Role of DNA sequence based structural features of promoters in transcription initiation and gene expression

D Regulatory information for transcription initiation is present in a stretch of genomic DNA, called the promoter region that is located upstream of the transcription start site (TSS) of the gene. The promoter region interacts with different transcription factors and RNA polymerase to initiate transcription and contains short stretches of transcription factor binding sites (TFBSs), as well as structurally unique elements. Recent experimental and computational analyses of promoter sequences show that they often have non-B-DNA structural motifs, as well as some conserved structural properties, such as stability, bendability, nucleosome positioning preference and curvature, across a class of organisms. Here, we briefly describe these structural features, the differences observed in various organisms and their possible role in regulation of gene expression.

Magnetic field induced tailoring of mechanical behavior of fluid filled micro porous carbon nanotube foam

Compressive loading of the carbon nanotube (CNT) has attracted much attention due to its entangled cellular like structure (CNT foam). This report investigates the mechanical behavior of magnetorheological fluid impregnated micro porous CNT foam that has not been realized before at this scale. Compressive behavior of CNT foam is found to greatly depend on the variation in both fluid viscosity as well as magnetic field intensity. Moreover, maximum achieved stress and energy absorption in CNT foam followed a power law behavior with the magnetic field intensity. Magnetic field induced movement of both CNT and iron oxide particles along the field direction is shown to dominate compressive behavior of CNT foam over highly attractive van der Waals forces between individual CNT. Therefore, this study demonstrates a method for tailoring the mechanical behavior of the fluid impregnated CNT foam. (C) 2014 AIP Publishing LLC.

Hot deformation behavior of Ni-Fe-Ga-based ferromagnetic shape memory alloy - A study using processing map

Ni-Fe-Ga-based alloys form a new class of ferromagnetic shape memory alloys (FSMAs) that show considerable formability because of the presence of a disordered fcc gamma-phase. The current study explores the deformation processing of this alloy using an off-stoichiometric Ni55Fe59Ga26 alloy that contains the ductile gamma-phase. The hot deformation behavior of this alloy has been characterized on the basis of its flow stress variation obtained by isothermal constant true strain rate compression tests in the 1123-1323 K temperature range and strain rate range of 10(-3)-10 s(-1) and using a combination of constitutive modeling and processing map. The dynamic recrystallization (DRX) regime for thermomechanical processing has been identified for this Heusler alloy on the basis of the processing maps and the deformed microstructures. This alloy also shows evidence of dynamic strain-aging (DSA) effect which has not been reported so far for any Heusler FSMAs. Similar effect is also noticed in a Ni-Mn-Ga-based Heusler alloy which is devoid of any gamma-phase. (C) 2014 Elsevier Ltd. All rights reserved.

Modelling of optical transport behavior of organic photovoltaic devices with nano-pillar transparent conducting electrodes

Optical transport behavior of organic photo-voltaic devices with nano-pillar transparent electrodes is investigated in this paper in order to understand possible enhancement of their charge-collection efficiency. Modeling and simulations of optical transport due to this architecture show an interesting regime of length-scale dependent optical characteristics. An electromagnetic wave propagation model is employed with simulation objectives toward understanding the mechanism of optical scattering and waveguide effects due to the nano-pillars and effective transmission through the active layer. Partial filling of gaps between the nano-pillars due to the nano-fabrication process is taken into consideration. Observations made in this paper will facilitate appropriate design rules for nano-pillar electrodes. (C) 2014 AIP Publishing LLC.

Combinatorial effect of rolling and carbonaceous nanoparticles on the evolution of crystallographic texture and structural properties of ultra high molecular weight polyethylene

Ultra high molecular weight polyethylene (PE) is a structural polymer widely used in biomedical implants. The mechanical properties of PE can be improved either by controlled crystalline orientation (texture) or by the addition of reinforcing agents. However, the combinatorial effect has not received much attention. The objective of this study was to characterize the structure and mechanical properties of PE composites incorporating multiwall carbon nanotubes (MWCNT) and reduced graphene oxide (RGO) subjected to hot rolling. The wide angle X-ray diffraction studies revealed that mechanical deformation resulted in a mixture of orthorhombic and monoclinic crystals. Furthermore, the presence of nanoparticles resulted in lower crystallinity in PE with smaller crystallite size, more so in RGO than in MWCNT composites. Rolling strengthened the texture of both orthorhombic and the monoclinic phases in PE. Presence of RGO weakened the texture of both phases of PE after rolling whereas MWCNT only mildly weakened the texture. This resulted in a reduction in the elastic modulus of RGO composites whereas moduli of neat polymer and the MWCNT composite increased after rolling. This study provides new insight into the role of nanoparticles in texture evolution during polymer processing with implications for processing of structural polymer composites.

