Computation

This paper presents the mathematical modeling and experimental implementation of a Buck converter with hysteresis control. The system is described using a state-space model. Theoretical and simulation studies show that the zero hysteresis control leads to an equilibrium point with the implication of an infinite commutation frequency, while the use of a constant hysteresis band induces a limit cycle with a finite switching frequency. There exists a tradeoff between voltage output ripple and transistor switching frequency. An experimental prototype for the Buck power converter is built, and theoretical results are verified experimentally. In general terms, the Buck converter with the hysteresis control shows a robust control with respect to load variations, with undesired high switching frequency taking place for a very narrow hysteresis band, which is solved by tuning the hysteresis band properly. Full article

Metabolic pathway analysis is a key method to study a metabolism in its steady state, and the concept of elementary fluxes (EFs) plays a major role in the analysis of a network in terms of non-decomposable pathways. The supports of the EFs contain in particular those of the elementary flux modes (EFMs), which are the support-minimal pathways, and EFs coincide with EFMs when the only flux constraints are given by the irreversibility of certain reactions. Practical use of both EFMs and EFs has been hampered by the combinatorial explosion of their number in large, genome-scale systems. The EFs give the possible pathways in a steady state but the real pathways are limited by biological constraints, such as thermodynamic or, more generally, kinetic constraints and regulatory constraints from the genetic network. We provide results on the mathematical structure and geometrical characterization of the solution space in the presence of such biological constraints (which is no longer a convex polyhedral cone or a convex polyhedron) and revisit the concept of EFMs and EFs in this framework. We show that most of the results depend only on very general properties of compatibility of constraints with vector signs: either sign-invariance, satisfied by regulatory constraints, or sign-monotonicity (a stronger property), satisfied by thermodynamic and kinetic constraints. We show in particular that the solution space for sign-monotone constraints is a union of particular faces of the original polyhedral cone or polyhedron and that EFs still coincide with EFMs and are just those of the original EFs that satisfy the constraint, and we show how to integrate their computation efficiently in the double description method, the most widely used method in the tools dedicated to EFs computation. We show that, for sign-invariant constraints, the situation is more complex: the solution space is a disjoint union of particular semi-open faces (i.e., without some of their own faces of lesser dimension) of the original polyhedral cone or polyhedron and, if EFs are still those of the original EFs that satisfy the constraint, their computation cannot be incrementally integrated into the double description method, and the result is not true for EFMs, that are in general strictly more numerous than those of the original EFMs that satisfy the constraint. Full article

Predicting the state of a dynamic system influenced by a chaotic immersion environment is an extremely difficult task, in which the direct use of statistical extrapolation computational schemes is infeasible. This paper considers a version of precedent forecasting in which we use the aftereffects of retrospective observation segments that are similar to the current situation as a forecast. Furthermore, we employ the presence of relatively stable correlations between the parameters of the immersion environment as a regularizing factor. We pay special attention to the choice of similarity measures or distances used to find analog windows in arrays of retrospective multidimensional observations. Full article

(1) Background: The estimation of daily reproduction numbers throughout the contagiousness period is rarely considered, and only their sum R₀ is calculated to quantify the contagiousness level of an infectious disease. (2) Methods: We provide the equation of the discrete dynamics of the epidemic’s growth and obtain an estimation of the daily reproduction numbers by using a deconvolution technique on a series of new COVID-19 cases. (3) Results: We provide both simulation results and estimations for several countries and waves of the COVID-19 outbreak. (4) Discussion: We discuss the role of noise on the stability of the epidemic’s dynamics. (5) Conclusions: We consider the possibility of improving the estimation of the distribution of daily reproduction numbers during the contagiousness period by taking into account the heterogeneity due to several host age classes. Full article

