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.

Structural stability of adenylate kinase from the sulfate-reducing bacteria Desulfovibrio gigas

Biophysical Chemistry 110 (2004) 83–92

From local to global importance measures of uncertainty propagation in composite structures

The influence of uncertainties of input parameters on output response of composite structures is investigated in this paper. In particular, the effects of deviations in mechanical properties, ply angles, ply thickness and on applied loads are studied. The uncertainty propagation and the importance measure of input parameters are analysed using three different approaches: a first-order local method, a Global Sensitivity Analysis (GSA) supported by a variance-based method and an extension of local variance to estimate the global variance over the domain of inputs. Sample results are shown for a shell composite laminated structure built with different composite systems including multi-materials. The importance measures of input parameters on structural response based on numerical results are established and discussed as a function of the anisotropy of composite materials. Needs for global variance methods are discussed by comparing the results obtained from different proposed methodologies. The objective of this paper is to contribute for the use of GSA techniques together with low expensive local importance measures.

An approach for reliability-based robust design optimisation of angle-ply composites

Variations of manufacturing process parameters and environmental aspects may affect the quality and performance of composite materials, which consequently affects their structural behaviour. Reliability-based design optimisation (RBDO) and robust design optimisation (RDO) searches for safe structural systems with minimal variability of response when subjected to uncertainties in material design parameters. An approach that simultaneously considers reliability and robustness is proposed in this paper. Depending on a given reliability index imposed on composite structures, a trade-off is established between the performance targets and robustness. Robustness is expressed in terms of the coefficient of variation of the constrained structural response weighted by its nominal value. The Pareto normed front is built and the nearest point to the origin is estimated as the best solution of the bi-objective optimisation problem.

Uncertainty propagation in inverse reliability-based design of composite structures

An approach for the analysis of uncertainty propagation in reliability-based design optimization of composite laminate structures is presented. Using the Uniform Design Method (UDM), a set of design points is generated over a domain centered on the mean reference values of the random variables. A methodology based on inverse optimal design of composite structures to achieve a specified reliability level is proposed, and the corresponding maximum load is outlined as a function of ply angle. Using the generated UDM design points as input/output patterns, an Artificial Neural Network (ANN) is developed based on an evolutionary learning process. Then, a Monte Carlo simulation using ANN development is performed to simulate the behavior of the critical Tsai number, structural reliability index, and their relative sensitivities as a function of the ply angle of laminates. The results are generated for uniformly distributed random variables on a domain centered on mean values. The statistical analysis of the results enables the study of the variability of the reliability index and its sensitivity relative to the ply angle. Numerical examples showing the utility of the approach for robust design of angle-ply laminates are presented.

Análise estática não linear de um edifício em betão armado

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Civil

Synechocystis ferredoxin/ferredoxin-NADP+-reductase/NADP+ complex: Structural model obtained by NMR-restrained docking

FEBS Letters 579 (2005) 4585–4590

Projeto de fundações e estrutura de ampliação de escola no Açores utilizando os eurocódigos estruturais

Trabalho de Projeto para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Estruturas

In-situ X-ray diffraction studies during growth of Ni-Ti shape memory alloy films and their complementary ex-situ characterization

