Multimode Analysis of Nanoscale Biomolecular Interactions

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical calculations have been developed for the analysis of biomolecular interactions. Human neuroglobin (hNgb) and cytochrome c from equine heart (Cyt c) proteins have been used to optimize the customized SPR instrument. The obtained Kd value (~13 µM), from SPR results, for Cyt c-hNgb molecular interactions is in general agreement with a previously published result. The SPR results also confirmed no significant impact of the internal disulfide bridge between Cys 46 and Cys 55 on hNgb binding to Cyt c. Using SPR, E. coli topoisomerase I enzyme turnover during plasmid DNA relaxation was found to be enhanced in the presence of Mg2+. In addition, a new theoretical approach of analyzing biphasic SPR data has been introduced based on analytical solutions of the biphasic rate equations. In order to develop a new label free method to quantitatively study protein-protein interactions, quartz nanopipettes were chemically modified. The derived Kd (~20 µM) value for the Cyt c-hNgb complex formations matched very well with SPR measurements (Kd ~16 µM). The finite element numerical simulation results were similar to the nanopipette experimental results. These results demonstrate that nanopipettes can potentially be used as a new class of a label-free analytical method to quantitatively characterize protein-protein interactions in attoliter sensing volumes, based on a charge sensing mechanism. Moreover, the molecule-based selective nature of hydrophobic and nanometer sized carbon nanotube (CNT) pores was observed. This result might be helpful to understand the selective nature of cellular transport through transmembrane protein pores.

Modelagem numérica de uma estrutura de contenção de estacas espaçadas atirantadas em areia

Retaining walls design involves factors such as plastification, loading and unloading, pre-stressing, excessive displacements and earth and water thrust. Furthermore, the interaction between the retained soil and the structure is rather complex and hard to predict. Despite the advances in numerical simulation techniques and monitoring of forces and displacements with field instrumentation, design projects are still based on classical methods, whose simplifying assumptions may overestimate structural elements of the retaining wall. This dissertation involves a three-dimensional numerical study on the behavior of a retaining wall using the finite element method (FEM). The retaining wall structure is a contiguous bored pile wall with tie-back anchors. The numerical results were compared to data obtained from field instrumentation. The influence of the position of one or two layers of anchors and the effects of the construction of a slab bounded at the top of the retaining wall was evaluated. Furthermore, this study aimed at investigating the phenomenon of arching in the soil behind the wall. Arching was evaluated by analyzing the effects of pile spacing on horizontal stresses and displacements. Parametric analysis with one layers of anchors showed that the smallest horizontal displacements of the structure were achieved for between 0.3 and 0.5 times the excavation depth. Parametric analyses with two anchor layers showed that the smallest horizontal displacements were achieve for anchors positioned in depths of 0.4H and 0.7H. The construction of a slab at the top of the retaining wall decreased the horizontal displacements by 0.14% times the excavation depth as compared to analyses without the slab. With regard to the arching , analyzes showed an optimal range of spacing between the faces of the piles between 0.4 and 0.6 times the diameter of the pile

Structural Analysis and Form-Finding of Mycelium-Based Monolithic Domes

As sustainability becomes an integral design driver for current civil structures, new materials and forms are investigated. The aim of this study is to investigate analytically and numerically the mechanical behavior of monolithic domes composed of mycological fungi. The study focuses on hemispherical and elliptical forms, as the most typical solution for domes. The influence of different types of loading, geometrical parameters, material properties and boundary conditions is investigated in this study. For the cases covered by the classical shell theory, a comparison between the analytical and the finite element solution is given. Two case studies regarding the dome of basilica of “San Luca” (Bologna, Italy) and the dome of sanctuary of “Vicoforte” (Vicoforte, Italy) are included. After the linear analysis under loading, buckling is also investigated as a critical type of failure through a parametric study using finite elements model. Since shells rely on their shape, form-found domes are also investigated and a comparison between the behavior of the form-found domes and the hemispherical domes under the linear and buckling analysis is conducted. From the analysis it emerges that form-finding can enhance the structural response of mycelium-based domes, although buckling becomes even more critical for their design. Furthermore, an optimal height to span ratio for the buckling of form-found domes is identified. This study highlights the importance of investigating appropriate forms for the design of novel biomaterial-based structures.

