The design and synthesis of redox core-alpha amino acid composites based on thiol-disulfide exchange mechanism and a comparative study of their zinc abstraction potential from [CCXX] boxes in proteins

The design and synthesis of agents that can abstract zinc from their [CCXX] (C=cysteine; X=cysteine/histidine) boxes by thioldisulfide exchange-having as control, the redox parities of the core sulfur ligands of the reagent and the enzyme, has been illustrated, and their efficiency demonstrated by monitoring the inhibition of the transcription of calf thymus DNA by E. coli RNA polymerase, which harbors two zinc atoms in their [CCXX] boxes of which one is exchangeable. Maximum inhibition possible with removal of the exchangeable zinc was seen with redox-sulfanilamide-glutamate composite. In sharp contrast, normal chelating agents (EDTA, phenanthroline) even in a thousand fold excess showed only marginal inhibition, thus supporting an exchange mechanism for the metal removal. (C) 2002 Elsevier Science Ltd. All rights reserved.

Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism

Pyrrolysyl-tRNA synthetase (PyIRS) is an atypical enzyme responsible for charging tRNA(Pyl) with pyrrolysine, despite lacking precise tRNA anticodon recognition. This dimeric protein exhibits allosteric regulation of function, like any other tRNA synthetases. In this study we examine the paths of allosteric communication at the atomic level, through energy-weighted networks of Desulfitobacterium hafniense PyIRS (DhPyIRS) and its complexes with tRNA(Pyl) and activated pyrrolysine. We performed molecular dynamics simulations of the structures of these complexes to obtain an ensemble conformation-population perspective. Weighted graph parameters relevant to identifying key players and ties in the context of social networks such as edge/node betweenness, closeness index, and the concept of funneling are explored in identifying key residues and interactions leading to shortest paths of communication in the structure networks of DhPylRS. Further, the changes in the status of important residues and connections and the costs of communication due to ligand induced perturbations are evaluated. The optimal, suboptimal, and preexisting paths are also investigated. Many of these parameters have exhibited an enhanced asymmetry between the two subunits of the dimeric protein, especially in the pretransfer complex, leading us to conclude that encoding of function goes beyond the sequence/structure of proteins. The local and global perturbations mediated by appropriate ligands and their influence on the equilibrium ensemble of conformations also have a significant role to play in the functioning of proteins. Taking a comprehensive view of these observations, we propose that the origin of many functional aspects (allostery rand half-sites reactivity in the case of DhPyIRS) lies in subtle rearrangements of interactions and dynamics at a global level.

A new parallel overlapped domain decomposition method for nonlinear dynamic finite element analysis

In this paper a new parallel algorithm for nonlinear transient dynamic analysis of large structures has been presented. An unconditionally stable Newmark-beta method (constant average acceleration technique) has been employed for time integration. The proposed parallel algorithm has been devised within the broad framework of domain decomposition techniques. However, unlike most of the existing parallel algorithms (devised for structural dynamic applications) which are basically derived using nonoverlapped domains, the proposed algorithm uses overlapped domains. The parallel overlapped domain decomposition algorithm proposed in this paper has been formulated by splitting the mass, damping and stiffness matrices arises out of finite element discretisation of a given structure. A predictor-corrector scheme has been formulated for iteratively improving the solution in each step. A computer program based on the proposed algorithm has been developed and implemented with message passing interface as software development environment. PARAM-10000 MIMD parallel computer has been used to evaluate the performances. Numerical experiments have been conducted to validate as well as to evaluate the performance of the proposed parallel algorithm. Comparisons have been made with the conventional nonoverlapped domain decomposition algorithms. Numerical studies indicate that the proposed algorithm is superior in performance to the conventional domain decomposition algorithms. (C) 2003 Elsevier Ltd. All rights reserved.

Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair

Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg 128 into the DNA double helix and its interaction with the O6MG: C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.

Molecular insights into the mechanism of phenotypic tolerance to rifampicin conferred on mycobacterial RNA polymerase by MsRbpA

The protein MsRbpA from Mycobacterium smegmatis rescues RNA polymerase (RNAP) from the inhibitory effect of rifampicin (Rif). We have reported previously that MsRbpA interacts with the beta-subunit of RNAP and that the effect of MsRbpA on Rif-resistant (Rif(R)) RNAP is minimal. Here we attempted to gain molecular insights into the mechanism of action of this protein with respect to its role in rescuing RNAP from Rif-mediated transcription inhibition. Our experimental approach comprised multiple-round transcription assays, fluorescence spectroscopy, MS and surface plasmon resonance in order to meet the above objective. Based on our molecular studies we propose here that Rif is released from its binding site in the RNAP-Rif complex in the presence of MsRbpA. Biophysical studies reveal that the location of MsRbpA on RNAP is at the junction of the beta- and beta'-subunits, close to the Rif-binding site and the (i + 1) site on RNAP.

