Sequence-Structure Similarity: Do Sequentially Identical Peptide Fragments have Similar Three-Dimensional Structures?

The rapidly growing structure databases enhance the probability of finding identical sequences sharing structural similarity. Structure prediction methods are being used extensively to abridge the gap between known protein sequences and the solved structures which is essential to understand its specific biochemical and cellular functions. In this work, we plan to study the ambiguity between sequence-structure relationships and examine if sequentially identical peptide fragments adopt similar three-dimensional structures. Fragments of varying lengths (five to ten residues) were used to observe the behavior of sequence and its three-dimensional structures. The STAMP program was used to superpose the three-dimensional structures and the two parameters (Sequence Structure Similarity Score (Sc) and Root Mean Square Deviation value) were employed to classify them into three categories: similar, intermediate and dissimilar structures. Furthermore, the same approach was carried out on all the three-dimensional protein structures solved in the two organisms, Mycobacterium tuberculosis and Plasmodium falciparum to validate our results.

Two Novel Heterometallic Chains Featuring Mn-II and Na-I Ions in Trigonal-Prismatic Geometries Alternately Linked to Octahedral Mn-IV Ions: Synthesis, Structures, and Magnetic Behavior

Two new one-dimensional heterometallic complexes, Mn3Na(L)(4)(CH3CO2)(MeOH)(2)]-(ClO4)(2)center dot 3H(2)O (1), Mn3Na(L)(4)(CH3CH2CO2)-(MeOH)(2)](ClO4)(2)center dot 2MeOH center dot H2O (2) LH2 = 2-methyl-2-(2-pyridyl)propane-1,3-diol], have been synthesized and characterized by X-ray crystallography. Both complexes feature Mn-II and Na-I ions in trigonal-prismatic geometries that are linked to octahedral Mn-IV ions by alkoxy bridges. Variable-temperature direct- and alternating-current magnetic susceptibility data indicated a spin ground state of S = 11/2 for both complexes. Density functional theory calculations performed on 1 supported this conclusion.

Mixed-ligand aroylhydrazone complexes of molybdenum: Synthesis, structure and biological activity

The reaction of the benzoylhydrazone of 2-hydroxybenzaldehyde (H2L) with MoO2(acac)(2)] proceeds smoothly in refluxing ethanol to afford an orange complex MoO2L(C2H5OH)] (1). The substrate binding capacity of 1 has been demonstrated by the formation and isolation of two mononuclear MoO2L(Q)] {where Q = imidazole (2a) and 1-methylimidazole (2b)} and one dinuclear (MoO2L)(2)(Q)] {Q = 4,4'-bipyridine (3)} mixed-ligand oxomolybdenum complex. All the complexes have been characterized by elemental analysis, magnetic and spectroscopic (IR, UV-Vis and NMR) measurements. The molecular structures of all the oxomolybdenum(VI) complexes (1, 2a, 2b and 3) have been determined by X-ray crystallography. In each complex, the dianionic planar ligand is coordinated to the metal centre via one enolate oxygen, one phenolate oxygen and an azomethine nitrogen atom. The complexes have been screened for their antibacterial activity against Escherichia coli, Bacillus and Pseudomonas aeruginosa. The minimum inhibitory concentration of these complexes and their antibacterial activity indicates that compounds 2a and 2b are potential lead molecules for drug designing. (C) 2012 Elsevier Ltd. All rights reserved.

Guided-wave based structural health monitoring of built-up composite structures using spectral finite element method

The paper discusses basically a wave propagation based method for identifying the damage due to skin-stiffener debonding in a stiffened structure. First, a spectral finite element model (SFEM) is developed for modeling wave propagation in general built-up structures, using the concept of assembling 2D spectral plate elements and the model is then used in modeling wave propagation in a skin-stiffener type structure. The damage force indicator (DFI) technique, which is derived from the dynamic stiffness matrix of the healthy stiffened structure (obtained from the SFEM model) along with the nodal displacements of the debonded stiffened structure (obtained from 2D finite element model), is used to identify the damage due to the presence of debond in a stiffened structure.