Application of Numerical Methods to Study Arrangement and Fracture of Lithium-Ion Microstructure

The focus of this work is to develop and employ numerical methods that provide characterization of granular microstructures, dynamic fragmentation of brittle materials, and dynamic fracture of three-dimensional bodies.

We first propose the fabric tensor formalism to describe the structure and evolution of lithium-ion electrode microstructure during the calendaring process. Fabric tensors are directional measures of particulate assemblies based on inter-particle connectivity, relating to the structural and transport properties of the electrode. Applying this technique to X-ray computed tomography of cathode microstructure, we show that fabric tensors capture the evolution of the inter-particle contact distribution and are therefore good measures for the internal state of and electronic transport within the electrode.

We then shift focus to the development and analysis of fracture models within finite element simulations. A difficult problem to characterize in the realm of fracture modeling is that of fragmentation, wherein brittle materials subjected to a uniform tensile loading break apart into a large number of smaller pieces. We explore the effect of numerical precision in the results of dynamic fragmentation simulations using the cohesive element approach on a one-dimensional domain. By introducing random and non-random field variations, we discern that round-off error plays a significant role in establishing a mesh-convergent solution for uniform fragmentation problems. Further, by using differing magnitudes of randomized material properties and mesh discretizations, we find that employing randomness can improve convergence behavior and provide a computational savings.

The Thick Level-Set model is implemented to describe brittle media undergoing dynamic fragmentation as an alternative to the cohesive element approach. This non-local damage model features a level-set function that defines the extent and severity of degradation and uses a length scale to limit the damage gradient. In terms of energy dissipated by fracture and mean fragment size, we find that the proposed model reproduces the rate-dependent observations of analytical approaches, cohesive element simulations, and experimental studies.

Lastly, the Thick Level-Set model is implemented in three dimensions to describe the dynamic failure of brittle media, such as the active material particles in the battery cathode during manufacturing. The proposed model matches expected behavior from physical experiments, analytical approaches, and numerical models, and mesh convergence is established. We find that the use of an asymmetrical damage model to represent tensile damage is important to producing the expected results for brittle fracture problems.

The impact of this work is that designers of lithium-ion battery components can employ the numerical methods presented herein to analyze the evolving electrode microstructure during manufacturing, operational, and extraordinary loadings. This allows for enhanced designs and manufacturing methods that advance the state of battery technology. Further, these numerical tools have applicability in a broad range of fields, from geotechnical analysis to ice-sheet modeling to armor design to hydraulic fracturing.

Nonlinear soil-structure interaction for buried pressure pipes under differential ground motion

Pipelines extend thousands of kilometers across wide geographic areas as a network to provide essential services for modern life. It is inevitable that pipelines must pass through unfavorable ground conditions, which are susceptible to natural disasters. This thesis investigates the behaviour of buried pressure pipelines experiencing ground distortions induced by normal faulting. A recent large database of physical modelling observations on buried pipes of different stiffness relative to the surrounding soil subjected to normal faults provided a unique opportunity to calibrate numerical tools. Three-dimensional finite element models were developed to enable the complex soil-structure interaction phenomena to be further understood, especially on the subjects of gap formation beneath the pipe and the trench effect associated with the interaction between backfill and native soils. Benchmarked numerical tools were then used to perform parametric analysis regarding project geometry, backfill material, relative pipe-soil stiffness and pipe diameter. Seismic loading produces a soil displacement profile that can be expressed by isoil, the distance between the peak curvature and the point of contraflexure. A simplified design framework based on this length scale (i.e., the Kappa method) was developed, which features estimates of longitudinal bending moments of buried pipes using a characteristic length, ipipe, the distance from peak to zero curvature. Recent studies indicated that empirical soil springs that were calibrated against rigid pipes are not suitable for analyzing flexible pipes, since they lead to excessive conservatism (for design). A large-scale split-box normal fault simulator was therefore assembled to produce experimental data for flexible PVC pipe responses to a normal fault. Digital image correlation (DIC) was employed to analyze the soil displacement field, and both optical fibres and conventional strain gauges were used to measure pipe strains. A refinement to the Kappa method was introduced to enable the calculation of axial strains as a function of pipe elongation induced by flexure and an approximation of the longitudinal ground deformations. A closed-form Winkler solution of flexural response was also derived to account for the distributed normal fault pattern. Finally, these two analytical solutions were evaluated against the pipe responses observed in the large-scale laboratory tests.

