Reduced three-wave model to study the hard transition to chaotic dynamics in Alfven wave-fronts

The derivative nonlinear Schrödinger (DNLS) equation, describing propagation of circularly polarized Alfven waves of finite amplitude in a cold plasma, is truncated to explore the coherent, weakly nonlinear, cubic coupling of three waves near resonance, one wave being linearly unstable and the other waves damped. In a reduced three-wave model (equal damping of daughter waves, three-dimensional flow for two wave amplitudes and one relative phase), no matter how small the growth rate of the unstable wave there exists a parametric domain with the flow exhibiting chaotic dynamics that is absent for zero growth-rate. This hard transition in phase-space behavior occurs for left-hand (LH) polarized waves, paralelling the known fact that only LH time-harmonic solutions of the DNLS equation are modulationally unstable.

Fully 3-wave model to study the hard transition to chaotic dynamics in alfven wave-fronts

The derivative nonlinear Schrödinger (DNLS) equation, describing propagation of circularly polarized Alfven waves of finite amplitude in a cold plasma, is truncated to explore the coherent, weakly nonlinear coupling of three waves near resonance, one wave being linearly unstable and the other waves damped. No matter how small the growth rate of the unstable wave, the four-dimensional flow for the three wave amplitudes and a relative phase, with both resistive damping and linear Landau damping, exhibits chaotic relaxation oscillations that are absent for zero growth-rate. This hard transition in phase-space behavior occurs for left-hand (LH) polarized waves, paralleling the known fact that only LH time-harmonic solutions of the DNLS equation are modulationally unstable. The parameter domain developing chaos is much broader than the corresponding domain in a reduced 3-wave model that assumes equal dampings of the daughter waves

Computational model for local damage assesment of structures

In the last years many studies have been developed to analyze the seismic behavior throug the damage concept. In fact, the evaluation of the structural damage is important in order to quantify the safety of new and existing structures and, also, to establish a framework for seismic retrofitting decision making of structures. Most proposed models are based on a post-earthquake evaluation in such a way they uncouple the computation of the structural response from that of damage. However, there are other models which include explicity the existing coupling between the degradation and the structural mechanical beaviour. Those models are closer to the physical reality and its formulation is based on the principles of Continuum Damage Mechanics. In the present work, a coupled model is formulated using a simplified application of the Continuum Damage Mechanics to the analysis of frames and allows its representation in standard finite element programs. This work is part of the activities developed by the Structural Mechanics Department (UPM) within ICONS (European Research Project on Innovative Seismic Design Concepts for New and Existing Structures).

A model of the spatially dependent mechanical properties of the axon during its growth

Neuronal growth is a complex process involving many intra- and extracellular mechanisms which are collaborating conjointly to participate to the development of the nervous system. More particularly, the early neocortical development involves the creation of a multilayered structure constituted by neuronal growth (driven by axonal or dendritic guidance cues) as well as cell migration. The underlying mechanisms of such structural lamination not only implies important biochemical changes at the intracellular level through axonal microtubule (de)polymerization and growth cone advance, but also through the directly dependent stress/stretch coupling mechanisms driving them. Efforts have recently focused on modeling approaches aimed at accounting for the effect of mechanical tension or compression on the axonal growth and subsequent soma migration. However, the reciprocal influence of the biochemical structural evolution on the mechanical properties has been mostly disregarded. We thus propose a new model aimed at providing the spatially dependent mechanical properties of the axon during its growth. Our in-house finite difference solver Neurite is used to describe the guanosine triphosphate (GTP) transport through the axon, its dephosphorylation in guanosine diphosphate (GDP), and thus the microtubules polymerization. The model is calibrated against experimental results and the tensile and bending mechanical stiffnesses are ultimately inferred from the spatially dependent microtubule occupancy. Such additional information is believed to be of drastic relevance in the growth cone vicinity, where biomechanical mechanisms are driving axonal growth and pathfinding. More specifically, the confirmation of a lower stiffness in the distal axon ultimately participates in explaining the controversy associated to the tensile role of the growth cone.

