The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have attracted attention. There are several limitations to experimentally testing such hypotheses, Recent developments in computational methods facilitate the study of active site-ligand complexes to high levels of accuracy, Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

Testing threshold functions using implied minterm structure

A geometrical structure called the implied minterm structure (IMS) has been developed from the properties of minterms of a threshold function. The IMS is useful for the manual testing of linear separability of switching functions of up to six variables. This testing is done just by inspection of the plot of the function on the IMS.

Testing approximate theories of first-order phase transitions on the two-dimensional Potts model

The two-dimensional,q-state (q>4) Potts model is used as a testing ground for approximate theories of first-order phase transitions. In particular, the predictions of a theory analogous to the Ramakrishnan-Yussouff theory of freezing are compared with those of ordinary mean-field (Curie-Wiess) theory. It is found that the Curie-Weiss theory is a better approximation than the Ramakrishnan-Yussouff theory, even though the former neglects all fluctuations. It is shown that the Ramakrishnan-Yussouff theory overestimates the effects of fluctuations in this system. The reasons behind the failure of the Ramakrishnan-Yussouff approximation and the suitability of using the two-dimensional Potts model as a testing ground for these theories are discussed.

Rationale of Length Scale-Down Model Span Testing of Transmission Lines

Length scale-down (LS) model tests have been traditionally employed for laboratory studies on aeolian vibration of transmission line conductors. The span adopted is normally 30 m and is recommended by the relevant Indian, as well as other, standards. The traditionally adopted length of the LS model is reexamined herein to establish the rationale behind the choice. Based on the theoretical studies discussed, certain guidelines for the choice of model span of conductor are emphasized. In addition, the adequacy of the LS span as a tool for predicting the performance of the full span is reestablished.

New approach to improved detection and tracking performance in track-while-scan radars. Part 3: Performance prediction, optimisation and testing

The paper presents, in three parts, a new approach to improve the detection and tracking performance of a track-while-scan radar. Part 1 presents a review of the current status of the subject. Part 2 details the new approach. It shows how a priori information provided by the tracker can be used to improve detection. It also presents a new multitarget tracking algorithm. In the present Part, analytical derivations are presented for assessing, a priori, the performance of the TWS radar system. True track initiation, false track initiation, true track continuation and false track deletion characteristics have been studied. It indicates how the various thresholds can be chosen by the designer to optimise performance. Simulation results are also presented.

A Microprocessor-Based Scheme for Testing Protective Relays

This paper presents a general hardware scheme for testing protective relays using microprocessor based systems. The microprocessor simulates the relaying signals for test purpose and monitors the relay performance. Based on the proposed hardware, a teat procedure for directional overcurrent relays is presented in detail. Typical test results of various routine tests conducted on a commercial single phase directional over-current relay clearly demonstrate the efficacy of the proposed technique for conducting tests on commercial relays.

Shock tunnel testing of a Mach 6 hypersonic waverider

A waverider is a lifting body configuration whose upper surface is parallel to the free stream, and the lower surface aerodynamically so designed, that the resulting shock at the design Mach number, is always attached with the leading edge of the vehicle. This prevents spillage from high pressure (lower) surface to the low pressure (upper) surface.In the present study a conical waverider has been designed, fabricated and tested at Mach 6 in the IISc hypersonic shock tunnel HST2. The measurements show that the waverider has a lift to drag ratio of 4.28 at the designed Mach number. Exhaustive FEM and CFD studies are also carried out to complement the force measurements in the tunnel.

Mechanism of failure in a free-standing Pt-aluminide bond coat during tensile testing at room temperature

The room temperature (RT) tensile behaviour of a free-standing high activity Pt-aluminide bond coat has been evaluated by microtensile testing technique. The coating had a typical three-layer microstructure. The stress-strain plot for the free-standing coating was linear, indicating the coating to be brittle at RT. Different fracture features were observed across the coating layers, namely quasi-cleavage in the outer layer and inner interdiffusion zone, and cleavage in the intermediate layer. By employing interrupted tensile test and observing the cross-sectional microstructure of the tested specimens, it was determined that failure of the microtensile samples occurred by the initiation of a single crack in the intermediate layer of the coating and its subsequent inside-out propagation. Such a mechanism of failure has been explained in terms of the fracture features observed across the sample thickness. This mechanism of failure is consistent with fracture toughness values of the individual coating layers. (C) 2009 Elsevier B.V. All rights reserved.

Testing and Modeling of MR Damper and Its Application to SDOF Systems Using Integral Backstepping Technique

Magnetorheological dampers are intrinsically nonlinear devices, which make the modeling and design of a suitable control algorithm an interesting and challenging task. To evaluate the potential of magnetorheological (MR) dampers in control applications and to take full advantages of its unique features, a mathematical model to accurately reproduce its dynamic behavior has to be developed and then a proper control strategy has to be taken that is implementable and can fully utilize their capabilities as a semi-active control device. The present paper focuses on both the aspects. First, the paper reports the testing of a magnetorheological damper with an universal testing machine, for a set of frequency, amplitude, and current. A modified Bouc-Wen model considering the amplitude and input current dependence of the damper parameters has been proposed. It has been shown that the damper response can be satisfactorily predicted with this model. Second, a backstepping based nonlinear current monitoring of magnetorheological dampers for semi-active control of structures under earthquakes has been developed. It provides a stable nonlinear magnetorheological damper current monitoring directly based on system feedback such that current change in magnetorheological damper is gradual. Unlike other MR damper control techniques available in literature, the main advantage of the proposed technique lies in its current input prediction directly based on system feedback and smooth update of input current. Furthermore, while developing the proposed semi-active algorithm, the dynamics of the supplied and commanded current to the damper has been considered. The efficiency of the proposed technique has been shown taking a base isolated three story building under a set of seismic excitation. Comparison with widely used clipped-optimal strategy has also been shown.

