A Bayesian hurdle model for analysis of an insect resistance monitoring database

Motivated by the analysis of the Australian Grain Insect Resistance Database (AGIRD), we develop a Bayesian hurdle modelling approach to assess trends in strong resistance of stored grain insects to phosphine over time. The binary response variable from AGIRD indicating presence or absence of strong resistance is characterized by a majority of absence observations and the hurdle model is a two step approach that is useful when analyzing such a binary response dataset. The proposed hurdle model utilizes Bayesian classification trees to firstly identify covariates and covariate levels pertaining to possible presence or absence of strong resistance. Secondly, generalized additive models (GAMs) with spike and slab priors for variable selection are fitted to the subset of the dataset identified from the Bayesian classification tree indicating possibility of presence of strong resistance. From the GAM we assess trends, biosecurity issues and site specific variables influencing the presence of strong resistance using a variable selection approach. The proposed Bayesian hurdle model is compared to its frequentist counterpart, and also to a naive Bayesian approach which fits a GAM to the entire dataset. The Bayesian hurdle model has the benefit of providing a set of good trees for use in the first step and appears to provide enough flexibility to represent the influence of variables on strong resistance compared to the frequentist model, but also captures the subtle changes in the trend that are missed by the frequentist and naive Bayesian models. © 2014 Springer Science+Business Media New York.

Regularized numerical integration of multibody dynamics with the generalized alpha method*

This paper discusses the consistent regularization property of the generalized α method when applied as an integrator to an initial value high index and singular differential-algebraic equation model of a multibody system. The regularization comes from within the discretization itself and the discretization remains consistent over the range of values the regularization parameter may take. The regularization involves increase of the smallest singular values of the ill-conditioned Jacobian of the discretization and is different from Baumgarte and similar techniques which tend to be inconsistent for poor choice of regularization parameter. This regularization also helps where pre-conditioning the Jacobian by scaling is of limited effect, for example, when the scleronomic constraints contain multiple closed loops or singular configuration or when high index path constraints are present. The feed-forward control in Kane's equation models is additionally considered in the numerical examples to illustrate the effect of regularization. The discretization presented in this work is adopted to the first order DAE system (unlike the original method which is intended for second order systems) for its A-stability and same order of accuracy for positions and velocities.

Homogeneous model theory of metric structures

This thesis studies homogeneous classes of complete metric spaces. Over the past few decades model theory has been extended to cover a variety of nonelementary frameworks. Shelah introduced the abstact elementary classes (AEC) in the 1980s as a common framework for the study of nonelementary classes. Another direction of extension has been the development of model theory for metric structures. This thesis takes a step in the direction of combining these two by introducing an AEC-like setting for studying metric structures. To find balance between generality and the possibility to develop stability theoretic tools, we work in a homogeneous context, thus extending the usual compact approach. The homogeneous context enables the application of stability theoretic tools developed in discrete homogeneous model theory. Using these we prove categoricity transfer theorems for homogeneous metric structures with respect to isometric isomorphisms. We also show how generalized isomorphisms can be added to the class, giving a model theoretic approach to, e.g., Banach space isomorphisms or operator approximations. The novelty is the built-in treatment of these generalized isomorphisms making, e.g., stability up to perturbation the natural stability notion. With respect to these generalized isomorphisms we develop a notion of independence. It behaves well already for structures which are omega-stable up to perturbation and coincides with the one from classical homogeneous model theory over saturated enough models. We also introduce a notion of isolation and prove dominance for it.

Catalyst effectiveness factor for redox model kinetic equation

A generalized isothermal effectiveness factor correlation has been proposed for catalytic reactions whose intrinsic kinetics are based on the redox model. In this correlation which is exact for asymptotic values of the Thiele parameter the effect of the parameters appearing in the model, the order of the reaction and particle geometry are incorporated in a modified form of Thiele parameter. The relationship takes the usual form: Image and predicts effectiveness factor with an error of less than 2% in a range of Thiele parameter that accommodates both the kinetic and diffusion control regimes.

Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Anomalous reaction-diffusion as a model of nonexponential DNA escape kinetics

We show that data from recent experiments carried out on the kinetics of DNA escape from alpha-hemolysin nanopores [M. Wiggin, C. Tropini, C. T. Cossa, N. N. Jetha, and A. Marziali, Biophys. J. 95, 5317 (2008)] may be rationalized by a model of chain dynamics based on the anomalous diffusion of a particle moving in a harmonic well in the presence of a delta function sink. The experiments of Wiggin found, among other things, that the occasional occurrence of unusually long escape times in the distribution of chain trapping events led to nonexponential decays in the survival probability, S(t), of the DNA molecules within the nanopore. Wiggin ascribed this nonexponentiality to the existence of a distribution of trapping potentials, which they suggested was theresult of stochastic interactions between the bases of the DNA and the amino acids located on the surface of the nanopore. Based on this idea, they showed that the experimentally determined S(t) could be well fit in both the short and long time regimes by a function of the form (1+t/tau)(-alpha) (the so called Becquerel function). In our model, S(t) is found to be given by a Mittag-Leffler function at short times and by a generalized Mittag-Leffler function at long times. By suitable choice of certain parameter values, these functions are found to fit the experimental S(t) even better than the Becquerel function. Anomalous diffusion of DNA within the trap prior to escape over a barrier of fixed height may therefore provide a second, plausible explanation of the data, and may offer fresh perspectives on similar trapping and escape problems.

A Model of Anomalous Chain Translocation Dynamics

A model of polymer translocation based on the stochastic dynamics of the number of monomers on one side of a pore-containing surface is formulated in terms of a one-dimensional generalized Langevin equation, in which the random force is assumed to be characterized by long-ranged temporal correlations. The model is introduced to rationalize anomalies in measured and simulated values of the average time of passage through the pore, which in general cannot be satisfactorily accounted for by simple Brownian diffusion mechanisms. Calculations are presented of the mean first passage time for barrier crossing and of the mean square displacement of a monomeric segment, in the limits of strong and weak diffusive bias. The calculations produce estimates of the exponents in various scaling relations that are in satisfactory agreement with available data.

A New Threshold Voltage Model for Omega Gate Cylindrical Nanowire Transistor

In this work, for the first time, we present a physically based analytical threshold voltage model for omega gate silicon nanowire transistor. This model is developed for long channel cylindrical body structure. The potential distribution at each and every point of the of the wire is derived with a closed form solution of two dimensional Poisson's equation, which is then used to model the threshold voltage. Proposed model can be treated as a generalized model, which is valid for both surround gate and semi-surround gate cylindrical transistors. The accuracy of proposed model is verified for different device geometry against the results obtained from three dimensional numerical device simulators and close agreement is observed.

A model Integrating the Facilities Management Process with the Building End User’s Business Process (ProFacil)

The ProFacil model is a generic process model defined as a framework model showing the links between the facilities management process and the building end user’s business process. The purpose of using the model is to support more detailed process modelling. The model has been developed using the IDEF0 modelling method. The ProFacil model describes business activities from the generalized point of view as management-, support-, and core processes and their relations. The model defines basic activities in the provision of a facility. Examples of these activities are “operate facilities”, “provide new facilities”, “provide re-build facilities”, “provide maintained facilities” and “perform dispose of facilities”. These are all generic activities providing a basis for a further specialisation of company specific FM activities and their tasks. A facilitator can establish a specialized process model using the ProFacil model and interacting with company experts to describe their company’s specific processes. These modelling seminars or interviews will be done in an informal way, supported by the high-level process model as a common reference.

A non-orthogonal distributed space-time coded protocol - Part 1:Signal model and design criteria

In this two-part series of papers, a generalized non-orthogonal amplify and forward (GNAF) protocol which generalizes several known cooperative diversity protocols is proposed. Transmission in the GNAF protocol comprises of two phases - the broadcast phase and the cooperation phase. In the broadcast phase, the source broadcasts its information to the relays as well as the destination. In the cooperation phase, the source and the relays together transmit a space-time code in a distributed fashion. The GNAF protocol relaxes the constraints imposed by the protocol of Jing and Hassibi on the code structure. In Part-I of this paper, a code design criteria is obtained and it is shown that the GNAF protocol is delay efficient and coding gain efficient as well. Moreover GNAF protocol enables the use of sphere decoders at the destination with a non-exponential Maximum likelihood (ML) decoding complexity. In Part-II, several low decoding complexity code constructions are studied and a lower bound on the Diversity-Multiplexing Gain tradeoff of the GNAF protocol is obtained.

