Ligand-Induced structural changes in TEM‑1 probed by molecular dynamics and relative binding free energy calculations

The TEM family of enzymes has had a crucial impact on the pharmaceutical industry due to their important role in antibiotic resistance. Even with the latest technologies in structural biology and genomics, no 3D structure of a TEM- 1/antibiotic complex is known previous to acylation. Therefore, the comprehension of their capability in acylate antibiotics is based on the protein macromolecular structure uncomplexed. In this work, molecular docking, molecular dynamic simulations, and relative free energy calculations were applied in order to get a comprehensive and thorough analysis of TEM-1/ampicillin and TEM-1/amoxicillin complexes. We described the complexes and analyzed the effect of ligand binding on the overall structure. We clearly demonstrate that the key residues involved in the stability of the ligand (hot-spots) vary with the nature of the ligand. Structural effects such as (i) the distances between interfacial residues (Ser70−Oγ and Lys73−Nζ, Lys73−Nζ and Ser130−Oγ, and Ser70−Oγ−Ser130−Oγ), (ii) side chain rotamer variation (Tyr105 and Glu240), and (iii) the presence of conserved waters can be also influenced by ligand binding. This study supports the hypothesis that TEM-1 suffers structural modifications upon ligand binding.

On a generalized Laguerre operational matrix of fractional integration

A new operationalmatrix of fractional integration of arbitrary order for generalized Laguerre polynomials is derived.The fractional integration is described in the Riemann-Liouville sense.This operational matrix is applied together with generalized Laguerre tau method for solving general linearmultitermfractional differential equations (FDEs).Themethod has the advantage of obtaining the solution in terms of the generalized Laguerre parameter. In addition, only a small dimension of generalized Laguerre operational matrix is needed to obtain a satisfactory result. Illustrative examples reveal that the proposedmethod is very effective and convenient for linear multiterm FDEs on a semi-infinite interval.

Power law analysis of financial index dynamics

Power law PL and fractional calculus are two faces of phenomena with long memory behavior. This paper applies PL description to analyze different periods of the business cycle. With such purpose the evolution of ten important stock market indices DAX, Dow Jones, NASDAQ, Nikkei, NYSE, S&P500, SSEC, HSI, TWII, and BSE over time is studied. An evolutionary algorithm is used for the fitting of the PL parameters. It is observed that the PL curve fitting constitutes a good tool for revealing the signal main characteristics leading to the emergence of the global financial dynamic evolution.

On development of fractional calculus during the last fifty years

Fractional calculus generalizes integer order derivatives and integrals. During the last half century a considerable progress took place in this scientific area. This paper addresses the evolution and establishes an assertive measure of the research development.

Application of continuous wavelet transform to the analysis of the modulus of the fractional Fourier transform bands for resolving two component mixture

In this paper, the fractional Fourier transform (FrFT) is applied to the spectral bands of two component mixture containing oxfendazole and oxyclozanide to provide the multicomponent quantitative prediction of the related substances. With this aim in mind, the modulus of FrFT spectral bands are processed by the continuous Mexican Hat family of wavelets, being denoted by MEXH-CWT-MOFrFT. Four modulus sets are obtained for the parameter a of the FrFT going from 0.6 up to 0.9 in order to compare their effects upon the spectral and quantitative resolutions. Four linear regression plots for each substance were obtained by measuring the MEXH-CWT-MOFrFT amplitudes in the application of the MEXH family to the modulus of the FrFT. This new combined powerful tool is validated by analyzing the artificial samples of the related drugs, and it is applied to the quality control of the commercial veterinary samples.

Optimal controllers with complex order derivatives

This paper studies the optimization of complex-order algorithms for the discrete-time control of linear and nonlinear systems. The fundamentals of fractional systems and genetic algorithms are introduced. Based on these concepts, complexorder control schemes and their implementation are evaluated in the perspective of evolutionary optimization. The results demonstrate not only that complex-order derivatives constitute a valuable alternative for deriving control algorithms, but also the feasibility of the adopted optimization strategy.

And I say to myself: “What a fractional world!”

This paper discusses several complex systems in the perspective of fractional dynamics. For prototype systems are considered the cases of deoxyribonucleic acid decoding, financial evolution, earthquakes events, global warming trend, and musical rhythms. The application of the Fourier transform and of the power law trendlines leads to an assertive representation of the dynamics and to a simple comparison of their characteristics. Moreover, the gallery of different systems, both natural and man made, demonstrates the richness of phenomena that can be described and studied with the tools of fractional calculus.

