Molecular Mechanics Studies of Homopolymeric and Mixed Sequence Py.Pu*Pu Triple Helices,

DNA triple helices containing two purine strands and one pyrimidine strand (C.G*G and T.A*A) have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that in the C.G*G case the structure with a parallel orientation of the third strand, resulting from Hoogsteen hydrogen bonds between the third strand and the Watson-Crick duplex, is energetically the most favourable while in the T.A*A case the antiparallel orientation of the third strand, resulting from reverse Hoogsteen hydrogen bonds, is energetically the most favourable. These studies when extended to the mixed sequence triplexes, in which the second strand is a mixture of G and A, correspondingly the third strand is a mixture of G and APT, show that though the parallel orientation is still energetically more favourable, the antiparallel orientation becomes energetically comparable with an increasing number of thymines in the third strand. Structurally, for the mixed triplexes containing G and T in the third strand, it is seen that the basepair non-isomorphism between the C.G*G and the T.A*T triplets can be overcome with some changes in the base pair parameters without much distortion of either the backbone or the hydrogen bonds.

Structural Polymorphism in d(T).d(A)*d(T) Triple Helices

DNA triple helices containing two thymine strands and one adenine strand have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that the structure with a parallel orientation of the third strand, in which the third strand base forms Hoogsteen hydrogen bonds with the adenine base in the Watson-Crick duplex, is energetically the most favourable. An antiparallel orientation of the third strand is also possible, in which the third strand base hydrogen bonds to both the bases in the Watson-Crick duplex. This structure is energetically comparable to the parallel structure. For the parallel triplex a 200ps molecular dynamics simulation starting from two different starting structures indicates that at 300K significant structural heterogeneity exists in this tripler structure. The results are compared with existing structural data on this class of triplexes derived from theoretical and NMR techniques.

(2E)-3-(4-Ethoxyphenyl)-1-(2-methyl-4-phenylquinolin-3-yl)prop-2-en-1-on e monohydrate

The title hydrate, C27H23NO2 center dot H2O, features an almost planar quinoline residue (r.m.s. deviation = 0.015 angstrom) with the benzene dihedral angle = 63.80 (7)degrees] and chalcone C-C-C-O torsion angle = -103.38 (18)degrees] substituents twisted significantly out of its plane. The configuration about the C=C bond 1.340 (2) angstrom] is E. In the crystal, molecules related by the 21 symmetry operation are linked along the b axis via water molecules that form O-H center dot center dot center dot O-c and O-H center dot center dot center dot N-q hydrogen bonds (c = carbonyl and q = quinoline). A C-H center dot center dot center dot O interaction also occurs.

A parity-violatingU4-gravitation theory

The general structure of a metric-torsion theory of gravitation allows a parity-violating contribution to the complete action which is linear in the curvature tensor and vanishes identically in the absence of torsion. The resulting action involves, apart from the constant ¯K E =8pgr/c4, a coupling (B) which governs the strength of the parity interaction mediated by torsion. In this model the Brans-Dicke scalar field generates the torsion field, even though it has zero spin. The interesting consequence of the theory is that its results for the solar-system differ very little from those obtained from Brans-Dicke (BD) theory. Therefore the theory is indistinguishable from BD theory in solar-system experiments.

Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes

Different modes of binding of pyrimidine monophosphates 2'-UMP, 3'-UMP, 2'-CMP and 3'-CMP to ribonuclease (RNase) A are studied by energy minimization in torsion angle and subsequently in Cartesian coordinate space. The results are analysed in the light of primary binding sites. The hydrogen bonding pattern brings out roles for amino acids such as Asn44 and Ser123 apart from the well known active site residues viz., His12,Lys41,Thr45 and His119. Amino acid segments 43-45 and 119-121 seem to be guiding the ligand binding by forming a pocket. Many of the active site charged residues display considerable movement upon nucleotide binding.

1H NMR Study of Molecular Motions and Phase Transitions in Methyl Ammonium Hexabromo Selenate [(CH3NH3)2SeBr6]

The temperature dependence of 1H spin-lattice relaxation time, T1, and that of the second moment, M2, are analysed in the temperature range 390 K to 77 K. A plot of T1 vs inverse temperature shows three phase transitions at 250 K, 167 K and 111 K. At 167 K, T1 displays a large jump while it shows changes in slope at 250 K and 111 K. In the high temperature phase (> 167 K), the correlated motion of CH3 and NH3 groups is found to cause the relaxation while their uncorrelated motion takes over in the low temperature phases (< 167 K). The unusual T1 behaviour in phase II (250 K-167 K) is ascribed to the small angle torsion of the cation. A constant M2 value of ∼ 9.7 G2, throughout the range of temperature studied, indicates the presence of reorientation of CH3 and NH3 groups.

