Binding site of brefeldin A at the interface between the small G protein ADP-ribosylation factor 1 (ARF1) and the nucleotide-exchange factor Sec7 domain

Sec7 domains (Sec7d) catalyze the exchange of guanine nucleotide on ARFs. Recent studies indicated that brefeldin A (BFA) inhibits Sec7d-catalyzed nucleotide exchange on ARF1 in an uncompetitive manner by trapping an early intermediate of the reaction: a complex between GDP-bound ARF1 and Sec7d. Using 3H-labeled BFA, we show that BFA binds to neither isolated Sec7d nor isolated ARF1–GDP, but binds to the transitory Sec7d–ARF1–GDP complex and stabilizes it. Two pairs of residues at positions 190–191 and 198–208 (Arno numbering) in Sec7d contribute equally to the stability of BFA binding, which is also sensitive to mutation of H80 in ARF1. The catalytic glutamic (E156) residue of Sec7d is not necessary for BFA binding. In contrast, BFA does not bind to the intermediate catalytic complex between nucleotide-free ARF1 and Sec7d. These results suggest that, on initial docking steps between ARF1–GDP and Sec7d, BFA inserts like a wedge between the switch II region of ARF1–GDP and a surface encompassing residues 190–208, at the border of the characteristic hydrophobic groove of Sec7d. Bound BFA would prevent the switch regions of ARF1–GDP from reorganizing and forming tighter contacts with Sec7d and thereby would maintain the bound GDP of ARF1 at a distance from the catalytic glutamic finger of Sec7d.

Electrostatic surface plasmon resonance: Direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches

We demonstrate that in situ optical surface plasmon resonance spectroscopy can be used to monitor hybridization kinetics for unlabeled DNA in tethered monolayer nucleic acid films on gold in the presence of an applied electrostatic field. The dc field can enhance or retard hybridization and can also denature surface-immobilized DNA duplexes. Discrimination between matched and mismatched hybrids is achieved by simple adjustment of the electrode potential. Although the electric field at the interface is extremely large, the tethered single-stranded DNA thiol probes remain bound and can be reused for subsequent hybridization reactions without loss of efficiency. Only capacitive charging currents are drawn; redox reactions are avoided by maintaining the gold electrode potential within the ideally polarizable region. Because of potential-induced changes in the shape of the surface plasmon resonance curve, we account for the full curve rather than simply the shift in the resonance minimum.

Protein-protein interaction: a genetic selection for compensating mutations at the barnase-barstar interface.

Barnase and barstar are trivial names of the extracellular RNase and its intracellular inhibitor produced by Bacillus amyloliquefaciens. Inhibition involves the formation of a very tight one-to-one complex of the two proteins. With the crystallographic solution of the structure of the barnase-barstar complex and the development of methods for measuring the free energy of binding, the pair can be used to study protein-protein recognition in detail. In this report, we describe the isolation of suppressor mutations in barstar that compensate for the loss in interaction energy caused by a mutation in barnase. Our suppressor search is based on in vivo selection for barstar variants that are able to protect host cells against the RNAse activity of those barnase mutants not properly inhibited by wild-type barstar. This approach utilizes a plasmid system in which barnase expression is tightly controlled to keep the mutant barnase gene silent. When expression of barnase is turned on, failure to form a complex between the mutant barnase and barstar has a lethal effect on host cells unless overcome by substitution of the wild-type barstar by a functional suppressor derivative. A set of barstar suppressors has been identified for barnase mutants with substitutions in two amino acid positions (residues 102 and 59), which are critically involved in both RNase activity and barstar binding. The mutations selected as suppressors could not have been predicted on the basis of the known protein structures. The single barstar mutation with the highest information content for inhibition of barnase (H102K) has the substitution Y30W. The reduction in binding caused by the R59E mutation in barnase can be partly reversed by changing Glu-76 of barstar, which forms a salt bridge with the Arg-59 in the wild-type complex, to arginine, thus completing an interchange of the two charges.

Preparation of poly (alkylcyanoacrylate) nanoparticles by polymerization of water-free microemulsions

Phase diagrams of the pseudoternary systems ethyloleate, polyoxyethylene 20 sorbitan mono-oleate/sorbitan monolaurate and propylene glycol with and without butanol as a co-surfactant were prepared. Areas containing optically isotropic, one-phase systems were identified and samples therein designated as droplet, bicontinuous or solution type microemulsions using conductivity, viscosity and self-diffusion NMR. Nanoparticles were prepared by polymerization of selected microemulsions with ethyl-2-cyanoacrylate and the morphology of the particles was investigated. Addition of monomer to all types of microemulsions led to the formation of nanoparticles, which had an average size of 244 +/- 25 nm, an average polydispersity index of 0.15 +/- 0.04 and a zeta-potential of -17 +/- 3 mV. The formation of particles from water-free microemulsions of different types is surprising, particularly considering that polymerization is expected to occur at a water-oil interface by base-catalysed polymerization. It would appear that propylene glycol is sufficiently nucleophilic to initiate the polymerization. The use of water-free microemulsions as templates for the preparation of poly (alkylcyanoacrylate) nanoparticles opens up interesting opportunities for the encapsulation of bioactives which do not have suitable properties for encapsulation on the basis of water-containing microemulsions.