A class of bivariate integer-valued time series models was constructed via copula theory. Each series follows a Markov chain with the serial dependence captured using copula-based transition probabilities from the Poisson and the zero-inflated Poisson (ZIP) margins. The copula theory was also used again to capture the dependence between the two series using either the bivariate Gaussian or “t-copula” functions. Such a method provides a flexible dependence structure that allows for positive and negative correlation, as well. In addition, the use of a copula permits applying different margins with a complicated structure such as the ZIP distribution. Likelihood-based inference was used to estimate the models’ parameters with the bivariate integrals of the Gaussian or t-copula functions being evaluated using standard randomized Monte Carlo methods. To evaluate the proposed class of models, a comprehensive simulated study was conducted. Then, two sets of real-life examples were analyzed assuming the Poisson and the ZIP marginals, respectively. The results showed the superiority of the proposed class of models. Full article

Automation is becoming ubiquitous in all laboratory activities, moving towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models describe physical processes, while protocols define the steps carried out during an experiment: neither cover the domain of the other, although they both attempt to characterize the same phenomena. We should ideally start from an integrated description of both the model and the steps carried out to test it, to concurrently analyze uncertainties in model parameters, equipment tolerances, and data collection. To this end, we present a language to model and optimize experimental biochemical protocols that facilitates such an integrated description, and that can be combined with experimental data. We provide probabilistic semantics for our language in terms of Gaussian processes (GPs) based on the linear noise approximation (LNA) that formally characterizes the uncertainties in the data collection, the underlying model, and the protocol operations. In a set of case studies, we illustrate how the resulting framework allows for automated analysis and optimization of experimental protocols, including Gibson assembly protocols. Full article

Genetic expression analysis is a principal tool to explain the behavior of genes in an organism when exposed to different experimental conditions. In the state of art, many clustering algorithms have been proposed. It is overwhelming the amount of biological data whose high-dimensional structure exceeds mostly current computational architectures. The computational time and memory consumption optimization actually become decisive factors in choosing clustering algorithms. We propose a clustering algorithm based on Non-negative Matrix Factorization and K-means to reduce data dimensionality but whilst preserving the biological context and prioritizing gene selection, and it is implemented within parallel GPU-based environments through the CUDA library. A well-known dataset is used in our tests and the quality of the results is measured through the Rand and Accuracy Index. The results show an increase in the acceleration of 6.22× compared to the sequential version. The algorithm is competitive in the biological datasets analysis and it is invariant with respect to the classes number and the size of the gene expression matrix. Full article

There is a myriad of career opportunities stemming from science, technology, engineering, and mathematics (STEM) disciplines. In addition to careers in corporate settings, teaching is a viable career option for individuals pursuing degrees in STEM disciplines. With national shortages of secondary STEM teachers, efforts to recruit, train, and retain quality STEM teachers is greatly important. Prior to exploring ways to attract potential STEM teacher candidates to pursue teacher training programs, it is important to understand the perceived value that potential recruits place on STEM careers, disciplines, and the teaching profession. The purpose of this study was to explore students’ perceptions of the usefulness of STEM disciplines and their value in supporting students’ careers. A novel statistical method was utilized, combining exploratory-factor analysis, the analysis of variance, generalized estimating equation evaluations under the framework of a generalized linear model, and quantile regression. Using the outputs from each statistical measure, students’ valuation of each STEM discipline and their interest in pursuing teaching as a career option were assessed. Our results indicate a high correlation of liking and perceived usability of the STE disciplines relative to careers. Conversely, our results also display a low correlation of the liking and perceived usability of mathematics relative to future careers. The significance of these diametrically related results suggests the need for promotion of the interrelatedness of mathematics and STE. Full article

We discuss the Simple Equations Method (SEsM) for obtaining exact solutions of a class of nonlinear differential equations containing polynomial nonlinearities. We present an amended version of the methodology, which is based on the use of composite functions. The number of steps of the SEsM was reduced from seven to four in the amended version of the methodology. For the case of nonlinear differential equations with polynomial nonlinearities, SEsM can reduce the solved equations to a system of nonlinear algebraic equations. Each nontrivial solution of this algebraic system leads to an exact solution of the solved nonlinear differential equations. We prove the theorems and present examples for the use of composite functions in the methodology of the SEsM for the following three kinds of composite functions: (i) a composite function of one function of one independent variable; (ii) a composite function of two functions of two independent variables; (iii) a composite function of three functions of two independent variables. Full article

