DoSA: Database of Structural Alignments

Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159 780 conformationally similar and 56 140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function.

Patterned growth and differentiation of neural cells on polymer derived carbon substrates with micro/nano structures in vitro

The growth of neuroblastoma (N2a) and Schwann cells has been explored on polymer derived carbon substrates of varying micro and nanoscale geometries: resorcinol-formaldehyde (RE) gel derived carbon films and electrospun nanofibrous (similar to 200 nm diameter) mat and SU-8 (a negative photoresist) derived carbon micro-patterns. MTT assay and complementary lactate dehydrogenase (LDH) assay established cytocompatibility of RE derived carbon films and fibers over a period of 6 days in culture. The role of length scale of surface patterns in eliciting lineage-specific adaptive response along, across and on the interspacing between adjacent micropatterns (i.e., ``on'', ``across'' and ``off'') has been assayed. Textural features were found to affect 3',5'-cyclic AMP sodium salt-induced neurite outgrowth, over a wide range of length scales: from similar to 200 nm (carbon fibers) to similar to 60 mu m (carbon patterns). Despite their innate randomness, carbon nanofibers promoted preferential differentiation of N2a cells into neuronal lineage, similar to ordered micro-patterns. Our results, for the first time, conclusively demonstrate the potential of RE-gel and SU-8 derived carbon substrates as nerve tissue engineering platforms for guided proliferation and differentiation of neural cells in vitro. (C) 2013 Elsevier Ltd. All rights reserved.

Auto-ignition based synthesis of Y2O3 for photo- and thermo-luminescent applications

We present a simple route for synthesis of Y2O3 for both photoluminescent (PL) and thermoluminescent (TL) applications. We show that by simply switching the fuel from ethylene di-amine tetracetic acid (EDTA) to its disodium derivative (Na-2-EDTA), we obtain a better photoluminescent material. On the other hand, use of EDTA aids in formation of Y2O3 which is a better thermoluminescent material. In both cases pure cubic nano-Y2O3 is obtained. For both the material systems, structural characterization, photoluminescence, thermoluminescence, and absorbance spectra are reported and analyzed. Use of EDTA results in nano Y2O3 with crystallite size similar to 10 nm. Crystallinity improves, and crystallite size is larger (similar to 30 nm) when Na-2-EDTA is used. TL response of Y2O3 nanophosphors prepared by both fuels is examined using UV radiation. Samples prepared with EDTA show well resolved glow curve at 140 degrees C, while samples prepared with Na-2-EDTA shows a glow curve at 155 degrees C. Effect of UV exposure time on TL characteristics is investigated. The TL kinetic parameters are also calculated using glow curve shape method. Results indicate that the TL behavior of both the samples follow a second order kinetic model. (C) 2013 Elsevier B.V. All rights reserved.

Better early osteogenesis of electroconductive hydroxyapatite-calcium titanate composites in a rabbit animal model

In view of the fact that bone healing can be enhanced due to external electric field application, it is important to assess the influence of the implant conductivity on the bone regeneration in vivo. To address this issue, this study reports the in vivo biocompatibility property of multistage spark plasma sintered hydroxyapatite (HA)-80 wt % calcium titanate (CaTiO3) composites and monolithic HA, which have widely different conductivity property (14 orders of magnitude difference). The ability of bone regeneration was assessed by implantation in cylindrical femoral bone defects of rabbit animal model for varying time period of 1, 4, and 12 weeks. The overall assessment of the histology results suggests that the progressive healing of bone defects around HA-80 wt % CaTiO3 is associated with a better efficacy with respect to (w.r.t) early stage neobone formation, which is histomorphometrically around 140% higher than monolithic HA. Overall, this study demonstrates that the in vivo biocompatibility property of HA-80 wt % CaTiO3 with respect to local effects after 12 weeks of implantation is not compromised both qualitatively and quantitatively, and a comparison with control implant (HA) points toward the critical role of electrical conductivity on better early stage bone regeneration. (c) 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 842-851, 2014.

