The estimation of the thermodynamic properties of ternary alloys from binary data using the shortest distance composition path

A new composition path, Xi-Xj=constant, is suggested for the semi-empirical calculation of the thermodynamic properties of ternary ‘substitutional’ solutions from binary data, when the binary systems show deviations from the regular solution model. A comparison is made between the results obtained for integral and partial properties using this composition path and those calculated employing other composition paths suggested in literature. It appears that the best estimate of the ternary properties is obtained when binary data at compositions closest to the ternary composition are used.

Allosteric Communication in Cysteinyl tRNA Synthetase A NETWORK OF DIRECT AND INDIRECT READOUT

Protein structure networks are constructed for the identification of long-range signaling pathways in cysteinyl tRNA synthetase (CysRS). Molecular dynamics simulation trajectory of CysRS-ligand complexes were used to determine conformational ensembles in order to gain insight into the allosteric signaling paths. Communication paths between the anticodon binding region and the aminoacylation region have been identified. Extensive interaction between the helix bundle domain and the anticodon binding domain, resulting in structural rigidity in the presence of tRNA, has been detected. Based on the predicted model, six residues along the communication paths have been examined by mutations (single and double) and shown to mediate a coordinated coupling between anticodon recognition and activation of amino acid at the active site. This study on CysRS clearly shows that specific key residues, which are involved in communication between distal sites in allosteric proteins but may be elusive in direct structure analysis, can be identified from dynamics of protein structure networks.

Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-alpha method

Biochemical pathways involving chemical kinetics in medium concentrations (i.e., at mesoscale) of the reacting molecules can be approximated as chemical Langevin equations (CLE) systems. We address the physically consistent non-negative simulation of the CLE sample paths as well as the issue of non-Lipschitz diffusion coefficients when a species approaches depletion and any stiffness due to faster reactions. The non-negative Fully Implicit Stochastic alpha (FIS alpha) method in which stopped reaction channels due to depleted reactants are deleted until a reactant concentration rises again, for non-negativity preservation and in which a positive definite Jacobian is maintained to deal with possible stiffness, is proposed and analysed. The method is illustrated with the computation of active Protein Kinase C response in the Protein Kinase C pathway. (C) 2011 Elsevier Inc. All rights reserved.

Parallel Computation of 2D Morse-Smale Complexes

The Morse-Smale complex is a useful topological data structure for the analysis and visualization of scalar data. This paper describes an algorithm that processes all mesh elements of the domain in parallel to compute the Morse-Smale complex of large two-dimensional data sets at interactive speeds. We employ a reformulation of the Morse-Smale complex using Forman's Discrete Morse Theory and achieve scalability by computing the discrete gradient using local accesses only. We also introduce a novel approach to merge gradient paths that ensures accurate geometry of the computed complex. We demonstrate that our algorithm performs well on both multicore environments and on massively parallel architectures such as the GPU.

Null Dereference Verification via Over-approximated Weakest Pre-conditions Analysis

Null dereferences are a bane of programming in languages such as Java. In this paper we propose a sound, demand-driven, inter-procedurally context-sensitive dataflow analysis technique to verify a given dereference as safe or potentially unsafe. Our analysis uses an abstract lattice of formulas to find a pre-condition at the entry of the program such that a null-dereference can occur only if the initial state of the program satisfies this pre-condition. We use a simplified domain of formulas, abstracting out integer arithmetic, as well as unbounded access paths due to recursive data structures. For the sake of precision we model aliasing relationships explicitly in our abstract lattice, enable strong updates, and use a limited notion of path sensitivity. For the sake of scalability we prune formulas continually as they get propagated, reducing to true conjuncts that are less likely to be useful in validating or invalidating the formula. We have implemented our approach, and present an evaluation of it on a set of ten real Java programs. Our results show that the set of design features we have incorporated enable the analysis to (a) explore long, inter-procedural paths to verify each dereference, with (b) reasonable accuracy, and (c) very quick response time per dereference, making it suitable for use in desktop development environments.

mRegistry: a registry representation for fault diagnosis

Microsoft Windows uses the notion of registry to store all configuration information. The registry entries have associations and dependencies. For example, the paths to executables may be relative to some home directories. The registry being designed with faster access as one of the objectives does not explicitly capture these relations. In this paper, we explore a representation that captures the dependencies more explicitly using shared and unifying variables. This representation, called mRegistry exploits the tree-structured hierarchical nature of the registry, is concept-based and obtained in multiple stages. mRegistry captures intra-block, inter-block and ancestor-children dependencies (all leaf entries of a parent key in a registry put together as an entity constitute a block thereby making the block as the only child of the parent). In addition, it learns the generalized concepts of dependencies in the form of rules. We show that mRegistry has several applications: fault diagnosis, prediction, comparison, compression etc.

