Network, nodes and nexus: systems approach to multitarget therapeutics

Systems biology is revealing multiple layers of regulatory networks that manifest spatiotemporal variations. Since genes and environment also influence the emergent property of a cell, the biological output requires dynamic understanding of various molecular circuitries. The metabolic networks continually adapt and evolve to cope with the changing milieu of the system, which could also include infection by another organism. Such perturbations of the functional networks can result in disease phenotypes, for instance tuberculosis and cancer. In order to develop effective therapeutics, it is important to determine the disease progression profiles of complex disorders that can reveal dynamic aspects and to develop mutitarget systemic therapies that can help overcome pathway adaptations and redundancy.

Physics and chemistry of CdTe/CdS thin film heterojunction photovoltaic devices: fundamental and critical aspects

Among the armoury of photovoltaic materials, thin film heterojunction photovoltaics continue to be a promising candidate for solar energy conversion delivering a vast scope in terms of device design and fabrication. Their production does not require expensive semiconductor substrates and high temperature device processing, which allows reduced cost per unit area while maintaining reasonable efficiency. In this regard, superstrate CdTe/CdS solar cells are extensively investigated because of their suitable bandgap alignments, cost effective methods of production at large scales and stability against proton/electron irradiation. The conversion efficiencies in the range of 6-20% are achieved by structuring the device by varying the absorber/window layer thickness, junction activation/annealing steps, with more suitable front/back contacts, preparation techniques, doping with foreign ions, etc. This review focuses on fundamental and critical aspects like: (a) choice of CdS window layer and CdTe absorber layer; (b) drawbacks associated with the device including environmental problems, optical absorption losses and back contact barriers; (c) structural dynamics at CdS-CdTe interface; (d) influence of junction activation process by CdCl2 or HCF2Cl treatment; (e) interface and grain boundary passivation effects; (f) device degradation due to impurity diffusion and stress; (g) fabrication with suitable front and back contacts; (h) chemical processes occurring at various interfaces; (i) strategies and modifications developed to improve their efficiency. The complexity involved in understanding the multiple aspects of tuning the solar cell efficiency is reviewed in detail by considering the individual contribution from each component of the device. It is expected that this review article will enrich the materials aspects of CdTe/CdS devices for solar energy conversion and stimulate further innovative research interest on this intriguing topic.

In vitro and in silico biological studies of novel thiazolo3,2-a]pyrimidine-6-carboxylate derivatives

In the present study, we report the synthesis, characterization of new series of thiazolo3,2-a]pyrimidine-6-carboxylate derivatives 3a-f and 4a-f. The newly synthesized compounds were screened for in vitro antimicrobial and antiviral activities. The probable mode of action of these active compounds was determined through in silico docking study by docking the receptor methionyl-tRNA synthetase and human inosine-5'-monophosphate dehydrogenase (IMPDH) for antibacterial and antiviral activities, respectively. Among the compounds, 4c exhibited excellent in vitro antimicrobial activity against all tested strains with binding and docking energies -35.6 and -12.4 kcal/mol, respectively. The antiviral studies were carried out for the selected compounds in which 4a exhibited 73.69 and 54.42 % of inhibition of buffalopox and camelpox viruses, respectively. Furthermore, compound 4a showed minimum docking and binding energy along with the maximum hydrogen/hydrophobic interaction with IMPDH. The study contributes towards identification and screening of potential antimicrobial and antiviral agent's against the pathogens.

A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.

Scientific and technological aspects of fixed bed biomass gasification

In recent years new emphasis has been placed on problems of the environmental aspects of waste disposal, especially investigating alternatives to landfill, sea dumping and incineration. There is also a strong emphasis on clean, economic and efficient processes for electric power generation. These two topics may at first appear unrelated. Nevertheless, the technological advances are now such that a solution to both can be combined in a novel approach to power generation based on waste-derived fuels, including refuse-derived fuel (RDF) and sludge power (SP) by utilising a slagging gasifier and advance fuel technology (AFT). The most appropriate gasification technique for such waste utilisation is the British Gas/Lurgi (BGL) high pressure, fixed bed slagging gasifier where operation on a range of feedstocks has been well-documented. This gasifier is particularly amenable to briquette fuel feeding and, operating in an integrated gasification combined cycle mode (IGCC), is particularly advantageous. Here, the author details how this technology has been applied to Britain's first AFT-IGCC Power Station which is now under development at Fife Energy Ltd., in Scotland, the former British Gas Westfield Development Centre.

