Thermomechanical behaviour of pin joints subjected to sheet loads

An important problem regarding pin joints in a thermal environment is addressed. The motivation emerges from structural safety requirements in nuclear and aerospace engineering. A two-dimensional model of a smooth, rigid misfit pin in a large isotropic sheet is considered as an abstraction. The sheet is subjected to a biaxial stress system and far-field unidirectional heat flow. The thermoelastic analysis is complex due to non-linear load-dependent contact and separation conditions at the pin-hole interface and the absence of existence and uniqueness theorems for the class of frictionless thermoelastic contact problems. Identification of relevant parameters and appropriate synthesis of thermal and mechanical variables enables the thermomechanical generalization of pin-joint behaviour. This paper then proceeds to explore the possibility of multiple solutions in such problems, especially interface contact configuration.

Thermomechanical generalization of pin joints in finite plates

The understanding of thermoelastic behaviour of joints is significant in order to ensure the integrity of large and complex structures exposed to a thermal environment, particularly in fields such as aerospace and nuclear engineering. Thermomechanical generalization of partial contact behaviour of a pin joint under combined in-plane mechanical loading and on-axis unidirectional heat flow has already been established by the authors for the analytically simpler domains of large plates. This paper successfully extends the on-going investigation to a single pin in a finite rectangular isotropic plate as a two-dimensional abstraction from a practical situation of a multipin fastener joint. The finite element method is used to analyse the joint problem under on-axis thermomechanical loading and unified load-contact relationships are established for a class of loading conditions.

WOMM: A Weak Operational Memory Model

Memory models of shared memory concurrent programs define the values a read of a shared memory location is allowed to see. Such memory models are typically weaker than the intuitive sequential consistency semantics to allow efficient execution. In this paper, we present WOMM (abbreviation for Weak Operational Memory Model) that formally unifies two sources of weak behavior in hardware memory models: reordering of instructions and weakly consistent memory. We show that a large number of optimizations are allowed by WOMM. We also show that WOMM is weaker than a number of hardware memory models. Consequently, if a program behaves correctly under WOMM, it will be correct with respect to those hardware memory models. Hence, WOMM can be used as a formally specified abstraction of the hardware memory models. Moreover; unlike most weak memory models, WOMM is described using operational semantics, making it easy to integrate into a model checker for concurrent programs. We further show that WOMM has an important property - it has sequential consistency semantics for datarace-free programs.

Further studies on Norrish type II reactions including a reaction in the first excited singlet state and cyclization of 1:4 biradicals

The Norrish type II processes of methyl-2,2-dimethyl- cyclopropyl ketone, alpha-alkoxy acetones and alkyl pyruvates have been examined using the AM1 semi-empirical molecular orbital method with complete geometry optimization at the partial configuration interaction level in the restricted Hartree-Fock (RHF) frame. The results reveal that the methyl-substituted cyclopropyl ketone has a constrained geometry favourable for hydrogen abstraction from the gamma-position relative to the carbonyl group in the excited singlet state. The presence of the ether oxygen atom in the beta-position relative to the carbonyl group in alkoxy acetones and alkyl pyruvates leads to increased reactivity relative to alkyl monoketones and diketones respectively. The cyclization of 1:4 biradicals has been studied in the unrestricted Hartree-Fock (UHF) frame, and the results reveal that the 1:4 biradical derived from alkoxy acetones readily cyclizes to form oxetanols. On the other hand, in the 1:4 biradicals derived from methyl-substituted cyclopropyl ketone, the three-membered ring breaks readily to form an enol intermediate. Delocalization of an odd electron in 1:4 biradicals derived from alkyl pyruvates is thought to make cyclization difficult.

Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis

Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP) dependent enzyme that catalyses degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild-type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the cofactor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modelling suggests that Thr166 may be involved in abstraction of proton from the C alpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses a, b elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.

Tree structure for efficient data mining using rough sets

In data mining, an important goal is to generate an abstraction of the data. Such an abstraction helps in reducing the space and search time requirements of the overall decision making process. Further, it is important that the abstraction is generated from the data with a small number of disk scans. We propose a novel data structure, pattern count tree (PC-tree), that can be built by scanning the database only once. PC-tree is a minimal size complete representation of the data and it can be used to represent dynamic databases with the help of knowledge that is either static or changing. We show that further compactness can be achieved by constructing the PC-tree on segmented patterns. We exploit the flexibility offered by rough sets to realize a rough PC-tree and use it for efficient and effective rough classification. To be consistent with the sizes of the branches of the PC-tree, we use upper and lower approximations of feature sets in a manner different from the conventional rough set theory. We conducted experiments using the proposed classification scheme on a large-scale hand-written digit data set. We use the experimental results to establish the efficacy of the proposed approach. (C) 2002 Elsevier Science B.V. All rights reserved.

