A path-based framework for analyzing large markov models

Reliability and dependability modeling can be employed during many stages of analysis of a computing system to gain insights into its critical behaviors. To provide useful results, realistic models of systems are often necessarily large and complex. Numerical analysis of these models presents a formidable challenge because the sizes of their state-space descriptions grow exponentially in proportion to the sizes of the models. On the other hand, simulation of the models requires analysis of many trajectories in order to compute statistically correct solutions. This dissertation presents a novel framework for performing both numerical analysis and simulation. The new numerical approach computes bounds on the solutions of transient measures in large continuous-time Markov chains (CTMCs). It extends existing path-based and uniformization-based methods by identifying sets of paths that are equivalent with respect to a reward measure and related to one another via a simple structural relationship. This relationship makes it possible for the approach to explore multiple paths at the same time,· thus significantly increasing the number of paths that can be explored in a given amount of time. Furthermore, the use of a structured representation for the state space and the direct computation of the desired reward measure (without ever storing the solution vector) allow it to analyze very large models using a very small amount of storage. Often, path-based techniques must compute many paths to obtain tight bounds. In addition to presenting the basic path-based approach, we also present algorithms for computing more paths and tighter bounds quickly. One resulting approach is based on the concept of path composition whereby precomputed subpaths are composed to compute the whole paths efficiently. Another approach is based on selecting important paths (among a set of many paths) for evaluation. Many path-based techniques suffer from having to evaluate many (unimportant) paths. Evaluating the important ones helps to compute tight bounds efficiently and quickly.

A Flexible Architecture for the Computation of Direct and Inverse Transforms in H.264/AVC Video Codecs

A new high throughput and scalable architecture for unified transform coding in H.264/AVC is proposed in this paper. Such flexible structure is capable of computing all the 4x4 and 2x2 transforms for Ultra High Definition Video (UHDV) applications (4320x7680@ 30fps) in real-time and with low hardware cost. These significantly high performance levels were proven with the implementation of several different configurations of the proposed structure using both FPGA and ASIC 90 nm technologies. In addition, such experimental evaluation also demonstrated the high area efficiency of theproposed architecture, which in terms of Data Throughput per Unit of Area (DTUA) is at least 1.5 times more efficient than its more prominent related designs(1).

The underestimation of compliance to direct help requests explained by adaptive sampling

Helping behavior is any intentional behavior that benefits another living being or group (Hogg & Vaughan, 2010). People tend to underestimate the probability that others will comply with their direct requests for help (Flynn & Lake, 2008). This implies that when they need help, they will assess the probability of getting it (De Paulo, 1982, cited in Flynn & Lake, 2008) and then they will tend to estimate one that is actually lower than the real chance, so they may not even consider worth asking for it. Existing explanations for this phenomenon attribute it to a mistaken cost computation by the help seeker, who will emphasize the instrumental cost of “saying yes”, ignoring that the potential helper also needs to take into account the social cost of saying “no”. And the truth is that, especially in face-to-face interactions, the discomfort caused by refusing to help can be very high. In short, help seekers tend to fail to realize that it might be more costly to refuse to comply with a help request rather than accepting. A similar effect has been observed when estimating trustworthiness of people. Fetchenhauer and Dunning (2010) showed that people also tend to underestimate it. This bias is reduced when, instead of asymmetric feedback (getting feedback only when deciding to trust the other person), symmetric feedback (always given) was provided. This cause could as well be applicable to help seeking as people only receive feedback when they actually make their request but not otherwise. Fazio, Shook, and Eiser (2004) studied something that could be reinforcing these outcomes: Learning asymmetries. By means of a computer game called BeanFest, they showed that people learn better about negatively valenced objects (beans in this case) than about positively valenced ones. This learning asymmetry esteemed from “information gain being contingent on approach behavior” (p. 293), which could be identified with what Fetchenhauer and Dunning mention as ‘asymmetric feedback’, and hence also with help requests. Fazio et al. also found a generalization asymmetry in favor of negative attitudes versus positive ones. They attributed it to a negativity bias that “weights resemblance to a known negative more heavily than resemblance to a positive” (p. 300). Applied to help seeking scenarios, this would mean that when facing an unknown situation, people would tend to generalize and infer that is more likely that they get a negative rather than a positive outcome from it, so, along with what it was said before, people will be more inclined to think that they will get a “no” when requesting help. Denrell and Le Mens (2011) present a different perspective when trying to explain judgment biases in general. They deviate from the classical inappropriate information processing (depicted among other by Fiske & Taylor, 2007, and Tversky & Kahneman, 1974) and explain this in terms of ‘adaptive sampling’. Adaptive sampling is a sampling mechanism in which the selection of sample items is conditioned by the values of the variable of interest previously observed (Thompson, 2011). Sampling adaptively allows individuals to safeguard themselves from experiences they went through once and turned out to lay negative outcomes. However, it also prevents them from giving a second chance to those experiences to get an updated outcome that could maybe turn into a positive one, a more positive one, or just one that regresses to the mean, whatever direction that implies. That, as Denrell and Le Mens (2011) explained, makes sense: If you go to a restaurant, and you did not like the food, you do not choose that restaurant again. This is what we think could be happening when asking for help: When we get a “no”, we stop asking. And here, we want to provide a complementary explanation for the underestimation of the probability that others comply with our direct help requests based on adaptive sampling. First, we will develop and explain a model that represents the theory. Later on, we will test it empirically by means of experiments, and will elaborate on the analysis of its results.

