Trifurcated (four-center) hydrogen bond in solid state crystal structure of 5'-amino-5'-deoxyadenosine p-toluenesulfonate

The crystal structure of 5'-amino-5'-deoxyadenosine (5'-Am.dA) p-toluenesulfonate has been determined by X-ray crystallographic methods. It belongs to the orthorhombic space group P2(1)2(1)2(1) with a = 7.754(3)Angstrom, b = 8.065(1)Angstrom and c = 32.481(2)Angstrom. This nucleoside side shows a syn conformation about the glycosyl bond and C2'-endo-C3'-exo puckering for the ribose sugar. The orientation of N5' atom is gauche-trans about the exocyclic C4'-C5' bond. The amino nitrogen N5' forms a trifurcated hydrogen bond with N3, O9T and O4' atoms. Adenine bases form A.A.A triplets through hydrogen bonding between N6, N7 and N1 atoms of symmetry related nucleoside molecules.

Modeling of heat and mass transfer for solid state fermentation process in tray bioreactor

A mathematical model is developed to simulate oxygen consumption, heat generation and cell growth in solid state fermentation (SSF). The fungal growth on the solid substrate particles results in the increase of the cell film thickness around the particles. The model incorporates this increase in the biofilm size which leads to decrease in the porosity of the substrate bed and diffusivity of oxygen in the bed. The model also takes into account the effect of steric hindrance limitations in SSF. The growth of cells around single particle and resulting expansion of biofilm around the particle is analyzed for simplified zero and first order oxygen consumption kinetics. Under conditions of zero order kinetics, the model predicts upper limit on cell density. The model simulations for packed bed of solid particles in tray bioreactor show distinct limitations on growth due to simultaneous heat and mass transport phenomena accompanying solid state fermentation process. The extent of limitation due to heat and/or mass transport phenomena is analyzed during different stages of fermentation. It is expected that the model will lead to better understanding of the transport processes in SSF, and therefore, will assist in optimal design of bioreactors for SSF.

Semi-active vibration isolation using a near-zero-spring-rate device:steady state analysis of a single-degree-of-freedom model

A vibration isolator is described which incorporates a near-zero-spring-rate device within its operating range. The device is an assembly of a vertical spring in parallel with two inclined springs. A low spring rate is achieved by combining the equivalent stiffness in the vertical direction of the inclined springs with the stiffness of the vertical central spring. It is shown that there is a relation between the geometry and the stiffness of the individual springs that results in a low spring rate. Computer simulation studies of a single-degree-of-freedom model for harmonic base input show that the performance of the proposed scheme is superior to that of the passive schemes with linear springs and skyhook damping configuration. The response curves show that, for small to large amplitudes of base disturbance, the system goes into resonance at low frequencies of excitation. Thus, it is possible to achieve very good isolation over a wide low-frequency band. Also, the damper force requirements for the proposed scheme are much lower than for the damper force of a skyhook configuration or a conventional linear spring with a semi-active damper.

Soft gluon k(t)-resummation and the Froissart bound

We study soft gluon k(t)-resurnmation and the relevance of InfraRed (IR) gluons for the energy dependence of total hadronic cross-sections. In our model, consistency with the Froissart bound is directly related to the ansatz that the IR behaviour of the QCD coupling constant follows an inverse power law.

Structural Investigation of Activated Lattice Oxygen in Ce1-xSnxO2 and Ce1-x-ySnxPdyO2-delta by EXAFS and DFT calculation

Substitution of Sn4+ ion in CeO2 creates activated oxygen in Ce0.8Sn0.2O2 leading to higher oxygen storage capacity compared to Ce0.8Zr0.2O2. With Pd ion substitution in Ce0.8Sn0.2O2,activation of oxygen is further enhanced as observed from the H-2/TPR study. Both EXAFS analysis and DFT calculation reveal that in the solid solution Ceexhibits 4 + 4 coordination, Sri exhibits 4 + 2 + 2 coordination and Pd has 4 + 3 coordination. While the oxygen in the First four coordination with short M-O bonds are strongly held in the lattice, the oxygens in the second and higher coordinations with long M-O bonds are weakly bound, and they are the activated oxygen ill the lattice. Bond valence analysis shows that oxygen with valencies as low its 1.65 are created by the Sn and Pd ion Substitution. Another interesting observation is that H-2/TPR experiment of Ce1-xSnxO2 shows a broad peak starting from 200 to 500 degrees C, while the same reduction is achieved in a single step at similar to 110 degrees C in presence Pd2+ on. Substitution of Pd2+ ion thus facilitates synergistic reduction of the catalyst at lower temperature. We have shown that simultaneous reduction of the Ce4+ and Sr4+ ions by Pd-0 is the synergistic interaction leading to high oxygen storage capacity at low temperature.