Complex order van der Pol oscillator

In this paper a complex-order van der Pol oscillator is considered. The complex derivative Dα±ȷβ , with α,β∈R + is a generalization of the concept of integer derivative, where α=1, β=0. By applying the concept of complex derivative, we obtain a high-dimensional parameter space. Amplitude and period values of the periodic solutions of the two versions of the complex-order van der Pol oscillator are studied for variation of these parameters. Fourier transforms of the periodic solutions of the two oscillators are also analyzed.

Analysis of financial data series using fractional Fourier transform and multidimensional scaling

The goal of this study is the analysis of the dynamical properties of financial data series from worldwide stock market indexes during the period 2000–2009. We analyze, under a regional criterium, ten main indexes at a daily time horizon. The methods and algorithms that have been explored for the description of dynamical phenomena become an effective background in the analysis of economical data. We start by applying the classical concepts of signal analysis, fractional Fourier transform, and methods of fractional calculus. In a second phase we adopt the multidimensional scaling approach. Stock market indexes are examples of complex interacting systems for which a huge amount of data exists. Therefore, these indexes, viewed from a different perspectives, lead to new classification patterns.

Fractional control with a smith predictor

The advantageous use of fractional calculus (FC) in the modeling and control of many dynamical systems has been recognized. In this paper, we study the control of a heat diffusion system based on the application of the FC concepts. Several algorithms are investigated and compared, when integrated within a Smith predictor control structure. Simulations are presented assessing the performance of the proposed fractional algorithms.

Complex order biped rhythms

Animal locomotion is a complex process, involving the central pattern generators (neural networks, located in the spinal cord, that produce rhythmic patterns), the brainstem command systems, the steering and posture control systems and the top layer structures that decide which motor primitive is activated at a given time. Pinto and Golubitsky studied an integer CPG model for legs rhythms in bipeds. It is a four-coupled identical oscillators' network with dihedral symmetry. This paper considers a new complex order central pattern generator (CPG) model for locomotion in bipeds. A complex derivative Dα±jβ, with α, β ∈ ℜ+, j = √-1, is a generalization of the concept of an integer derivative, where α = 1, β = 0. Parameter regions where periodic solutions, identified with legs' rhythms in bipeds, occur, are analyzed. Also observed is the variation of the amplitude and period of periodic solutions with the complex order derivative.

A fractional approach for the motion planning of redundant and hyper-redundant manipulators

The trajectory planning of redundant robots through the pseudoinverse control leads to undesirable drift in the joint space. This paper presents a new technique to solve the inverse kinematics problem of redundant manipulators, which uses a fractional differential of order α to control the joint positions. Two performance measures are defined to examine the strength and weakness of the proposed method. The positional error index measures the precision of the manipulator's end-effector at the target position. The repeatability performance index is adopted to evaluate if the joint positions are repetitive when the manipulator execute repetitive trajectories in the operational workspace. Redundant and hyper-redundant planar manipulators reveal that it is possible to choose in a large range of possible values of α in order to get repetitive trajectories in the joint space.

Application of fractional calculus in engineering

Fractional Calculus (FC) goes back to the beginning of the theory of differential calculus. Nevertheless, the application of FC just emerged in the last two decades. It has been recognized the advantageous use of this mathematical tool in the modelling and control of many dynamical systems. Having these ideas in mind, this paper discusses a FC perspective in the study of the dynamics and control of several systems. The paper investigates the use of FC in the fields of controller tuning, legged robots, electrical systems and digital circuit synthesis.

Optimal tuning of fractional controllers using genetic algorithms

This study addresses the optimization of fractional algorithms for the discrete-time control of linear and non-linear systems. The paper starts by analyzing the fundamentals of fractional control systems and genetic algorithms. In a second phase the paper evaluates the problem in an optimization perspective. The results demonstrate the feasibility of the evolutionary strategy and the adaptability to distinct types of systems.

Entropy analysis of integer and fractional dynamical systems

This paper investigates the adoption of entropy for analyzing the dynamics of a multiple independent particles system. Several entropy definitions and types of particle dynamics with integer and fractional behavior are studied. The results reveal the adequacy of the entropy concept in the analysis of complex dynamical systems.