Generation Function Research Articles

Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise.

System-environment interactions are essential in determining charge-transfer (CT) rates and mechanisms. We developed a computationally accessible method, suitable to simulate CT in flexible molecules (i.e., DNA) with hundreds of sites, where the system-environment interactions are explicitly treated with numerical noise modeling of time-dependent site energies and couplings. The properties of the noise are tunable, providing us a flexible tool to investigate the detailed effects of correlated thermal fluctuations on CT mechanisms. The noise is parametrizable by molecular simulation and quantum calculation results of specific molecular systems, giving us better molecular resolution in simulating the system-environment interactions than sampling fluctuations from generic spectral density functions. The spatially correlated thermal fluctuations among different sites are naturally built-in in our method but are not readily incorporated using approximate spectral densities. Our method has quantitative accuracy in systems with small redox potential differences (<kbT) and provides qualitative insights into systems with wide redox potential differences (≫kbT). Specifically, we find that the temporal correlations of site energies are critical in determining the coherent-incoherent transition, while the role of spatial correlations depends on the nature of the systems. In a system with repeated bridge units of the same chemistry, spatially correlated fluctuations enhance the charge delocalization and charge-transfer rates; however, in a system of units with different site energies, spatial correlations slow the fluctuations to bring units into degeneracy, in turn, slowing the charge-transfer rates. The spatial and temporal correlations of condensed phase medium fluctuations provide another source to control and tune the kinetics and dynamics of charge-transfer systems.

Simplified seismic loss functions for suspended ceilings and drywall partitions

Post-disaster reconnaissance reports frequently list non-structural components (NSCs) as a major source of financial loss in earthquakes. Moreover, minimizing their damage is also of vital significance to the uninterrupted functionality of a building. For efficient decision making, it is important to be able to estimate the cost and downtime associated with the repair of the damage likely to be caused at different hazard levels used in seismic design. Generalized loss functions for two important NSCs commonly used in New Zealand, namely suspended ceilings and drywall partitions are developed in this study. The methodology to develop the loss functions, in the form of engineering demand parameter vs. expected loss due to the considered components, is based on the existing framework for the storey level loss estimation. Nevertheless, exhaustive construction/field data are employed to make these loss functions more generic. In order to estimate financial losses resulting from the failure of suspended ceilings, generalized ceiling fragility functions are developed and combined with the cost functions, which give the loss associated with typical ceilings at various peak acceleration demands. Similarly, probabilities of different damage states in drywall partitions are combined with their associated repair/replacement costs to find the cumulative distribution of the expected loss due to partitions at various drift levels, which is then normalized in terms of the total building cost. Efficiencies of the developed loss functions are investigated through detailed loss assessment of case study reinforced concrete (RC) buildings. It is observed that the difference between the expected losses for ceilings, predicted by the developed generic loss function, and the losses obtained from the detailed loss estimation method is within 5%. Similarly, the developed generic loss function for partitions is able to estimate the partition losses within 2% of that from the detailed loss assessment. The results confirm the accuracy of the proposed generic seismic loss functions.

Refined beam finite elements for static and dynamic analysis of hull structures

The accuracy and reliability of structural analyses are significantly compromised owing to the utilization of simple beam elements to model the global mechanical behaviour of ship hulls. These 1D models entail various assumptions and do not provide accurate and reliable results for hulls with complex structural details, such as cut-outs or reinforcements. The 3D FEM solutions, on the other hand, are computationally expensive. In the present study, refined 1D FE models for the analysis of simplified naval engineering structures have been developed by using the well-known Carrera Unified Formulation (CUF). According to CUF, refined kinematics beam models that go beyond classical theories (Euler, Timoshenko) can be easily developed by expressing the displacement field as an expansion in terms of generic functions, whose form and order are arbitrary. Hence, the stiffness and mass matrices are written in terms of fundamental nuclei, which are independent of the adopted class of beam theory and the FE approximation along the beam axis. As a particular class of CUF models, Lagrange polynomials have been used to formulate beam models at the component scale. According to this approach, each structural component (e.g. hull, longerons, bulkheads, and floors) can be modelled by means of the same 1D formulation. The results clearly demonstrate the enhanced capabilities of the proposed formulation, which is able to replicate solid/shell ANSYS solutions with very low computational efforts.

