The Structure of the Thioredoxin-Triosephosphate Isomerase Complex Provides Insights into the Reversible Glutathione-Mediated Regulation of Triosephosphate Isomerase

Protein-protein interactions are crucial for many biological functions. The redox interactome encompasses numerous weak transient interactions in which thioredoxin plays a central role. Proteomic studies have shown that thioredoxin binds to numerous proteins belonging to various cellular processes, including energy metabolism. Thioredoxin has cross talk with other redox mechanisms involving glutathionylation and has functional overlap with glutaredoxin in deglutathionylation reactions. In this study, we have explored the structural and biochemical interactions of thioredoxin with the glycolytic enzyme, triosephosphate isomerase. Nuclear magnetic resonance chemical shift mapping methods and molecular dynamics-based docking have been applied in deriving a structural model of the thioredoxin-triosephosphate isomerase complex. The spatial proximity of active site cysteine residues of thioredoxin to reactive thiol groups on triosephosphate isomerase provides a direct link to the observed deglutathionylation of cysteine 217 in triosephosphate isomerase, thereby reversing the inhibitory effect of S-glutathionylation of triosephosphate isomerase.

The Structure of the Thioredoxin−Triosephosphate Isomerase Complex Provides Insights into the Reversible Glutathione-Mediate Regulation of Triosephosphate Isomerase

Protein−protein interactions are crucial for many biological functions. The redox interactome encompasses numerous weak transient interactions in which thioredoxin plays a central role. Proteomic studies have shown that thioredoxin binds to numerous proteins belonging to various cellular processes, including energy metabolism. Thioredoxin has cross talk with other redox mechanisms involving glutathionylation and has functional overlap with glutaredoxin in deglutathionylation reactions. In this study, we have explored the structural and biochemical interactions of thioredoxin with the glycolytic enzyme, triosephosphate isomerase. Nuclear magnetic resonance chemical shift mapping methods and molecular dynamics-based docking have been applied in deriving a structural model of the thioredoxin−triosephosphate isomerase complex. The spatial proximity of active site cysteine residues of thioredoxin to reactive thiol groups on triosephosphate isomerase provides a direct link to the observed deglutathionylation of cysteine 217 in triosephosphate isomerase, thereby reversing the inhibitory effect of S-glutathionylation of triosephosphate isomerase.

A versatile resolving agent for diffusion edited separation of enantiomers, complex mixtures and constitutional isomers

The study is the first report of the utilization of a crown ether as a new and versatile resolving agent for the diffusion edited separation of enantiomers, complex mixtures and constitutional isomers. As a consequence of different binding affinities of enantiomers of a chiral molecule and individual components of the complex mixtures with the crown ether, the molecules diffuse at different rates. The enhanced separation achieved due to matrix assisted diffusion permitted their separation in the diffusion dimension. The generality and wide utility of the new resolving agent and the methodology are demonstrated on diverse examples, such as an organic chiral molecule, constitutional isomers and complex mixture of molecules possessing different functional groups that possess nearly identical molecular weights.

Microwave Spectroscopic and Atoms in Molecules Theoretical Investigations on the ArPropargyl Alcohol Complex: ArHO, Ar, and ArC Interactions

The structure of the Arpropargyl alcohol (ArPA) complex is determined from the rotational spectra of the parent complex and its two deuterated isotopologues, namely ArPA-D(OD) and ArPA-D(CD). The spectra confirm a geometry in which PA exists in the gauche form with Ar located in between OH and CCH groups. All a, b and c types of transitions show small splitting due to some large-amplitude motion dominated by COH torsion, as in the monomer. Splittings in a- and b-type transitions are of the order of a few kilohertz, whereas splitting in the c-type transitions is relatively larger (0.92.6 MHz) and decreases in the order ArPA>ArPA-D(CD)>ArPA-D(OD). The assignments are well supported by ab initio calculations. Atoms in molecules (AIM) and electrostatic potential calculations are used to explore the nature of the interactions in this complex. AIM calculations not only reveal the expected OHAr and Ar interactions in the Argauche-PA complex, but also novel CAr (of CH2OH group) and OHAr interactions in the Artrans-PA complex. Similar interactions are also present in the Armethanol complex.

