Computer-based analysis of the binding steps in protein complex formation

Computer models were used to examine whether and under what conditions the multimeric protein complex is inhibited by high concentrations of one of its components—an effect analogous to the prozone phenomenon in precipitin tests. A series of idealized simple “ball-and-stick” structures representing small oligomeric complexes of protein molecules formed by reversible binding reactions were analyzed to determine the binding steps leading to each structure. The equilibrium state of each system was then determined over a range of starting concentrations and Kds and the steady-state concentration of structurally complete oligomer calculated for each situation. A strong inhibitory effect at high concentrations was shown by any protein molecule forming a bridge between two or more separable parts of the complex. By contrast, proteins linked to the outside of the complex by a single bond showed no inhibition whatsoever at any concentration. Nonbridging, multivalent proteins in the body of the complex could show an inhibitory effect or not depending on the structure of the complex and the strength of its bonds. On the basis of this study, we suggest that the prozone phenomenon will occur widely in living cells and that it could be a crucial factor in the regulation of protein complex formation.

Avaliação de métodos numéricos de análise linear de estabilidade para perfis de aço formados a frio.

Para o projeto de estruturas com perfis de aço formados a frio, é fundamental a compreensão dos fenômenos da instabilidade local e global, uma vez que estes apresentam alta esbeltez e baixa rigidez à torção. A determinação do carregamento crítico e a identificação do modo de instabilidade contribuem para o entendimento do comportamento dessas estruturas. Este trabalho avalia três metodologias para a análise linear de estabilidade de perfis de aço formados a frio isolados, com o objetivo de determinar os carregamentos críticos elásticos de bifurcação e os modos de instabilidade associados. Estritamente, analisa-se perfis de seção U enrijecido e Z enrijecido isolados, de diversos comprimentos e diferentes condições de vinculação e carregamento. Determinam-se os carregamentos críticos elásticos de bifurcação e os modos de instabilidade globais e locais por meio de: (i) análise com o Método das Faixas Finitas (MFF), através do uso do programa computacional CUFSM; (ii) análise com elementos finitos de barra baseados na Teoria Generalizada de Vigas (MEF-GBT), via uso do programa GBTUL; e (iii) análise com elementos finitos de casca (MEF-cascas) por meio do uso do programa ABAQUS. Algumas restrições e ressalvas com relação ao uso do MFF são apresentadas, assim como limitações da Teoria Generalizada de Viga e precauções a serem tomadas nos modelos de cascas. Analisa-se também a influência do grau de discretização da seção transversal. No entanto, não é feita avaliação em relação aos procedimentos normativos e tampouco análises não lineares, considerando as imperfeições geométricas iniciais, tensões residuais e o comportamento elastoplástico do material.

Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii

We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gin and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15degrees-98degreesC) were used to generate IIII modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gin, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60degreesC, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes. from psychrophiles to hyperthermophiles

Atomic nanolithography patterning of submicron features: writing an organic self-assembled monolayer with cold bright Cs atom beams

Cs atom beams, transversely collimated and cooled, passing through material masks in the form of arrays of reactive-ion-etched hollow Si pyramidal tips and optical masks formed by intense standing light waves, write submicron features on self-assembled monolayers (SAMs). Features with widths as narrow as 43 ± 6 nm and spatial resolution limited only by the grain boundaries of the substrate have been realized in SAMs of alkanethiols. The material masks write two-dimensional arrays of submicron holes; the optical masks result in parallel lines spaced by half the optical wavelength. Both types of feature are written to the substrate by exposure of the masked SAM to the Cs flux and a subsequent wet chemical etch. For the arrays of pyramidal tips, acting as passive shadow masks, the resolution and size of the resultant feature depends on the distance of the mask array from the SAM, an effect caused by the residual divergence of the Cs atom beam. The standing wave optical mask acts as an array of microlenses focusing the atom flux onto the substrate. Atom 'pencils' writing on SAMs have the potential to create arbitrary submicron figures in massively parallel arrays. The smallest features and highest resolutions were realized with SAMs grown on smooth, sputtered gold substrates.

