Fletcher–Reeves based Particle Swarm Optimization for prediction of molecular structure

The determination of the most stable conformers of a molecule can be formulated as a global optimization problem. Knowing the stable conformers of a molecule is important because it allows us to understand its properties and behavior based on its structure. The most stable conformation is that involving the global minimum of potential energy. The problem of finding this global minimum is highly complex, and is computationally difficult because of the number of local minima, which grows exponentially with molecular size. In this paper, we propose a hybrid approach combining Particle Swarm Optimization (PSO) and the Fletcher–Reeves algorithm to minimize the potential energy function. The proposed hybrid algorithm is applied to a simplified molecular potential energy function in problems with up to 100 degrees of freedom and also to a realistic potential energy function modeling a pseudoethane molecule. The computational results for both the cases show that the proposed method performs significantly better than the other algorithms.     

Modeling structure–activity relationships of prodiginines with antimalarial activity using GA/MLR and OPS/PLS

In the present study, we performed a multivariate quantitative structure-activity relationship (QSAR) analysis of 52 prodiginines with antimalarial activity. Variable selection was based on the genetic algorithm (GA) and ordered predictor selection (OPS) approaches, and the models were built using the multiple linear regression (MLR) and partial least squares (PLS) regression methods. The leave-N-out crossvalidation and y-randomization tests showed that the models were robust and free from chance correlation. The mechanistic interpretation of the results was supported by earlier findings. In addition, the comparison of our models with those previously described indicated that the OPS/PLS-based model had a higher quality of external prediction. Thus, this study provides a comprehensive approach to the evaluation of the antimalarial activity of prodiginines, which may be used as a support tool in designing new therapeutic agents for malaria.     

A numerical study of the ground state and dynamics of atomic–molecular Bose–Einstein condensates

In this paper, we numerically investigate the ground-state structure and dynamics of atomic–molecular Bose–Einstein condensates at zero temperature, which are modeled by coupled Gross–Pitaevskii equations (GPEs). To get the ground state, we evolve a gradient flow with discrete normalization numerically. To study the dynamics, we employ an efficient numerical method—the time-splitting Fourier pseudospectral method for solving the coupled GPEs. The proposed numerical methods have been numerically tested and employed in studying the mechanism on how an atomic condensate can be converted into an atomic–molecular mixture or a pure molecular condensate from an atomic condensate either in equilibrium or dynamically.     

On the structure of multivariate concentration — some relationships among the concentration surface and two variate mean difference and regressions

First, concentration surface L(x, y) and Gini's coefficient G_xy with respect to two variates x and y are defined and discussed. Mean difference Δ_xy and mean deviation δ_xy of x and y are also defined in connection with L(x,y) and G_xy. Some other statistical measures working like correlation coefficient and regression coefficient are newly introduced based on the geometrical properties of the concentration surface and are discussed in comparison with moment measures corresponding to them.Non-linear regression is also discussed based on certain representative income distributions.The close relations between Gini's coefficient G_xy and the regression residuals are pointed out in the case of both linear and non-linear regressions.Finally, elasticity analysis is tried on the family budget data of Japan in 1981.     

Structure–property relationships of energetic nitrogen-rich salts composed of triaminoguanidinium or ammonium cation and tetrazole-based anions

Density functional theory and volume-based thermodynamics calculations have been performed to study the crystal densities, heats of formation (HOFs), energetic properties, and thermodynamics of formation for a series of ionic salts composed of triaminoguanidinium or ammonium cations and tetrazole-based anions. Substitution with NF₂, CH₂NF₂, CF₂NF₂, or C(NO₂)₂NF₂ groups increased the densities of the salts. The densities of the tetrazole-based salts are affected not only by different substituents but also by different cations. The CN or N₃ groups are effective substituents for increasing the HOFs of the salts. The triaminoguanidinium cation is more effective than the ammonium cation for increasing the HOF of the tetrazole-based salts. Substitution with NO₂, NF₂, or C(NO₂)₂NF₂ groups enhances the explosive properties of the salts. The thermodynamics of formation of the salts reveal that all of the tetrazole-based salts with the triaminoguanidinium or ammonium cation could be synthesized using the proposed reactions. Our calculated methods provide a straightforward and inexpensive route for screening a large number of potentially energetic ionic salts.     