NanoLAB Triboprobe: Characterizing Dynamic Wear, Friction and Fatigue at the Nanoscale

In-situ transmission electron microscopy (TEM) has developed rapidly over the last decade. In particular, with the inclusion of scanning probes in TEM holders, allows both mechanical and electrical testing to be performed whilst simultaneously imaging the microstructure at high resolution. In-situ TEM nanoindentation and tensile experiments require only an axial displacement perpendicular to the test surface. However, here, through the development of a novel in-situ TEM triboprobe, other surface characterisation experiments are now possible, with the introduction of a fully programmable 3D positioning system. Programmable lateral displacement control allows scratch tests to be performed at high resolution with simultaneous imaging of the changing microstructure. With the addition of repeated cyclic movements, both nanoscale fatigue and friction experiments can also now be performed. We demonstrate a range of movement profiles for a variety of applications, in particular, lateral sliding wear. The developed NanoLAB TEM triboprobe also includes a new closed loop vision control system for intuitive control during positioning and alignment. It includes an automated online calibration to ensure that the fine piezotube is controlled accurately throughout any type of test. Both the 3D programmability and the closed loop vision feedback system are demonstrated here.

Dynamic subspace clustering for very large high-dimensional databases

Emerging high-dimensional data mining applications needs to find interesting clusters embeded in arbitrarily aligned subspaces of lower dimensionality. It is difficult to cluster high-dimensional data objects, when they are sparse and skewed. Updations are quite common in dynamic databases and they are usually processed in batch mode. In very large dynamic databases, it is necessary to perform incremental cluster analysis only to the updations. We present a incremental clustering algorithm for subspace clustering in very high dimensions, which handles both insertion and deletions of datapoints to the backend databases.

A Flexure-based Deployable Stereo Vision Mechanism and Temperature and Force Sensors for Laparoscopic Tools

This paper presents concepts, designs, and working prototypes of enhanced laparoscopic surgical tools. The enhancements are in equipping the tool with force and temperature sensing as well as image acquisition for stereo vision. Just as the pupils of our eyes are adequately spaced out and the distance between them is adjustable, two minute cameras mounted on a mechanism in our design can be moved closer or farther apart inside the inflated abdomen during the surgery. The cameras are fitted to a deployable mechanism consisting of flexural joints so that they can be inserted through a small incision and then deployed and moved as needed.A temperature sensor and a force sensor are mounted on either of the gripping faces of the surgical grasping tool to measure the temperature and gripping force, which need to be controlled for safe laparoscopic surgery. The sensors are small enough and hence they do not cause interference during surgery and insertion.Prototyping and working of the enhanced laparoscopic tool are presented with details

An Improved Compact Compliant Mechanism for an External Pipe-Crawler

An external pipe-crawling device presented in this paper aids the inspection of pipes in hazardous environments and areas inaccessible to humans. The principal component of our design, which uses inchworm type motion, is a compliant ring mechanism actuated using shape memory alloy (SMA) wire. It was fabricated and tested and was reported in our earlier work. But this device had a drawback of low crawling speed (about 1 mm/min) owing to the delay in heating and cooling of the SMA strips in the linear actuation. Additionally, that design also had the difficulties of mounting on pipes with closed ends, large radial span, and the need for housing for electrical insulation and guiding of the SMA wire. In this paper we present a compact design that overcomes the difficulties of the earlier design. In particular, we present a compact compliant mechanism with two halves so as to enable mounting and un-mounting on any closed or open pipe. Another feature is the presence of insulation and guiding of the SMA wire without housing. This design results in a reduction of the radial span of the ring from 22 mm to 12 mm, and the stiffness of the mechanism and the SMA wire are matched. An SMA helical spring is to used in the place of an SMA strip to increase the crawling speed of the device. A microcontroller-based circuitry is also fitted to cyclically.activate the SMA wires and springs.