External Costs as Competitiveness Factors for Freight Transport — A State of the Art

ABSTRACTExternal costs have been a key issue in the last years of transport research. In Europe, this trend is in line with the political willingness to internalize externalities in transport pricing policies. This paper has two purposes. It first identifies the recent work achieved in the field of external costs of road and intermodal freight transport, where each paper is assessed in terms of its perspective (academic or project oriented), its objective (prescription, application, projection), the type of externality (air pollution, climate change, noise, accidents, congestion) and the type of cost (marginal, average, total) that is considered. The literature review reveals a gap in the development of generic mathematical functions for external costs of transport. The second objective of the paper is thus to highlight the usefulness of such functions by identifying the main parameters that influence freight transport competitiveness in terms of external costs, and by determining which of these parameters should be incorporated in further research works.

General relativity as an attractor for scalar-torsion cosmology

We study flat Friedmann-Lemaitre-Robertson-Walker cosmological models for a scalar field coupled nonminimally to teleparallel gravity with generic coupling and potential functions. The goal of this paper is to determine the conditions under which the cosmological evolution tends to the limit where the variation of the gravitational "constant" ceases and the system evolves close to general relativity. These conditions can be read off from the approximate analytical solutions describing the process in matter and potential domination eras. Only those models where the GR limit exists and is an attractor can be considered viable. We expect the results to hold in the original "pure tetrad" formulation as well as in the recently suggested covariant formulation of the teleparallel theory. In the former case the GR attractor simultaneously provides a mechanism how cosmological evolution suppresses the problematic degrees of freedom stemming from the lack of local Lorentz invariance.

Number of appearances of events in random sequences: A new approach to non-overlapping runs

ABSTRACTDistributions of non-overlapping runs in multistate systems are derived using a new generating function (GF) approach, which has been applied previously mainly to exact length runs. By utilizing this method, univariate and multivariate joint distributions of non-overlapping runs are derived in a unified way. The GF approach also leads naturally to the asymptotic Gaussian distributions, with the mean, variance, and covariance linear in the size of the system.

Capabilities of 1D CUF-based models to analyse metallic/composite rotors

The Carrera Unified Formulation (CUF) is here extended to perform free-vibrational analyses of rotating structures. CUF is a hierarchical formulation which makes it possible to obtain refined structural theories by writing the unknown displacement variables using generic functions of the cross-section coordinates (x,z), which are, in this paper, Taylor-like expansions of N-order. The increase of the theory order leads to three-dimensional solutions while, the classical beam models are obtained as particular cases of the linear theory (N=1). The Finite Element method is used to derive the weak form of the three-dimensional differential equations of motion in term of 'fundamental nuclei', whose forms do not depend on the approximation used. Including both gyroscopic and stiffening contributions, structures rotating about either transversal or longitudinal axis can be considered. In particular, the dynamic characteristics of thin-walled composite shafts and blades are investigated in order to predict critical speeds and instabilities. The results reveal that the present one-dimensional approach combines a remarkable accuracy with a very low computational cost compared with the available 2D and 3D solutions. The advantages are especially evident when shafts with deformable discs, thick metallic/laminated cylinders and box beams are analyzed.

Dynamics of Two-Sided Markets

AbstractThis paper considers a dynamical system, which models a two-sided market. I evaluate the volume of users from each side of the market as a function of time. I formulate and prove theorems describing the long-term behavior and tendency of the market. Even though I consider generic attachment functions, I obtain a concrete result, formulated in terms of properties of attachment functions. This result is followed by examples (defined by the most popular in economics attachment functions), which illustrate behavior of the two-sided markets. I also simulate some two-sided market scenarios, showing how adjustments of attachment functions can influence the users’ dynamics. The dynamical system’s approach to the study of two-sided market problem allows natural generalization to multi-sided market, where one can utilize the same technique and obtain similar results in higher dimensions.