Monte Carlo derivation of filtered tungsten anode X-ray spectra for dose computation in digital mammography

Abstract Objective: Derive filtered tungsten X-ray spectra used in digital mammography systems by means of Monte Carlo simulations. Materials and Methods: Filtered spectra for rhodium filter were obtained for tube potentials between 26 and 32 kV. The half-value layer (HVL) of simulated filtered spectra were compared with those obtained experimentally with a solid state detector Unfors model 8202031-H Xi R/F & MAM Detector Platinum and 8201023-C Xi Base unit Platinum Plus w mAs in a Hologic Selenia Dimensions system using a direct radiography mode. Results: Calculated HVL values showed good agreement as compared with those obtained experimentally. The greatest relative difference between the Monte Carlo calculated HVL values and experimental HVL values was 4%. Conclusion: The results show that the filtered tungsten anode X-ray spectra and the EGSnrc Monte Carlo code can be used for mean glandular dose determination in mammography.

Inhibition of dendritic Ca2+ spikes by GABAB receptors in cortical pyramidal neurons is mediated by a direct Gi/o- -subunit interaction with Cav1 channels

Voltage-dependent calcium channels (VDCCs) serve a wide range of physiological functions and their activity is modulated by different neurotransmitter systems. GABAergic inhibition of VDCCs in neurons has an important impact in controlling transmitter release, neuronal plasticity, gene expression and neuronal excitability. We investigated the molecular signalling mechanisms by which GABAB receptors inhibit calcium-mediated electrogenesis (Ca2+ spikes) in the distal apical dendrite of cortical layer 5 pyramidal neurons. Ca2+ spikes are the basis of coincidence detection and signal amplification of distal tuft synaptic inputs characteristic for the computational function of cortical pyramidal neurons. By combining dendritic whole-cell recordings with two-photon fluorescence Ca2+ imaging we found that all subtypes of VDCCs were present in the Ca2+ spike initiation zone, but that they contribute differently to the initiation and sustaining of dendritic Ca2+ spikes. Particularly, Cav1 VDCCs are the most abundant VDCC present in this dendritic compartment and they generated the sustained plateau potential characteristic for the Ca2+ spike. Activation of GABAB receptors specifically inhibited Cav1 channels. This inhibition of L-type Ca2+ currents was transiently relieved by strong depolarization but did not depend on protein kinase activity. Therefore, our findings suggest a novel membrane-delimited interaction of the Gi/o-βγ-subunit with Cav1 channels identifying this mechanism as the general pathway of GABAB receptor-mediated inhibition of VDCCs. Furthermore, the characterization of the contribution of the different VDCCs to the generation of the Ca2+ spike provides new insights into the molecular mechanism of dendritic computation.