Multimodal 'Eyes-Free' interaction techniques for mobile devices

Mobile and wearable computers present input/output prob-lems due to limited screen space and interaction techniques. When mobile, users typically focus their visual attention on navigating their environment - making visually demanding interface designs hard to operate. This paper presents two multimodal interaction techniques designed to overcome these problems and allow truly mobile, 'eyes-free' device use. The first is a 3D audio radial pie menu that uses head gestures for selecting items. An evaluation of a range of different audio designs showed that egocentric sounds re-duced task completion time, perceived annoyance, and al-lowed users to walk closer to their preferred walking speed. The second is a sonically enhanced 2D gesture recognition system for use on a belt-mounted PDA. An evaluation of the system with and without audio feedback showed users' ges-tures were more accurate when dynamically guided by au-dio-feedback. These novel interaction techniques demon-strate effective alternatives to visual-centric interface de-signs on mobile devices.

Progettazione e sviluppo di un framework in ambiente Android per la realizzazione di interfacce utente see-through e hands-free

La tesi tratta l'esplorazione dell'idea per una nuova tipologia di interfacce utente, progettate specificatamente per dispositivi wearable hands free (più nel dettaglio per un'accoppiata smart glass Android based e gesture recognizer). Per facilitare lo sviluppo di applicazioni basate su questi dispositivi è stato realizzato un framework che permetta di costruire, in maniera relativamente semplice, interfacce utente innovative, che consentano all'utente di interagire con i contenuti digitali senza interrompere il suo contatto con la realtà e senza costringerlo a utilizzare le mani.

A New Method for Modeling Free Surface Flows and Fluid-structure Interaction with Ocean Applications

The computational modeling of ocean waves and ocean-faring devices poses numerous challenges. Among these are the need to stably and accurately represent both the fluid-fluid interface between water and air as well as the fluid-structure interfaces arising between solid devices and one or more fluids. As techniques are developed to stably and accurately balance the interactions between fluid and structural solvers at these boundaries, a similarly pressing challenge is the development of algorithms that are massively scalable and capable of performing large-scale three-dimensional simulations on reasonable time scales. This dissertation introduces two separate methods for approaching this problem, with the first focusing on the development of sophisticated fluid-fluid interface representations and the second focusing primarily on scalability and extensibility to higher-order methods.

We begin by introducing the narrow-band gradient-augmented level set method (GALSM) for incompressible multiphase Navier-Stokes flow. This is the first use of the high-order GALSM for a fluid flow application, and its reliability and accuracy in modeling ocean environments is tested extensively. The method demonstrates numerous advantages over the traditional level set method, among these a heightened conservation of fluid volume and the representation of subgrid structures.

Next, we present a finite-volume algorithm for solving the incompressible Euler equations in two and three dimensions in the presence of a flow-driven free surface and a dynamic rigid body. In this development, the chief concerns are efficiency, scalability, and extensibility (to higher-order and truly conservative methods). These priorities informed a number of important choices: The air phase is substituted by a pressure boundary condition in order to greatly reduce the size of the computational domain, a cut-cell finite-volume approach is chosen in order to minimize fluid volume loss and open the door to higher-order methods, and adaptive mesh refinement (AMR) is employed to focus computational effort and make large-scale 3D simulations possible. This algorithm is shown to produce robust and accurate results that are well-suited for the study of ocean waves and the development of wave energy conversion (WEC) devices.

Interface microstructure of alumina mechanically metallized with Ti brazed to Fe–Ni–Co using different fillers

NASCIMENTO,R.M. et al.Interface microstructure of alumina mechanically metallized with Ti brazed to Fe–Ni–Co using different fillers. Materials Science and Engineering A, v.466, n.1/2, p. 195-200, 2007.

Three-dimensional free surface modelling in an unstructured mesh environment for metal processing applications

In the casting of metals, tundish flow, welding, converters, and other metal processing applications, the behaviour of the fluid surface is important. In aluminium alloys, for example, oxides formed on the surface may be drawn into the body of the melt where they act as faults in the solidified product affecting cast quality. For this reason, accurate description of wave behaviour, air entrapment, and other effects need to be modelled, in the presence of heat transfer and possibly phase change. The authors have developed a single-phase algorithm for modelling this problem. The Scalar Equation Algorithm (SEA) (see Refs. 1 and 2), enables the transport of the property discontinuity representing the free surface through a fixed grid. An extension of this method to unstructured mesh codes is presented here, together with validation. The new method employs a TVD flux limiter in conjunction with a ray-tracing algorithm, to ensure a sharp bound interface. Applications of the method are in the filling and emptying of mould cavities, with heat transfer and phase change.