A Compliant Mechanism Kit with Flexible Beams and Connectors

We present the concept, prototypes, and an optimal design method for a compliant mechanism kit as a parallel to the kits available for rigid-body mechanisms. The kit consists of flexible beams and connectors that can be easily hand-assembled using snap fits. It enables users, using their creativity and mechanics intuition, to quickly realize a compliant mechanism. The mechanisms assembled in this manner accurately capture the essential behavior of the topology, shape, size and material aspects and thereby can lead the way for a real compliant mechanism for practical use. Also described in this paper are the design of the connector to which flexible beams can be added in eight different directions; and prototyping of the spring steel connectors as well as beams using wire-cut electro discharge machining. It is noted in this paper that the concept of the kit also resolves a discrepancy in the finite element (FE) modeling of beam-based compliant mechanisms. The discrepancy arises when two or more beams are joining at one point and thus leading to increased stiffness. After resolving this discrepancy, this work extends the topology optimization to automatically generate designs that can be assembled with the kit. Thus, the kit and the accompanying analysis and optimal synthesis procedures comprise a self-contained educational as well as a research and pragmatic toolset for compliant mechanisms. The paper also illustrates how human creativity finds new ways of using the kit beyond the original intended use and how it is useful even for a novice to design compliant mechanisms.

The Effect of Evacuated Backside Cavity on the Dynamic Characteristics of a Capacitive Micromachined Ultrasonic Transducer

In this paper, we investigate the effect of vacuum sealing the backside cavity of a Capacitive Micromachined Ultrasonic Transducer (CMUT). The presence or absence of air inside the cavity has a marked effect upon the system parameters, such as the natural frequency, damping, and the pull-in voltage. The presence of vacuum inside the cavity of the device causes a reduction in the effective gap height which leads to a reduction in the pull-in voltage. We carry out ANSYS simulations to quantify this reduction. The presence of vacuum inside the cavity of the device causes stress stiffening of the membrane, which changes the natural frequency of the device. A prestressed modal analysis is carried out to determine the change in natural frequency due to stress stiffening. The equivalent circuit method is used to evaluate the performance of the device in the receiver mode. The lumped parameters of the device are obtained and an equivalent circuit model of the device is constructed to determine the open circuit receiving sensitivity of the device. The effect of air in the cavity is included by incorporating an equivalent compliance and an equivalent resistance in the equivalent circuit.

Mathematical model of COREX melter gasifier: Part II. Dynamic model

A dynamic model of the COREX melter gasifier is developed to study the transient behavior of the furnace. The effect of pulse disturbance and step disturbance on the process performance has been studied. This study shows that the effect of pulse disturbance decays asymptotically. The step change brings the system to a new steady state after a delay of about 5 hours. The dynamic behavior of the melter gasifier with respect to a shutdown/blow-on condition and the effect of tapping are also studied. The results show that the time response of the melter gasifier is much less than that of a blast furnace.

The effect of T-stress on plane strain dynamic crack growth in elastic-plastic materials

In this paper, the effects of T -stress on steady, dynamic crack growth in an elastic-plastic material are examined using a modified boundary layer formulation. The analyses are carried out under mode I, plane strain conditions by employing a special finite element procedure based on moving crack tip coordinates. The material is assumed to obey the J (2) flow theory of plasticity with isotropic power law hardening. The results show that the crack opening profile as well as the opening stress at a finite distance from the tip are strongly affected by the magnitude and sign of the T -stress at any given crack speed. Further, it is found that the fracture toughness predicted by the analyses enhances significantly with negative T -stress for both ductile and cleavage mode of crack growth.

Pyrochlore ``dynamic spin-ice'' Pr(2)Sn(2)O(7) and monoclinic Pr(2)Ti(2)O(7): A comparative temperature-dependent Raman study

Here we report a temperature-dependent Raman study of the pyrochlore ``dynamic spin-ice'' compound Pr(2)Sn(2)O(7) and compare the results with its non-pyrochlore (monoclinic) counterpart Pr(2)Ti(2)O(7). In addition to phonon modes, we observe two bands associated with electronic Raman scattering involving crystal field transitions in Pr(2)Sn(2)O(7) at similar to 135 and 460 cm(-1) which couple strongly to phonons. Anomalous temperature dependence of phonon frequencies that are observed in Pyrochlore Pr(2)Sn(2)O(7) are absent in monoclinic Pr(2)Ti(2)O(7). This, therefore, confirms that the strong phonon-phonon anharmonic interactions, responsible for the temperature-dependent anomalous behavior of phonons, arise due to the inherent vacant sites in the pyrochlore structure. (C) 2011 Elsevier Inc. All rights reserved.