Direct effects of increased CO2 concentrations in seawater on the net primary production of charophytes in a shallow, coastal, brackish-water ecosystem

Charophytes are found in fresh and brackish waters across the globe and play key roles in coastal ecosystems. However, their response to increasing CO2 is not well understood. The aim of the study was to detect the effects of elevated CO2 on the physiology of charophyte species growing in the brackish Baltic Sea by measuring net primary production. Mesocosm experiments were conducted in the Kõiguste Bay (N Gulf of Riga) during the field season of 2012. Separate mesocosms were maintained at different pCO2 levels: 2000, 1000 and 200 µatm. The experiments were carried out with three species of charophytes: Chara aspera, C. tomentosa and C. horrida. The short-term photosynthetic responses of charophytes to different treatments were measured by the oxygen method. The results show that elevated CO2 levels in brackish water may enhance the photosynthetic activity of charophyte species and suggest that increasing CO2 in the Baltic Sea could have implications for interspecific competition and community structure in a future high CO2 world.

Computation of nonlinear streaky structures in boundary layer flow

En esta tesis se integran numéricamente las ecuaciones reducidas de Navier Stokes (RNS), que describen el flujo en una capa límite tridimensional que presenta también una escala característica espacial corta en el sentido transversal. La formulación RNS se usa para el cálculo de “streaks” no lineales de amplitud finita, y los resultados conseguidos coinciden con los existentes en la literatura, obtenidos típicamente utilizando simulación numérica directa (DNS) o nonlinear parabolized stability equations (PSE). El cálculo de los “streaks” integrando las RNS es mucho menos costoso que usando DNS, y no presenta los problemas de estabilidad que aparecen en la formulación PSE cuando la amplitud del “streak” deja de ser pequeña. El código de integración RNS se utiliza también para el cálculo de los “streaks” que aparecen de manera natural en el borde de ataque de una placa plana en ausencia de perturbaciones en la corriente uniforme exterior. Los resultados existentes hasta ahora calculaban estos “streaks” únicamente en el límite lineal (amplitud pequeña), y en esta tesis se lleva a cabo el cálculo de los mismos en el régimen completamente no lineal (amplitud finita). En la segunda parte de la tesis se generaliza el código RNS para incluir la posibilidad de tener una placa no plana, con curvatura en el sentido transversal que varía lentamente en el sentido de la corriente. Esto se consigue aplicando un cambio de coordenadas, que transforma el dominio físico en uno rectangular. La formulación RNS se integra también expresada en las correspondientes coordenadas curvilíneas. Este código generalizado RNS se utiliza finalmente para estudiar el flujo de capa límite sobre una placa con surcos que varían lentamente en el sentido de la corriente, y es usado para simular el flujo sobre surcos que crecen en tal sentido. Abstract In this thesis, the reduced Navier Stokes (RNS) equations are numerically integrated. This formulation describes the flow in a three-dimensional boundary layer that also presents a short characteristic space scale in the spanwise direction. RNS equations are used to calculate nonlinear finite amplitude “streaks”, and the results agree with those reported in the literature, typically obtained using direct numerical simulation (DNS) or nonlinear parabolized stability equations (PSE). “Streaks” simulations through the RNS integration are much cheaper than using DNS, and avoid stability problems that appear in the PSE when the amplitude of the “streak” is not small. The RNS integration code is also used to calculate the “streaks” that naturally emerge at the leading edge of a flat plate boundary layer in the absence of any free stream perturbations. Up to now, the existing results for these “streaks” have been only calculated in the linear limit (small amplitude), and in this thesis their calculation is carried out in the fully nonlinear regime (finite amplitude). In the second part of the thesis, the RNS code is generalized to include the possibility of having a non-flat plate, curved in the spanwise direction and slowly varying in the streamwise direction. This is achieved by applying a change of coordinates, which transforms the physical domain into a rectangular one. The RNS formulation expressed in the corresponding curvilinear coordinates is also numerically integrated. This generalized RNS code is finally used to study the boundary layer flow over a plate with grooves which vary slowly in the streamwise direction; and this code is used to simulate the flow over grooves that grow in the streamwise direction.