Modeling Equitable Distribution of Water: Dynamic Inversion-Based Controller Approach

It is a well-known fact that most of the developing countries have intermittent water supply and the quantity of water supplied from the source is also not distributed equitably among the consumers. Aged pipelines, pump failures, and improper management of water resources are some of the main reasons for it. This study presents the application of a nonlinear control technique to overcome this problem in different zones in the city of Bangalore. The water is pumped to the city from a large distance of approximately 100km over a very high elevation of approximately 400m. The city has large undulating terrain among different zones, which leads to unequal distribution of water. The Bangalore, inflow water-distribution system (WDS) has been modeled. A dynamic inversion (DI) nonlinear controller with proportional integral derivative (PID) features (DI-PID) is used for valve throttling to achieve the target flows to different zones of the city. This novel approach of equitable water distribution using DI-PID controllers that can be used as a decision support system is discussed in this paper.

Temperature dependent electrical behaviour of Cu2SnS3 films

The temperature dependent electrical properties of the dropcasted Cu2SnS3 films have been measured in the temperature range 140 K to 317 K. The log I versus root V plot shows two regions. The region at lower bias is due to electrode limited Schottky emission and the higher bias region is due to bulk limited Poole Frenkel emission. The ideality factor is calculated from the ln I versus V plot for different temperatures fitted with the thermionic emission model and is found to vary from 6.05 eV to 12.23 eV. This large value is attributed to the presence of defects or amorphous layer at the Ag / Cu2SnS3 interface. From the Richardson's plot the Richardson's constant and the barrier height were calculated. Owing to the inhomogeneity in the barrier heights, the Richardson's constant and the barrier height were also calculated from the modified Richardson's plot. The I-V-T curves were also fitted using the thermionic field emission model. The barrier heights were found to be higher than those calculated using thermionic emission model. From the fit of the I-V-T curves to the field emission model, field emission was seen to dominate in the low temperature range of 140 K to 177 K. The temperature dependent current graphs show two regions of different mechanisms. The log I versus 1000/T plot gives activation energies E-a1 = 0.367095 - 0.257682 eV and E-a2 = 0.038416 - 0.042452 eV. The log ( I/T-2) versus 1000/T graph gives trap depths Phi(o1) = 0.314159 - 0.204752 eV and Phi(o2) = 0.007425- 0.011163 eV. With increasing voltage the activation energy E-a1 and the trap depth Phi(o1) decrease. From the ln (IT1/ 2) versus 1/T-1/ 4 graph, the low temperature region is due to variable range hopping mechanism and the high temperature region is due to thermionic emission. (C) 2014 Author(s).

Vertical Uplift Resistance of Two Interfering Horizontal Anchors in Clay

The vertical uplift resistance of two interfering rigid strip plate anchors embedded horizontally at the same level in clay has been examined. The lower and upper bound theorems of the limit analysis in combination with finite-elements and linear optimization have been employed to compute the failure load in a bound form. The analysis is meant for an undrained condition and it incorporates the increase of cohesion with depth. For different clear spacing (S) between the anchors, the magnitude of the efficiency factor (eta c gamma) resulting from the combined components of soil cohesion (c) and soil unit weight (gamma), has been computed for different values of embedment ratio (H/B), the rate of linear increase of cohesion with depth (m) and normalized unit weight (gamma H/c). The magnitude of eta c gamma has been found to reduce continuously with a decrease in the spacing between the anchors, and the uplift resistance becomes minimum for S/B=0. It has been noted that the critical spacing between the anchors required to eliminate the interference effect increases continuously with (1) an increase in H/B, and (2) a decrease in m.

Solving Axisymmetric Stability Problems by Using Upper Bound Finite Elements, Limit Analysis, and Linear Optimization

A numerical formulation has been proposed for solving an axisymmetric stability problem in geomechanics with upper bound limit analysis, finite elements, and linear optimization. The Drucker-Prager yield criterion is linearized by simulating a sphere with a circumscribed truncated icosahedron. The analysis considers only the velocities and plastic multiplier rates, not the stresses, as the basic unknowns. The formulation is simple to implement, and it has been employed for finding the collapse loads of a circular footing placed over the surface of a cohesive-frictional material. The formulation can be used to solve any general axisymmetric geomechanics stability problem.