Group behaviour in physical, chemical and biological systems

Groups exhibit properties that either are not perceived to exist, or perhaps cannot exist, at the individual level. Such `emergent' properties depend on how individuals interact, both among themselves and with their surroundings. The world of everyday objects consists of material entities. These are, ultimately, groups of elementary particles that organize themselves into atoms and molecules, occupy space, and so on. It turns out that an explanation of even the most commonplace features of this world requires relativistic quantum field theory and the fact that Planck's constant is discrete, not zero. Groups of molecules in solution, in particular polymers ('sols'), can form viscous clusters that behave like elastic solids ('gels'). Sol-gel transitions are examples of cooperative phenomena. Their occurrence is explained by modelling the statistics of inter-unit interactions: the likelihood of either state varies sharply as a critical parameter crosses a threshold value. Group behaviour among cells or organisms is often heritable and therefore can evolve. This permits an additional, typically biological, explanation for it in terms of reproductive advantage, whether of the individual or of the group. There is no general agreement on the appropriate explanatory framework for understanding group-level phenomena in biology.

Some Thermodynamic Aspects of the Oxides of Chromium

To understand Cr emissions from slag melts to a vapor phase, an assessment of the stabilities of the chromium oxides at high temperatures has been carried out. The objective of the present study is to present a set of consistent data corresponding to the thermodynamic properties of the oxides of chromium, with special reference to the emission of hexavalent chromium from slags. In the current work, critical analysis of the experimental data available and a third analysis in the case of Cr2O3 have been carried out. Commercial databases, Fact Sage and ThermoCalc along with NIST-JANAF Thermochemical Tables, have been used for the analysis and comparisons of the results that are presented. The significant discrepancies in the available data have been pointed out. The data from NIST-JANAF Thermochemical Tables have been found to provide a set of consistent data for the various chromium oxides. An Ellingham diagram and the equations for the Delta G degrees (standard Gibbs free energy change) of formation of CrOx have been proposed. The present analysis shows that CrO3(g) is likely to be emitted from slag melts at high oxygen partial pressures. (C) The Minerals, Metals & Materials Society and ASM International 2014

THE LEGACY OF GN RAMACHANDRAN AND THE DEVELOPMENT OF STRUCTURAL BIOLOGY IN INDIA

G.N. Ramachandran is among the founding fathers of structural molecular biology. He made pioneering contributions in computational biology, modelling and what we now call bioinformatics. The triple helical coiled coil structure of collagen proposed by him forms the basis of much of collagen research at the molecular level. The Ramachandran map remains the simplest descriptor and tool for validation of protein structures. He has left his imprint on almost all aspects of biomolecular conformation. His contributions in the area of theoretical crystallography have been outstanding. His legacy has provided inspiration for the further development of structural biology in India. After a pause, computational biology and bioinformatics are in a resurgent phase. One of the two schools established by Ramachandran pioneered the development of macromolecular crystallography, which has now grown into an important component of modern biological research in India. Macromolecular NMR studies in the country are presently gathering momentum. Structural biology in India is now poised to again approach heights of the kind that Ramachandran conquered more than a generation ago.

Intense Acoustic Burst Ultrasound Modulated Optical Tomography for Elasticity Mapping of Soft Biological Tissue Mimicking Phantom: A Laser Speckle Contrast Analysis Study

This report addresses the assessment of variation in elastic property of soft biological tissues non-invasively using laser speckle contrast measurement. The experimental as well as the numerical (Monte-Carlo simulation) studies are carried out. In this an intense acoustic burst of ultrasound (an acoustic pulse with high power within standard safety limits), instead of continuous wave, is employed to induce large modulation of the tissue materials in the ultrasound insonified region of interest (ROI) and it results to enhance the strength of the ultrasound modulated optical signal in ultrasound modulated optical tomography (UMOT) system. The intensity fluctuation of speckle patterns formed by interference of light scattered (while traversing through tissue medium) is characterized by the motion of scattering sites. The displacement of scattering particles is inversely related to the elastic property of the tissue. We study the feasibility of laser speckle contrast analysis (LSCA) technique to reconstruct a map of the elastic property of a soft tissue-mimicking phantom. We employ source synchronized parallel speckle detection scheme to (experimentally) measure the speckle contrast from the light traversing through ultrasound (US) insonified tissue-mimicking phantom. The measured relative image contrast (the ratio of the difference of the maximum and the minimum values to the maximum value) for intense acoustic burst is 86.44 % in comparison to 67.28 % for continuous wave excitation of ultrasound. We also present 1-D and 2-D image of speckle contrast which is the representative of elastic property distribution.