Efficient computation of the pressures developed during high-speed train passing events

The paper resumes the results obtained applying various implementations of the direct boundary element method (BEM) to the solution of the Laplace Equation governing the potential flow problem during everyday service manoeuvres of high-speed trains. In particular the results of train passing events at three different speed combinations are presented. Some recommendations are given in order to reduce calculation times which as is demonstrated can be cut down to not exceed reasonable limits even when using nowadays office PCs. Thus the method is shown to be a very valuable tool for the design engineer.

An efficient nonlinear transformation for the numerical computation of the singular integrals appearing in the 2-D Boundary Element Method

We discuss several methods, based on coordinate transformations, for the evaluation of singular and quasisingular integrals in the direct Boundary Element Method. An intrinsec error of some of these methods is detected. Two new transformations are suggested which improve on those currently available.

Direct and adjoint global stability analysis of turbulent transonic flows over a NACA0012 profile

In this work, various turbulent solutions of the two-dimensional (2D) and three-dimensional compressible Reynolds averaged Navier?Stokes equations are analyzed using global stability theory. This analysis is motivated by the onset of flow unsteadiness (Hopf bifurcation) for transonic buffet conditions where moderately high Reynolds numbers and compressible effects must be considered. The buffet phenomenon involves a complex interaction between the separated flow and a shock wave. The efficient numerical methodology presented in this paper predicts the critical parameters, namely, the angle of attack and Mach and Reynolds numbers beyond which the onset of flow unsteadiness appears. The geometry, a NACA0012 profile, and flow parameters selected reproduce situations of practical interest for aeronautical applications. The numerical computation is performed in three steps. First, a steady baseflow solution is obtained; second, the Jacobian matrix for the RANS equations based on a finite volume discretization is computed; and finally, the generalized eigenvalue problem is derived when the baseflow is linearly perturbed. The methodology is validated predicting the 2D Hopf bifurcation for a circular cylinder under laminar flow condition. This benchmark shows good agreement with the previous published computations and experimental data. In the transonic buffet case, the baseflow is computed using the Spalart?Allmaras turbulence model and represents a mean flow where the high frequency content and length scales of the order of the shear-layer thickness have been averaged. The lower frequency content is assumed to be decoupled from the high frequencies, thus allowing a stability analysis to be performed on the low frequency range. In addition, results of the corresponding adjoint problem and the sensitivity map are provided for the first time for the buffet problem. Finally, an extruded three-dimensional geometry of the NACA0012 airfoil, where all velocity components are considered, was also analyzed as a Triglobal stability case, and the outcoming results were compared to the previous 2D limited model, confirming that the buffet onset is well detected.

Quantum computation by communication

We present here a new approach to scalable quantum computing - a 'qubus computer' - which realizes qubit measurement and quantum gates through interacting qubits with a quantum communication bus mode. The qubits could be 'static' matter qubits or 'flying' optical qubits, but the scheme we focus on here is particularly suited to matter qubits. There is no requirement for direct interaction between the qubits. Universal two-qubit quantum gates may be effected by schemes which involve measurement of the bus mode, or by schemes where the bus disentangles automatically and no measurement is needed. In effect, the approach integrates together qubit degrees of freedom for computation with quantum continuous variables for communication and interaction.

Computation of rare transitions in the barotropic quasi-geostrophic equations

We investigate the theoretical and numerical computation of rare transitions in simple geophysical turbulent models. We consider the barotropic quasi-geostrophic and two-dimensional Navier–Stokes equations in regimes where bistability between two coexisting large-scale attractors exist. By means of large deviations and instanton theory with the use of an Onsager–Machlup path integral formalism for the transition probability, we show how one can directly compute the most probable transition path between two coexisting attractors analytically in an equilibrium (Langevin) framework and numerically otherWe adapt a class of numerical optimization algorithms known as minimum action methods to simple geophysical turbulent models. We show that by numerically minimizing an appropriate action functional in a large deviation limit, one can predict the most likely transition path for a rare transition between two states. By considering examples where theoretical predictions can be made, we show that the minimum action method successfully predicts the most likely transition path. Finally, we discuss the application and extension of such numerical optimization schemes to the computation of rare transitions observed in direct numerical simulations and experiments and to other, more complex, turbulent systems.