Adiabatic eigenfunction-based approach for coherent excitation transfer: An almost analytical treatment of the Fenna-Matthews-Olson complex

We suggest a method of studying coherence in finite-level systems coupled to the environment and use it for the Hamiltonian that has been used to describe the light-harvesting pigment-protein complex. The method works with the adiabatic states and transforms the Hamiltonian to a form in which the terms responsible for decoherence and population relaxation are separated out. Decoherence is then accounted for nonperturbatively and population relaxation using a Markovian master equation. Almost analytical results can be obtained for the seven-level system, and the calculations are very simple for systems with more levels. We apply the treatment to the seven-level system, and the results are in excellent agreement with the exact numerical results of Nalbach et al. Nalbach, Braun, and Thorwart, Phys. Rev. E 84, 041926 (2011)]. Our approach is able to account for decoherence and population relaxation separately. It is found that decoherence causes only damping of oscillations and does not lead to transfer to the reaction center. Population relaxation is necessary for efficient transfer to the reaction center, in agreement with earlier findings. Our results show that the transformation to the adiabatic basis followed by a Redfield type of approach leads to results in good agreement with exact simulation.

Domains in complex surfaces with a noncompact automorphism group - II

Let X be an arbitrary complex surface and D subset of X a domain that has a noncompact group of holomorphic automorphisms. A characterization of those domains D that admit a smooth real analytic, finite type, boundary orbit accumulation point and whose closures are contained in a complete hyperbolic domain D' subset of X is obtained.

Constraining complex aquifer geometry with geophysics (2-D ERT and MRS measurements) for stochastic modelling of groundwater flow

Stochastic modelling is a useful way of simulating complex hard-rock aquifers as hydrological properties (permeability, porosity etc.) can be described using random variables with known statistics. However, very few studies have assessed the influence of topological uncertainty (i.e. the variability of thickness of conductive zones in the aquifer), probably because it is not easy to retrieve accurate statistics of the aquifer geometry, especially in hard rock context. In this paper, we assessed the potential of using geophysical surveys to describe the geometry of a hard rock-aquifer in a stochastic modelling framework. The study site was a small experimental watershed in South India, where the aquifer consisted of a clayey to loamy-sandy zone (regolith) underlain by a conductive fissured rock layer (protolith) and the unweathered gneiss (bedrock) at the bottom. The spatial variability of the thickness of the regolith and fissured layers was estimated by electrical resistivity tomography (ERT) profiles, which were performed along a few cross sections in the watershed. For stochastic analysis using Monte Carlo simulation, the generated random layer thickness was made conditional to the available data from the geophysics. In order to simulate steady state flow in the irregular domain with variable geometry, we used an isoparametric finite element method to discretize the flow equation over an unstructured grid with irregular hexahedral elements. The results indicated that the spatial variability of the layer thickness had a significant effect on reducing the simulated effective steady seepage flux and that using the conditional simulations reduced the uncertainty of the simulated seepage flux. As a conclusion, combining information on the aquifer geometry obtained from geophysical surveys with stochastic modelling is a promising methodology to improve the simulation of groundwater flow in complex hard-rock aquifers. (C) 2013 Elsevier B.V. All rights reserved.

Improved perfect space-time block codes

Perfect space-time block codes (STBCs) are based on four design criteria-full-rateness, nonvanishing determinant, cubic shaping, and uniform average transmitted energy per antenna per time slot. Cubic shaping and transmission at uniform average energy per antenna per time slot are important from the perspective of energy efficiency of STBCs. The shaping criterion demands that the generator matrix of the lattice from which each layer of the perfect STBC is carved be unitary. In this paper, it is shown that unitariness is not a necessary requirement for energy efficiency in the context of space-time coding with finite input constellations, and an alternative criterion is provided that enables one to obtain full-rate (rate of complex symbols per channel use for an transmit antenna system) STBCs with larger normalized minimum determinants than the perfect STBCs. Further, two such STBCs, one each for 4 and 6 transmit antennas, are presented and they are shown to have larger normalized minimum determinants than the comparable perfect STBCs which hitherto had the best-known normalized minimum determinants.