A simplified finite element model for assessing steel fibre reinforced concrete structural performance

The present numerical investigation offers evidence concerning the validity and objectivity of the predictions of a simple, yet practical, finite element model concerning the responses of steel fibre reinforced concrete structural elements under static monotonic and cyclic loading. Emphasis is focused on realistically describing the fully brittle tensile behaviour of plain concrete and the contribution of steel fibres on the post-cracking behaviour it exhibits. The good correlation exhibited between the numerical predictions and their experimental counterparts reveals that, despite its simplicity, the subject model is capable of providing realistic predictions concerning the response of steel fibre reinforced concrete structural configurations exhibiting both ductile and brittle modes of failure without requiring recalibration.

A more reliable PCR for detection of Mycobacterium tuberculosis in clinical samples

Diagnostic techniques based on PCR have two major problems: false-positive reactions due to contamination with DNA fragments from previous PCRs (amplicons) and false-negative reactions caused by inhibitors that interfere with the PCR. We have improved our previously reported PCR based on the amplification of a fragment of the Mycobacterium tuberculosis complex-specific insertion element IS6110 with respect to both problems. False-positive reactions caused by amplicon contamination were prevented by the use of uracil-N-glycosylase and dUTP instead of dTTP. We selected a new set of primers outside the region spanned by the formerly used primers to avoid false-positive reactions caused by dTTP-containing amplicons still present in the laboratory. With this new primer set, 16 copies of the IS6110 insertion element, the equivalent of two bacteria, could be amplified 10(10) times in 40 cycles, resulting in a mean efficiency of 77% per cycle. To detect the presence of inhibitors of the Taq polymerase, which may cause false-negative reactions, part of each sample was spiked with M. tuberculosis DNA. The DNA purification method using guanidinium thiocyanate and diatoms effectively removed most or all inhibitors of the PCR. However, this was not suitable for blood samples, for which we developed a proteinase K treatment followed by phenol-chloroform extraction. This method permitted detection of 20 M. tuberculosis bacteria per ml of whole blood. Various laboratory procedures were introduced to reduce failure or inhibition of PCR and avoid DNA cross contamination. We have tested 218 different clinical specimens obtained from patients suspected of having tuberculosis. The samples included sputum (n=145), tissue biopsy samples (n=25), cerebrospinal fluid (n=15), blood (n=14), pleural fluid (n=9), feces, (n=7), fluid from fistulae (n=2), and pus from a wound (n=1). The results obtained by PCR were consistent with those obtained with culture, which is the "gold standard." We demonstrate that PCR is a useful technique for the rapid diagnosis of tuberculosis at various sites.

Algoritmos de otimização e o problema inverso aplicados à identificação de danos estruturais com o uso do MEF

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Civil e Ambiental, 2015.

