Ab initio modelling of the N-terminal domain of the secretin receptors

G protein coupled receptors of the secretin family are activated by peptide hormones of about 30 residues in length. There is considerable sequence homology within both the hormone and receptor families. The receptors possess in addition to the integral membrane domain a characteristic extracellular domain of about 120 residues in length, having conserved cysteine residues, which are involved in disulphide bridge formation, and tryptophanes, which have been shown to be critical for hormone binding. This extracellular domain does not have detectable homology to any known protein fold. In order to be able to propose a structure for this domain we have used ab initio prediction methods combined with constraints based on experimental results for the disulphide connectivity. The results of computational tools for predicting secondary structure and accessibility, together with ligand binding and mutational data and other structural considerations were used in the ab initio protein folding programs DRAGON and GADGET and also the simpler program RAMBLE, which was able to explore different permutations of disulphide bond connectivity, tryptophan side chain orientation and chain topology. The methods generated a limited number of plausible models but no single unique solution was found under the constraints. One of these was refined into a full atomic model that contained a possible peptide binding site comprising the most conserved residues.     

Simultaneous quantification of reduced and oxidized glutathione in plasma using a two-dimensional chromatographic system with parallel porous graphitized carbon columns coupled with fluorescence and coulometric electrochemical detection

A method for the simultaneous quantification of reduced and oxidized glutathione in human plasma employing a two-dimensional chromatographic system with parallel porous graphitized carbon (PGC) columns coupled with fluorescence (FLD) and coulometric electrochemical detection (ED) has been developed. Post-sampling oxidation of reduced glutathione (GSH) was prevented by derivatizing the -SH group with monobromobimane (MBB) and the glutathione-bimane adduct (GSMB) was detected by FLD. Oxidized glutathione (GSSG) was detected by ED optimized to give lowest possible limits of detection (LOD). The method is fully validated and is currently used for determination of GSH, GSSG and its redox potential in different clinical studies.     

A revisit to the bending problem of a thin elliptic aelotropic plate with simply supported edge and uniform lateral load

The complex solution method of Okubo for the deflection of a thin circular aelotropic plate with simply supported edge and uniform lateral load was extended to an elliptic plate by Ohasi. In his work however several inconsistencies appear, of which at least one disqualifies a central part. From a revisit to the works of Okubo and Ohasi a new solution for the deflection of a thin elliptic aelotropic plate with simply supported edge and uniform lateral load emerged. The solution is a generalisation of Okubo’s solution and is valid for any angle between material and geometric principal axes. Previously known solutions, including those for circular plates, are reproduced as special cases of the new solution and results of numerical calculations in new situations appear reasonable.     

GELATION KINETICS OF POLYMERS CONFINED IN WATER/ OIL-SATURATED POROUS MATERIALS PROBED BY NMR

Abstract

The gelation of polyvinylalcohol with glutaraldehyde confined in a water/ oil (= 3/1 in volume ratio) saturated sandstone (Bentheimer) was characterized by H NMR spin-lattice relaxation rate (1/ T)measurements and Pulse Field Gradient (PFG) NMR diffusion measurements. The gelation rate was found to be (12.8 ± 1.3) 10^?1 5^?1 at 340 K, which is approximately an order of magnitude faster than in bulk solution. In comparison, the gelation rate within the same porous material containing no oil phase was even faster, by a factor of 2.     

In Situ Studies on Reaction Mechanisms in Atomic Layer Deposition

During the past decade, atomic layer deposition (ALD) has become an important thin-film deposition method in microelectronics industry, and it has also gained a lot of interest in many other areas, such as nanotechnology. The success of ALD is built on proper surface reactions. In this paper, in situ reaction mechanism studies on ALD processes are reviewed with the aim of building a general understanding on similarities and differences exhibited by various processes and process groups. Also, levels of understanding reaction mechanisms in ALD are discussed. The main methods used to study ALD chemistry in situ under typical process conditions are quadrupole mass spectrometry (QMS), quartz crystal microbalance (QCM), and infrared (IR) spectrometry. These are presented in detail in the review. Various other optical methods, ellipsometry in particular, have been used to study ALD processes too, but they provide little information about the reaction mechanisms. Competent in situ investigations solve the ALD reaction mechanism as balanced equations for the ALD half-reactions. The majority of ALD processes are exploiting ligand exchange reactions, where the ligands of the metal precursor are eliminated by bonding to the Lewis acids of the nonmetal precursors, most commonly hydrogen. These volatile byproducts are usually released during both precursor pulses, and determining their relative amounts is the important task in reaction mechanism studies of such processes. These processes are mechanistically fairly well understood, though some of these also display side-reactions to the ligand exchange reactions. There are also whole groups of processes that are using chemistry almost entirely different from the ligand exchange reactions. The most important such processes involve combustion chemistry, with oxygen, oxygen plasma, or ozone as a precursor or co-reactant. The mechanisms of these processes are complicated and less understood compared with the mechanisms of the ligand exchange reaction processes.     

Parallel systems under two sequential attacks with contest intensity variation

Single and double attacks against a system of parallel elements are analyzed. The vulnerability of each element depends on an attacker-defender contest success function. The contest intensity may change from the first to the second attack as determined by a contest intensity variation factor. The defender allocates its resource between deploying elements to provide redundancy, and protecting each element. The attacker allocates its resource optimally across the two attacks, may attack a subset of the elements in the first attack, observes which elements are destroyed in the first attack, and attacks all surviving elements in the second attack. A minmax two period game is analyzed where the defender moves first and the attacker moves second. The paper shows how the contest intensity variation factor affects the defense and attack strategies.     

Mathematical modeling and parameters estimation of a car crash using data-based regressive model approach

In this paper we present the application of regressive models to simulation of car-to-pole impacts. Three models were investigated: RARMAX, ARMAX and AR. Their suitability to estimate physical system parameters as well as to reproduce car kinematics was examined. It was found out that they not only estimate the one quantity which was used for their creation (car acceleration) but also describe the car’s acceleration, velocity and crush. A virtual experiment was performed to obtain another set of data for use in further research. An AR model to predict the behavior of a low-speed car impacting a rigid barrier was created and verified.     

False targets efficiency in defense strategy

The paper analyzes the efficiency of deploying false targets as part of a defense strategy. It is assumed that the defender has a single object that can be destroyed by the attacker. The defender distributes its resource between deploying false targets and protecting the object from outside attacks. The attacker cannot distinguish the false targets from the defended object (genuine target). Therefore the attacker has no preferences for attacking one target rather than another target. The defender decides how many false targets to deploy whereas the attacker decides how many targets to attack. The article assumes that both the defender and attacker have complete information and full rationality. The optimal number of false targets and the attacked targets are obtained for the case of fixed and variable resources of the defender and the attacker as solutions of a non-cooperative game between the two agents.