Efficient Strategies for Calculating Blockwise Likelihoods Under the Coalescent.

The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno.

Integrating nurse researchers in clinical practice - a challenging, but necessary task for nurse leaders.

To create awareness among nurse leaders, of what they may need to consider, when integrating nurse researchers as advanced nurse practitioners (ANP) at PhD-level among their staff. In a time of transition nurse leaders may be challenged by the change towards evidence-based clinical nursing, including integrating nurse researchers in ANP positions. A collective case study including three ANPs took place at a large regional hospital in Denmark. The cases were first analysed by focusing on the generic features, functions and skills of ANPs, and second by focusing on the approaches to evidence-based practice seen in the cases. Regardless of same position, formal level of research expertise and overall responsibility, different approaches related to each ANPs professional profile, interest, academic ambitions and personality were seen. Nurse leaders must ensure a process where the content and expectations of the particular role are mutually clarified and adjusted to the individual ANP and to the specific context, in order to create a harmonious match. In order to clarify expectations regarding the inclusion of nurse researchers as ANPs at PhD level, the paper provides firm recommendations that may guide the process.

Human Resource Management Practices in Bangladesh: Current Scenario and Future Challenges

The aim of this study is to assess current HRM practices in Bangladesh, as well as the future challenges the country faces. Based on secondary sources, we explain the institutional contexts of the four main generic HRM functions: recruitment and selection, training and development, pay and performance appraisal and industrial relations practices. Here, we also highlight recent developments and future challenges with regard to HRM practices. While credible research on HRM practices in Bangladesh is still rare, this study will be beneficial to researchers and HRM practitioners interested in Bangladesh and other developing countries and, we hope, will encourage future research.

Sustainability management: insights from the Viable System Model

A review of current literature on sustainability standards reveals a significant gap between their adoption and the implementation of sustainability into every level of the organisation. In this paper, it is argued that in order to overcome this challenge, an appropriate model of an organisation is needed. The Viable System Model (VSM) is proposed as such a model and, in order to illustrate this argument, it is used to interpret the ISO 26000 standard on Social Responsibility (SR). First, the VSM theory is introduced and presented by modelling the hypothetical company Widget Co. Then, the clauses of ISO 26000 are mapped on the Widget Co. model, together with detailed descriptions and examples on the organisational and managerial implications of its adopting the standard's guidelines. The result is the identification of generic SR functions that need to be performed by the various organisational governance systems, as well as their dynamic interrelations, thus clarifying implementation issues. Moreover, by identifying different SR management layers, VSM is suggested as a way forward to develop an integration model for SR issues and respective sustainability tools. Finally, a discussion is given on the implications of using this approach to integrate sustainability standards and the way this research contributes to recent developments in sustainability research.

Distributions of Runs Revisited

Distributions of runs have important applications in many fields, including biological sequence analysis. The generating function (GF) method provides a unified approach to tackle different run-related problems in multistate trials. By utilizing this method, various run-related distributions are derived in a systematic way for both conditional and unconditional models. The GF approach also naturally yields the asymptotic distributions. For all the distributions considered, the limiting distributions are Gaussian, with mean, variance, and covariance linear functions in the size of the system.

Quantitative information flow under generic leakage functions and adaptive adversaries

We put forward a model of action-based randomization mechanisms to analyse quantitative information flow (QIF) under generic leakage functions, and under possibly adaptive adversaries. This model subsumes many of the QIF models proposed so far. Our main contributions include the following: (1) we identify mild general conditions on the leakage function under which it is possible to derive general and significant results on adaptive QIF; (2) we contrast the efficiency of adaptive and non-adaptive strategies, showing that the latter are as efficient as the former in terms of length up to an expansion factor bounded by the number of available actions; (3) we show that the maximum information leakage over strategies, given a finite time horizon, can be expressed in terms of a Bellman equation. This can be used to compute an optimal finite strategy recursively, by resorting to standard methods like backward induction.