Massively parallelizable list-mode reconstruction using a Monte Carlo-based elliptical Gaussian model

Purpose: A fully three-dimensional (3D) massively parallelizable list-mode ordered-subsets expectation-maximization (LM-OSEM) reconstruction algorithm has been developed for high-resolution PET cameras. System response probabilities are calculated online from a set of parameters derived from Monte Carlo simulations. The shape of a system response for a given line of response (LOR) has been shown to be asymmetrical around the LOR. This work has been focused on the development of efficient region-search techniques to sample the system response probabilities, which are suitable for asymmetric kernel models, including elliptical Gaussian models that allow for high accuracy and high parallelization efficiency. The novel region-search scheme using variable kernel models is applied in the proposed PET reconstruction algorithm. Methods: A novel region-search technique has been used to sample the probability density function in correspondence with a small dynamic subset of the field of view that constitutes the region of response (ROR). The ROR is identified around the LOR by searching for any voxel within a dynamically calculated contour. The contour condition is currently defined as a fixed threshold over the posterior probability, and arbitrary kernel models can be applied using a numerical approach. The processing of the LORs is distributed in batches among the available computing devices, then, individual LORs are processed within different processing units. In this way, both multicore and multiple many-core processing units can be efficiently exploited. Tests have been conducted with probability models that take into account the noncolinearity, positron range, and crystal penetration effects, that produced tubes of response with varying elliptical sections whose axes were a function of the crystal's thickness and angle of incidence of the given LOR. The algorithm treats the probability model as a 3D scalar field defined within a reference system aligned with the ideal LOR. Results: This new technique provides superior image quality in terms of signal-to-noise ratio as compared with the histogram-mode method based on precomputed system matrices available for a commercial small animal scanner. Reconstruction times can be kept low with the use of multicore, many-core architectures, including multiple graphic processing units. Conclusions: A highly parallelizable LM reconstruction method has been proposed based on Monte Carlo simulations and new parallelization techniques aimed at improving the reconstruction speed and the image signal-to-noise of a given OSEM algorithm. The method has been validated using simulated and real phantoms. A special advantage of the new method is the possibility of defining dynamically the cut-off threshold over the calculated probabilities thus allowing for a direct control on the trade-off between speed and quality during the reconstruction.

Finite elastic deformations of transversely isotropic circular cylindrical tubes

We consider the finite radially symmetric deformation of a circular cylindrical tube of a homogeneous transversely isotropic elastic material subject to axial stretch, radial deformation and torsion, supported by axial load, internal pressure and end moment. Two different directions of transverse isotropy are considered: the radial direction and an arbitrary direction in planes normal locally to the radial direction, the only directions for which the considered deformation is admissible in general. In the absence of body forces, formulas are obtained for the internal pressure, and the resultant axial load and torsional moment on the ends of the tube in respect of a general strain-energy function. For a specific material model of transversely isotropic elasticity, and material and geometrical parameters, numerical results are used to illustrate the dependence of the pressure, (reduced) axial load and moment on the radial stretch and a measure of the torsional deformation for a fixed value of the axial stretch.

Finite element simulation of sandwich panels of plasterboard and rock wool under mixed mode fracture

This paper presents the results of research on mixed mode fracture of sandwich panels of plasterboard and rock wool. The experimental data of the performed tests are supplied. The specimens were made from commercial panels. Asymmetrical three-point bending tests were performed on notched specimens. Three sizes of geometrically similar specimens were tested for studying the size effect. The paper also includes the numerical simulation of the experimental results by using an embedded cohesive crack model.The involved parameters for modelling are previously measured by standardised tests.

Win-win transport strategies: searching for sinergies

In order to achieve to minimize car-based trips, transport planners have been particularly interested in understanding the factors that explain modal choices. In the transport modelling literature there has been an increasing awareness that socioeconomic attributes and quantitative variables are not sufficient to characterize travelers and forecast their travel behavior. Recent studies have also recognized that users? social interactions and land use patterns influence travel behavior, especially when changes to transport systems are introduced, but links between international and Spanish perspectives are rarely deal. In this paper, factorial and path analyses through a Multiple-Indicator Multiple-Cause (MIMIC) model are used to understand and describe the relationship between the different psychological and environmental constructs with social influence and socioeconomic variables. The MIMIC model generates Latent Variables (LVs) to be incorporated sequentially into Discrete Choice Models (DCM) where the levels of service and cost attributes of travel modes are also included directly to measure the effect of the transport policies that have been introduced in Madrid during the last three years in the context of the economic crisis. The data used for this paper are collected from a two panel smartphone-based survey (n=255 and 190 respondents, respectively) of Madrid.