An Empirical Evaluation of Novelty-SAPPhIRE Relationship

The research shown in this paper is to check whether a framework for designing: GEMS of SAPPhIRE as req-sol, developed earlier, can support in the designing of novel concepts. This is done by asking the questions: (a) Is there a relationship between the constructs of the framework and novelty? (b) If there is a relationship, what is the degree of this relationship? A hypothesis — an increase in the size and variety of ideas used while designing should enhance the variety of concepts produced, leading to an increase in the novelty of the concept space — is developed to explain the relationship between novelty and the constructs. Eight existing observational studies of designing sessions, each involving an individual designer solving a conceptual design problem by following a think aloud protocol are used for the analysis. The hypothesis is verified empirically using the observational studies. Results also show a strong correlation between novelty and the constructs of the framework; correlation value decreases as the abstraction level of the constructs reduces, signifying the importance of using constructs at higher abstraction levels especially for novelty.

Displacement Amplifying Compliant Mechanisms for Two-axis High-resolution Monolithic Inertial Sensors

Novel designs for two-axis, high-resolution, monolithic inertial sensors are presented in this paper. Monolithic, i.e., joint-less single-piece compliant designs are already common in micromachined inertial sensors such as accelerometers and gyroscopes. Here, compliant mechanisms are used not only to achieve de-coupling between motions along two orthogonal axes but also to amplify the displacements of the proof-mass. Sensitivity and resolution capabilities are enhanced because the amplified motion is used for sensing the measurand. A particular symmetric arrangement of displacement-amplifying compliant mechanisms (DaCMs) leads to de-coupled and amplified motion. An existing DaCM and a new topology-optimized DaCM are presented as a building block in the new arrangement. A spring-mass-lever model is presented as a lumped abstraction of the new arrangement. This model is useful for arriving at the optimal parameters of the DaCM and for performing system-level simulation. The new designs improved the performance by a factor of two or more.

Executable Analysis using Abstract Interpretation with Circular Linear Progressions

We propose a new abstract domain for static analysis of executable code. Concrete states are abstracted using circular linear progressions (CLPs). CLPs model computations using a finite word length as is seen in any real life processor. The finite abstraction allows handling overflow scenarios in a natural and straight-forward manner. Abstract transfer functions have been defined for a wide range of operations which makes this domain easily applicable for analyzing code for a wide range of ISAs. CLPs combine the scalability of interval domains with the discreteness of linear congruence domains. We also present a novel, lightweight method to track linear equality relations between static objects that is used by the analysis to improve precision. The analysis is efficient, the total space and time overhead being quadratic in the number of static objects being tracked.

WCET Estimation for Executables in the Presence of Data Caches

This paper describes techniques to estimate the worst case execution time of executable code on architectures with data caches. The underlying mechanism is Abstract Interpretation, which is used for the dual purposes of tracking address computations and cache behavior. A simultaneous numeric and pointer analysis using an abstraction for discrete sets of values computes safe approximations of access addresses which are then used to predict cache behavior using Must Analysis. A heuristic is also proposed which generates likely worst case estimates. It can be used in soft real time systems and also for reasoning about the tightness of the safe estimate. The analysis methods can handle programs with non-affine access patterns, for which conventional Presburger Arithmetic formulations or Cache Miss Equations do not apply. The precision of the estimates is user-controlled and can be traded off against analysis time. Executables are analyzed directly, which, apart from enhancing precision, renders the method language independent.

H-DBUG: A High-level Debugging Framework for Protocol Verification using Assertions

The success of an ABV IP depends highly on the associated debugging environment. An efficient debugging environment helps the user to find out the exact location of the failure. Moreover, it provides information to the user in a refined detail of abstraction and permit adequate interaction. It has also been realized that adequate visualization support helps in tracking the behavioral aspects of the Design Under Test (DUT). Currently, the debugging tools provide information in the signal level and do not provide any information about the high-level behavior of the DUT. We present a debugging framework that takes the design specification, assertions and the user intent in a simple format and provides detailed information by processing the design trace on-line, or off-line. We also present a visualization framework to ease the debugging procedure. We have experimented with industrial standard on-chip bus protocols that ensure that this utility can be incorporated successfully in the present functional verification flow.