Design Aspects of Luminescent Organic Crystals

With the progress of modern material science and successful commercialisations of organic-electronics, the field of organic luminescent materials has gained much attention in recent years. For a long time, the concepts and knowledge of photoluminescence (i.e. fluorescence and phosphorescence) were restricted to the solution phase as the exceptions of fluorescence quenching in condensed state were yet to be discovered. However, in the last few decades, researchers around the globe have come up with a number of promising strategies and concepts to systematically design solid-state emissive organic materials. In particular, the manipulations of ordered solid state structures and intermolecular strong and weak interactions provide a basis for understanding structure-property relationship and serve as an important tool for the design of newer, better and more efficient luminescent materials. In this short review, recent developments in this field will be presented.

Rapid, microwave-assisted synthesis of Gd2O3 and Eu:Gd2O3 nanocrystals: characterization, magnetic, optical and biological studies

Ultra-small crystals of undoped and Eu-doped gadolinium oxide (Gd2O3) were synthesised by a simple, rapid microwave-assisted route, using benzyl alcohol as the reaction solvent. XRD, XPS and TEM analysis reveal that the as-prepared powder material consists of nearly monodisperse Gd2O3 nanocrystals with an average diameter of 5.2 nm. The nanocrystals show good magnetic behaviour and exhibit a larger reduction in relaxation time of water protons than the standard Gd-DTPA complex currently used in MRI imaging. Cytotoxicity studies (both concentration- and time-dependent) of the Gd2O3 nanocrystals show no adverse effect on cell viability, evidencing their high biological compatibility. Finally, Eu:Gd2O3 nanocrystals were prepared by a similar route and the red luminescence of Eu3+ activator ions was used to study the cell permeability of the nanocrystals. Red fluorescence from Eu3+ ions observed by fluorescence microscopy shows that the nanocrystals (Gd2O3 and Eu:Gd2O3) can permeate not only the cell membrane but can also enter the cell nucleus, rendering them candidate materials not only for MRI imaging but also for drug delivery when tagged or functionalized with specific drug molecules.

High-quality ZnO nanorod based flexible devices for electronic and biological applications

Vertically aligned zinc oxide nanorods (ZnO NRs) were synthesized on kapton flexible sheets using a simple and cost-effective three-step process (electrochemical seeding, annealing under ambient conditions, and chemical solution growth). Scanning electron microscopy studies reveal that ZnO NRs grown on seed-layers, developed by electrochemical deposition at a negative potential of 1.5 V over a duration of 2.5 min and annealed at 200 degrees C for 2 h, consist of uniform morphology and good chemical stoichiometry. Transmission electron microscopy analyses show that the as-grown ZnO NRs have single crystalline hexagonal structure with a preferential growth direction of < 001 >. Highly flexible p-n junction diodes fabricated by using p-type conductive polymer exhibited excellent diode characteristics even under the fold state.

Social insect colony as a biological regulatory system: modelling information flow in dominance networks

Social insects provide an excellent platform to investigate flow of information in regulatory systems since their successful social organization is essentially achieved by effective information transfer through complex connectivity patterns among the colony members. Network representation of such behavioural interactions offers a powerful tool for structural as well as dynamical analysis of the underlying regulatory systems. In this paper, we focus on the dominance interaction networks in the tropical social wasp Ropalidia marginata-a species where behavioural observations indicate that such interactions are principally responsible for the transfer of information between individuals about their colony needs, resulting in a regulation of their own activities. Our research reveals that the dominance networks of R. marginata are structurally similar to a class of naturally evolved information processing networks, a fact confirmed also by the predominance of a specific substructure-the `feed-forward loop'-a key functional component in many other information transfer networks. The dynamical analysis through Boolean modelling confirms that the networks are sufficiently stable under small fluctuations and yet capable of more efficient information transfer compared to their randomized counterparts. Our results suggest the involvement of a common structural design principle in different biological regulatory systems and a possible similarity with respect to the effect of selection on the organization levels of such systems. The findings are also consistent with the hypothesis that dominance behaviour has been shaped by natural selection to co-opt the information transfer process in such social insect species, in addition to its primal function of mediation of reproductive competition in the colony.

