Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral twofold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon =g(-), xi =t) B-II conformation at the 10(th) position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures

Insights into conformational and packing features in a series of aryl substituted ethyl-6-methyl-4-phenyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate

The supramolecular structures of eight aryl protected ethyl-6-methyl-4-phenyl-2-oxo-1,2,3,4-tetrahydropyrimidine- 5-carboxylates have been analyzed to determine the role of different functional groups on the molecular geometry, conformational characteristics and the packing of these molecules in the crystal lattice. Out of these the para fluoro substituted compound on the aryl ring exhibits conformational polymorphism, due to the different conformation of the ester moiety. This behaviour has been characterized using both powder and single-crystal X-ray diffraction, optical microscopy and differential scanning calorimetry performed on both these polymorphs. The compounds pack via the cooperative interplay of strong N-H center dot center dot center dot O=C intermolecular dimers and chains forming a sheet like structure. In addition, weak C-H center dot center dot center dot O=C and C-H center dot center dot center dot pi interactions impart additional stability to the crystal packing.

Training-Symbol Embedded, High-Rate Complex Orthogonal Designs for Relay Networks

Distributed Space-Time Block Codes (DSTBCs) from Complex Orthogonal Designs (CODs) (both square and non-square CODs other than the Alamouti design) are known to lose their single-symbol ML decodable (SSD) property when used in two-hop wireless relay networks using the amplify and forward protocol. For such a network, a new class of high rate, training-symbol embedded (TSE) SSD DSTBCs are proposed from TSE-CODs. The constructed codes include the training symbols within the structure of the code which is shown to be the key point to obtain high rate along with the SSD property. TSE-CODs are shown to offer full-diversity for arbitrary complex constellations. Non-square TSE-CODs are shown to provide better rates (in symbols per channel use) compared to the known SSD DSTBCs for relay networks when the number of relays is less than 10. Importantly, the proposed DSTBCs do not contain zeros in their codewords and as a result, antennas of the relay nodes do not undergo a sequence of switch on and off transitions within every codeword use. Hence, the proposed DSTBCs eliminate the antenna switching problem.

Code Generation Paradigms On Optical Orthogonal And Other Codes In a Fiber Optic CDMA Lan

Code Division Multiple Access (CDMA) techniques, by far, had been applied to LAN problems by many investigators, An analytical study of well known algorithms for generation of Orthogonal codes used in FO-CDMA systems like those for prime, quasi-Prime, Optical Orthogonal and Matrix codes has been presented, Algorithms for OOCs like Greedy/Modified Greedy/Accelerated Greedy algorithms are implemented. Many speed-up enhancements. for these algorithms are suggested. A novel Synthetic Algorithm based on Difference Sets (SADS) is also proposed. Investigations are made to vectorise/parallelise SADS to implement the source code on parallel machines. A new matrix for code families of OOCs with different seed code-words but having the same (n,w,lambda) set is formulated.

Studies in crystal engineering: Effect of fluorine substitution in crystal packing and topological photodimerization of styryl coumarins in the solid state

Styryl coumarins generally yield centrosymmetric (alpha-mode, anti-HT) photodimers when subjected to irradiation in the solid state, However, the substitution of fluorine dramatically alters the packing mode and steers the molecules 4-(4-fluorostyryl)coumarin 1 and 4-(2-fluorostyryl)coumarin 2 to form a stereospecific photodimer, beta-mode, syn-HH across the styrenic double bond (yield 78-85%). The stereochemistry of the photodimer 2a has been established by X-ray crystallography. There is no evidence for the presence of C-H ... F interactions. The true nature of the weak atom-atom interactions called into play when fluorine is substituted is not clear, It is observed that the fluoro substituted compounds have greater crystal density than the corresponding unsubstituted ones.