Input–output structure and growth in China

The fast and steady economic growth in China during the 1990s has attracted much international attention. Using the three most recent Chinese input–output tables, this paper investigates industry structure and inter-industry relationships and the relationship of both to economic growth. The input–output tables contain intermediate demand and final demand for six broad industries, namely, Agriculture, Industry, Construction, Transportation, Post and Telecommunications, Services, and Others, for 1992, 1995 and 1997, which enables computing of input–output coefficients for three time periods. As direct and indirect input–output coefficients characterise industry structure during a particular time period, changes over time reflect the patterns in industry structure evolvement. Furthermore, output growth in a particular industry can be analysed from two different sources, namely the changes in input–output coefficients that reflect technological change, and the change in final demand. This paper sheds light on four different issues over the five-year period from 1992 to 1997: (1) Was growth driven by technological changes or final demand increases? (2) As a result of the interdependence of industries, how did an increase in final demand in one industry affect growth in another? (3) How has the bottleneck of an insufficient capability in the transportation, post and telecommunications sectors to cope with demands from other sectors been affected during this period? (4) Has the industry structure of the economy been shifting in conformity with traditional growth theory, namely, with a decline in the agricultural sector and a rise in the modern industrial sector?     

Numerical studies on fluid–structure interactions of stent deployment and stented arteries

This study is to investigate the mechanical behaviors of angioplasty stents during and after implantation and blood flow in the stented artery using the immersed finite element method. In this study, the mechanical behaviors such as the expansion mechanism, stress distribution on the stent during the implantation, and stent responses toward various vascular conditions are analyzed. Furthermore, pulsatile blood flow in stented artery is also examined to identify potential regions where the blood clots form and potentially induce reactions leading to thrombus formation. We found that the wall shear stress and the residence time are the highest at the entrance and the exit of the stent while they decrease significantly in between stent struts. The results suggested that platelets/particles are most likely to be activated near the entrance; they form aggregates in between struts where the shear stress is very low and eventually reside at the end of the stent where the resident time is the highest. Our numerical observations agree quite well with in vitro experimental studies. This analysis will assist in the development of novel stent designs and stent deployment protocols to minimize vascular injury during stenting and reduce restenosis.     

Efficient and extendible class scheme for the combined reaction–diffusion of multiple molecular species

When dealing with large numbers of cells in biophysical simulations, it is important to properly manage the different substances that diffuse and react in and around cells. Although in an object-oriented programming environment it seems more natural to define cells as the basic objects, it turns out that individual substances are better suited to take this role. Here we describe the biophysical problem and our computational solution, and display the results obtained with a toy model. We find that the new implementation does not decrease performance and yet it leads to a much better structured and modular code. This will make more realistic programs with many molecular pathways much more modular and readily extendible.     

DFT simulation towards evaluation the molecular structure and properties of the heterogeneous C16Mg8O8 nano–cage as selective nano–sensor for H2 and N2 gases

Adsorption of hydrogen (H₂) and nitrogen (N₂) molecules was analyzed on a new fullerene–like C₁₆Mg₈O₈ nano–cage, composed of magnesium, oxygen, and carbon, using density functional theory. A detailed analysis of the energy, geometry, and electronic structure of various H₂ and N₂ adsorptions on the cluster surface was performed. The adsorption energies of H₂ and N₂ were estimated to ranging from −0.16 to −0.52 eV, respectively. The most stable adsorption configurations were those in which the H or N atoms of the adsorbates were located near the Mg atom of the cluster surface at different sides. It was found that the heterogeneous C₁₆Mg₈O₈ nano–cluster selectively act against the H₂ and N₂ gaseous molecules. The electrical conductivity of the cluster, arising from HOMO/LUMO energy gap, was more sensitive to N₂ gaseous molecule rather than H₂ one, indicating that the heterogeneous C₁₆Mg₈O₈ nano–cage may be potential nano–sensor for N₂ molecule. These findings were specified by analyzing the characteristics in the electron density of states (DOS).     