Highly compressible behavior of polymer mediated three-dimensional network of graphene foam

The compressive behavior of graphene foam (GF) and its polymer (polydimethyl siloxane) (PDMS) infiltrated structure are presented. While GF showed an irreversible compressibility, the GF/PDMS structure revealed a highly reversible mechanical behavior up to many cycles of compression and also possesses a six times higher compressive strength. In addition, the strain rate demonstrated a negligible effect on both the maximum achieved stress and energy absorption in the GF/PDMS structure. The mechanical responses of both GF and GF/PDMS structure are compared with carbon nanotubes based cellular structure and its composite with PDMS, where GF/PDMS presented a dominant mechanical characteristic among other carbon based micro foam structures. Therefore, the improved mechanical properties of GF/PDMS suggest its potential for dampers, cushions, packaging, etc.

On the Utility of Microscopy and C-Scan Techniques in the Study of Defects Arising From Resin Infusion Process and a Study on the Influence of Voids on the Impact Behavior of CFRP Composites

Carbon Fiber Reinforced Plastic composites were fabricated through vacuum resin infusion technology by adopting two different processing conditions, viz., vacuum only in the first and vacuum plus external pressure in the next, in order to generate two levels of void-bearing samples. They were relatively graded as higher and lower void-bearing ones, respectively. Microscopy and C-scan techniques were utilized to describe the presence of voids arising from the two different processing parameters. Further, to determine the influence of voids on impact behavior, the fabricated +45 degrees/90 degrees/-45 degrees composite samples were subjected to low velocity impacts. The tests show impact properties like peak load and energy to peak load registering higher values for the lower void-bearing case where as the total energy, energy for propagation and ductility indexes were higher for the higher void-bearing ones. Fractographic analysis showed that higher void-bearing samples display lower number of separation of layers in the laminate. These and other results are described and discussed in this report.

Combinatorial Crystal Synthesis: Structural Landscape of Phloroglucinol:1,2-bis(4-pyridyl)ethylene and Phloroglucinol:Phenazine

A large number of crystal forms, polymorphs and pseudopolymorphs, have been isolated in the phloroglucinol-dipyridylethylene (PGL:DPE) and phloroglucinol-phenazine (PGL:PHE) systems. An understanding of the intermolecular interactions and synthon preferences in these binary systems enables one to design a ternary molecular solid that consists of PGL, PHE, and DPE, and also others where DPE is replaced by other heterocycles. Clean isolation of these ternary cocrystals demonstrates synthon amplification during crystallization. These results point to the lesser likelihood of polymorphism in multicomponent crystals compared to single-component crystals. The appearance of several crystal forms during crystallization of a multicomponent system can be viewed as combinatorial crystal synthesis with synthon selection from a solution library. The resulting polymorphs and pseudopolymorphs that are obtained constitute a crystal structure landscape.

Evaluating shock absorption behavior of small-sized systems under programmable electric field

A simple ball-drop impact tester is developed for studying the dynamic response of hierarchical, complex, small-sized systems and materials. The developed algorithm and set-up have provisions for applying programmable potential difference along the height of a test specimen during an impact loading; this enables us to conduct experiments on various materials and smart structures whose mechanical behavior is sensitive to electric field. The software-hardware system allows not only acquisition of dynamic force-time data at very fast sampling rate (up to 2 x 10(6) samples/s), but also application of a pre-set potential difference (up to +/- 10 V) across a test specimen for a duration determined by feedback from the force-time data. We illustrate the functioning of the set-up by studying the effect of electric field on the energy absorption capability of carbon nanotube foams of 5 x 5 x 1.2 mm(3) size under impact conditions. (C) 2014 AIP Publishing LLC.