Endonuclease Controlled Aggregation of Gold Nanoparticles for the Ultrasensitive Detection of Pathogenic Bacterial DNA

The development of an ultrasensitive biosensor for the low-cost and on-site detection of pathogenic DNA could transform detection capabilities within food safety, environmental monitoring and clinical diagnosis. Herein, we present an innovative approach exploiting endonuclease-controlled aggregation of plasmonic gold nanoparticles (AuNPs) for label-free and ultrasensitive detection of bacterial DNA. The method utilizes RNA-functionalized AuNPs which form DNA-RNA heteroduplex structures through specific hybridization with target DNA. Once formed, the DNA-RNA heteroduplex is susceptible to RNAse H enzymatic cleavage of the RNA probe, allowing the target DNA to liberate and hybridize with another RNA probe. This continuously happens until all of the RNA probes are cleaved, leaving the nanoparticles unprotected and thus aggregated upon exposure to a high electrolytic medium. The assay is ultrasensitive, allowing the detection of target DNA at femtomolar level by simple spectroscopic analysis (40.7 fM and 2.45 fM as measured by UV-vis and dynamic light scattering (DLS), respectively). The target DNA spiked food matrix (chicken meat) is also successfully detected at a concentration of 1.2 pM (by UV-vis) or 18.0 fM (by DLS). In addition to the ultra-high sensitivity, the total analysis time of the assay is less than 3 hours, thus demonstrating its practicality for food analysis.

Clustering of Rab11 vesicles in influenza A virus infected cells creates hotspots containing the 8 viral ribonucleoproteins

Influenza A virus is an important human pathogen causative of yearly epidemics and occasional pandemics. The ability to replicate within the host cell is a determinant of virulence, amplifying viral numbers for host-to-host transmission. This process requires multiple rounds of entering permissive cells, replication, and virion assembly at the plasma membrane, the site of viral budding and release. The assembly of influenza A virus involves packaging of several viral (and host) proteins and of a segmented genome, composed of 8 distinct RNAs in the form of viral ribonucleoproteins (vRNPs). The selective assembly of the 8-segment core remains one of the most interesting unresolved problems in virology. The recycling endosome regulatory GTPase Rab11 was shown to contribute to the process, by transporting vRNPs to the periphery, giving rise to enlarged cytosolic puncta rich in Rab11 and the 8 vRNPs. We recently reported that vRNP hotspots were formed of clustered vesicles harbouring protruding electron-dense structures that resembled vRNPs. Mechanistically, vRNP hotspots were formed as vRNPs outcompeted the cognate effectors of Rab11, the Rab11-Family-Interacting-Proteins (FIPs) for binding, and as a consequence impair recycling sorting at an unknown step. Here, we speculate on the impact that such impairment might have in host immunity, membrane architecture and viral assembly.

An application of reliability-based robustness assessment of steel moment resisting frame structures under post-mainshock cascading events

The paper presented herein proposes a reliability-based framework for quantifying the structural robustness considering the occurrence of a major earthquake (mainshock) and subsequent cascading hazard events, such as aftershocks that are triggered by the mainshock. These events can significantly increase the probability of failure of buildings, especially for structures that are damaged during the mainshock. The application of the proposed framework is exemplified through three numerical case studies. The case studies correspond to three SAC steel moment frame buildings of 3-, 9-, and 20- stories, which were designed to pre-Northridge codes and standards. Twodimensional nonlinear finite element models of the buildings are developed using the Open System for Earthquake Engineering Simulation framework (OpenSees), using a finite-length plastic hinge beam model and a bilinear constitutive law with deterioration, and are subjected to multiple mainshock-aftershock seismic sequences. For the three buildings analyzed herein, it is shown that the structural reliability under a single seismic event can be significantly different from that under a sequence of seismic events. The reliability-based robustness indicator used shows that the structural robustness is influenced by the extent by which a structure can distribute damage.

Crack width control in RC elements with recycled steel fibres and applications to integral structures : theoretical and experimental study