Leveraging Partially Enhanced Scan for Improved Observability in Delay Fault Testing

Enhanced Scan design can significantly improve the fault coverage for two pattern delay tests at the cost of exorbitantly high area overhead. The redundant flip-flops introduced in the scan chains have traditionally only been used to launch the two-pattern delay test inputs, not to capture tests results. This paper presents a new, much lower cost partial Enhanced Scan methodology with both improved controllability and observability. Facilitating observation of some hard to observe internal nodes by capturing their response in the already available and underutilized redundant flip-flops improves delay fault coverage with minimal or almost negligible cost. Experimental results on ISCAS'89 benchmark circuits show significant improvement in TDF fault coverage for this new partial enhance scan methodology.

Multi-Tone Testing of Linear and Nonlinear Analog Circuits using Polynomial Coefficients

A method of testing for parametric faults of analog circuits based on a polynomial representation of fault-free function of the circuit is presented. The response of the circuit under test (CUT) is estimated as a polynomial in the applied input voltage at relevant frequencies in addition to DC. Classification or Cur is based on a comparison of the estimated polynomial coefficients with those of the fault free circuit. This testing method requires no design for test hardware as might be added to the circuit fly some other methods. The proposed method is illustrated for a benchmark elliptic filter. It is shown to uncover several parametric faults causing deviations as small as 5% from the nominal values.

Selective attention in a synchronising bushcricket: physiology

Synchronising bushcricket males achieve synchrony by delaying their chirps in response to calling neighbours. In multi-male choruses, males that delay chirps in response to all their neighbours would remain silent most of the time and be unable to attract mates. This problem could be overcome if the afferent auditory system exhibited selective attention, and thus a male interacted only with a subset of neighbours. We investigated whether individuals of the bushcricket genus Mecopoda restricted their attention to louder chirps neurophysiologically, behaviourally and through spacing. We found that louder leading chirps were preferentially represented in the omega neuron but the representation of softer following chirps was not completely abolished. Following chirps that were 20 dB louder than leading chirps were better represented than leading chirps. During acoustic interactions, males synchronised with leading chirps even when the following chirps were 20 dB louder. Males did not restrict their attention to louder chirps during interactions but were affected by all chirps above a particular threshold. In the field, we found that males on average had only one or two neighbours whose calls were above this threshold. Selective attention is thus achieved in this bushcricket through spacing rather than neurophysiological filtering of softer signals.

Selective attention in a synchronising bushcricket: physiology, behaviour and ecology

Synchronising bushcricket males achieve synchrony by delaying their chirps in response to calling neighbours. In multi-male choruses, males that delay chirps in response to all their neighbours would remain silent most of the time and be unable to attract mates. This problem could be overcome if the afferent auditory system exhibited selective attention, and thus a male interacted only with a subset of neighbours. We investigated whether individuals of the bushcricket genus Mecopoda restricted their attention to louder chirps neurophysiologically, behaviourally and through spacing. We found that louder leading chirps were preferentially represented in the omega neuron but the representation of softer following chirps was not completely abolished. Following chirps that were 20 dB louder than leading chirps were better represented than leading chirps. During acoustic interactions, males synchronised with leading chirps even when the following chirps were 20 dB louder. Males did not restrict their attention to louder chirps during interactions but were affected by all chirps above a particular threshold. In the field, we found that males on average had only one or two neighbours whose calls were above this threshold. Selective attention is thus achieved in this bushcricket through spacing rather than neurophysiological filtering of softer signals.

Selective attention in a synchronising bushcricket: physiology, behaviour and ecology

Synchronising bushcricket males achieve synchrony by delaying their chirps in response to calling neighbours. In multi-male choruses, males that delay chirps in response to all their neighbours would remain silent most of the time and be unable to attract mates. This problem could be overcome if the afferent auditory system exhibited selective attention, and thus a male interacted only with a subset of neighbours. We investigated whether individuals of the bushcricket genus Mecopoda restricted their attention to louder chirps neurophysiologically, behaviourally and through spacing. We found that louder leading chirps were preferentially represented in the omega neuron but the representation of softer following chirps was not completely abolished. Following chirps that were 20 dB louder than leading chirps were better represented than leading chirps. During acoustic interactions, males synchronised with leading chirps even when the following chirps were 20 dB louder. Males did not restrict their attention to louder chirps during interactions but were affected by all chirps above a particular threshold. In the field, we found that males on average had only one or two neighbours whose calls were above this threshold. Selective attention is thus achieved in this bushcricket through spacing rather than neurophysiological filtering of softer signals.

Tool wear monitoring using ant behaviour

In this paper we show the applicability of Ant Colony Optimisation (ACO) techniques for pattern classification problem that arises in tool wear monitoring. In an earlier study, artificial neural networks and genetic programming have been successfully applied to tool wear monitoring problem. ACO is a recent addition to evolutionary computation technique that has gained attention for its ability to extract the underlying data relationships and express them in form of simple rules. Rules are extracted for data classification using training set of data points. These rules are then applied to set of data in the testing/validation set to obtain the classification accuracy. A major attraction in ACO based classification is the possibility of obtaining an expert system like rules that can be directly applied subsequently by the user in his/her application. The classification accuracy obtained in ACO based approach is as good as obtained in other biologically inspired techniques.