Shape Memory Alloy (SMA) Ni-Ti films have attracted much interest as functional and smart materials due to their unique properties. However, there are still important issues unresolved like formation of film texture and its control as well as substrate effects. Thus, the main challenge is not only the control of the microstructure, including stoichiometry and precipitates, but also the identification and control of the preferential orientation since it is a crucial factor in determining the shape memory behaviour. The aim of this PhD thesis is to study the optimisation of the deposition conditions of films of Ni-Ti in order to obtain the material fully crystallized at the end of the deposition, and to establish a clear relationship between the substrates and texture development. In order to achieve this objective, a two-magnetron sputter deposition chamber has been used allowing to heat and to apply a bias voltage to the substrate. It can be mounted into the six-circle diffractometer of the Rossendorf Beamline (ROBL) at the European Synchrotron Radiation Facility (ESRF), Grenoble, France, enabling an in-situ characterization by X-ray diffraction(XRD) of the films during their growth and annealing. The in-situ studies enable us to identify the different steps of the structural evolution during deposition with a set of parameters as well as to evaluate the effect of changing parameters on the structural characteristics of the deposited film. Besides the in-situ studies, other complementary ex-situ characterization techniques such as XRD at a laboratory source, Rutherford backscattering spectroscopy(RBS), Auger electron spectroscopy (AES), cross-sectional transmission electron microscopy (X-TEM), scanning electron microscopy (SEM), and electrical resistivity (ER) measurements during temperature cycling have been used for a fine structural characterization. In this study, mainly naturally and thermally oxidized Si(100) substrates, TiN buffer layers with different thicknesses (i.e. the TiN topmost layer crystallographic orientation is thickness dependent) and MgO(100) single crystals were used as substrates. The chosen experimental procedure led to a controlled composition and preferential orientation of the films. The type of substrate plays an important role for the texture of the sputtered Ni-Ti films and according to the ER results, the distinct crystallographic orientations of the Ni-Ti films influence their phase transformation characteristics.

Structural and mechanistic studies of iron containing proteins

Dissertação apresentada para obtenção do Grau de Doutor em Bioquímica, ramo de Bioquímica-Física, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

A wireless sensor network platform for structural health monitoring: enabling accurate and synchronized measurements through COTS+custom-based design

Structural health monitoring has long been identified as a prominent application of Wireless Sensor Networks (WSNs), as traditional wired-based solutions present some inherent limitations such as installation/maintenance cost, scalability and visual impact. Nevertheless, there is a lack of ready-to-use and off-the-shelf WSN technologies that are able to fulfill some most demanding requirements of these applications, which can span from critical physical infrastructures (e.g. bridges, tunnels, mines, energy grid) to historical buildings or even industrial machinery and vehicles. Low-power and low-cost yet extremely sensitive and accurate accelerometer and signal acquisition hardware and stringent time synchronization of all sensors data are just examples of the requirements imposed by most of these applications. This paper presents a prototype system for health monitoring of civil engineering structures that has been jointly conceived by a team of civil, and electrical and computer engineers. It merges the benefits of standard and off-the-shelf (COTS) hardware and communication technologies with a minimum set of custom-designed signal acquisition hardware that is mandatory to fulfill all application requirements.

Feasibility of the extended finite element method for the simulation of composite bonded joints

Adhesive-bonding for the unions in multi-component structures is gaining momentum over welding, riveting and fastening. It is vital for the design of bonded structures the availability of accurate damage models, to minimize design costs and time to market. Cohesive Zone Models (CZM’s) have been used for fracture prediction in structures. The eXtended Finite Element Method (XFEM) is a recent improvement of the Finite Element Method (FEM) that relies on traction-separation laws similar to those of CZM’s but it allows the growth of discontinuities within bulk solids along an arbitrary path, by enriching degrees of freedom. This work proposes and validates a damage law to model crack propagation in a thin layer of a structural epoxy adhesive using the XFEM. The fracture toughness in pure mode I (GIc) and tensile cohesive strength (sn0) were defined by Double-Cantilever Beam (DCB) and bulk tensile tests, respectively, which permitted to build the damage law. The XFEM simulations of the DCB tests accurately matched the experimental load-displacement (P-d) curves, which validated the analysis procedure.