Full-rate full-diversity finite feedback space-time schemes with minimum feedback and transmission duration

A Finite Feedback Scheme (FFS) for a quasi-static MIMO block fading channel with finite N-ary delay-free noise-free feedback consists of N Space-Time Block Codes (STBCs) at the transmitter, one corresponding to each possible value of feedback, and a function at the receiver that generates N-ary feedback. A number of FFSs are available in the literature that provably attain full-diversity. However, there is no known full-diversity criterion that universally applies to all FFSs. In this paper a universal necessary condition for any FFS to achieve full-diversity is given, and based on this criterion the notion of Feedback-Transmission duration optimal (FT-optimal) FFSs is introduced, which are schemes that use minimum amount of feedback N for the given transmission duration T, and minimum T for the given N to achieve full-diversity. When there is no feedback (N = 1) an FT-optimal scheme consists of a single STBC, and the proposed condition reduces to the well known necessary and sufficient condition for an STBC to achieve full-diversity. Also, a sufficient criterion for full-diversity is given for FFSs in which the component STBC yielding the largest minimum Euclidean distance is chosen, using which full-rate (N-t complex symbols per channel use) full-diversity FT-optimal schemes are constructed for all N-t > 1. These are the first full-rate full-diversity FFSs reported in the literature for T < N-t. Simulation results show that the new schemes have the best error performance among all known FFSs.

Adiabatic Eigenfunction Based Approach to Coherent Transfer: Application to the Fenna-Matthews-Olson (FMO) Complex and the Role of Correlations in the Efficiency of Energy Transfer

We have recently suggested a method (Pallavi Bhattacharyya and K. L. Sebastian, Physical Review E 2013, 87, 062712) for the analysis of coherence in finite-level systems that are coupled to the surroundings and used it to study the process of energy transfer in the Fenna-Matthews-Olson (FMO) complex. The method makes use of adiabatic eigenstates of the Hamiltonian, with a subsequent transformation of the Hamiltonian into a form where the terms responsible for decoherence and population relaxation could be separated out at the lowest order. Thus one can account for decoherence nonperturbatively, and a Markovian type of master equation could be used for evaluating the population relaxation. In this paper, we apply this method to a two-level system as well as to a seven-level system. Comparisons with exact numerical results show that the method works quite well and is in good agreement with numerical calculations. The technique can be applied with ease to systems with larger numbers of levels as well. We also investigate how the presence of correlations among the bath degrees of freedom of the different bacteriochlorophyll a molecules of the FMO Complex affect the rate of energy transfer. Surprisingly, in the cases that we studied, our calculations suggest that the presence of anticorrelations, in contrast to correlations, make the excitation transfer more facile.

Prediction of the stiffness of nanoclay-polypropylene composites using a monte carlo finite element analysis approach

The present work deals with the prediction of stiffness of an Indian nanoclay-reinforced polypropylene composite (that can be termed as a nanocomposite) using a Monte Carlo finite element analysis (FEA) technique. Nanocomposite samples are at first prepared in the laboratory using a torque rheometer for achieving desirable dispersion of nanoclay during master batch preparation followed up with extrusion for the fabrication of tensile test dog-bone specimens. It has been observed through SEM (scanning electron microscopy) images of the prepared nanocomposite containing a given percentage (3–9% by weight) of the considered nanoclay that nanoclay platelets tend to remain in clusters. By ascertaining the average size of these nanoclay clusters from the images mentioned, a planar finite element model is created in which nanoclay groups and polymer matrix are modeled as separate entities assuming a given homogeneous distribution of the nanoclay clusters. Using a Monte Carlo simulation procedure, the distribution of nanoclay is varied randomly in an automated manner in a commercial FEA code, and virtual tensile tests are performed for computing the linear stiffness for each case. Values of computed stiffness modulus of highest frequency for nanocomposites with different nanoclay contents correspond well with the experimentally obtained measures of stiffness establishing the effectiveness of the present approach for further applications.