Estudo experimental e numérico de juntas adesivas em T com aderentes de alumínio

Nos dias de hoje, a ligação adesiva de estruturas complexas que não poderiam ou não seriam tão fáceis de ser fabricadas numa só peça é cada vez mais usual. As juntas adesivas têm vindo a substituir muitos outros métodos de ligação, como por exemplo ligações aparafusadas, rebitas ou soldadas, devido às vantagens de facilidade na sua fabricação, resistência superior e capacidade de unir materiais diferentes. Por esta razão as juntas adesivas têm vindo a ser aplicadas cada vez mais em várias industrias como aeroespacial, aeronáutica, automóvel, naval e calçado. O tipo de adesivo a usar em determinada aplicação é principalmente escolhido consoante as suas características mecânicas e o tipo de resposta pretendida às solicitações impostas. Como exemplo de adesivo resistente e frágil existe o Araldite® AV138. Por outro lado, o adesivo Araldite® 2015 é menos resistente, mas apresenta maior ductilidade e flexibilidade. Além dos adesivos Araldite® comerciais, existem adesivos de poliuretano que combinam características de elevada resistência com características de grande ductilidade e flexibilidade, como por exemplo o Sikaforce® 7752. Esta dissertação tem como objetivo estudar experimentalmente e numericamente, através de modelos de dano coesivo (MDC), o comportamento de diferentes configurações de junta em T quando sujeitas a solicitações de arrancamento. Consideram-se os adesivos anteriormente mencionados para testar as juntas sob diferentes tipos de adesivos. A junta em T é constituída por 2 aderentes em L de alumínio e um aderente base também em alumínio, unidos por uma camada de adesivo. Experimentalmente é feito um estudo da resistência da junta com a variação da espessura dos aderentes em L (tP2). Com a análise numérica são estudadas as distribuições de tensões, evolução do dano, modos de rotura e resistência. Além disso, realizou-se um estudo numérico da existência ou não de adesivo de preenchimento na zona da curvatura dos aderentes em L nas tensões e na resistência da junta. Mostrouse que a variação da geometria nos aderentes em L, a presença de adesivo de preenchimento e o tipo de adesivo têm uma influência direta na resistência de junta. Os ensaios experimentais validaram os resultados numéricos e permitiram concluir que os MDC são uma técnica precisa para o estudo das geometrias das juntas em T.

Estudo comparativo de pás para aerogeradores de grande porte fabricadas em materiais compósitos reforçadas com fibra de carbono ou fibra de vidro

The research and development of wind turbine blades are essential to keep pace with worldwide growth in the renewable energy sector. Although currently blades are typically produced using glass fiber reinforced composite materials, the tendency for larger size blades, particularly for offshore applications, has increased the interest on carbon fiber reinforced composites because of the potential for increased stiffness and weight reduction. In this study a model of blade designed for large generators (5 MW) was studied on a small scale. A numerical simulation was performed to determine the aerodynamic loading using a Computational Fluid Dynamics (CFD) software. Two blades were then designed and manufactured using epoxy matrix composites: one reinforced with glass fibers and the other with carbon fibers. For the structural calculations, maximum stress failure criterion was adopted. The blades were manufactured by Vacuum Assisted Resin Transfer Molding (VARTM), typical for this type of component. A weight comparison of the two blades was performed and the weight of the carbon fiber blade was approximately 45% of the weight of the fiberglass reinforced blade. Static bending tests were carried out on the blades for various percentages of the design load and deflections measurements were compared with the values obtained from finite element simulations. A good agreement was observed between the measured and calculated deflections. In summary, the results of this study confirm that the low density combined with high mechanical properties of carbon fibers are particularly attractive for the production of large size wind turbine blades

A finite element framework for the interplay between delamination and buckling of rubber-like bi-material systems and stretchable electronics

In this study, a finite element (FE) framework for the analysis of the interplay between buckling and delamination of thin layers bonded to soft substrates is proposed. The current framework incorporates the following modeling features: (i) geometrically nonlinear solid shell elements, (ii) geometrically nonlinear cohesive interface elements, and (iii) hyperelastic material constitutive response for the bodies that compose the system. A fully implicit Newton–Raphson solution strategy is adopted to deal with the complex simultaneous presence of geometrical and material nonlinearities through the derivation of the consistent FE formulation. Applications to a rubber-like bi-material system under finite bending and to patterned stiff islands resting on soft substrate for stretchable solar cells subjected to tensile loading are proposed. The results obtained are in good agreement with benchmark results available in the literature, confirming the accuracy and the capabilities of the proposed numerical method for the analysis of complex three-dimensional fracture mechanics problems under finite deformations.

