Parallel implementation of AutoDock

Computational docking of ligands to protein structures is a key step in structure-based drug design. Currently, the time required for each docking run is high and thus limits the use of docking in a high-throughput manner, warranting parallelization of docking algorithms. AutoDock, a widely used tool, has been chosen for parallelization. Near-linear increases in speed were observed with 96 processors, reducing the time required for docking ligands to HIV-protease from 81 min, as an example, on a single IBM Power-5 processor ( 1.65 GHz), to about 1 min on an IBM cluster, with 96 such processors. This implementation would make it feasible to perform virtual ligand screening using AutoDock.

The partition of unity finite element method for elastic wave propagation in Reissner-Mindlin plates

This paper reports a numerical method for modelling the elastic wave propagation in plates. The method is based on the partition of unity approach, in which the approximate spectral properties of the infinite dimensional system are embedded within the space of a conventional finite element method through a consistent technique of waveform enrichment. The technique is general, such that it can be applied to the Lagrangian family of finite elements with specific waveform enrichment schemes, depending on the dominant modes of wave propagation in the physical system. A four-noded element for the Reissner-indlin plate is derived in this paper, which is free of shear locking. Such a locking-free property is achieved by removing the transverse displacement degrees of freedom from the element nodal variables and by recovering the same through a line integral and a weak constraint in the frequency domain. As a result, the frequency-dependent stiffness matrix and the mass matrix are obtained, which capture the higher frequency response with even coarse meshes, accurately. The steps involved in the numerical implementation of such element are discussed in details. Numerical studies on the performance of the proposed element are reported by considering a number of cases, which show very good accuracy and low computational cost. Copyright (C)006 John Wiley & Sons, Ltd.

Semi-empirical procedures for estimation of residual velocity and ballistic limit for impact on mild steel plates by projectiles

This paper deals with the development of simplified semi-empirical relations for the prediction of residual velocities of small calibre projectiles impacting on mild steel target plates, normally or at an angle, and the ballistic limits for such plates. It has been shown, for several impact cases for which test results on perforation of mild steel plates are available, that most of the existing semi-empirical relations which are applicable only to normal projectile impact do not yield satisfactory estimations of residual velocity. Furthermore, it is difficult to quantify some of the empirical parameters present in these relations for a given problem. With an eye towards simplicity and ease of use, two new regression-based relations employing standard material parameters have been discussed here for predicting residual velocity and ballistic limit for both normal and oblique impact. The latter expressions differ in terms of usage of quasi-static or strain rate-dependent average plate material strength. Residual velocities yielded by the present semi-empirical models compare well with the experimental results. Additionally, ballistic limits from these relations show close correlation with the corresponding finite element-based predictions.

Influence of tilt angle of plate on friction and transfer layer—A study of aluminium pin sliding against steel plate

In the present investigation, unidirectional grinding marks were attained on the steel plates. Then aluminium (Al) pins were slid at 0.2°, 0.6°, 1.0°, 1.4°, 1.8°, 2.2° and 2.6° tilt angles of the plate with the grinding marks perpendicular and parallel to the sliding direction under both dry and lubricated conditions using a pin-on-plate inclined sliding tester to understand the influence of tilt angle and grinding marks direction of the plate on coefficient of friction and transfer layer formation. It was observed that the transfer layer formation and the coefficient of friction depend primarily on the grinding marks direction of the harder mating surface. Stick-slip phenomenon was observed only under lubricated conditions. For the case of pins slid perpendicular to the unidirectional grinding marks stick-slip phenomenon was observed for tilt angles exceeding 0.6°, the amplitude of which increases with increasing tilt angles. However, for the case of the pins slid parallel to the unidirectional grinding marks the stick-slip phenomena was observed for angles exceeding 2.2°, the amplitude of which also increases with increasing tilt angle. The presence of stick-slip phenomena under lubricated conditions could be attributed to the molecular deformation of the lubricant component confined between asperities.

