From anomalies in neat liquid to structure, dynamics and function in the biological world

Water brings its remarkable thermodynamic and dynamic anomalies in the pure liquid state to biological world where water molecules face a multitude of additional interactions that frustrate its hydrogen bond network. Yet the water molecules participate and control enormous number of biological processes in manners which are yet to be understood at a molecular level. We discuss thermodynamics, structure, dynamics and properties of water around proteins and DNA, along with those in reverse micelles. We discuss the roles of water in enzyme kinetics, in drug-DNA intercalation and in kinetic-proof reading ( the theory of lack of errors in biosynthesis). We also discuss how water may play an important role in the natural selection of biomolecules. (C) 2011 Elsevier B. V. All rights reserved.

Learning polyhedral classifiers using logistic function

In this paper we propose a new algorithm for learning polyhedral classifiers. In contrast to existing methods for learning polyhedral classifier which solve a constrained optimization problem, our method solves an unconstrained optimization problem. Our method is based on a logistic function based model for the posterior probability function. We propose an alternating optimization algorithm, namely, SPLA1 (Single Polyhedral Learning Algorithm1) which maximizes the loglikelihood of the training data to learn the parameters. We also extend our method to make it independent of any user specified parameter (e.g., number of hyperplanes required to form a polyhedral set) in SPLA2. We show the effectiveness of our approach with experiments on various synthetic and real world datasets and compare our approach with a standard decision tree method (OC1) and a constrained optimization based method for learning polyhedral sets.

DeNOx Study in Diesel Engine Exhaust Using Barrier Discharge Corona Assisted by V2O5/TiO2 Catalyst

A plasma-assisted catalytic reactor was used to remove nitrogen oxides (NOx) from diesel engine exhaust operated under different load conditions. Initial studies were focused on plasma reactor (a dielectric barrier discharge reactor) treatment of diesel exhaust at various temperatures. The nitric oxide (NO) removal efficiency was lowered when high temperature exhaust was treated using plasma reactor. Also, NO removal efficiency decreased when 45% load exhaust was treated. Studies were then made with plasma reactor combined with a catalytic reactor consisting of a selective catalytic reduction (SCR) catalyst, V2O5/TiO2. Ammonia was used as a reducing agent for SCR process in a ratio of 1:1 to NOx. The studies were focused on temperatures of the SCR catalytic reactor below 200°C. The plasma-assisted catalytic reactor was operated well to remove NOx under no-load and load conditions. For an energy input of 96 J/l, the NOx removal efficiencies obtained under no-load and load conditions were 90% and 72% respectively at an exhaust temperature of 100°C.

Treatment of NOx from Diesel Engine Exhaust by Dielectric Barrier Discharge Method

This paper reports improved performance of discharge plasma in filtered engine exhaust treatment. Our paper deals about the removal of NOX emissions from the diesel exhaust by electric discharge plasma. For the treatment of diesel exhaust a new type of reactor referred to as crossflow dielectric barrier discharge reactor has been used, where the gas flow is perpendicular to the corona electrode. Experiments were conducted at different flow rates ranging from 2 l/min to 10 l/min. The discharge plasma assisted barrier discharge reactor has shown promising results in NOX removal at high flow rates.

Barrier Inhomogeneity and Electrical Properties of InN Nanodots/Si Heterojunction Diodes

The electrical transport behavior of n-n indium nitride nanodot-silicon (InN ND-Si) heterostructure Schottky diodes is reported here, which have been fabricated by plasma-assisted molecular beam epitaxy. InN ND structures were grown on a 20 nm InN buffer layer on Si substrates. These dots were found to be single crystalline and grown along [0 0 0 1] direction. Temperature-dependent current density-voltage plots (J-V-T) reveal that the ideality factor (eta) and Schottky barrier height (SBH) (Phi(B)) are temperature dependent. The incorrect values of the Richardson constant (A**) produced suggest an inhomogeneous barrier. Descriptions of the experimental results were explained by using two models. First one is barrier height inhomogeneities (BHIs) model, in which considering an effective area of the inhomogeneous contact provided a procedure for a correct determination of A**. The Richardson constant is extracted similar to 110 A cm(-2) K(-2) using the BHI model and that is in very good agreement with the theoretical value of 112 A cm(-2) K(-2). The second model uses Gaussian statistics and by this, mean barrier height Phi(0) and A** were found to be 0.69 eV and 113 A cm(-2) K(-2), respectively.