El presente trabajo trata de elementos reforzados con barras de armadura y Fibras Metálicas Recicladas (FMR). El objetivo principal es mejorar el comportamiento a fisuración de elementos sometidos a flexión pura y a flexión compuesta, aumentando en consecuencia las prestaciones en servicio de aquellas estructuras con requerimientos estrictos con respecto al control de fisuración. Entre éstas últimas se encuentran las estructuras integrales, es decir aquellas estructuras sin juntas (puentes o edificios), sometidas a cargas gravitatorias y deformaciones impuestas en los elementos horizontales debidas a retracción, fluencia y temperatura. Las FMR son obtenidas a partir de los neumáticos fuera de uso, y puesto que el procedimiento de reciclado se centra en el caucho en vez que en el acero, su forma es aleatoria y con longitud variable. A pesar de que la eficacia del fibrorefuerzo mediante FMR ha sido demostrada en investigaciones anteriores, la innovación que representa este trabajo consiste en proponer la acción combinada de barras convencionales y FMR en la mejora del comportamiento a fisuración. El objetivo es por tanto mejorar la sostenibilidad del proyecto de la estructura en HA al utilizar materiales reciclados por un lado, y aumentando por el otro la durabilidad. En primer lugar, se presenta el estado del arte con respecto a la fisuración en elementos de HA, que sucesivamente se amplía a elementos reforzados con barras y fibras. Asimismo, se resume el método simplificado para el análisis de columnas de estructuras sin juntas ya propuesto por Pérez et al., con particular énfasis en aquellos aspectos que son incompatibles con la acción de las fibras a nivel seccional. A continuación, se presenta un modelo para describir la deformabilidad seccional y la fisuración en elementos en HA, que luego se amplía a aquellos elementos reforzados con barras y fibras, teniendo en cuenta también los efectos debidos a la retracción (tension stiffening negativo). El modelo es luego empleado para ampliar el método simplificado para el análisis de columnas. La aportación consiste por tanto en contar con una metodología amplia de análisis para este tipo de elementos. Seguidamente, se presenta la campaña experimental preliminar que ha involucrado vigas a escala reducida sometidas a flexión simple, con el objetivo de validar la eficiencia y la usabilidad en el hormigón de las FMR de dos diferentes tipos, y su comportamiento con respecto a fibras de acero comerciales. Se describe a continuación la campaña principal, consistente en ensayos sobre ocho vigas en flexión simple a escala 1:1 (variando contenido en FRM, Ø/s,eff y recubrimiento) y doce columnas a flexión compuesta (variando contenido en FMR, Ø/s,eff y nivel de fuerza axil). Los resultados obtenidos en la campaña principal son presentados y comentados, resaltando las mejoras obtenidas en el comportamiento a fisuración de las vigas y columnas, y la rigidez estructural de las columnas. Estos resultados se comparan con las predicciones del modelo propuesto. Los principales parámetros estudiados para describir la fisuración y el comportamiento seccional de las vigas son: la separación entre fisuras, el alargamiento medio de las armaduras y la abertura de fisura, mientras que en los ensayos de las columnas se ha contrastado las leyes momento/curvatura, la tensión en las barras de armadura y la abertura de fisura en el empotramiento en la base. La comparación muestra un buen acuerdo entre las predicciones y los resultados experimentales. Asimismo, se nota la mejora en el comportamiento a fisuración debido a la incorporación de FMR en aquellos elementos con cuantías de armadura bajas en flexión simple, en elementos con axiles bajos y para el control de la fisuración en elementos con grandes recubrimientos, siendo por tanto resultados de inmediato impacto en la práctica ingenieril (diseño de losas, tanques, estructuras integrales, etc.). VIIIComo punto final, se presentan aplicaciones de las FMR en estructuras reales. Se discuten dos casos de elementos sometidos a flexión pura, en particular una viga simplemente apoyada y un tanque para el tratamiento de agua. En ambos casos la adicción de FMR al hormigón lleva a mejoras en el comportamiento a fisuración. Luego, utilizando el método simplificado para el análisis en servicio de columnas de estructuras sin juntas, se calcula la máxima longitud admisible en casos típicos de puentes y edificación. En particular, se demuestra que las limitaciones de la práctica ingenieril actual (sobre todo en edificación) pueden ser aumentadas considerando el comportamiento real de las columnas en HA. Finalmente, los mismos casos son modificados para considerar el uso de MFR, y se presentan las mejoras tanto en la máxima longitud admisible como en la abertura de fisura para una longitud y deformación impuesta. This work deals with elements reinforced with both rebars and Recycled Steel Fibres (RSFs). Its main objective is to improve cracking behaviour of elements subjected to pure bending and bending and axial force, resulting in better serviceability conditions for these structures demanding keen crack width control. Among these structures a particularly interesting type are the so-called integral structures, i.e. long jointless structures (bridges and buildings) subjected to gravitational loads and imposed deformations due to shrinkage, creep and temperature. RSFs are obtained from End of Life Tyres, and due to the recycling process that is focused on the rubber rather than on the steel they come out crooked and with variable length. Although the effectiveness of RSFs had already been proven by previous research, the innovation of this work consists in the proposing the combined action of conventional rebars and RSFs to improve cracking behaviour. Therefore, the objective is to improve the sustainability of RC structures by, on the one hand, using recycled materials, and on the other improving their durability. A state of the art on cracking in RC elements is firstly drawn. It is then expanded to elements reinforced with both rebars and fibres (R/FRC elements). Finally, the simplified method for analysis of columns of long jointless structures already proposed by Pérez et al. is resumed, with a special focus on the points that conflict when taking into account the action of fibres. Afterwards, a model to describe sectional deformability and cracking of R/FRC elements is presented, taking also into account the effect of shrinkage (negative tension stiffening). The model is then used to implement the simplified method for columns. The novelty represented by this is that a comprehensive methodology to analyse this type of elements is presented. A preliminary experimental campaign consisting in small beams subjected to pure bending is described, with the objective of validating the effectiveness and usability in concrete of RSFs of two different types, and their behaviour when compared with commercial steel fibres. With the results and lessons learnt from this campaign in mind, the main experimental campaign is then described, consisting in cracking tests of eight unscaled beams in pure bending (varying RSF content, Ø/s,eff and concrete cover) and twelve columns subjected to imposed displacement and axial force (varying RSF content, Ø/s,eff and squashing load ratio). The results obtained from the main campaign are presented and discussed, with particular focus on the improvement in cracking behaviour for the beams and columns, and structural stiffness for the columns. They are then compared with the proposed model. The main parameters studied to describe cracking and sectional behaviours of the beam tests are crack spacing, mean steel strain and crack width, while for the column tests these were moment/curvature, stress in rebars and crack with at column embedment. The comparison showed satisfactory agreement between experimental results and model predictions. Moreover, it is pointed out the improvement in cracking behaviour due to the addition of RSF for elements with low reinforcement ratios, elements with low squashing load ratios and for crack width control of elements with large concrete covers, thus representing results with a immediate impact in engineering practice (slab design, tanks, integral structures, etc.). Applications of RSF to actual structures are finally presented. Two cases of elements in pure bending are presented, namely a simple supported beam and a water treatment tank. In both cases the addition of RSF to concrete leads to improvements in cracking behaviour. Then, using the simplified model for the serviceability analysis of columns of jointless structures, the maximum achievable jointless length of typical cases of a bridge and building is obtained. In XIIparticular, it is shown how the limitations of current engineering practice (this is especially the case of buildings) can be increased by considering the actual behaviour of RC supports. Then, the same cases are modified considering the use of RSF, and the improvements both in maximum achievable length and in crack width for a given length and imposed strain at the deck/first floor are shown.