Tunable device properties of free-standing inorganic/organic flexible hybrid structures obtained by exfoliation

We report the fabrication of free-standing flexible inorganic/organic hybrid structures by exfoliating ZnO nanostructured films from the flat indium tin oxide (ITO)/silicon/sapphire substrates using poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS). Strong interaction between ZnO and PEDOT: PSS and the thermomechanical response of PEDOT: PSS are the key issues for the exfoliation to prevail. The performance of the free-standing hybrid structures as rectifiers and photodetectors is better as compared to ITO supported hybrid structures. It is also shown that device properties of hybrid structures can be tuned by using different electrode materials. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4729550]

Damage-tolerant design optimization of laminated composite structures using dispersion of ply angles by genetic algorithm

This article aims to obtain damage-tolerant designs with minimum weight for a laminated composite structure using genetic algorithm. Damage tolerance due to impacts in a laminated composite structure is enhanced by dispersing the plies such that too many adjacent plies do not have the same angle. Weight of the structure is minimized and the Tsai-Wu failure criterion is considered for the safe design. Design variables considered are the number of plies and ply orientation. The influence of dispersed ply angles on the weight of the structure for a given loading conditions is studied by varying the angles in the range of 0 degrees-45 degrees, 0 degrees-60 degrees and 0 degrees-90 degrees at intervals of 5 degrees and by using specific ply angles tailored to loading conditions. A comparison study is carried out between the conventional stacking sequence and the stacking sequence with dispersed ply angles for damage-tolerant weight minimization and some useful designs are obtained. Unconventional stacking sequence is more damage tolerant than the conventional stacking sequence is demonstrated by performing a finite element analysis under both tensile as well as compressive loading conditions. Moreover, a new mathematical function called the dispersion function is proposed to measure the dispersion of ply angles in a laminate. The approach for dispersing ply angles to achieve damage tolerance is especially suited for composite material design space which has multiple local minima.

Stabilization of O-Mn-O clusters (Mn-5) in three dimensionally extended MOF structures: synthesis, structure and properties

Four new three-dimensional Mn2+ ion-containing compounds have been prepared by employing a hydrothermal reaction between Mn(CH3COO)(2)center dot 4H(2)O, sulfodibenzoic acid (H(2)SDBA), imidazole, alkali hydroxide and water at 220 degrees C for 1 day. The compounds have Mn-5 (1-4) clusters connected by SDBA, forming the three-dimensional structure. A time and temperature dependent study on the synthesis mixture revealed the formation of a one-dimensional compound, Mn(SDBA)(H2O)(2), at lower temperatures (T <= 180 degrees C). The stabilization of the fcu related topology in the compounds is noteworthy. Magnetic studies indicate strong anti-ferromagnetic interactions between the Mn2+ ions within the clusters in the temperature range 75-300 K. The rare participation of a sulfonyl group in the bonding is important and can pave way for the design of new structures.

Radiative and non-radiative effects of a substrate on localized plasmon resonance of particles

Experiments have shown strong effects of some substrates on the localized plasmons of metallic nano particles but they are inconclusive on the affecting parameters. Here, we have used discrete dipole approximation in conjunction with Sommerfeld integral relations to explain the effect of the substrates as a function of the parameters of incident radiation. The radiative coupling can both quench and enhance the resonance and its dependence on the angle and polarization of incident radiation with respect to the surface is shown. Non-radiative interaction with the substrate enhances the plasmon resonance of the particles and can shift the resonances from their free-space energies significantly. The non-radiative interaction of the substrate is sensitive to the shape of particles and polarization of incident radiation with respect to substrate. Our results show that the plasmon resonances in coupled and single particles can be significantly altered from their free-space resonances and are quenched or enhanced by the choice of substrate and polarization of incident radiation. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4736544]

Structural landscape of benzoic acid: using experimental crystal structures of fluorobenzoic acids as a probe

Experimental crystal structures of mono and polyfluorinated benzoic acids correspond to high energy computed crystal structures of benzoic acid itself, thereby permitting access to its structural landscape.