The asymptotic structure of the Morris–Lecar model

In this paper, the asymptotic structure of the Morris–Lecar (ML) model in the concepts of slow manifold and fast foliation is analyzed based on the Tikhonov's theorem. The rationality of the well-known V, N reduced ML system is discussed, and a new V, N reduced ML system is derived from a more reasonable asymptotic structures of the original ML system, which we propose.     

Neural networks and non-linear statistical methods: an application to the modelling of price–quality relationships

This paper examines the potential of a neural network (NN) approach to the analysis of ‘hedonic’ regressions, in which price is dependent on quality characteristics. The aim of the regressions is to measure, using objective data, the valuation consumers place on these characteristics. A neural network approach is employed because of potential non-linearities in the hedonic functions, using the property of ‘universal approximation’. Our NN implementation goes beyond the now-orthodox approach in using the Polytope algorithm, which we compare with Backpropagation, and uses two hidden layers. The results obtained provide an improvement on linear formulations, but the improvement in this case is relatively marginal. We view NN modelling as a useful means of specification testing and hence our results imply some support for a linear formulation as an adequate approximation. From a managerial perspective, the linear model is more easily interpreted. NN modelling is potentially very time-consuming, especially with the Polytope algorithm, and requires a good deal of technical skill.Scope and purposeThe application area studied in the paper involves ‘hedonic’ regressions, which is the term usually employed for regressions of prices on the characteristics of goods. These employ objective data rather than subjective evaluations of intent and as well as having predictive capacity they serve to indicate the valuation placed on characteristics by consumers. In the extensive literature on the subject there is extensive debate on the appropriate functional form for the regressions. We have employed neural networks (NNs) in order to cast some light on the issue, because of their property of ‘universal approximation’ which, although in danger of being taken too literally means a capacity to ‘mimic’ a wide variety of shapes. We specifically employ an NN model as a test of linearity for hedonic functions, using the Polytope algorithm as an alternative to the standard Backpropagation method. Our results indicate that only a marginal improvement in goodness of fit is obtained, despite various theoretical arguments against a linear formulation. The linear model is given some support in our work as an adequate working approximation.     

Fokker–Planck approximation of the master equation in molecular biology

The master equation of chemical reactions is solved by first approximating it by the Fokker–Planck equation. Then this equation is discretized in the state space and time by a finite volume method. The difference between the solution of the master equation and the discretized Fokker–Planck equation is analyzed. The solution of the Fokker–Planck equation is compared to the solution of the master equation obtained with Gillespie’s Stochastic Simulation Algorithm (SSA) for problems of interest in the regulation of cell processes. The time dependent and steady state solutions are computed and for equal accuracy in the solutions, the Fokker–Planck approach is more efficient than SSA for low dimensional problems and high accuracy.     

The impact of technological,organizational and environmental characteristics on electronic collaboration and relationship performance in international customer–supplier relationships

The literature suggests that advances in information and communication technologies have been a major driver of the restructuring of multinational enterprises and their cross-border supply chain management. However, the role of information technology usage for collaboration and its antecedents and performance implications in cross-border exchange relationships have not been clearly specified. In response to this claim, this study examines the determinants of electronic collaboration (E-collaboration) and its outcomes for suppliers with regard to their international customers. Drawing on an empirical foundation of 240 Taiwanese-based electronics equipment manufacturers, we test the effects of technological, organizational and environmental dimensions on E-collaboration and its impact on relationship performance in international exchange. The findings on the pertinence of E-collaboration in international customer–supplier relationships are presented and discussed.     