Experimental analysis of the cyclic response of traditional timber joints and their influence on the seismic capacity of timber frame structures

Timber connections represent the crucial part of a timber structure and a great variability exists in terms of types of connections and mechanisms. Taking as case study the widespread traditional timber frame structures, in particular the Portuguese Pombalino buildings, one of the most common timber connection is the half-lap joint. Connections play a major role in the overall behaviour of a structure, particularly when assessing their seismic response, since damage is concentrated at the connections. For this reason, an experimental campaign was designed and distinct types of tests were carried out on traditional half-lap joints to assess their in-plane response. In particular, pull-out and in-plane cyclic tests were carried out on real scale unreinforced connections. Subsequently, the connections were retrofitted, using strengthening techniques such as self-tapping screws, steel plates and GFRP sheets. The tests chosen were meant to capture the hysteretic behaviour and dissipative capacity of the connections and characterise their response and, therefore, their influence on the seismic response of timber frame walls, particularly concerning their uplifting and rotation capacity, that could lead to rocking in the walls. In this paper, the results of the experimental campaign are presented in terms of hysteretic curves, dissipated energy and equivalent viscous damping ratio. Moreover, recommendations are provided on the most appropriate retrofitting solutions.

Product costing model for laser welded hollow core steel panels

The aim of the study was to create an easily upgradable product costing model for laser welded hollow core steel panels to help in pricing decisions. The theory section includes a literature review to identify traditional and modern cost accounting methodologies, which are used by manufacturing companies. The theory section also presents the basics of steel panel structures and their manufacturing methods and manufacturing costs based on previous research. Activity-Based costing turned out to be the most appropriate methodology for the costing model because of wide product variations. Activity analysis and the determination of cost drivers based on observations and interviews were the key steps in the creation of the model. The created model was used to test how panel parameters affect the costs caused by the main manufacturing stages and materials. By comparing cost structures, it was possible to find the panel types that are the most economic and uneconomic to manufacture. A sensitivity analysis proved that the model gives sufficiently reliable cost information to support pricing decisions. More reliable cost information could be achieved by determining the cost drivers more accurately. Alternative methods for manufacturing the cores were compared with the model. The comparison proved that roll forming can be more advantageous and flexible than press brake bending. However, more extensive research showed that roll forming is possible only when the cores are designed to be manufactured by roll forming. Due to that fact, when new panels are designed consideration should be given to the possibility of using roll forming.