Molecularly imprinted polymers (MIPs) are synthetic receptors engineered towards the selective binding of a target molecule; however, the manner in which MIPs interact with other molecules is of great importance. Being able to rapidly analyze the binding of potential molecular interferences and determine the selectivity of a MIP can be a long tedious task, being time- and resource-intensive. Identifying computational models capable of reliably predicting and reporting the binding of molecular species is therefore of immense value in both a research and commercial setting. This research therefore sets focus on comparing the use of machine learning algorithms (multitask regressor, graph convolution, weave model, DAG model, and inception) to predict the binding of various molecular species to a MIP designed towards 2-methoxphenidine. To this end, each algorithm was “trained” with an experimental dataset, teaching the algorithms the structures and binding affinities of various molecular species at varying concentrations. A validation experiment was then conducted for each algorithm, comparing experimental values to predicted values and facilitating the assessment of each approach by a direct comparison of the metrics. The research culminates in the construction of binding isotherms for each species, directly comparing experimental vs. predicted values and identifying the approach that best emulates the real-world data. Full article

Models of computation are fundamental notions in computer science; consequently, they have been the subject of countless research papers, with numerous novel models proposed even in recent years. Amongst a multitude of different approaches, many of these methods draw inspiration from the biological processes observed in nature. P systems, or membrane systems, make an analogy between the communication in computing and the flow of information that can be perceived in living organisms. These systems serve as a basis for various concepts, ranging from the fields of computational economics and robotics to the techniques of data clustering. In this paper, such utilization of these systems—membrane system–based clustering—is taken into focus. Considering the growing number of data stored worldwide, more and more data have to be handled by clustering algorithms too. To solve this issue, bringing these methods closer to the data, their main element provides several benefits. Database systems equip their users with, for instance, well-integrated security features and more direct control over the data itself. Our goal is if the type of the database management system is given, e.g., NoSQL, but the corporation or the research team can choose which specific database management system is used, then we give a perspective, how the algorithms written like this behave in such an environment, so that, based on this, a more substantiated decision can be made, meaning which database management system should be connected to the system. For this purpose, we discover the possibilities of a clustering algorithm based on P systems when used alongside NoSQL database systems, that are designed to manage big data. Variants over two competing databases, MongoDB and Redis, are evaluated and compared to identify the advantages and limitations of using such a solution in these systems. Full article

Anisotropic materials are of great interest due to their unique direction-dependent optical properties. Borophene, the two-dimensional analog of graphene consisting of boron atoms, has attracted immense research interest due to its exciting anisotropic electronic and mechanical properties. Its synthesis in several structural polymorphic configurations has recently been reported. The present work reports the layer-dependent optical absorption and hyperpolarizabilities of the buckled borophene (δ6-borophene). The results, based on density functional theory, show that multilayer borophene is nearly transparent with only a weak absorbance in the visible region, reflecting its anisotropic structural characteristics. The static first-order hyperpolarizability significantly increases with the number of layers, due mainly to interactions among the frontier orbitals in multilayer borophene. Transparency in the visible region combined with enhanced nonlinear optical properties makes the multilayer borophene important for future photonics technologies. Full article

In this work, a new adaptive controller is designed for substrate control of a fed-batch bioreactor in the presence of input saturation and unknown varying control gain with unknown upper and lower bounds. The output measurement noise and the unknown varying nature of reaction rate and biomass concentration and water volume are also handled. The design is based on dead zone quadratic forms. The designed controller ensures the convergence of the modified tracking error and the boundedness of the updated parameters. As the first distinctive feature, a new robust adaptive auxiliary system is proposed in order to tackle input saturation and control gain uncertainty. As the second distinctive feature, the modified tracking error converges to a compact region whose bound is user-defined, in contrast to related studies where the convergence region depends on upper bounds of either external disturbances, system states, model parameters or terms and model parameter values. Simulations confirm the properties of the closed loop behavior. Full article