Structure-function relationship in serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT), a pyridoxal-5V-phosphate (PLP)-dependent enzyme catalyzes thetetrahydrofolate (H4-folate)- dependent retro-aldol cleavage of serine to form 5,10-methylene H4-folate and glycine. The structure–function relationship of SHMT wasstudied in our laboratory initially by mutation of residues that are conserved in all SHMTs and later by structure-based mutagenesis of residues located in the active site. The analysis of mutants showed that K71, Y72, R80, D89, W110, S202, C203, H304, H306 and H356 residues are involved in maintenance of the oligomeric structure. The mutation of D227, a residue involved in charge relay system, led to the formation of inactive dimers, indicating that this residue has a role in maintaining the tetrameric structure and catalysis. E74, a residue appropriately positioned in the structure of the enzyme to carry out proton abstraction, was shown by characterization of E74Q and E74K mutants to be involved in conversion of the enzyme from an ‘open’ to ‘closed’ conformation rather than proton abstraction from the hydroxylgroup of serine. K256, the residue involved in the formation of Schiffs base with PLP, also plays a crucial role in the maintenance of the tetrameric structure. Mutation of R262 residue established the importance of distal interactions in facilitating catalysis and Y82 is not involved in the formaldehyde transfer via the postulated hemiacetal intermediate but plays a role in stabilizing the quinonoid intermediate.The mutational analysis of scSHMT along with the structure of recombinant Bacillus stearothermophilus SHMT and its substrate(s)complexes was used to provide evidence for a direct transfer mechanism rather than retro-aldol cleavage for the reaction catalyzed by SHMT.

Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase

Salmonella typhimurium DCyD (StDCyD) is a fold type II pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes the degradation of D-Cys to H2S and pyruvate. It also efficiently degrades beta-chloro-D-alanine (beta CDA). D-Ser is a poor substrate while the enzyme is inactive with respect to L-Ser and 1-amino-1-carboxy cyclopropane (ACC). Here, we report the X-ray crystal structures of StDCyD and of crystals obtained in the presence of D-Cys, beta CDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 angstrom. The polypeptide fold of StDCyD consisting of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) resembles other fold type II PLP dependent enzymes. The structures obtained in the presence of D-Cys and beta CDA show the product, pyruvate, bound at a site 4.0-6.0 angstrom away from the active site. ACC forms an external aldimine complex while D- and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at C alpha proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggest formation of PMP by the hydrolysis of cycloserines. Mutational studies suggest that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for C alpha proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed.

Virtually cool ternary content addressable memory

Fast content addressable data access mechanisms have compelling applications in today's systems. Many of these exploit the powerful wildcard matching capabilities provided by ternary content addressable memories. For example, TCAM based implementations of important algorithms in data mining been developed in recent years; these achieve an an order of magnitude speedup over prevalent techniques. However, large hardware TCAMs are still prohibitively expensive in terms of power consumption and cost per bit. This has been a barrier to extending their exploitation beyond niche and special purpose systems. We propose an approach to overcome this barrier by extending the traditional virtual memory hierarchy to scale up the user visible capacity of TCAMs while mitigating the power consumption overhead. By exploiting the notion of content locality (as opposed to spatial locality), we devise a novel combination of software and hardware techniques to provide an abstraction of a large virtual ternary content addressable space. In the long run, such abstractions enable applications to disassociate considerations of spatial locality and contiguity from the way data is referenced. If successful, ideas for making content addressability a first class abstraction in computing systems can open up a radical shift in the way applications are optimized for memory locality, just as storage class memories are soon expected to shift away from the way in which applications are typically optimized for disk access locality.

Current trends in modeling hostpathogen interactions

The rapid emergence of infectious diseases calls for immediate attention to determine practical solutions for intervention strategies. To this end, it becomes necessary to obtain a holistic view of the complex hostpathogen interactome. Advances in omics and related technology have resulted in massive generation of data for the interacting systems at unprecedented levels of detail. Systems-level studies with the aid of mathematical tools contribute to a deeper understanding of biological systems, where intuitive reasoning alone does not suffice. In this review, we discuss different aspects of hostpathogen interactions (HPIs) and the available data resources and tools used to study them. We discuss in detail models of HPIs at various levels of abstraction, along with their applications and limitations. We also enlist a few case studies, which incorporate different modeling approaches, providing significant insights into disease. (c) 2013 Wiley Periodicals, Inc.