Direct linkage between dimethyl sulfide production and microzooplankton grazing, resulting from prey composition change under high partial pressure of carbon dioxide conditions

Oceanic dimethyl sulfide (DMS) is the enzymatic cleavage product of the algal metabolite dimethylsulfoniopropionate (DMSP) and is the most abundant form of sulfur released into the atmosphere. To investigate the effects of two emerging environmental threats (ocean acidification and warming) on marine DMS production, we performed a large-scale perturbation experiment in a coastal environment. At both ambient temperature and 2 °C warmer, an increase in partial pressure of carbon dioxide (pCO2) in seawater (160-830 ppmv pCO2) favored the growth of large diatoms, which outcompeted other phytoplankton species in a natural phytoplankton assemblage and reduced the growth rate of smaller, DMSP-rich phototrophic dinoflagellates. This decreased the grazing rate of heterotrophic dinoflagellates (ubiquitous micrograzers), resulting in reduced DMS production via grazing activity. Both the magnitude and sign of the effect of pCO2 on possible future oceanic DMS production were strongly linked to pCO2-induced alterations to the phytoplankton community and the cellular DMSP content of the dominant species and its association with micrograzers.

DIRECT NUMERICAL SIMULATION OF INCOMPRESSIBLE MULTIPHASE FLOW WITH PHASE CHANGE

Phase change problems arise in many practical applications such as air-conditioning and refrigeration, thermal energy storage systems and thermal management of electronic devices. The physical phenomenon in such applications are complex and are often difficult to be studied in detail with the help of only experimental techniques. The efforts to improve computational techniques for analyzing two-phase flow problems with phase change are therefore gaining momentum. The development of numerical methods for multiphase flow has been motivated generally by the need to account more accurately for (a) large topological changes such as phase breakup and merging, (b) sharp representation of the interface and its discontinuous properties and (c) accurate and mass conserving motion of the interface. In addition to these considerations, numerical simulation of multiphase flow with phase change introduces additional challenges related to discontinuities in the velocity and the temperature fields. Moreover, the velocity field is no longer divergence free. For phase change problems, the focus of developmental efforts has thus been on numerically attaining a proper conservation of energy across the interface in addition to the accurate treatment of fluxes of mass and momentum conservation as well as the associated interface advection. Among the initial efforts related to the simulation of bubble growth in film boiling applications the work in \cite{Welch1995} was based on the interface tracking method using a moving unstructured mesh. That study considered moderate interfacial deformations. A similar problem was subsequently studied using moving, boundary fitted grids \cite{Son1997}, again for regimes of relatively small topological changes. A hybrid interface tracking method with a moving interface grid overlapping a static Eulerian grid was developed \cite{Juric1998} for the computation of a range of phase change problems including, three-dimensional film boiling \cite{esmaeeli2004computations}, multimode two-dimensional pool boiling \cite{Esmaeeli2004} and film boiling on horizontal cylinders \cite{Esmaeeli2004a}. The handling of interface merging and pinch off however remains a challenge with methods that explicitly track the interface. As large topological changes are crucial for phase change problems, attention has turned in recent years to front capturing methods utilizing implicit interfaces that are more effective in treating complex interface deformations. The VOF (Volume of Fluid) method was adopted in \cite{Welch2000} to simulate the one-dimensional Stefan problem and the two-dimensional film boiling problem. The approach employed a specific model for mass transfer across the interface involving a mass source term within cells containing the interface. This VOF based approach was further coupled with the level set method in \cite{Son1998}, employing a smeared-out Heaviside function to avoid the numerical instability related to the source term. The coupled level set, volume of fluid method and the diffused interface approach was used for film boiling with water and R134a at the near critical pressure condition \cite{Tomar2005}. The effect of superheat and saturation pressure on the frequency of bubble formation were analyzed with this approach. The work in \cite{Gibou2007} used the ghost fluid and the level set methods for phase change simulations. A similar approach was adopted in \cite{Son2008} to study various boiling problems including three-dimensional film boiling on a horizontal cylinder, nucleate boiling in microcavity \cite{lee2010numerical} and flow boiling in a finned microchannel \cite{lee2012direct}. The work in \cite{tanguy2007level} also used the ghost fluid method and proposed an improved algorithm based on enforcing continuity and divergence-free condition for the extended velocity field. The work in \cite{sato2013sharp} employed a multiphase model based on volume fraction with interface sharpening scheme and derived a phase change model based on local interface area and mass flux. Among the front capturing methods, sharp interface methods have been found to be particularly effective both for implementing sharp jumps and for resolving the interfacial velocity field. However, sharp velocity jumps render the solution susceptible to erroneous oscillations in pressure and also lead to spurious interface velocities. To implement phase change, the work in \cite{Hardt2008} employed point mass source terms derived from a physical basis for the evaporating mass flux. To avoid numerical instability, the authors smeared the mass source by solving a pseudo time-step diffusion equation. This measure however led to mass conservation issues due to non-symmetric integration over the distributed mass source region. The problem of spurious pressure oscillations related to point mass sources was also investigated by \cite{Schlottke2008}. Although their method is based on the VOF, the large pressure peaks associated with sharp mass source was observed to be similar to that for the interface tracking method. Such spurious fluctuation in pressure are essentially undesirable because the effect is globally transmitted in incompressible flow. Hence, the pressure field formation due to phase change need to be implemented with greater accuracy than is reported in current literature. The accuracy of interface advection in the presence of interfacial mass flux (mass flux conservation) has been discussed in \cite{tanguy2007level,tanguy2014benchmarks}. The authors found that the method of extending one phase velocity to entire domain suggested by Nguyen et al. in \cite{nguyen2001boundary} suffers from a lack of mass flux conservation when the density difference is high. To improve the solution, the authors impose a divergence-free condition for the extended velocity field by solving a constant coefficient Poisson equation. The approach has shown good results with enclosed bubble or droplet but is not general for more complex flow and requires additional solution of the linear system of equations. In current thesis, an improved approach that addresses both the numerical oscillation of pressure and the spurious interface velocity field is presented by featuring (i) continuous velocity and density fields within a thin interfacial region and (ii) temporal velocity correction steps to avoid unphysical pressure source term. Also I propose a general (iii) mass flux projection correction for improved mass flux conservation. The pressure and the temperature gradient jump condition are treated sharply. A series of one-dimensional and two-dimensional problems are solved to verify the performance of the new algorithm. Two-dimensional and cylindrical film boiling problems are also demonstrated and show good qualitative agreement with the experimental observations and heat transfer correlations. Finally, a study on Taylor bubble flow with heat transfer and phase change in a small vertical tube in axisymmetric coordinates is carried out using the new multiphase, phase change method.