Solid-state photobehaviour and crystal packing of o-chlorobenzylidene-DL-piperitone: influence of molecular topology on photobehaviour

C17H19ClO, M(r) = 274.7, triclinic, P1BAR, a = 11.154 (3), b = 12.685 (2), c = 12.713 (2) angstrom, alpha = 100.68 (1), beta = 113.58 (1), gamma = 104.50 (2)-degrees, V = 1511.1 (6) angstrom3, Z = 4, D(m) = 1.22, D(x) = 1.215 Mg m-3, Cu K-alpha, lambda = 1.5418 angstrom, mu = 2.16 mm-1, F(000) = 584, T = 293 K, R = 0.057 for 3481 observed reflections. The title compound is photostable in the crystalline state and lattice-energy calculations have been employed to rationalize the photobehaviour. The well-known beta-steering ability of the chloro group is not operative in this system as there are no Cl...Cl interactions in the crystal lattice. All five benzylidene-DL-piperitone structures so far studied are alpha-packed and the molecular topology appears to be a deciding factor even in the presence of steering groups.

Studies in crystal engineering: Crystal packing, topological photodimerization and structure-reactivity correlations in fluoro-substituted styrylcoumarins

In continuation of our studies on the influence of fluoro substitution on the solid state photobehaviour and packing pattern of styrylcoumarins, the results obtained for 4-(3-fluorostyryl)coumarin 1, 4-styryl-6-fluorocoumarin 2 and 4-styryl-7-fluorocoumarin 3 are presented. The configuration of the dimers was established on the basis of crystal packing of 1 and 2 (alpha-packed). A rationale for the significantly lower dimer yield in the crystal for 2 is proposed. In the observed centrosymmetric arrangement of the reactants the C=O ...pi (phenyl) contacts seem to provide additional attractive interactions. C-H ... O and C-H ... F hydrogen bonding seems to provide stability in these structures.

The Equations of Equilibrium in Orthogonal Curvilinear Reference Coordinates

Analytical solutions to problems in finite elasticity are most often derived using the semi-inverse approach along with the spatial form of the equations of motion involving the Cauchy stress tensor. This procedure is somewhat indirect since the spatial equations involve derivatives with respect to spatial coordinates while the unknown functions are in terms of material coordinates, thus necessitating the use of the chain rule. In this classroom note, we derive compact expressions for the components of the divergence, with respect to orthogonal material coordinates, of the first Piola-Kirchhoff stress tensor. The spatial coordinate system is also assumed to be an orthogonal curvilinear one, although, not necessarily of the same type as the material coordinate system. We show by means of some example applications how analytical solutions can be derived more directly using the derived results.

Wavelength/Time orthogonal codes with FEC offer dual advantage

To meet the growing demands of the high data rate applications, suitable asynchronous schemes such as Fiber-Optic Code Division Multiple Access (FO-CDMA) are required in the last mile. FO-CDMA scheme offers potential benefits and at the same time it faces many challenges. Wavelength/Time (W/T) 2-D codes for use in FO-CDMA, can be classified mainly into two types: 1) hybrid codes and 2) matrix codes, to reduce the 'time' like property, have been proposed. W/T single-pulse-per-row (SPR) are energy efficient codes as this family of codes have autocorrelation sidelobes of '0', which is unique to this family and the important feature of the W/T multiple-pulses-per-row (MPR) codes is that the aspect ratio can be varied by trade off between wavelength and temporal lengths. These W/T codes have improved cardinality and spectral efficiency over other W/T codes and at the same time have lowest crosscorrelation values. In this paper, we analyze the performances of the FO-CDMA networks using W/T SPR codes and W/T MPR codes, with and without forward error correction (FEC) coding and show that with FEC there is dual advantage of error correction and reduced spread sequence length.