Numerical model for the study of hydrodynamics on bays and estuaries

A nonlinear implicit finite element model for the solution of two-dimensional (2-D) shallow water equations, based on a Galerkin formulation of the 2-D estuaries hydrodynamic equations, has been developed. Spatial discretization has been achieved by the use of isoparametric, Lagrangian elements. To obtain the different element matrices, Simpson numerical integration has been applied. For time integration of the model, several schemes in finite differences have been used: the Cranck-Nicholson iterative method supplies a superior accuracy and allows us to work with the greatest time step Δt; however, central differences time integration produces a greater velocity of calculation. The model has been tested with different examples to check its accuracy and advantages in relation to computation and handling of matrices. Finally, an application to the Bay of Santander is also presented.

Finite element simulation of dispersion in the Bay of Santander

Two mathematical models are used to simulate pollution in the Bay of Santander. The first is the hydrodynamic model that provides the velocity field and height of the water. The second gives the pollutant concentration field as a resultant. Both models are formulated in two-dimensional equations. Linear triangular finite elements are used in the Galerkin procedure for spatial discretization. A finite difference scheme is used for the time integration. At each time step the calculated results of the first model are input to the second model as field data. The efficiency and accuracy of the models are tested by their application to a simple illustrative example. Finally a case study in simulation of pollution evolution in the Bay of Santander is presented

Some consistent finite element formulations of 1-D beam models: a comparative study

A consistent Finite Element formulation was developed for four classical 1-D beam models. This formulation is based upon the solution of the homogeneous differential equation (or equations) associated with each model. Results such as the shape functions, stiffness matrices and consistent force vectors for the constant section beam were found. Some of these results were compared with the corresponding ones obtained by the standard Finite Element Method (i.e. using polynomial expansions for the field variables). Some of the difficulties reported in the literature concerning some of these models may be avoided by this technique and some numerical sensitivity analysis on this subject are presented.

Neurite, a finite difference large scale parallel program for the simulation of the electrical signal propagation in neurites under mechanical loading

With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, function of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells has only very recently been proposed (Jerusalem et al., 2013). In this paper, we present the implementation details of Neurite: the finite difference parallel program used in this reference. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to simulate the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The simulation of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the simulated cells grows. The solvers implemented in Neurite-explicit and implicit-were therefore parallelized using graphics processing units in order to reduce the burden of the simulation costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between lectrophysiology and mechanics (Jerusalem et al., 2013). This paper provides the details of the parallel implementation of Neurite, along with three different application examples: a long myelinated axon, a segmented dendritic tree, and a damaged axon. The capabilities of the program to deal with large scale scenarios, segmented neuronal structures, and functional deficits under mechanical loading are specifically highlighted.

Classifying GABAergic interneurons with semi-supervised projected model-based clustering

Objectives: A recently introduced pragmatic scheme promises to be a useful catalog of interneuron names.We sought to automatically classify digitally reconstructed interneuronal morphologies according tothis scheme. Simultaneously, we sought to discover possible subtypes of these types that might emergeduring automatic classification (clustering). We also investigated which morphometric properties weremost relevant for this classification.Materials and methods: A set of 118 digitally reconstructed interneuronal morphologies classified into thecommon basket (CB), horse-tail (HT), large basket (LB), and Martinotti (MA) interneuron types by 42 of theworld?s leading neuroscientists, quantified by five simple morphometric properties of the axon and fourof the dendrites. We labeled each neuron with the type most commonly assigned to it by the experts. Wethen removed this class information for each type separately, and applied semi-supervised clustering tothose cells (keeping the others? cluster membership fixed), to assess separation from other types and lookfor the formation of new groups (subtypes). We performed this same experiment unlabeling the cells oftwo types at a time, and of half the cells of a single type at a time. The clustering model is a finite mixtureof Gaussians which we adapted for the estimation of local (per-cluster) feature relevance. We performedthe described experiments on three different subsets of the data, formed according to how many expertsagreed on type membership: at least 18 experts (the full data set), at least 21 (73 neurons), and at least26 (47 neurons).Results: Interneurons with more reliable type labels were classified more accurately. We classified HTcells with 100% accuracy, MA cells with 73% accuracy, and CB and LB cells with 56% and 58% accuracy,respectively. We identified three subtypes of the MA type, one subtype of CB and LB types each, andno subtypes of HT (it was a single, homogeneous type). We got maximum (adapted) Silhouette widthand ARI values of 1, 0.83, 0.79, and 0.42, when unlabeling the HT, CB, LB, and MA types, respectively,confirming the quality of the formed cluster solutions. The subtypes identified when unlabeling a singletype also emerged when unlabeling two types at a time, confirming their validity. Axonal morphometricproperties were more relevant that dendritic ones, with the axonal polar histogram length in the [pi, 2pi) angle interval being particularly useful.Conclusions: The applied semi-supervised clustering method can accurately discriminate among CB, HT, LB, and MA interneuron types while discovering potential subtypes, and is therefore useful for neuronal classification. The discovery of potential subtypes suggests that some of these types are more heteroge-neous that previously thought. Finally, axonal variables seem to be more relevant than dendritic ones fordistinguishing among the CB, HT, LB, and MA interneuron types.