Processing map for hot working of stainless steel type AISI 316L

Processing and instability maps using a dynamic materials model have been developed for stainless steel type AISI 316L in the temperature range 600-1250-degrees-C and strain rate range 0.001-100 s-1 with a view to optimising its hot workability. Stainless steel type AISI 316L undergoes dynamic recrystallisation, with a peak efficiency of 35% at 1250-degrees-C and 0.05 s-1, which are the optimum parameters for hot working this material. The material undergoes dynamic recovery at 900-degrees-C and 0.001 s-1. The increase in the dynamic recrystallisation and dynamic recovery temperatures in comparison with stainless steel type AISI 304L is attributed to the presence of a backstress caused by the molybdenum additions. These results are in general agreement with those reported elsewhere on stainless steel type 316 deformed in hot extrusion and hot torsion. At temperatures < 850-degrees-C and strain rates > 10 s-1, the material exhibits flow localisation owing to adiabatic shear band formation, whereas at higher temperatures (> 850-degrees-C) and strain rates (> 10 s-1) mechanical twinning and wavy slip bands are observed. (C) 1993 The Institute of Materials.

Anomalin. A Dihydropyranocoumarin Derivative from the Plant Lingusticum elatum

The title compound, 9,10-dihydro-8,8-dimethyl-2-oxo-2H,8H-benzo[1,2-b:3,4-b']dipyran-9,10-diyl 2-methyl-2-butenoate, C24H26O7, contains a highly planar coumarin nucleus and a substituted dihydropyran ring (C), which has a distorted half-chair conformation, with an 8 alpha,9 beta orientation. The conformation of ring C is further supported by the two angelyloxy (2-methyl-2-butenoyloxy) substituents at positions C9 and C10, which are cis oriented and thus cannot both occupy equatorial positions with respect to the plane of ring C. The conformations of the two angelyloxy substituents are different, as indicated by their endocyclic torsion angles. The most striking of these angles are O1'-C2'-C4'=C6' and O1'-C2'-C4'-C5' [-137.7 (5) and 43.7 (5)degrees, respectively, in the chain at C10 and 155.8 (5) and -24.7 (9)degrees, respectively in the chain at C9]. These variations are due to two intramolecular hydrogen bonds, namely, C16-H161 ... O1' [C16 ... O1' 3.056 (7) Angstrom] and C7''-H7Y ... O3'' [C7'' ... O3'' 2.955 (12) Angstrom]. The methyl substituents, C15 and C16, at position C8 are alpha and beta oriented, respectively. The crystal structure is stabilized by a weak C4-H41 ... O3' hydrogen bond [C4 ... O3' 3.297 (6) Angstrom] between the screw-related molecules.

Molecular dynamics studies on nucleoside 2',3'-cyclic phosphates

2',3'-cyclic nucleotides are intermediates and substrates of Ribonuclease (RNase)-catalysed reactions. The characterization of the equilibrium conformation as well as the flexibility inherent in these molecules helps in understanding the enzymatic action of RNases. The present study explores parameters like phase angle, glycosydic torsion angle and hydrogen bond to find possible interrelationship between them through Molecular Dynamics (MD) simulations on 3'-GMP, 3'-UMP, A>p, G>p, U>p, C>p, GpA>p and UpA>p. Interesting results of the effect of cyclisation and other constraints such as hydrogen bond between certain groups on the equilibrium ribose conformation have emerged from this study.

Influence of strain rate and state-of-stress on the formation of ferrite in stainless steel type AISI 304 during hot working

The influence of strain rate and state-of-stress on the formation of ferrite in stainless steel type AISI 304L, 304 and 304 as-cast, during hot working has been studied. Compression and torsion tests were conducted in the temperature range 1100 to 1250 degrees C and strain rate range 0.001 to 100 s(-1) on these materials, Ferrite formation occurs during deformation at temperatures above 1150 degrees C and strain rates above 10 s(-1), in stainless steel type AISI 304L and 304. The tendency for the formation of ferrite is more in as-cast 304 than in wrought 304, In as-cast 304 the ferrite forms at lower temperatures and strain rates, The tendency for the ferrite formation is more in torsion than in compression.