Development of a Generic Safety Narrative for a UK Geological Disposal Facility

AbstractThe UK has published a generic Disposal System Safety Case for a geological disposal facility (NDA, 2010) and is planning to update this in 2016. However, it is a challenge to present a meaningful safety case when the location and hence the design of a geological disposal facility are not known. Consequently, this paper describes our aim to present a narrative, explaining how we can have confidence in the long-term safety of a geological disposal facility. This narrative is based on an understanding of the environmental safety functions of a geological disposal facility and the features, events and processes (FEPs) that support them. The highest level environmental safety functions required for a geological disposal facility are isolation and containment. By isolation we mean removal of the wastes from people and the surface environment. By containment we mean retaining the radioactivity from the wastes within various parts of the disposal facility for as long as required to achieve safety. Beneath these top-level environmental safety functions we have identified generic environmental safety functions associated with each of the key safety barriers within a geological disposal facility, namely: the wasteform, the container, the local buffer or backfill, the mass backfill (in the access tunnels and service ways), the plugs and seals and the geosphere. This paper discusses the application of environmental safety functions and FEPs to building a safety narrative and explains how it is proposed to use such an approach to develop a generic environmental safety case for the UK to provide confidence in the longterm safety of a geological disposal facility after it has been sealed and closed.

Cognitive phylogenies, the Darwinian logic of descent, and the inadequacy of cladistic thinking

There has been a reappraisal of phylogenetic issues in cognitive science, as reconstructing cognitive phylogenies has been considered a key for unveiling the cognitive novelties that set the stage for what makes humans special. In our opinion, the studies made until now have approached cognitive phylogenies in a non-optimal way, and we wish to both highlight their problems, drawing on recent considerations in philosophy of biology. The inadequacy of current visions on cognitive phylogenies stems from the influence of the traditional “linear cladograms,” according to which every seemingly new or more sophisticated feature of a cognitive mechanism, viewed as a novelty, is represented as a node on top of the old and shared elements. We claim that this kind of cladograms does not succeed in depicting the complexity with which traits are distributed across species and, furthermore, that the labels of the nodes of these traditional representational systems fail to capture the “tinkering” nature of evolution. We argue that if we are to conceive of cognitive mechanisms in a multi-dimensional, bottom-up perspective, in accordance with the Darwinian logic of descent, we should rather focus on decomposing these mechanisms into lower-level, generic functions, which have the additional advantage of being implementable in neural matter, which ultimately produces cognition. Doing so renders current constructions of cognitive phylogenies otiose.

Accurate Response of Wing Structures to Free-Vibration, Load Factors, and Nonstructural Masses

Based on the Carrera unified formulation, this work extends variable kinematic finite beam elements to include load factors and nonstructural masses for the static and vibration analyses of complex, metallic wing structures. According to the Carrera unified formulation, variable kinematic beam theories are formulated in an automatic and hierarchical manner by expressing the displacement field as an arbitrary expansion through generic cross-sectional functions. Both Taylor-like and Lagrange polynomials are used in this paper to develop refined beam kinematics, and the related theories are referred to as Taylor expansion and Lagrange expansion, respectively. The generalized unknowns of Taylor expansion models are the beam axis displacements and the -order displacement derivatives, with being a free parameter of the analysis. Classical beam theories are clearly particular cases of the linear () Taylor expansion model. On the other hand, Lagrange expansion models have only pure translational displacements as unknowns. By exploiting this characteristic of Lagrange expansion, a componentwise approach is implemented and used for the analysis of multicomponent reinforced-shell structures. Numerical applications are developed by classical finite element procedures, and both static response and free vibration analyses are addressed. Various configurations of a benchmark wing are considered, and the capabilities of the present methodologies when dealing with higher-order effects due to deformable cross sections and geometrical discontinuities (for example, underside windows) are evaluated. The attention is focused on the applicability of the present refined beam models to problems involving complex, external inertial loadings. The results are compared to finite element solutions from commercial tools, including full three-dimensional models and models obtained by assembling two-dimensional shell and one-dimensional finite elements.