Finite element code-based modeling of a multi-feature isolation system and passive alleviation of possible inner pounding

The existing seismic isolation systems are based on well-known and accepted physical principles, but they are still having some functional drawbacks. As an attempt of improvement, the Roll-N-Cage (RNC) isolator has been recently proposed. It is designed to achieve a balance in controlling isolator displacement demands and structural accelerations. It provides in a single unit all the necessary functions of vertical rigid support, horizontal flexibility with enhanced stability, resistance to low service loads and minor vibration, and hysteretic energy dissipation characteristics. It is characterized by two unique features that are a self-braking (buffer) and a self-recentering mechanism. This paper presents an advanced representation of the main and unique features of the RNC isolator using an available finite element code called SAP2000. The validity of the obtained SAP2000 model is then checked using experimental, numerical and analytical results. Then, the paper investigates the merits and demerits of activating the built-in buffer mechanism on both structural pounding mitigation and isolation efficiency. The paper addresses the problem of passive alleviation of possible inner pounding within the RNC isolator, which may arise due to the activation of its self-braking mechanism under sever excitations such as near-fault earthquakes. The results show that the obtained finite element code-based model can closely match and accurately predict the overall behavior of the RNC isolator with effectively small errors. Moreover, the inherent buffer mechanism of the RNC isolator could mitigate or even eliminate direct structure-tostructure pounding under severe excitation considering limited septation gaps between adjacent structures. In addition, the increase of inherent hysteretic damping of the RNC isolator can efficiently limit its peak displacement together with the severity of the possibly developed inner pounding and, therefore, alleviate or even eliminate the possibly arising negative effects of the buffer mechanism on the overall RNC-isolated structural responses.

A methodology to calibrate structural finite element models for reinforced concrete structures subject to blast loads

Civil buildings are not specifically designed to support blast loads, but it is important to take into account these potential scenarios because of their catastrophic effects, on persons and structures. A practical way to consider explosions on reinforced concrete structures is necessary. With this objective we propose a methodology to evaluate blast loads on large concrete buildings, using LS-DYNA code for calculation, with Lagrangian finite elements and explicit time integration. The methodology has three steps. First, individual structural elements of the building like columns and slabs are studied, using continuum 3D elements models subjected to blast loads. In these models reinforced concrete is represented with high precision, using advanced material models such as CSCM_CONCRETE model, and segregated rebars constrained within the continuum mesh. Regrettably this approach cannot be used for large structures because of its excessive computational cost. Second, models based on structural elements are developed, using shells and beam elements. In these models concrete is represented using CONCRETE_EC2 model and segregated rebars with offset formulation, being calibrated with continuum elements models from step one to obtain the same structural response: displacement, velocity, acceleration, damage and erosion. Third, models basedon structural elements are used to develop large models of complete buildings. They are used to study the global response of buildings subjected to blast loads and progressive collapse. This article carries out different techniques needed to calibrate properly the models based on structural elements, using shells and beam elements, in order to provide results of sufficient accuracy that can be used with moderate computational cost.