Correlation between thermodynamic anomalies and pathways of ice nucleation in supercooled water

The well-known classical nucleation theory (CNT) for the free energy barrier towards formation of a nucleus of critical size of the new stable phase within the parent metastable phase fails to take into account the influence of other metastable phases having density/order intermediate between the parent metastable phase and the final stable phase. This lacuna can be more serious than capillary approximation or spherical shape assumption made in CNT. This issue is particularly significant in ice nucleation because liquid water shows rich phase diagram consisting of two (high and low density) liquid phases in supercooled state. The explanations of thermodynamic and dynamic anomalies of supercooled water often invoke the possible influence of a liquid-liquid transition between two metastable liquid phases. To investigate both the role of thermodynamic anomalies and presence of distinct metastable liquid phases in supercooled water on ice nucleation, we employ density functional theoretical approach to find nucleation free energy barrier in different regions of phase diagram. The theory makes a number of striking predictions, such as a dramatic lowering of nucleation barrier due to presence of a metastable intermediate phase and crossover in the dependence of free energy barrier on temperature near liquid-liquid critical point. These predictions can be tested by computer simulations as well as by controlled experiments. (C) 2014 AIP Publishing LLC.

Effect of quantum nuclear motion on hydrogen bonding

This work considers how the properties of hydrogen bonded complexes, X-H center dot center dot center dot Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H center dot center dot center dot O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4-3.0 angstrom, i.e., from strong to weak hydrogen bonds. The position of the proton (which determines the X-H bond length) and its longitudinal vibrational frequency, along with the isotope effects in both are described quantitatively. An analysis of the secondary geometric isotope effect, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of bending modes is also considered: their quantum effects compete with those of the stretching mode for weak to moderate H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several trends. (C) 2014 AIP Publishing LLC.

A Gibbs-ensemble based technique for Monte Carlo simulation of electric double layer capacitors (EDLC) at constant voltage

Current methods for molecular simulations of Electric Double Layer Capacitors (EDLC) have both the electrodes and the electrolyte region in a single simulation box. This necessitates simulation of the electrode-electrolyte region interface. Typical capacitors have macroscopic dimensions where the fraction of the molecules at the electrode-electrolyte region interface is very low. Hence, large systems sizes are needed to minimize the electrode-electrolyte region interfacial effects. To overcome these problems, a new technique based on the Gibbs Ensemble is proposed for simulation of an EDLC. In the proposed technique, each electrode is simulated in a separate simulation box. Application of periodic boundary conditions eliminates the interfacial effects. This in addition to the use of constant voltage ensemble allows for a more convenient comparison of simulation results with experimental measurements on typical EDLCs. (C) 2014 AIP Publishing LLC.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with x(TBA) approximate to 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at x(TBA) approximate to 0.05. We note that ``islands'' of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, x(TBA) approximate to 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level. (C) 2014 AIP Publishing LLC.

Model for triplet state engineering in organic light emitting diodes

Engineering the position of the lowest triplet state (T-1) relative to the first excited singlet state (S-1) is of great importance in improving the efficiencies of organic light emitting diodes and organic photovoltaic cells. We have carried out model exact calculations of substituted polyene chains to understand the factors that affect the energy gap between S-1 and T-1. The factors studied are backbone dimerisation, different donor-acceptor substitutions, and twisted geometry. The largest system studied is an 18 carbon polyene which spans a Hilbert space of about 991 x 10(6). We show that for reverse intersystem crossing process, the best system involves substituting all carbon sites on one half of the polyene with donors and the other half with acceptors. (C) 2014 AIP Publishing LLC.

Stability of Unsupported Vertical Circular Excavations

A methodology has been presented for determining the stability of unsupported vertical cylindrical excavations by using an axisymmetric upper bound limit analysis approach in conjunction with finite elements and linear optimization. For the purpose of excavation design, stability numbers (S-n) have been generated for both (1) cohesive-frictional soils and (2) pure cohesive soils, with an additional provision accounting for linearly increasing cohesion with increasing depth by means of a nondimensional factor m. The variation of S-n with H/b has been established for different values of m and phi, where H and b refer to the height and radius of the cylindrical excavation. A number of useful observations have been gathered about the variation of the stability number and nodal velocity patterns as H/b, phi, and m change. The results of the analysis compare quite well with the different solutions reported in the literature. (C) 2014 American Society of Civil Engineers.