A unified model for auxiliary switch commutated DC-DC converters

A novel ZVS auxiliary switch commutated variation for all DGDC converter topologies has been proposed in 2006. With proper designation of the circuit variables (throw current I and the pole voltage V), all these converters are seen to be governed by an identical set of equations. With idealized switches, the steady-state performance is obtainable in an analytical form. The conversion ratio of the converter topologies is obtained. A generalized equivalent circuit emerges for all these converters from the steady-state conversion ratio. It also provides a dynamic model as well. With these generalized steady-state equivalent circuits, small signal analysis of these converters may be carried out readily. It enables one to use the familiar state space averaged results of the standard PWM DGDC converters for the resonant counterparts. Th dc and ac models reveals that dc and low frequency behaviour of the proposed family of converters is similiar to that of its PWM parent

Double time window targeting technique: Real-time DMRG dynamics in the Pariser-Parr-Pople model

We present a generalized adaptive time-dependent density matrix renormalization-group (DMRG) scheme, called the double time window targeting (DTWT) technique, which gives accurate results with nominal computational resources, within reasonable computational time. This procedure originates from the amalgamation of the features of pace keeping DMRG algorithm, first proposed by Luo et al. [Phys. Rev. Lett. 91, 049701 (2003)] and the time-step targeting algorithm by Feiguin and White [Phys. Rev. B 72, 020404 (2005)]. Using the DTWT technique, we study the phenomena of spin-charge separation in conjugated polymers (materials for molecular electronics an spintronics), which have long-range electron-electron interactions and belong to the class of strongly correlated low-dimensional many-body systems. The issue of real-time dynamics within the Pariser-Parr-Pople (PPP) model which includes long-range electron correlations has not been addressed in the literature so far. The present study on PPP chains has revealed that, (i) long-range electron correlations enable both the charge and spin degree of freedom of the electron, to propagate faster in the PPP model compared to Hubbard model, (ii) for standard parameters of the PPP model as applied to conjugated polymers, the charge velocity is almost twice that of the spin velocity, and (iii) the simplistic interpretation of long-range correlations by merely renormalizing the U value of the Hubbard model fails to explain the dynamics of doped holes/electrons in the PPP model.

Generalized asymptotic expansions for coupled wavenumbers in fluid-filled cylindrical shells

Analytical expressions are found for the coupled wavenumbers in an infinite fluid-filled cylindrical shell using the asymptotic methods. These expressions are valid for any general circumferential order (n).The shallow shell theory (which is more accurate at higher frequencies)is used to model the cylinder. Initially, the in vacua shell is dealt with and asymptotic expressions are derived for the shell wavenumbers in the high-and the low-frequency regimes. Next, the fluid-filled shell is considered. Defining a relevant fluid-loading parameter p, we find solutions for the limiting cases of small and large p. Wherever relevant, a frequency scaling parameter along with some ingenuity is used to arrive at an elegant asymptotic expression. In all cases.Poisson's ratio v is used as an expansion variable. The asymptotic results are compared with numerical solutions of the dispersion equation and the dispersion relation obtained by using the more general Donnell-Mushtari shell theory (in vacuo and fluid-filled). A good match is obtained. Hence, the contribution of this work lies in the extension of the existing literature to include arbitrary circumferential orders(n). (C) 2010 Elsevier Ltd. All rights reserved.

Probabilistic extension to realistic abductive reasoning model

In this paper, we give a method for probabilistic assignment to the Realistic Abductive Reasoning Model, The knowledge is assumed to be represented in the form of causal chaining, namely, hyper-bipartite network. Hyper-bipartite network is the most generalized form of knowledge representation for which, so far, there has been no way of assigning probability to the explanations, First, the inference mechanism using realistic abductive reasoning model is briefly described and then probability is assigned to each of the explanations so as to pick up the explanations in the decreasing order of plausibility.

Mean field lattice model for adsorption isotherms in zeolite NaA

Using a lattice model for adsorption in microporous materials, pure component adsorption isotherms are obtained within a mean field approximation for methane at 300 K and xenon at 300 and 360 K in zeolite NaA. It is argued that the increased repulsive adsorbate-adsorbate interactions at high coverages must play an important role in determining the adsorption behavior. Therefore, this feature is incorporated through a "coverage-dependent interaction'' model, which introduces a free, adjustable parameter. Another important feature, the site volume reduction, has been treated in two ways: a van der Waal model and a 1D hard-rod theory [van Tassel et al., AIChE J. 40, 925 (1994)]; we have also generalized the latter to include all possible adsorbate overlap scenarios. In particular, the 1D hard-rod model, with our coverage-dependent interaction model, is shown to be in best quantitative agreement with the previous grand canonical Monte Carlo isotherms. The expressions for the isosteric heats of adsorption indicate that attractive and repulsive adsorbate-adsorbate interactions increase and decrease the heats of adsorption, respectively. It is concluded that within the mean field approximation, our simple model for repulsive interactions and the 1D hard-rod model for site volume reduction are able to capture most of the important features of adsorption in confined regions. (C) 1999 American Institute of Physics. [S0021-9606(99)70515-5].