An Inspection System to Identify Fatigue Damage on Steel-Bridge Structures

Crack formation and growth in steel bridge structural elements may be due to loading oscillations. The welded elements are liable to internal discontinuities along welded joints and sensible to stress variations. The evaluation of the remaining life of a bridge is needed to make cost-effective decisions regarding inspection, repair, rehabilitation, and replacement. A steel beam model has been proposed to simulate crack openings due to cyclic loads. Two possible alternatives have been considered to model crack propagation, which the initial phase is based on the linear fracture mechanics. Then, the model is extended to take into account the elastoplastic fracture mechanic concepts. The natural frequency changes are directly related to moment of inertia variation and consequently to a reduction in the flexural stiffness of a steel beam. Thus, it is possible to adopt a nondestructive technique during steel bridge inspection to quantify the structure eigenvalue variation that will be used to localize the grown fracture. A damage detection algorithm is developed for the proposed model and the numerical results are compared with the solutions achieved by using another well know computer code.

Structural capacity of steel tubular cast-in-place piling

Steel tubular cast-in-place pilings are used throughout the country for many different project types. These piles are a closed-end pipe with varying wall thicknesses and outer diameters, that are driven to depth and then the core is filled with concrete. These piles are typically used for smaller bridges, or secondary structures. Mostly the piling is designed based on a resistance based method which is a function of the soil properties of which the pile is driven through, however there is a structural capacity of these members that is considered to be the upper bound on the loading of the member. This structural capacity is given by the AASHTO LRFD (2010), with two methods. These two methods are based on a composite or non-composite section. Many state agencies and corporations use the non-composite equation because it is requires much less computation and is known to be conservative. However with the trends of the time, more and more structural elements are being investigated to determine ways to better understand the mechanics of the members, which could lead to more efficient and safer designs. In this project, a set of these piling are investigated. The way the cross section reacts to several different loading conditions, along with a more detailed observation of the material properties is considered as part of this research. The evaluation consisted of testing stub sections of pile with varying sizes (10-¾”, 12-¾”), wall thicknesses (0.375”, 0.5”), and testing methods (whole compression, composite compression, push through, core sampling). These stub sections were chosen as they would represent a similar bracing length to many different soils. In addition, a finite element model was developed using ANSYS to predict the strains from the testing of the pile cross sections. This model was able to simulate the strains from most of the loading conditions and sizes that were tested. The bond between the steel shell and the concrete core, along with the concrete strength through the depth of the cross section were some of the material properties of these sections that were investigated.

NDT flaw mapping of steel surfaces by continuous magnetic Barkhausen noise: Volumetric flaw detection case

This paper reports the use of a non-destructive, continuous magnetic Barkhausen noise (CMBN) technique to investigate the size and thickness of volumetric defects, in a 1070 steel. The magnetic behavior of the used probe was analyzed by numerical simulation, using the finite element method (FEM). Results indicated that the presence of a ferrite coil core in the probe favors MBN emissions. The samples were scanned with different speeds and probe configurations to determine the effect of the flaw on the CMBN signal amplitude. A moving smooth window, based on a second-order statistical moment, was used for analyzing the time signal. The results show the technique`s good repeatability, and high capacity for detection of this type of defect. (C) 2009 Elsevier Ltd. All rights reserved.

Crack detection in hollow section structures through coupled response measurements

Detection of a circumferential crack in a hollow section beam is investigated using coupled response measurements. The crack section is represented by a local flexibility matrix connecting two undamaged beam segments. This matrix defines the relationship between the displacements and forces across the crack section and is derived by applying fundamental fracture mechanics theory. The suitability of the mode coupling methodology is first demonstrated analytically. Laboratory test results are then presented for circular hollow section beams with artificially generated cracks of varying severity. It is shown that this method has the potential as a damage detection tool for mechanical structures. (C) 2002 Elsevier Science Ltd. All rights reserved.