A bio-attuned ratiometric hydrogen sulfate ion selective receptor in aqueous solvent: structural proof of the H-bonded adduct

A new cell permeable quinazoline based receptor (1) selectively senses HSO4- ions of nanomolar region in 0.1 M HEPES buffer (ethanol-water: 1/5, v/v) at biological pH over other competitive ions through the proton transfer followed by hydrogen bond formation and subsequent anion coordination to yield the LHSO4]-LH+center dot 3H(2)O (2) ensemble, which has been crystallographically characterised to ensure the structure property relationship. This non-cytotoxic HSO4- ion selective biomarker has great potential to recognize the intercellular distribution of HSO4- ions in HeLa cells under fluorescence microscope.

Antioxidant activity and electrochemical elucidation of the enigmatic redox behavior of curcumin and its structurally modified analogues

Here, we report studies on the antioxidant activity and redox behavior of curcumin and its structurally modified synthetic analogues. We have synthesized a number of analogues of curcumin which abrogate its keto-enol tautomerism or substitute the methylene group at the centre of its heptadione moiety implicated in the hydride transfer and studied their redox property. From cyclic voltammetric studies, it is demonstrated that H-atom transfer from CH2 group at the center of the heptadione link also plays an important role in the antioxidant properties of curcumin along with that of its phenolic -OH group. In addition, we also show that the conversion of 1, 3-dicarbonyl moiety of curcumin to an isosteric heterocycle as in pyrazole curcumin, which decreases its rotational freedom, leads to an improvement of its redox properties as well as its antioxidant activity. (C) 2014 Elsevier Ltd. All rights reserved.

An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles

Rich data bearing on the structural and evolutionary principles of protein protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial `driver' mutations in oncogenesis. They also provide the foundation toward the design of protein protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview. (C) 2014 Elsevier Ltd. All rights reserved.

Synergistic Effect of Mo plus Cu Codoping on the Photocatalytic Behavior of Metastable TiO2 Solid Solutions

Codoping with Cu and Mo is shown to have a synergistic effect on the photocatalytic activity of TiO2. The enhancement in activity is observed only if the synthesis route results in TiO2 in which (Cu, Mo) codopants are forced into the TiO2 lattice. Using X-ray photoelectron spectroscopy, Cu and Mo are shown to be present in the +2 and +6 oxidation states, respectively. A systematic study of the ternary system shows that TiO2 containing 6 mol % CuO and 1.5 mol % MoO3 is the most active ternary composition. Ab initio calculations show that codoping of TiO2 using (Mo, Cu) introduces levels above the valence band, and below the conduction band, resulting in a significant reduction in the band gap (similar to 0.8 eV). However, codoping also introduces deep defect states, which can have a deleterious impact on photoactivity. This helps rationalize the narrow compositional window over which the enhancement in photocatalytic activity is observed.

Optimal control analysis of the dynamic growth behavior of microorganisms

Understanding the growth behavior of microorganisms using modeling and optimization techniques is an active area of research in the fields of biochemical engineering and systems biology. In this paper, we propose a general modeling framework, based on Monad model, to model the growth of microorganisms. Utilizing the general framework, we formulate an optimal control problem with the objective of maximizing a long-term cellular goal and solve it analytically under various constraints for the growth of microorganisms in a two substrate batch environment. We investigate the relation between long term and short term cellular goals and show that the objective of maximizing cellular concentration at a fixed final time is equivalent to maximization of instantaneous growth rate. We then establish the mathematical connection between the generalized framework and optimal and cybernetic modeling frameworks and derive generalized governing dynamic equations for optimal and cybernetic models. We finally illustrate the influence of various constraints in the cybernetic modeling framework on the optimal growth behavior of microorganisms by solving several dynamic optimization problems using genetic algorithms. (C) 2014 Published by Elsevier Inc.

First-Principles Study on Structural Stability of Belite

A first-principles study was carried out to investigate the stability of the crystal structure of beta-form belite (beta-C2S) substituted by Sr atoms as trace impurities for Ca atoms in CaOx polyhedra. The effect of the connection types of CaOx polyhedral, in the form of common-edge bond and common-face bond, upon the crystal stability is described. The Ca-Ca interatomic distance closely relates to the hydraulic activity of beta-C2S. The beta-C2S substituted by an Sr atom for Ca(1) atoms having seven Ca-O bonds is energetically more stable than that substituted by an Sr atom for Ca(2) atoms having eight Ca-O bonds. The Sr-doped beta-C2S having a common face bond with SrOx polyhedra is energetically more favorable and results in structural stability compared with that having a common edge bond with SrOx polyhedra.