Generation of an eight node brick element using Papcovitch-Neuber functions

Some conventional finite elements suffer from drawbacks, such as shear locking, membrane locking, etc. To overcome them researchers have developed various techniques, termed as tricks by some and variational crimes by others. Many attempts have been made, but satisfactory explanations for why some of these techniques work have not been obtained, especially in the case of solid elements. This paper attempts a simple non-conforming solid element using assumed displacement fields which satisfy the Navier equation exactly. Its behaviour under simple loadings like bending, torsion and tension is examined and comparisons are made with existing elements.

Stochastic Aeroelastic Analysis of Composite Helicopter Rotor

The effect of uncertainty in composite material properties on the aeroelastic response, vibratory loads, and stability of a hingeless helicopter rotor is investigated. The uncertainty impact on rotating natural frequencies of the blade is studied with Monte Carlo simulations and first-order reliability methods. The stochastic aeroelastic analyses in hover and forward flight are carried out with Monte Carlo simulations. The flap, lag, and torsion responses show considerable scatter from their baseline values, and the uncertainty impact varies with the azimuth angle. Furthermore, the blade response shows finite probability of resonance-type conditions caused by modal frequencies approaching multiples of the rotor speed. The 4/rev vibratory forces show large deviations from their baseline values. The lag mode damping shows considerable scatter due to uncertain material properties with an almost 40% probability of instability in hover.

Health monitoring,of a helicopter rotor in forward flight using fuzzy logic

A fuzzy logic system is developed for helicopter rotor system fault isolation. Inputs to the fuzzy logic system are measurement deviations of blade bending and torsion response and vibration from a "good" undamaged helicopter rotor. The rotor system measurements used are flap and lag bending tip deflections, elastic twist deflection at the tip, and three forces and three moments at the rotor hub. The fuzzy logic system uses rules developed from an aeroelastic model of the helicopter rotor with implanted faults to isolate the fault while accounting for uncertainty in the measurements. The faults modeled include moisture absorption, loss of trim mass, damaged lag damper, damaged pitch control system, misadjusted pitch link, and damaged flap. Tests with simulated data show that the fuzzy system isolates rotor system faults with an accuracy of about 90-100%. Furthermore, the fuzzy system is robust and gives excellent results, even when some measurements are not available. A rule-based expert system based on similar rules from the aeroelastic model performs much more poorly than the fuzzy system in the presence of high levels of uncertainty.

On the importance of backbone loop and peptide flip in the Walker sequence in F-1-ATPase action

The Walker sequence, GXXXXGKT, present in all the six subunits of F-1-ATPase exists in a folded form, known as phosphate-binding loop (P-loop). Analysis of the Ramachandran angles showed only small RMS deviation between the nucleotide-bound and nucleotide-free forms. This indicated a good overlap of the backbone loops. The catalytic beta-subunits (chains D, E and F) showed significant changes in the Ramachandran angles and the side chain torsion angles, but not the structural alpha-subunits (chains A, B and C). Most striking among these are the changes associated with Val160 and Gly161 corresponding to a flip in the peptide unit between them when a nucleotide is bound (chains D or F compared to nucleotide-free chain E). The conformational analysis further revealed a hitherto unnoticed hydrogen bond between amide-N of the flipped Gly161 and terminal phosphate-O of the nucleotide. This assigns a role for this conserved amino acid, otherwise ignored, of making an unusual direct interaction between the peptide backbone of the enzyme protein and the incoming nucleotide substrate. Significance of this interaction is enhanced, as it is limited only to the catalytic subunits, and also likely to involve a mechanical rotation of bonds of the peptide unit. Hopefully this is part of the overall events that link the chemical hydrolysis of ATP with the mechanical rotation of this molecule, now famous as tiny molecular motor.

Optimum design of a helicopter rotor for low vibration using aeroelastic analysis and response surface methods

An aeroelastic analysis based on finite elements in space and time is used to model the helicopter rotor in forward flight. The rotor blade is represented as an elastic cantilever beam undergoing flap and lag bending, elastic torsion and axial deformations. The objective of the improved design is to reduce vibratory loads at the rotor hub that are the main source of helicopter vibration. Constraints are imposed on aeroelastic stability, and move limits are imposed on the blade elastic stiffness design variables. Using the aeroelastic analysis, response surface approximations are constructed for the objective function (vibratory hub loads). It is found that second order polynomial response surfaces constructed using the central composite design of the theory of design of experiments adequately represents the aeroelastic model in the vicinity of the baseline design. Optimization results show a reduction in the objective function of about 30 per cent. A key accomplishment of this paper is the decoupling of the analysis problem and the optimization problems using response surface methods, which should encourage the use of optimization methods by the helicopter industry. (C) 2002 Elsevier Science Ltd. All rights reserved.