Monoclinic polymorph of Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe(anhydrous). Parallel packing of 3(10)-/alpha-helices and a transition of helix type

The structures of two crystal forms of Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe have been determined. The triclinic form (P1, Z = 1) from DMSO/H2O crystallizes as a dihydrate (Karle, Sukumar & Balaram (1986) Proc, Natl, Acad. Sci. USA 83, 9284-9288). The monoclinic form (P2(1), Z = 2) crystallized from dioxane is anhydrous. The conformation of the peptide is essentially the same in both crystal system, but small changes in conformational angles are associated with a shift of the helix from a predominantly alpha-type to a predominantly 3(10)-type. The r.m.s. deviation of 33 atoms in the backbone and C beta positions of residues 2-8 is only 0.29 A between molecules in the two polymorphs. In both space groups, the helical molecules pack in a parallel fashion, rather than antiparallel. The only intermolecular hydrogen bonding is head-to-tail between helices. There are no lateral hydrogen bonds. In the P2(1) cell, a = 9.422(2) A, b = 36.392(11) A, c = 10.548(2) A, beta = 111.31(2) degrees and V = 3369.3 A for 2 molecules of C60H97N11O13 per cell.

Parallel and antiparallel aggregation of alpha-helices. Crystal structures of two apolar decapeptides X-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe (X = Boc, Ac)

An apolar helical decapeptide with different end groups, Boc- or Ac-, crystallizes in a completely parallel fashion for the Boc-analog and in an antiparallel fashion for the Ac-analog. In both crystals, the packing motif consists of rows of parallel molecules. In the Boc-crystals, adjacent rows assemble with the helix axes pointed in the same direction. In the Ac-crystals, adjacent rows assemble with the helix axes pointed in opposite directions. The conformations of the molecules in both crystals are quite similar, predominantly alpha-helical, except for the tryptophanyl side chain where chi 1 congruent to 60 degrees in the Boc- analog and congruent to 180 degrees in the Ac-analog. As a result, there is one lateral hydrogen bond between helices, N(1 epsilon)...O(7), in the Ac-analog. The structures do not provide a ready rationalization of packing preference in terms of side-chain interactions and do not support a major role for helix dipole interactions in determining helix orientation in crystals. The crystal parameters are as follow. Boc-analog: C60H97N11O13.C3H7OH, space group Pl with a = 10.250(3) A, b = 12.451(4) A, c = 15.077(6) A, alpha = 96.55(3) degrees, beta = 92.31(3) degrees, gamma = 106.37(3) degrees, Z = 1, R = 5.5% for 5581 data ([F] greater than 3.0 sigma(F)), resolution 0.89 A. Ac-analog: C57H91N11O12, space group P2(1) with a = 9.965(1) A, b = 19.707(3) A, c = 16.648(3) A, beta = 94.08(1), Z = 2, R = 7.2% for 2530 data ([F] greater than 3.0 sigma(F)), resolution 1.00 A.

BER-optimized linear parallel interference cancellers for multicarrier DS-CDMA systems

In this paper, we consider the design and bit-error performance analysis of linear parallel interference cancellers (LPIC) for multicarrier (MC) direct-sequence code division multiple access (DS-CDMA) systems. We propose an LPIC scheme where we estimate and cancel the multiple access interference (MAT) based on the soft decision outputs on individual subcarriers, and the interference cancelled outputs on different subcarriers are combined to form the final decision statistic. We scale the MAI estimate on individual subcarriers by a weight before cancellation. In order to choose these weights optimally, we derive exact closed-form expressions for the bit-error rate (BER) at the output of different stages of the LPIC, which we minimize to obtain the optimum weights for the different stages. In addition, using an alternate approach involving the characteristic function of the decision variable, we derive BER expressions for the weighted LPIC scheme, matched filter (MF) detector, decorrelating detector, and minimum mean square error (MMSE) detector for the considered multicarrier DS-CDMA system. We show that the proposed BER-optimized weighted LPIC scheme performs better than the MF detector and the conventional LPIC scheme (where the weights are taken to be unity), and close to the decorrelating and MMSE detectors.