UAV Grouping and Coordination Tactics for Ground Attack Missions

Grouping and coordination tactics for ground attack missions by a heterogeneous mix of reconnaissance, enemy suppression, and attack unmanned aerial vehicles (UAVs) is presented. Dubins' paths are used to determine the optimal number of attack UAVs and their positional and heading freedoms, as functions of weapon seeker range and field of view. A generic battlefield scenario with layered defense is created and the tactics are evaluated on a Group Flyer simulation platform for both nominal and off-nominal conditions.

Effect of cryogenic treatment on thermal conductivity properties of copper

Copper exhibits high thermal conductivity properties and hence it is extensively used in cryogenic applications like cold fingers, heat exchangers, etc. During the realization of such components, copper undergoes various machining operations from the raw material stage to the final component. During these machining processes, stresses are induced within the metal resulting in internal stresses, strains and dislocations. These effects build up resistance paths for the heat carriers which transfer heat from one location to the other. This in turn, results in reduction of thermal conductivity of the conducting metal and as a result the developed component will not perform as per expectations. In the process of cryogenic treatment, the metal samples are exposed to cryogenic temperature for extended duration of time for 24 hours and later tempered. During this process, the internal stresses and strains are reduced with refinement of the atomic structure. These effects are expected to favourably improve thermal conductivity properties of the metal. In this experimental work, OFHC copper samples were cryotreated for 24 hours at 98 K and part of them were tempered at 423K for one hour. Significant enhancement of thermal conductivity values were observed after cryotreating and tempering the copper samples.

Evolution of Texture and Microstructure in Commercially Pure Titanium with Change in Strain Path During Rolling

The evolution of microstructure and texture in commercially pure titanium has been studied as a function of strain path during rolling using experimental techniques and viscoplastic self-consistent simulations. Four different strain paths, namely unidirectional rolling, two-step cross rolling, multistep cross rolling, and reverse rolling, have been employed to decipher the effect of strain path change on the evolution of deformation texture and microstructure. The cross-rolled samples show higher hardness with lower microstrain and intragranular misorientation compared to the unidirectional rolled sample as determined from X-ray diffraction and electron backscatter diffraction, respectively. The higher hardness of the cross-rolled samples is attributed to orientation hardening due to the near basal texture. Viscoplastic self-consistent simulations are able to successfully predict the texture evolution of the differently rolled samples. Simulation results indicate the higher contribution of basal slip in the formation of near basal texture and as well as lower intragranular misorientation in the cross-rolled samples.

Grain-Size Effects on the High-Temperature Oxidation of Modified 304 Austenitic Stainless Steel

The high-temperature oxidation behavior of modified 304 austenitic stainless steels in a water vapor atmosphere was investigated. Samples were prepared by various thermo mechanical treatments to result in different grain sizes in the range 8-30 mu m. Similar I 3 pound grain boundary fraction was achieved to eliminate any grain-boundary characteristics effect. Samples were oxidized in an air furnace at 700 A degrees C with 20 % water vapor atmosphere. On the fine-grained sample, a uniform Cr2O3 layer was formed, which increased the overall oxidation resistance. Whereas on the coarse-grained sample, an additional Fe2O3 layer formed on the Cr-rich oxide layer, which resulted in a relatively high oxidation rate. In the fine-grained sample, grain boundaries act as rapid diffusion paths for Cr and provided enough Cr to form Cr2O3 oxide on the entire sample surface.

Influence of tool rotation speed and feed rate on the forming limit of friction stir welded AA6061-T6 sheets

In this study, the influence of tool rotation speed and feed rate on the forming limit of friction stir welded Al 6061-T651 sheets has been investigated. The forming limit curve was evaluated by limit dome height test performed on all the friction stir welded sheets. The welding trials were conducted at a tool rotation speed of 1300 and 1400 r/min and feed rate of 90 and 100 mm/min. A third trial of welding was performed at a rotational speed of 1500 r/min and feed rate 120 mm/min. It is found that with increase in the tool rotation speed, from 1300 to 1400 r/min, for a constant feed rate, the forming limit of friction stir welded blank has improved and with increase in feed rate, from 90 to 100 mm/min, for a constant tool rotation speed, it has decreased. The forming limit of friction stir welded sheets is better than unwelded sheets. The thickness gradient after forming is severe in the cases of friction stir welded blanks made at higher feed rate and lower rotation speed. The strain hardening exponent of weld (n) increases with increase in tool rotation speed and it decreases with increase in feed rate. It has been demonstrated that the change in the forming limit of friction stir welded sheets with respect to welding parameters is due to the thickness distribution severity and strain hardening exponent of the weld region during forming. There is not much variation in the dome height among the friction stir welded sheets tested. When compared with unwelded sheets, dome height of friction stir welded sheets is higher in near-plane-strain condition, but it is lesser in stretching strain paths.