Depalladation of Neutral Monoalkyne- and Dialkyne-Inserted Palladacycles and Alkyne Insertion/Depalladation Reactions of Cationic Palladacycles Derived from N,N `,N `'-Triarylguanidines as Facile Routes for Guanidine-Containing Heterocycles/Carbocycles: Synthetic, Structural, and Mechanistic Aspects

Depalladation of the monoalkyne-inserted cyclopalldated guanidines (kappa 2(C,N)Pd(2,6-Me2C5H3N)Br] (I and II) in PhCl under reflux conditions and that of the dialkyne-inserted cyclopalladated guanidine kappa(2)(C,N):eta(2)(C=C)PdBr] (III) in pyridine under reflux conditions afforded a guanidine-containing indole (1), imidaziondole (2), and benzazepine (3) in 80%, 67%, and 76%, yields, respectively. trans-L2PdBr2] species (L = 2,6-Me2C5H3N, C5H5N) were also isolated in the aforementioned reactions in 35%, 42%, and 40% yields. Further , the reaction of the cyclopalladated guanidine kappa(2)(C,N)Pd(mu-Br)](2) (IV) with AgBF4 in a CH2Cl2/MeCN mixture afforded the cationic pincer type cyclopalladated guanidine kappa(3)(C,N,O)Pd(MeCN)]BF4] (4) in 85% yield and this palladacycle upon crystallization in MeCN and the reaction of kappa(2)(C,N)Pd(mu-Br)](2) (V) with AgBf(4) in a CH2Cl2/MeCN mixture afforded the cationic palladacycles {kappa(2)(C,N)Pd(MeCN)(2)]BF4](5 and 6) in 89% and 91% yields, respectively. The separate reactions of 4 with 2 equiv of methyl phenylpropiolate (MPP) or diphenylacetylene (DPA) and the reaction of 5 with 2 equiv of MPP in PhCl at 110 degrees C afforded the guanidine-containing quinazolinium tetrafluoroborate 7 in 25-32% yields. The reaction of 6 with 2 equiv of DPA under otherwise identical conditions afforded the unsymmetrically substituted guanidinium tetrafluoroborate 8, containing a highly substituted naphthalene unit, in 82% yield. Compounds 1-8 were characterized by analytical and spectroscopic techniques, and all compounds except 4 were characterized by single-crystal X-ray diffraction. The Molecular structure of 2 and 3 are nove, as the framework in the former arises due to the formation of two C-N bonds upon depalladation while the butadienyl unit in the latter revealed cis,cis stereochemistry, a-feature unprecedented in alkyne insertion chemistry. Plausible pathways for the formation of heterocycles/carbocycles are proposed. the influence of substitutents on the aryl rings fo the cyclopalladated guanidine moiety and those on alkynes upon the nature of the products in addressed. Heterocycles 1 and 7 revealed the presence of two rotamers in about a 1.00:0.43 ratio in CDCl3 and in about a 1.00:0.14 ratio in CD3OD, respectively, as detected by H-1 NMR spectroscopy while in CD3CN and DMSO-d(6) (1) and CD3CN and CDCl3 (7), these heterocycles revealed the presence of a single rotamer. These spectral features are attributed to the restricted C-N single-bond rotation of the CN3 unit of the guanidine moiety, which possibly arises from steric constraint due to the formation of a N-H center dot center dot center dot Cl hydrogen bond with CDCl3 (1) and N-H center dot center dot center dot O and O-D center dot center dot center dot O hydrogen bonds with CD3OD (7).

A non-resonant mass sensor to eliminate the ``missing mass'' effect during mass measurement of biological materials

Resonant sensors and crystal oscillators for mass detection need to be excited at very high natural frequencies (MHz). Use of such systems to measure mass of biological materials affects the accuracy of mass measurement due to their viscous and/or viscoelastic properties. The measurement limitation of such sensor system is the difficulty in accounting for the ``missing mass'' of the biological specimen in question. A sensor system has been developed in this work, to be operated in the stiffness controlled region at very low frequencies as compared to its fundamental natural frequency. The resulting reduction in the sensitivity due to non-resonant mode of operation of this sensor is compensated by the high resolution of the sensor. The mass of different aged drosophila melanogaster (fruit fly) is measured. The difference in its mass measurement during resonant mode of operation is also presented. That, viscosity effects do not affect the working of this non-resonant mass sensor is clearly established by direct comparison. (C) 2014 AIP Publishing LLC.