Обобщенные функции и преобразования Хартли в многоосновных системах счисления

Обобщенные функции и преобразования Хартли в многоосновных системах счисления

A correction method for systematic error in (1)H-NMR time-course data validated through stochastic cell culture simulation.

BackgroundThe growing ubiquity of metabolomic techniques has facilitated high frequency time-course data collection for an increasing number of applications. While the concentration trends of individual metabolites can be modeled with common curve fitting techniques, a more accurate representation of the data needs to consider effects that act on more than one metabolite in a given sample. To this end, we present a simple algorithm that uses nonparametric smoothing carried out on all observed metabolites at once to identify and correct systematic error from dilution effects. In addition, we develop a simulation of metabolite concentration time-course trends to supplement available data and explore algorithm performance. Although we focus on nuclear magnetic resonance (NMR) analysis in the context of cell culture, a number of possible extensions are discussed.ResultsRealistic metabolic data was successfully simulated using a 4-step process. Starting with a set of metabolite concentration time-courses from a metabolomic experiment, each time-course was classified as either increasing, decreasing, concave, or approximately constant. Trend shapes were simulated from generic functions corresponding to each classification. The resulting shapes were then scaled to simulated compound concentrations. Finally, the scaled trends were perturbed using a combination of random and systematic errors. To detect systematic errors, a nonparametric fit was applied to each trend and percent deviations calculated at every timepoint. Systematic errors could be identified at time-points where the median percent deviation exceeded a threshold value, determined by the choice of smoothing model and the number of observed trends. Regardless of model, increasing the number of observations over a time-course resulted in more accurate error estimates, although the improvement was not particularly large between 10 and 20 samples per trend. The presented algorithm was able to identify systematic errors as small as 2.5 % under a wide range of conditions.ConclusionBoth the simulation framework and error correction method represent examples of time-course analysis that can be applied to further developments in 1H-NMR methodology and the more general application of quantitative metabolomics.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-015-0197-4) contains supplementary material, which is available to authorized users.

Modelling macroseismic observations for historical earthquakes: the cases of the M = 7.0, 1954 Sofades and M = 6.8, 1957 Velestino events (central Greece)

We attempt to model the spatial distribution of the strong ground motion for the large M = 7.0, 1954 Sofades and M = 6.8, 1957 Velestino events (southern Thessaly basin, central Greece), using the macroseismic intensities (I M M up to 9+) observed within the broader Thessaly area. For this reason, we employ a modified stochastic method realised by the EXSIM algorithm for extended sources, in order to reproduce the damage distribution of these earthquakes, in an attempt to combine existing earthquake information and appropriate scaling relations with surface geology and to investigate the efficiency of the available macroseismic data. For site-effects assessment, we use a new digital geological map of the broader Thessaly basin, where geological formations are grouped by age and mapped on appropriate NEHRP soil classes. Using the previous approach, we estimate synthetic time series for different rupture scenarios and employ various calibrating relations between PGA/PGV and macroseismic intensity, allowing the generation of synthetic (stochastic) isoseismals. Also, different site amplification factors proposed for the broader Aegean area, according to local geology, are tested. Finally, we also perform a sensitivity analysis of the fault location, taking into account the available neotectonic data for the broader southern Thessaly fault zone. The finally determined fault locations are different than previously proposed, in agreement with the available neotectonic information. The observed macroseismic intensities are in good agreement with the ones derived from the synthetic waveforms, verifying both the usefulness of the approach, as well as of the macroseismic data used. Finally, site-effects show clear correlation with the geological classification employed, with constant amplification factors for each soil class generally providing better results than generic transfer functions.