Periplasmic nitrate reductases: structural and spectroscopic studies

Dissertação apresentada para obtenção do grau de Doutor em Bioquímica, especialidade Bioquímica-Física, pela Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa

Shear strength of adhesively bonded polyolefins with minimal surface preparation

Interest in polyethylene and polypropylene bonding has increased in the last years. However, adhesive joints with adherends which are of low surface energy and which are chemically inert present several difficulties. Generally, their high degree of chemical resistance to solvents and dissimilar solubility parameters limit the usefulness of solvent bonding as a viable assembly technique. One successful approach to adhesive bonding of these materials involves proper selection of surface pre-treatment prior to bonding. With the correct pre-treatment it is possible to glue these materials with one or more of several adhesives required by the applications involved. A second approach is the use of adhesives without surface pre-treatment, such as hot melts, high tack pressure-sensitive adhesives, solvent-based specialty adhesives and, more recently, structural acrylic adhesives as such 3M DP-8005® and Loctite 3030®. In this paper, the shear strengths of two acrylic adhesives were evaluated using the lap shear test method ASTM D3163 and the block shear test method ASTM D4501. Two different industrial polyolefins (polyethylene and polypropylene) were used for adherends. However, the focus of this study was to measure the shear strength of polyethylene joints with acrylic adhesives. The effect of abrasion was also studied. Some test specimens were manually abraded using 180 and 320 grade abrasive paper. An additional goal of this work was to examine the effect of temperature and moisture on mechanical strength of adhesive joints.

A sensor classification strategy for robotic manipulators

In practice the robotic manipulators present some degree of unwanted vibrations. The advent of lightweight arm manipulators, mainly in the aerospace industry, where weight is an important issue, leads to the problem of intense vibrations. On the other hand, robots interacting with the environment often generate impacts that propagate through the mechanical structure and produce also vibrations. In order to analyze these phenomena a robot signal acquisition system was developed. The manipulator motion produces vibrations, either from the structural modes or from endeffector impacts. The instrumentation system acquires signals from several sensors that capture the joint positions, mass accelerations, forces and moments, and electrical currents in the motors. Afterwards, an analysis package, running off-line, reads the data recorded by the acquisition system and extracts the signal characteristics. Due to the multiplicity of sensors, the data obtained can be redundant because the same type of information may be seen by two or more sensors. Because of the price of the sensors, this aspect can be considered in order to reduce the cost of the system. On the other hand, the placement of the sensors is an important issue in order to obtain the suitable signals of the vibration phenomenon. Moreover, the study of these issues can help in the design optimization of the acquisition system. In this line of thought a sensor classification scheme is presented. Several authors have addressed the subject of the sensor classification scheme. White (White, 1987) presents a flexible and comprehensive categorizing scheme that is useful for describing and comparing sensors. The author organizes the sensors according to several aspects: measurands, technological aspects, detection means, conversion phenomena, sensor materials and fields of application. Michahelles and Schiele (Michahelles & Schiele, 2003) systematize the use of sensor technology. They identified several dimensions of sensing that represent the sensing goals for physical interaction. A conceptual framework is introduced that allows categorizing existing sensors and evaluates their utility in various applications. This framework not only guides application designers for choosing meaningful sensor subsets, but also can inspire new systems and leads to the evaluation of existing applications. Today’s technology offers a wide variety of sensors. In order to use all the data from the diversity of sensors a framework of integration is needed. Sensor fusion, fuzzy logic, and neural networks are often mentioned when dealing with problem of combing information from several sensors to get a more general picture of a given situation. The study of data fusion has been receiving considerable attention (Esteban et al., 2005; Luo & Kay, 1990). A survey of the state of the art in sensor fusion for robotics can be found in (Hackett & Shah, 1990). Henderson and Shilcrat (Henderson & Shilcrat, 1984) introduced the concept of logic sensor that defines an abstract specification of the sensors to integrate in a multisensor system. The recent developments of micro electro mechanical sensors (MEMS) with unwired communication capabilities allow a sensor network with interesting capacity. This technology was applied in several applications (Arampatzis & Manesis, 2005), including robotics. Cheekiralla and Engels (Cheekiralla & Engels, 2005) propose a classification of the unwired sensor networks according to its functionalities and properties. This paper presents a development of a sensor classification scheme based on the frequency spectrum of the signals and on a statistical metrics. Bearing these ideas in mind, this paper is organized as follows. Section 2 describes briefly the robotic system enhanced with the instrumentation setup. Section 3 presents the experimental results. Finally, section 4 draws the main conclusions and points out future work.