Finite size scaling in crossover among different random matrix ensembles in microscopic lattice models

Using numerical diagonalization we study the crossover among different random matrix ensembles (Poissonian, Gaussian orthogonal ensemble (GOE), Gaussian unitary ensemble (GUE) and Gaussian symplectic ensemble (GSE)) realized in two different microscopic models. The specific diagnostic tool used to study the crossovers is the level spacing distribution. The first model is a one-dimensional lattice model of interacting hard-core bosons (or equivalently spin 1/2 objects) and the other a higher dimensional model of non-interacting particles with disorder and spin-orbit coupling. We find that the perturbation causing the crossover among the different ensembles scales to zero with system size as a power law with an exponent that depends on the ensembles between which the crossover takes place. This exponent is independent of microscopic details of the perturbation. We also find that the crossover from the Poissonian ensemble to the other three is dominated by the Poissonian to GOE crossover which introduces level repulsion while the crossover from GOE to GUE or GOE to GSE associated with symmetry breaking introduces a subdominant contribution. We also conjecture that the exponent is dependent on whether the system contains interactions among the elementary degrees of freedom or not and is independent of the dimensionality of the system.

On Precoding for Constant K-User MIMO Gaussian Interference Channel With Finite Constellation Inputs

This paper considers linear precoding for the constant channel-coefficient K-user MIMO Gaussian interference channel (MIMO GIC) where each transmitter-i (Tx-i) requires the sending of d(i) independent complex symbols per channel use that take values from fixed finite constellations with uniform distribution to receiver-i (Rx-i) for i = 1, 2, ..., K. We define the maximum rate achieved by Tx-i using any linear precoder as the signal-to-noise ratio (SNR) tends to infinity when the interference channel coefficients are zero to be the constellation constrained saturation capacity (CCSC) for Tx-i. We derive a high-SNR approximation for the rate achieved by Tx-i when interference is treated as noise and this rate is given by the mutual information between Tx-i and Rx-i, denoted as I(X) under bar (i); (Y) under bar (i)]. A set of necessary and sufficient conditions on the precoders under which I(X) under bar (i); (Y) under bar (i)] tends to CCSC for Tx-i is derived. Interestingly, the precoders designed for interference alignment (IA) satisfy these necessary and sufficient conditions. Furthermore, we propose gradient-ascentbased algorithms to optimize the sum rate achieved by precoding with finite constellation inputs and treating interference as noise. A simulation study using the proposed algorithms for a three-user MIMO GIC with two antennas at each node with d(i) = 1 for all i and with BPSK and QPSK inputs shows more than 0.1-b/s/Hz gain in the ergodic sum rate over that yielded by precoders obtained from some known IA algorithms at moderate SNRs.

A versatile ternary ionic complex for chiral discrimination of molecules with diverse functionalities using H-1 NMR

This study reports a simple, efficient and versatile protocol developed for NMR spectroscopic enantiodiscrimination of molecules containing diverse functional -groups, such as amino alcohols, secondary alcohols, cyanohydrins, oxazolidones, diols, thiones and epoxides, using a phosphorous based three component mixture. The simple mixing and shaking of enantiopure 1,1'-binaphthyt-2,2'-diyl hydrogenphosphate (BNPA), 4-(dimethylamino)pyridine (DMAP) and a chiral analyte in the solvent CDCl3 served as a chiral solvating agent and resulted in well dispersed peaks for each enantiomer in the H-1 NMR spectrum. Discrimination could be achieved not only for the proton at the chiral centre, but also for multiple proton sites. The devised approach also permitted the precise measurement of the enantiomeric excess (ee).

ELLIPSE FITTING USING FINITE RATE OF INNOVATION PRINCIPLES

We address the problem of parameter estimation of an ellipse from a limited number of samples. We develop a new approach for solving the ellipse fitting problem by showing that the x and y coordinate functions of an ellipse are finite-rate-of-innovation (FRI) signals. Uniform samples of x and y coordinate functions of the ellipse are modeled as a sum of weighted complex exponentials, for which we propose an efficient annihilating filter technique to estimate the ellipse parameters from the samples. The FRI framework allows for estimating the ellipse parameters reliably from partial or incomplete measurements even in the presence of noise. The efficiency and robustness of the proposed method is compared with state-of-art direct method. The experimental results show that the estimated parameters have lesser bias compared with the direct method and the estimation error is reduced by 5-10 dB relative to the direct method.