Quasi-Orthogonal Design and Performance Analysis of Amplify-And-Forward Relay Networks with Multiple-Antennas

This paper is on the design and performance analysis of practical distributed space-time codes for wireless relay networks with multiple antennas terminals. The amplify-andforward scheme is used in a way that each relay transmits a scaled version of the linear combination of the received symbols. We propose distributed generalized quasi-orthogonal space-time codes which are distributed among the source antennas and relays, and valid for any number of relays. Assuming M-PSK and M-QAM signals, we derive a formula for the symbol error probability of the investigated scheme over Rayleigh fading channels. For sufficiently large SNR, this paper derives closed-form average SER expression. The simplicity of the asymptotic results provides valuable insights into the performance of cooperative networks and suggests means of optimizing them. Our analytical results have been confirmed by simulation results, using full-rate full-diversity distributed codes.

Effect of packing density and adsorption parameters on the throughput of a thermal compressor

Vapour adsorption refrigeration systems (VAdS) have the advantage of scalability over a wide range of capacities ranging from a few watts to several kilowatts. In the first instance, the design of a system requires the characteristics of the adsorbate-adsorbent pair. Invariably, the void volume in the adsorbent reduces the throughput of the thermal compressor in a manner similar to the clearance volume in a reciprocating compressor. This paper presents a study of the activated carbon +HFC-134a (1,1,1,2-tetrafluoroethane) system as a possible pair for a typical refrigeration application. The aim of this study is to unfold the nexus between the adsorption parameters, achievable packing densities of charcoal and throughput of a thermal compressor. It is shown that for a thermal compressor, the adsorbent should not only have a high surface area, but should also be able to provide a high packing density. Given the adsorption characteristics of an adsorbent-adsorbate pair and the operating conditions, this paper discloses a method for the calculation of the minimum packing density necessary for an effective throughput of a thermal compressor. (C) 2002 Elsevier Science Ltd. All rights reserved.

Twisted aromatics, 9-anthryl and 1-pyrenyl terpyridines organize into novel multi-directional 'ladder-like' motifs in the solid state

9-Anthryl and 1-pyrenyl terpyridines (1 and 2, respectively), key precursors for the design of novel fluorescent sensors have been synthesized and characterized by H-1 NMR, mass spectroscopy and X-ray crystallography. Twisted molecular conformations for each 1 and 2 were observed in their single crystal structures. Energy minimization calculations for the 1 and 2 using the semi-empirical AM1 method show that the 'twisted' conformation is intrinsic to these systems. We observe interconnected networks of edge-to-face CH...pi interactions, which appear to be cooperative in nature, in each of the crystal structures. The two twisted molecules, although having differently shaped polyaromatic hydrocarbon substituents, show similar patterns of edge-to-face CH...pi interactions.The presently described systems comprise of two aromatic surfaces that are almost orthogonal to each other. This twisted or orthogonal nature of the molecules leads to the formation of interesting multi-directional ladder like supramolecular organizations. A combination of edge-to-face and face-to-face packing modes helps to stabilize these motifs. The ladder like architecture in 1 is helical in nature. (C) 2002 Published by Elsevier Science B.V.

Channel Precoding for STBCs from Generalized Pseudo Orthogonal Designs

Statistical information about the wireless channel can be used at the transmitter side to enhance the performance of MIMO systems. This paper addresses how the concept of channel precoding can be used to enhance the performance of STBCs from Generalized Pseudo Orthogonal Designs which were first introduced by Zhu and Jafarkhani. Such designs include some important classes of STBCs that are directly derivable from Quasi-Orthogonal Designs and Co-ordinate Interleaved Orthogonal Designs.

Optimality of orthogonal sequences with multi-dimensional signaling

The sum capacity on a symbol-synchronous CDMA system having processing gain N and supporting K power constrained users is achieved by employing any set of N orthogonal sequences if a few users are allowed to signal along multiple dimensions. Analogously, the minimum received power (energy-per-chip) on the symbolsynchronous CDMA system supporting K users that demand specified data rates is attained by employing any set of N orthogonal sequences. At most (N - 1) users need to be split and if there are no oversized users, these split users need to signal only in two dimensions each. These results show that sum capacity or minimum sum power can be achieved with minimal downlink signaling.