, the pulse in the incoherent type-1 feedforward loop, the bistability nature of double positive and double negative feedback loops, the oscillatory behavior of the negative feedback loop, and the "lock-in" effect of positive autoregulation. Conclusions We present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. The basic motifs used to build more complex networks (that is, simple regulation, reciprocal regulation, feedback loop, feedforward loop, and autoregulation) can be faithfully described and their temporal dynamics can be analyzed. PMID:22536967
Neural network approaches for noisy language modeling.
Li, Jun; Ouazzane, Karim; Kazemian, Hassan B; Afzal, Muhammad Sajid
2013-11-01
Text entry from people is not only grammatical and distinct, but also noisy. For example, a user's typing stream contains all the information about the user's interaction with computer using a QWERTY keyboard, which may include the user's typing mistakes as well as specific vocabulary, typing habit, and typing performance. In particular, these features are obvious in disabled users' typing streams. This paper proposes a new concept called noisy language modeling by further developing information theory and applies neural networks to one of its specific application-typing stream. This paper experimentally uses a neural network approach to analyze the disabled users' typing streams both in general and specific ways to identify their typing behaviors and subsequently, to make typing predictions and typing corrections. In this paper, a focused time-delay neural network (FTDNN) language model, a time gap model, a prediction model based on time gap, and a probabilistic neural network model (PNN) are developed. A 38% first hitting rate (HR) and a 53% first three HR in symbol prediction are obtained based on the analysis of a user's typing history through the FTDNN language modeling, while the modeling results using the time gap prediction model and the PNN model demonstrate that the correction rates lie predominantly in between 65% and 90% with the current testing samples, and 70% of all test scores above basic correction rates, respectively. The modeling process demonstrates that a neural network is a suitable and robust language modeling tool to analyze the noisy language stream. The research also paves the way for practical application development in areas such as informational analysis, text prediction, and error correction by providing a theoretical basis of neural network approaches for noisy language modeling.
Surrogate modeling of deformable joint contact using artificial neural networks.
Eskinazi, Ilan; Fregly, Benjamin J
2015-09-01
Deformable joint contact models can be used to estimate loading conditions for cartilage-cartilage, implant-implant, human-orthotic, and foot-ground interactions. However, contact evaluations are often so expensive computationally that they can be prohibitive for simulations or optimizations requiring thousands or even millions of contact evaluations. To overcome this limitation, we developed a novel surrogate contact modeling method based on artificial neural networks (ANNs). The method uses special sampling techniques to gather input-output data points from an original (slow) contact model in multiple domains of input space, where each domain represents a different physical situation likely to be encountered. For each contact force and torque output by the original contact model, a multi-layer feed-forward ANN is defined, trained, and incorporated into a surrogate contact model. As an evaluation problem, we created an ANN-based surrogate contact model of an artificial tibiofemoral joint using over 75,000 evaluations of a fine-grid elastic foundation (EF) contact model. The surrogate contact model computed contact forces and torques about 1000 times faster than a less accurate coarse grid EF contact model. Furthermore, the surrogate contact