Treatment of NOx from Diesel Engine Exhaust by Dielectric Barrier Discharge Method

This paper reports improved performance of advantages when compared to its counterpart as it is cost discharge plasma in filtered engine exhaust treatment. Our effective, low capital and operation costs, salable by- paper deals about the removal of NOX emissions from the diesel products, and integration with the existing systems. In this exhaust by electric discharge plasma. For the treatment of diesel paper we describe an alternate reactor geometry referred to exhaust a new type of reactor referred to as cross-flow dielectric as cross-flow DBD reactor, where the exhaust gas flow barrier discharge reactor has been used, where the gas flow is perpendicular to the wire-cylinder reaction chamber. This perpendicular to the corona electrode. Experiments were reactor is used to treat the actual exhaust of a 3.75 kW diesel- conducted at different flow rates ranging from 2 l/min to 10 l/ generator set. The main emphasis is laid on the NOX treatment min. The discharge plasma assisted barrier discharge reactor of diesel engine exhaust. Experiments were carried out at has shown promising results in NOX removal at high flow rates.

Construction of equivalent circuit of a transformer winding from driving-point impedance function - analytical approach

Analytical solution is presented to convert a given driving-point impedance function (in s-domain) into a physically realisable ladder network with inductive coupling between any two sections and losses considered. The number of sections in the ladder network can vary, but its topology is assumed fixed. A study of the coefficients of the numerator and denominator polynomials of the driving-point impedance function of the ladder network, for increasing number of sections, led to the identification of certain coefficients, which exhibit very special properties. Generalised expressions for these specific coefficients have also been derived. Exploiting their properties, it is demonstrated that the synthesis method essentially turns out to be an exercise of solving a set of linear, simultaneous, algebraic equations, whose solution directly yields the ladder network elements. The proposed solution is novel, simple and guarantees a unique network. Presently, the formulation can synthesise a unique ladder network up to six sections.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

Chitosan-polyvinyl alcohol-sulfonated polyethersulfone mixed-matrix membranes as methanol-barrier electrolytes for DMFCs

Chitosan (CS)-polyvinyl alcohol (PVA) cross-linked with sulfosuccinic acid (SSA) and modified with sulfonated polyethersulfone (SPES) mixed-matrix membranes are reported for their application in direct methanol fuel cells (DMFCs). Polyethersulfone (PES) is sulfonated by chlorosulfonic acid and factors affecting the sulfonation reaction, such as time and temperature, are studied. The ion-exchange capacity, degree of sulfonation, sorption, and proton conductivity for the mixed-matrix membranes are investigated. The mixed-matrix membranes are also characterised for their mechanical and thermal properties. The methanol-crossover flux across the mixed-matrix membranes is studied by measuring the mass balance of methanol using the density meter. The methanol cross-over for these membranes is found to be about 33% lower in relation to Nafion-117 membrane. The DMFC employing CS-PVA-SPES mixed-matrix membrane with an optimum content of 25 wt % SPES delivers a peak power-density of 5.5 mW cm-2 at a load current-density of 25 mA cm-2 while operating at 70 degrees C. (C) 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012

Insights into differential modulation of receptor function by hinge region using novel agonistic lutropin receptor and inverse agonistic thyrotropin receptor antibodies

We report two antibodies, scFv 13B1 and MAb PD1.37, against the hinge regions of LHR and TSHR, respectively, which have similar epitopes but different effects on receptor function. While neither of them affected hormone binding, with marginal effects on hormone response, scFv 13B1 stimulated LHR in a dose-dependent manner, whereas MAb PD1.37 acted as an inverse agonist of TSHR. Moreover, PD1.37 could decrease the basal activity of hinge region CAMs, but had varied effects on those present in ECLs, whereas 13B1 was refractory to any CAMs in LHR. Using truncation mutants and peptide phage display, we compared the differential roles of the hinge region cysteine box-2/3 as well as the exoloops in the activation of these two homologus receptors. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Partition function for hindered, one-and multi-dimensional rotors

Writing the hindered rotor (hr) partition function as the trace of (rho) over cap = e(-beta(H) over cap hr), we approximate it by the sum of contributions from a set of points in position space. The contribution of the density matrix from each point is approximated by performing a local harmonic expansion around it. The highlight of this method is that it can be easily extended to multidimensional systems. Local harmonic expansion leads to a breakdown of the method a low temperatures. In order to calculate the partition function at low temperatures, we suggest a matrix multiplication procedure. The results obtained using these methods closely agree with the exact partition function at all temperature ranges. Our method bypasses the evaluation of eigenvalues and eigenfunctions and evaluates the density matrix for internal rotation directly. We also suggest a procedure to account for the antisymmetry of the total wavefunction in the same. (C) 2012 Elsevier B.V. All rights reserved.