In this study, we designed a framework in which three techniques—classification tree, association rules analysis (ASA), and the naïve Bayes classifier—were combined to improve the performance of the latter. A classification tree was used to discretize quantitative predictors into categories and ASA was used to generate interactions in a fully realized way, as discretized variables and interactions are key to improving the classification accuracy of the naïve Bayes classifier. We applied our methodology to three medical datasets to demonstrate the efficacy of the proposed method. The results showed that our methodology outperformed the existing techniques for all the illustrated datasets. Although our focus here was on medical datasets, our proposed methodology is equally applicable to datasets in many other areas. Full article

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence. Full article

This work is devoted to the description and comparative study of some methods of mathematical modeling. We consider methods that can be applied for building cyber-physical systems and digital twins. These application areas add to the usual accuracy requirements for a model the need to be adaptable to new data and the small computational complexity allows it to be used in embedded systems. First, we regard the finite element method as one of the “pure” physics-based modeling methods and the general neural network approach as a variant of machine learning modeling with physics-based regularization (or physics-informed neural networks) and their combination. A physics-based network architecture model class has been developed by us on the basis of a modification of classical numerical methods for solving ordinary differential equations. The model problem has a parameter at some values for which the phenomenon of stiffness is observed. We consider a fixed parameter value problem statement and a case when a parameter is one of the input variables. Thus, we obtain a solution for a set of parameter values. The resulting model allows predicting the behavior of an object when its parameters change and identifying its parameters based on observational data. Full article

This paper presents the performance of a boost converter controlled with a zero average dynamics technique to regulate direct current signals. The boost converter is modeled in a compact form, and a variable change is performed to depend only on the $\gamma$ parameter. A new sliding surface is proposed, where it is possible to regulate both the voltage and the current with low relative errors with respect to the reference signals. It is analytically demonstrated that the approximation of the switching surface by a piecewise linear technique is efficient in controlling the system. It is shown numerically that for certain operating conditions, the system is evolved into a chaotic attractor. The zero average dynamics technique implemented in the boost converter has good regulation, due to the presence of zones in the bi-parametric space. Furthermore, the zero average dynamics technique regulates the voltage well and presents a chaotic attractor with low steady-state error. Full article

A recent computational paper (Kalita et al., Phys. Chem. Chem. Phys. 2020, 22, 24178–24180) reports the existence of a quadruple bond between a carbon and an iron atom in the FeC(CO)${}_3$ molecule. In this communication, we perform several computations on the same system, using both density functional theory and post-Hartree–Fock methods and find that the results, and in particular the Fe-C bond length and stretching frequency depend strongly on the method used. We ascribe this behavior to a strong multireference character of the FeC(CO)${}_3$ ground state, which explains the non-conclusive results obtained with single-reference methods. We therefore conclude that, while the existence of a Fe-C quadruple bond is not disproved, further investigation is required before a conclusion can be drawn. Full article

Count data with excessive zeros are ubiquitous in healthcare, medical, and scientific studies. There are numerous articles that show how to fit Poisson and other models which account for the excessive zeros. However, in many situations, besides zero, the frequency of another count k tends to be higher in the data. The zero- and k-inflated Poisson distribution model (ZkIP) is appropriate in such situations The ZkIP distribution essentially is a mixture distribution of Poisson and degenerate distributions at points zero and k. In this article, we study the fundamental properties of this mixture distribution. Using stochastic representation, we provide details for obtaining parameter estimates of the ZkIP regression model using the Expectation–Maximization (EM) algorithm for a given data. We derive the standard errors of the EM estimates by computing the complete, missing, and observed data information matrices. We present the analysis of two real-life data using the methods outlined in the paper. Full article