Liberating or debilitating? An examination of romantic relationships,sexual relationships and friendships on the Net

Ever since the beginnings of the internet researchers have questioned its utility in developing and maintaining psychological healthy romantic and sexual relations. Advocates of the social presence theory and media richness theory purport that in leaner media individuals can be quite aggressive towards one another (e.g., in the form of flaming). In contrast, others believe that the lack of traditional cues in CMC can in fact be overcome and instead lead to more personal, intimate relationships. As this paper will demonstrate, when we consider how beneficial it is to form relationships online we also need to consider individuals’ characteristics (e.g., personality characteristics and physical attractiveness), the amount of time people spend online, the duration of online relationships, and how these relationships effect individuals’ offline activities and relationships. Overall, the view here is that online relationships can be empowering for many people; that is, cyberspace provides a unique environment for people to experience and learn about relationships and sexuality.     

An intuitionistic view of the Dempster–Shafer belief structure

We discuss the Dempster–Shafer belief theory and describe its role in representing imprecise probabilistic information. In particular, we note its use of intervals for representing imprecise probabilities. We note in fuzzy set theory that there are two related approaches used for representing imprecise membership grades: interval-valued fuzzy sets and intuitionistic fuzzy sets. We indicate the first of these, interval-valued fuzzy sets, is in the same spirit as Dempster–Shafer representation, both use intervals. Using a relationship analogous to the type of relationship that exists between interval-valued fuzzy sets and intuitionistic fuzzy sets, we obtain from the interval-valued view of the Dempster–Shafer model an intuitionistic view of the Dempster–Shafer model. Central to this view is the use of an intuitionistic statement, pair of values, (Bel(A) Dis(A)), to convey information about the value of a variable lying in the set A. We suggest methods for combining intuitionistic statements and making inferences from these type propositions.     

Two-dimensional simulation of fluid–structure interaction using lattice-Boltzmann methods

The development of flow instabilities due to high Reynolds number flow in artificial heart-value geometries inducing high strain rates and stresses often leads to hemolysis and related highly undesired effects. Geometric and functional optimization of artificial heart valves is therefore mandatory. In addition to experimental work in this field it is meanwhile possible to obtain increasing insight into flow dynamics by computer simulation of refined model problems. Here we present two-dimensional simulation results of the coupled fluid–structure problem defined by a model geometry of an artificial heart value with moving leaflets exposed to a channel flow driven by transient boundary conditions representing a physiologically relevant regime. A modified lattice-Boltzmann approach is used to solve the coupled problem.     

A logical approach to systems engineering artifacts: semantic relationships and dependencies beyond traceability—from requirements to functional and architectural views

Not only system assurance drives a need for semantically richer relationships across various artifacts, work products, and items of information than are implied in the terms “trace and traceability” as used in current standards and textbooks. This paper deals with the task of working out artifacts in software and system development, their representation, and the analysis and documentation of the relationships between their logical contents—herein referred to as tracing and traceability; this is a richer meaning of traceability than in standards like IEEE STD 830. Among others, key tasks in system development are as follows: capturing, analyzing, and documenting system-level requirements, the step to functional system specifications, the step to architectures given by the decomposition of systems into subsystems with their connections and behavioral interactions. Each of these steps produces artifacts for documenting the development, as a basis for a specification and a design rationale, for documentation, for verification, and impact analysis of change requests. Crucial questions are how to represent and formalize the content of these artifacts and how to relate their content to support, in particular, system assurance. When designing multi-functional systems, key artifacts are system-level requirements, functional specifications, and architectures in terms of their subsystem specifications. Links and traces between these artifacts are introduced to relate their contents. Traceability has the goal to relate artifacts. It is required for instance in standards for functional system safety such as the ISO 26262. An approach to specifying semantic relationships is shown, such that the activity of creating and using (navigating through) these relationships can be supported with automation.