Dielectric Barrier Discharge Cascaded with Red Mud Waste to Enhance NOX Removal from Diesel Engine Exhaust

Red mud is a waste by-product generated during the processing of bauxite, the most common ore of aluminium. With the presence of ferric oxide, high surface area, resistance to poisoning and low cost, red mud made itself a good alternative to the existing commercial automobile catalyst. The cascading of dielectric barrier discharge plasma with red mud improved the NOX removal from diesel engine exhaust significantly. The DeNO(X) efficiency with discharge plasma was 74% and that with red mud was 31%. The efficiency increased to 92% when plasma was cascaded with red mud catalyst operating at a temperature of 400 degrees C. The NOX removal was dominated by NO2 removal. The studies were conducted at different temperatures and the results were discussed.

An Online Actor-Critic Algorithm with Function Approximation for Constrained Markov Decision Processes

We develop an online actor-critic reinforcement learning algorithm with function approximation for a problem of control under inequality constraints. We consider the long-run average cost Markov decision process (MDP) framework in which both the objective and the constraint functions are suitable policy-dependent long-run averages of certain sample path functions. The Lagrange multiplier method is used to handle the inequality constraints. We prove the asymptotic almost sure convergence of our algorithm to a locally optimal solution. We also provide the results of numerical experiments on a problem of routing in a multi-stage queueing network with constraints on long-run average queue lengths. We observe that our algorithm exhibits good performance on this setting and converges to a feasible point.

The force distribution function of an oscillator model of polymer stretching at constant velocity

Recent simulations of the stretching of tethered biopolymers at a constant speed v (Ponmurugan and Vemparala, 2011 Phys. Rev. E 84 060101(R)) have suggested that for any time t, the distribution of the fluctuating forces f responsible for chain deformation is governed by a relation of the form P(+ f)/ P(- f) = expgamma f], gamma being a coefficient that is solely a function of v and the temperature T. This result, which is reminiscent of the fluctuation theorems applicable to stochastic trajectories involving thermodynamic variables, is derived in this paper from an analytical calculation based on a generalization of Mazonka and Jarzynski's classic model of dragged particle dynamics Mazonka and Jarzynski, 1999 arXiv:cond-\textbackslashmat/9912121v1]. However, the analytical calculations suggest that the result holds only if t >> 1 and the force fluctuations are driven by white rather than colored noise; they further suggest that the coefficient gamma in the purported theorem varies not as v(0.15)T-(0.7), as indicated by the simulations, but as vT(-1).

MS_RHII-RSD, a Dual-Function RNase HII-(p)ppGpp Synthetase from Mycobacterium smegmatis

In the noninfectious soil saprophyte Mycobacterium smegmatis, intracellular levels of the stress alarmones guanosine tetraphosphate and guanosine pentaphosphate, together termed (p)ppGpp, are regulated by the enzyme Rel(Msm). This enzyme consists of a single, bifunctional polypeptide chain that is capable of both synthesizing and hydrolyzing (p)ppGpp. The rel(Msm), knockout strain of M. smegmatis (Delta rel(Msm)) is expected to show a (p)ppGpp null (p)ppGpp(0)] phenotype. Contrary to this expectation, the strain is capable of synthesizing (p)ppGpp in vivo. In this study, we identify and functionally characterize the open reading frame (ORF), MSMEG_5849, that encodes a second functional (p)ppGpp synthetase in M. smegmatis. In addition to (p)ppGpp synthesis, the 567-amino-acid-long protein encoded by this gene is capable of hydrolyzing RNA(.)DNA hybrids and bears similarity to the conventional RNase HII enzymes. We have classified this protein as actRel(Msm) in accordance with the recent nomenclature proposed and have named it MS_RHII-RSD, indicating the two enzymatic activities present RHII, RNase HII domain, originally identified as (d) under bar omain of (u) under bar nknown (f) under bar unction 429 (DUF429), and RSD, RelA_SpoT nucleotidyl transferase domain, the SYNTH domain responsible for (p)ppGpp synthesis activity]. MS_RHII-RSD is expressed and is constitutively active in vivo and behaves like a monofunctional (p)ppGpp synthetase in vitro. The occurrence of the RNase HII and (p)ppGpp synthetase domains together on the same polypeptide chain is suggestive of an in vivo role for this novel protein as a link connecting the essential life processes of DNA replication, repair, and transcription to the highly conserved stress survival pathway, the stringent response.