Direct Kinematics of Underactuated Cable-Driven Parallel Robots: Sensitivity to Redundant Measurements

Underactuated cable-driven parallel robots (UACDPRs) shift a 6-degree-of-freedom end-effector (EE) with fewer than 6 cables. This thesis proposes a new automatic calibration technique that is applicable for under-actuated cable-driven parallel robots. The purpose of this work is to develop a method that uses free motion as an exciting trajectory for the acquisition of calibration data. The key point of this approach is to find a relationship between the unknown parameters to be calibrated (the lengths of the cables) and the parameters that could be measured by sensors (the swivel pulley angles measured by the encoders and roll-and-pitch angles measured by inclinometers on the platform). The equations involved are the geometrical-closure equations and the finite-difference velocity equations, solved using the least-squares algorithm. Simulations are performed on a parallel robot driven by 4 cables for validation. The final purpose of the calibration method is, still, the determination of the platform initial pose. As a consequence of underactuation, the EE is underconstrained and, for assigned cable lengths, the EE pose cannot be obtained by means of forward kinematics only. Hence, a direct-kinematics algorithm for a 4-cable UACDPR using redundant sensor measurements is proposed. The proposed method measures two orientation parameters of the EE besides cable lengths, in order to determine the other four pose variables, namely 3 position coordinates and one additional orientation parameter. Then, we study the performance of the direct-kinematics algorithm through the computation of the sensitivity of the direct-kinematics solution to measurement errors. Furthermore, position and orientation error upper limits are computed for bounded cable lengths errors resulting from the calibration procedure, and roll and pitch angles errors which are due to inclinometer inaccuracies.