Polymer thin film structures for ultra-low cost biosensing

Reflectance change due to binding of molecules on thin film structures has been exploited for bio-molecular sensing by several groups due to its potential in the development of sensitive, low cost, easy to fabricate, large area sensors with high multiplexing capabilities. However, all of these sensing platforms have been developed using traditional semiconductor materials and processing techniques, which are expensive. This article presents a method to fabricate disposable thin film reflectance biosensors using polymers, such as polycarbonate, which are 2-3 orders of magnitude cheaper than conventional semiconductor and dielectric materials and can be processed by alternate low cost methods, leading to significant reduction in consumable costs associated with diagnostic biosensing. (C) 2011 Elsevier GmbH. All rights reserved.

Conservative Failure Criteria for Optimal Design of Composite Structures Including Effect of Shear Loading

A minimum weight design of laminated composite structures is carried out for different loading conditions and failure criteria using genetic algorithm. The phenomenological maximum stress (MS) and Tsai-Wu (TW) criteria and the micro-mechanism-based failure mechanism based (FMB) failure criteria are considered. A new failure envelope called the Most Conservative Failure Envelope (MCFE) is proposed by combining the three failure envelopes based on the lowest absolute values of the strengths predicted. The effect of shear loading on the MCFE is investigated. The interaction between the loading conditions, failure criteria, and strength-based optimal design is brought out.

Nonlinear dynamic state estimation in instrumented structures with conditionally linear Gaussian substructures

Many problems of state estimation in structural dynamics permit a partitioning of system states into nonlinear and conditionally linear substructures. This enables a part of the problem to be solved exactly, using the Kalman filter, and the remainder using Monte Carlo simulations. The present study develops an algorithm that combines sequential importance sampling based particle filtering with Kalman filtering to a fairly general form of process equations and demonstrates the application of a substructuring scheme to problems of hidden state estimation in structures with local nonlinearities, response sensitivity model updating in nonlinear systems, and characterization of residual displacements in instrumented inelastic structures. The paper also theoretically demonstrates that the sampling variance associated with the substructuring scheme used does not exceed the sampling variance corresponding to the Monte Carlo filtering without substructuring. (C) 2012 Elsevier Ltd. All rights reserved.

Interplay of localized and itinerant character of Ru ions: Tl2Ru2O7 versus Hg2Ru2O7

We carry out a comparative study of the electronic structure of two pyrochlore ruthenate compounds, Tl2Ru2O7 and Hg2Ru2O7, in terms of first principles calculations. Our study reveals the Ru d electrons in Hg2Ru2O7 to be much more delocalized compared to that in Tl2Ru2O7. The subtle change in the Ru-d bandwidths in the two compounds, triggered by the differences in Hg 5d-Ru 4d hybridization compared to that of Tl 5d-Ru 4d, bring in the observed differences in behavior. Our study further shows that the development of long range noncollinear antiferromagnetic structure at low temperature is sufficient to produce the insulating solution in Hg2Ru2O7, in line with the prediction from recent nuclear magnetic resonance study.

Synthesis of zinc oxide porous structures by anodization with water as an electrolyte

We report a simple, reliable and one-step method of synthesizing ZnO porous structures at room temperature by anodization of zinc (Zn) sheet with water as an electrolyte and graphite as a counter electrode. We observed that the de-ionized (DI) water used in the experiment is slightly acidic (pH=5.8), which is due to the dissolution of carbon dioxide from the atmosphere forming carbonic acid. Porous ZnO is characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy and photoluminescence (PL) studies. The current-transient measurement is carried out using a Gamry Instruments Reference 3000 and the thickness of the deposited films is measured using a Dektak surface profilometer. The PL, Raman and X-ray photoelectron spectroscopy are used to confirm the presence of ZnO phase. We have demonstrated that the hybrid structures of ZnO and poly (3,4-ethylenedioxythiophene):poly (styrene sulfonate) (PEDOT:PSS) exhibit good rectifying characteristics. The evaluated barrier height and the ideality factor are 0.45 eV and 3.6, respectively.