Yanai waves in the western equatorial Indian Ocean

Observations and models have shown the presence of intraseasonal fluctuations in 20-30-day and 10-20-day bands in the equatorial Indian Ocean west of 60 degrees E (WEIO). Their spatial and temporal structures characterize them as Yanai waves, which we label low-frequency (LFYW) and high-frequency (HFYW) Yanai waves, respectively. We explore the dynamics of these intraseasonal signals, using an ocean general circulation model (Modular Ocean Model) and a linear, continuously stratified model. Yanai waves are forced by the meridional wind tau(y) everywhere in the WEIO most strongly during the monsoon seasons. They are forced both directly in the interior ocean and by reflection of the interior response from the western boundary; interference between the interior and boundary responses results in a complex surface pattern that propagates eastward and has nodes. Yanai waves are also forced by instabilities primarily during June/July in a region offshore from the western boundary (52-55 degrees E). At that time, eddies, generated by barotropic instability of the Southern Gyre, are advected southward to the equator. There, they generate a westward-propagating, cross-equatorial flow field, v(eq), with a wave number/frequency spectrum that fits the dispersion relation of a number of Yanai waves, and these waves are efficiently excited. Typically, Yanai waves associated with several baroclinic modes are excited by both wind and eddy forcing; and typically, they superpose to create beams that carry energy vertically and eastward along ray paths. The same processes generate LFYWs and HFYWs, and hence, their responses are similar; differences are traceable to the property that HFYWs have longer wavelengths than LFYWs for each baroclinic mode.

DMT of parallel-path and layered networks under the half-duplex constraint

In this paper, we study the diversity-multiplexing-gain tradeoff (DMT) of wireless relay networks under the half-duplex constraint. It is often unclear what penalty if any, is imposed by the half-duplex constraint on the DMT of such networks. We study two classes of networks; the first class, called KPP(I) networks, is the class of networks with the relays organized in K parallel paths between the source and the destination. While we assume that there is no direct source-destination path, the K relaying paths can interfere with each other. The second class, termed as layered networks, is comprised of relays organized in layers, where links exist only between adjacent layers. We present a communication scheme based on static schedules and amplify-and-forward relaying for these networks. We also show that for KPP(I) networks with K >= 3, the proposed schemes can achieve full-duplex DMT performance, thus demonstrating that there is no performance hit on the DMT due to the half-duplex constraint. We also show that, for layered networks, a linear DMT of d(max)(1 - r)(+) between the maximum diversity d(max) and the maximum MG, r(max) = 1 is achievable. We adapt existing DMT optimal coding schemes to these networks, thus specifying the end-to-end communication strategy explicitly.

Mining large-scale response networks reveals `topmost activities' in Mycobacterium tuberculosis infection

Mycobacterium tuberculosis owes its high pathogenic potential to its ability to evade host immune responses and thrive inside the macrophage. The outcome of infection is largely determined by the cellular response comprising a multitude of molecular events. The complexity and inter-relatedness in the processes makes it essential to adopt systems approaches to study them. In this work, we construct a comprehensive network of infection-related processes in a human macrophage comprising 1888 proteins and 14,016 interactions. We then compute response networks based on available gene expression profiles corresponding to states of health, disease and drug treatment. We use a novel formulation for mining response networks that has led to identifying highest activities in the cell. Highest activity paths provide mechanistic insights into pathogenesis and response to treatment. The approach used here serves as a generic framework for mining dynamic changes in genome-scale protein interaction networks.

Generation of Ligand Specificity and Modes of Oligomerization in beta-Prism I Fold Lectins

beta-Prism I fold lectins constitute one of the five widely occurring structural classes of plant lectins. Each single domain subunit is made up of three Greek key motifs arranged in a threefold symmetric fashion. The threefold symmetry is not reflected in the sequence except in the case of the lectin from banana, a monocot, which carries two sugar-binding sites instead of the one in other lectins of known three-dimensional structure, all from dicots. This is believed to be a consequence of the different evolutionary paths followed by the lectin in monocots and dicots. The galactose-specific lectins among them have two chains produced by posttranslational proteolysis and contain three aromatic residues at the binding site. The extended binding sites of galactose- and mannose-specific lectins have been thoroughly characterized. Ligand binding at the sites involves both conformational selection and induced fit. Molecular plasticity of some of the lectins in the family has been characterized. The plasticity appears to be such as to promote variability in quaternary association which could be dimeric, tetrameric, or octameric. Structural and evolutionary reasons for the variability have been explored, and the relation of oligomerization to ligand binding and conformational selection investigated.