Analise de marcha : protocolo experimental a partir de variaveis cinematicas e antropometricas

Universidade Estadual de Campinas . Faculdade de Educação Física

Benign focal seizures of adolescence and neuropsychological findings in patients from community

RATIONALE: Benign focal seizures of adolescence (BFSA) described by Loiseau et al in 1972, is considered a rare entity, but maybe underdiagnosed. Although mild neuropsychological deficits have been reported in patients with benign epilepsies of childhood, these evaluations have not so far been described in BFSA. The aim of this study is to evaluate neuropsychological functions in BFSA with new onset seizures (<12 months). METHODS: Eight patients with BFSA (according to Loiseau et al, 1972, focal or secondarily tonic clonic generalized seizures between the ages of 10-18 yrs., normal neurologic examination, normal EEG or with mild focal abnormalities) initiated in the last 12 months were studied between July 2008 to May 2009. They were referred from the Pediatric Emergency Section of the Hospital Universitário of the University of Sao Paulo, a secondary care regionalized facility located in a district of middle-low income in Sao Paulo city, Brazil. The study was approved by the Ethics Committee of the Institution. All patients performed neurological, EEG, brain CT and neuropsychological evaluation which consisted of Raven's Special Progressive Matrices - General and Special Scale (according to different ages), Wechsler Children Intelligence Scale-WISC III with ACID Profile, Trail Making Test A/B, Stroop Test, Bender Visuo-Motor Test, Rey Complex Figure, Rey Auditory Verbal Learning Test-RAVLT, Boston Naming Test, Fluency Verbal for phonological and also conceptual patterns - FAS/Animals and Hooper Visual Organization Test. For academic achievement, we used a Brazilian test for named "Teste do Desempenho Escolar", which evaluates abilities to read, write and calculate according to school grade. RESULTS: There were 2 boys and 6 girls, with ages ranging from 10 yrs. 9 m to 14 yrs. 3 m. Most (7/8) of the patients presented one to two seizures and only three of them received antiepileptic drugs (AEDs). Six had mild EEG focal abnormalities and all had normal brain CT. All were literate, attended regular public schools and scored in a median range for IQ, and seven showed discrete higher scores for the verbal subtests. There were low scores for attention in different modalities in six patients, mainly in alternated attention as well as inhibitory subtests (Stroop test and Trail Making Test part B). Four of the latter cases who showed impairment both in alternated and inhibitory attention were not taking AEDs. Visual memory was impaired in five patients (Rey Complex Figure). Executive functions analysis showed deficits in working memory in five, mostly observed in Digits Indirect Order and Arithmetic tests (WISC III). Reading and writing skills were below the expected average for school grade in six patients according to the achievement scholar performance test utilized. One patient of this series who had the best scores in all tests was taking phenobarbital. CONCLUSIONS: Neuropsychological imbalance between normal IQ and mild dysfunctions such as in attention domain and in some executive abilities like working memory and planning, as well as difficulties in visual memory and in reading and writing, were described in this group of patients with BFSA from community. This may reflect mild higher level neurological dysfunctions in adolescence idiopathic focal seizures probably caused by an underlying dysmaturative epileptogenic process. Although academic problems often have multiple causes, a specific educational approach may be necessary in these adolescents, in order to improve their scholastic achievements, helping in this way, to decrease the stigma associated to epileptic seizures in the community.

Analysis of the tip roundness effects on the micro- and macroindentation response of elastic-plastic materials

In this work, the effects of indenter tip roundness oil the load-depth indentation curves were analyzed using finite element modeling. The tip roundness level was Studied based on the ratio between tip radius and maximum penetration depth (R/h(max)), which varied from 0.02 to 1. The proportional Curvature constant (C), the exponent of depth during loading (alpha), the initial unloading slope (S), the correction factor (beta), the level of piling-up or sinking-in (h(c)/h(max)), and the ratio h(max)/h(f) are shown to be strongly influenced by the ratio R/h(max). The hardness (H) was found to be independent of R/h(max) in the range studied. The Oliver and Pharr method was successful in following the variation of h(c)/h(max) with the ratio R/h(max) through the variation of S with the ratio R/h(max). However, this work confirmed the differences between the hardness values calculated using the Oliver-Pharr method and those obtained directly from finite element calculations; differences which derive from the error in area calculation that Occurs when given combinations of indented material properties are present. The ratio of plastic work to total work (W(p)/W(t)) was found to be independent of the ratio R/h(max), which demonstrates that the methods for the Calculation of mechanical properties based on the *indentation energy are potentially not Susceptible to errors caused by tip roundness.