Determination of the orthotropic plate parameters of stiffened plates and grillages in free vibration

It is well known that the analysis of vibration of orthogonally stiffened rectangular plates and grillages may be simplified by replacing the actual structure by an orthotropic plate. This needs a suitable determination of the four elastic rigidity constants Dx, Dy, Dxy, D1 and the mass {Mathematical expression} of the orthotropic plate. A method is developed here for determining these parameters in terms of the sectional properties of the original plate-stiffener combination or the system of interconnected beams. Results of experimental work conducted on aluminium plates agree well with the results of the theory developed here.

Large deflections of rectangular plates

Approximate solutions for the non-linear bending of thin rectangular plates are presented considering large deflections for various boundary conditions. In the case of stress-free edges, solutions are given for von Kármán's equations in terms of the stress function and the deflection of the plate. In the case of immovable edges, equations are constructed in terms of the three displacements and these are solved. The solution is given by using double series consisting of the appropriate Beam Functions which satisfy the boundary conditions. The differential equations are satisfied by using the orthogonality properties of the series. Numerical results for square plates with uniform lateral load indicate good convergence of the series solution presented here.

Thermal stresses in rectangular plates

A method of determining the thermal stresses in a flat rectangular isotropic plate of constant thickness with arbitrary temperature distribution in the plane of the plate and with no variation in temperature through the thickness is presented. The thermal stress have been obtained in terms of Fourier series and integrals that satisfy the differential equation and the boundary conditions. Several examples have been presented to show the application of the method.

Buckling of clamped skew plates

IN this Note, a condensed version of Ref. 1, only the results are presented. The available results for buckling of clamped skew plates are few and far from complete.2'3 In the present investigation, results for several new plate configurations and loading conditions as well as more accurate results for configurations reported in previous literature are obtained.In general, for a given a/b, the critical values increase with increasing skew angle. The results also confirm the conjecture of Ref. 4 that in the case of buckling under shear (Nxv)> "two critical values exist, the positive shear (one tending to reduce the skew angle) being numerically greater than the negative shear. However, reliable values for positive shear could not be obtained in Ref. 4 because of convergence difficulties.

Bending, vibration and buckling of simply supported thick orthotropic rectangular plates and laminates

This paper presents a unified exact analysis for the statics and dynamics of a class of thick laminates. A three-dimensional, linear, small deformation theory of elasticity solution is developed for the bending, vibration and buckling of simply supported thick orthotropic rectangular plates and laminates. All the nine elastic constants of orthotropy are taken into account. The solution is formally exact and leads to simple infinite series for stresses and displacements in flexure, forced vibration and "beam-column" type problems and to closed form characteristic equations for free vibration and buckling problems. For free vibration of plates, the present analysis yields a triply infinite spectrum of frequencies instead of only one doubly infinite spectrum by thin plate theory or three doubly infinite spectra by Reissner-Mindlin type analyses. Some numerical results are presented for plates and laminates. Comparison of results from thin plate, Reissner and Mindlin analyses with these yield some important conclusions regarding the validity and effects of the assumptions made in the approximate theories.

Vibration of rectangular orthotropic plates

An approximate analytical procedure has been given to solve the problem of a vibrating rectangular orthotropic plate, with various combinations of simply supported and clamped boundary conditions. Numerical results have been given for the case of a clamped square plate. Nomenclature 2a, 2b sides of the rectangular plate h plate thickness Eprime x , Eprime y , EPrime, G elastic constants of te orthotropic material D x Eprime x h 3/12 D y Eprime y h 3/12 H xy EPrimeh 3/12+Gh 3/6 D x , D y and H xy are rigidity constants of the orthotropic platergr mass of the plate per unit area ngr Poisson's ratio W deflection of the plate p circular frequency gamma b/a ratio X m , Y characteristic functions of the vibrating beam problem -lambda rgrp 2 a 2 b 2/H xy the frequency parameter.