Interface microstructure of alumina mechanically metallized with Ti brazed to Fe–Ni–Co using different fillers

NASCIMENTO,R.M. et al.Interface microstructure of alumina mechanically metallized with Ti brazed to Fe–Ni–Co using different fillers. Materials Science and Engineering A, v.466, n.1/2, p. 195-200, 2007.

Interface properties and capacitance-voltage behaviour of diamond devices prepared by microwave-assisted CVD

Free standing diamond films were used to study the effect of diamond surface morphology and microstructure on the electrical properties of Schottky barrier diodes. By using free standing films both the rough top diamond surface and the very smooth bottom surface are available for post-metal deposition. Rectifying electrical contacts were then established either with the smooth or the rough surface. The estimate of doping density from the capacitance-voltage plots shows that the smooth surface has a lower doping density when compared with the top layers of the same film. The results also show that surface roughness does not contribute significantly to the frequency dispersion of the small signal capacitance. The electrical properties of an abrupt asymmetric n(+)(silicon)-p(diamond) junction have also been measured. The I-V curves exhibit at low temperatures a plateau near zero bias, and show inversion of rectification. Capacitance-voltage characteristics show a capacitance minimum with forward bias, which is dependent on the environment conditions. It is proposed that this anomalous effect arises from high level injection of minority carriers into the bulk.

Detecção de interface em tanques de petróleo usando transmissores de nível e controladores Fuzzy

This work presents a proposal to detect interface in atmospheric oil tanks by installing a differential pressure level transmitter to infer the oil-water interface. The main goal of this project is to maximize the quantity of free water that is delivered to the drainage line by controlling the interface. A Fuzzy Controller has been implemented by using the interface transmitter as the Process Variable. Two ladder routine was generated to perform the control. One routine was developed to calculate the error and error variation. The other was generate to develop the fuzzy controller itself. By using rules, the fuzzy controller uses these variables to set the output. The output is the position variation of the drainage valve. Although the ladder routine was implemented into an Allen Bradley PLC, Control Logix family it can be implemented into any brand of PLCs

Interface properties and capacitance-voltage behaviour of diamond devices prepared by microwave-assisted CVD

Free standing diamond films were used to study the effect of diamond surface morphology and microstructure on the electrical properties of Schottky barrier diodes. By using free standing films both the rough top diamond surface and the very smooth bottom surface are available for post-metal deposition. Rectifying electrical contacts were then established either with the smooth or the rough surface. The estimate of doping density from the capacitance-voltage plots shows that the smooth surface has a lower doping density when compared with the top layers of the same film. The results also show that surface roughness does not contribute significantly to the frequency dispersion of the small signal capacitance. The electrical properties of an abrupt asymmetric n(+)(silicon)-p(diamond) junction have also been measured. The I-V curves exhibit at low temperatures a plateau near zero bias, and show inversion of rectification. Capacitance-voltage characteristics show a capacitance minimum with forward bias, which is dependent on the environment conditions. It is proposed that this anomalous effect arises from high level injection of minority carriers into the bulk.

Chemical Reaction Dynamics of the Liquid/Vapor Interface Studied by Mass Spectrometry

This thesis presents investigations of chemical reactions occurring at the liquid/vapor interface studied using novel sampling methodologies coupled with detection by mass spectrometry. Chapters 2 and 3 utilize the recently developed technique of field-induced droplet ionization mass spectrometry (FIDI-MS), in which the application of a strong electric field to a pendant microliter droplet results in the ejection of highly charged progeny droplets from the liquid surface. In Chapter 2, this method is employed to study the base-catalyzed dissociation of a surfactant molecule at the liquid/vapor interface upon uptake of ammonia from the gas phase. This process is observed to occur without significant modulation of the bulk solution pH, suggesting a transient increase in surface pH following the uptake of gaseous ammonia. Chapter 3 presents real-time studies of the oxidation of the model tropospheric organic compound glycolaldehyde by photodissociation of iron (III) oxalate complexes. The oxidation products of glycolaldehyde formed in this process are identified, and experiments in a deoxygenated environment identify the role of oxygen in the oxidation pathway and in the regeneration of iron (III) following photo-initiated reduction. Chapter 4 explores alternative methods for the study of heterogeneous reaction processes by mass spectrometric sampling from liquid surfaces. Bursting bubble ionization (BBI) and interfacial sampling with an acoustic transducer (ISAT) generate nanoliter droplets from a liquid surface that can be sampled via the atmospheric pressure interface of a mass spectrometer. Experiments on the oxidation of oleic acid by ozone using ISAT are also presented. Chapters 5 and 6 detail mechanistic studies and applications of free-radical-initiated peptide sequencing (FRIPS), a technique employing gas-phase free radical chemistry to the sequencing of peptides and proteins by mass spectrometry. Chapter 5 presents experimental and theoretical studies on the anomalous mechanism of dissociation observed in the presence of serine and threonine residues in peptides. Chapter 6 demonstrates the combination of FRIPS with ion mobility-mass spectrometry (IM-MS) for the separation of isomeric peptides.