The Mycobacterial MsDps2 Protein Is a Nucleoid-Forming DNA Binding Protein Regulated by Sigma Factors sigma(A) and sigma(B)

The Dps (DNA-binding protein from starved cells) proteins from Mycobacterium smegmatis MsDps1 and MsDps2 are both DNA-binding proteins with some differences. While MsDps1 has two oligomeric states, with one of them responsible for DNA binding, MsDps2 has only one DNA-binding oligomeric state. Both the proteins however, show iron-binding activity. The MsDps1 protein has been shown previously to be induced under conditions of starvation and osmotic stress and is regulated by the extra cellular sigma factors sigma(H) and sigma(F). We show here, that the second Dps homologue in M. smegmatis, namely MsDps2, is purified in a DNA-bound form and exhibits nucleoid-like structures under the atomic force microscope. It appears that the N-terminal sequence of Dps2 plays a role in nucleoid formation. MsDps2, unlike MsDps1, does not show elevated expression in nutritionally starved or stationary phase conditions; rather its promoter is recognized by RNA polymerase containing sigma(A) or sigma(B), under in vitro conditions. We propose that due to the nucleoid-condensing ability, the expression of MsDps2 is tightly regulated inside the cells.

Free and ATP-bound structures of Ap(4)A hydrolase from Aquifex aeolicus V5

Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 angstrom resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alpha beta alpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.

Role of the triplet state in the green emission peak of polyfluorene films: A time evolution study

The blue emission of ethyl-hexyl substituted polyfluorene (PF2/6) films is accompanied by a low energy green emission peak around 500 nm in inert atmosphere. The intensity of this 500 nm peak is large in electroluminescence (EL) compared to photoluminescence (PL)measurements. Furthermore, the green emission intensity reduces dramatically in the presence of molecular oxygen. To understand this, we have modeled various nonradiative processes by time dependent quantum many body methods. These are (i) intersystem crossing to study conversion of excited singlets to triplets leading to a phosphorescence emission, (ii) electron-hole recombination (e-hR) process in the presence of a paramagnetic impurity to follow the yield of triplets in a polyene system doped with paramagnetic metal atom, and (iii) quenching of excited triplet states in the presence of oxygen molecules to understand the low intensity of EL emission in ambient atmosphere, when compared with that in nitrogen atmosphere. We have employed the Pariser-Parr-Pople Hamiltonian to model the molecules and have invoked electron-electron repulsions beyond zero differential approximation while treating interactions between the organic molecule and the rest of the system. Our time evolution methods show that there is a large cross section for triplet formation in the e-hR process in the presence of paramagnetic impurity with degenerate orbitals. The triplet yield through e-hR process far exceeds that in the intersystem crossing pathway, clearly pointing to the large intensity of the 500 nm peak in EL compared to PL measurements. We have also modeled the triplet quenching process by a paramagnetic oxygen molecule which shows a sizable quenching cross section especially for systems with large sizes. These studies show that the most probable origin of the experimentally observed low energy EL emission is the triplets.

Wigner distributions for finite-state systems without redundant phase-point operators

We set up Wigner distributions for N-state quantum systems following a Dirac-inspired approach. In contrast to much of the work in this study, requiring a 2N x 2N phase space, particularly when N is even, our approach is uniformly based on an N x N phase-space grid and thereby avoids the necessity of having to invoke a `quadrupled' phase space and hence the attendant redundance. Both N odd and even cases are analysed in detail and it is found that there are striking differences between the two. While the N odd case permits full implementation of the marginal property, the even case does so only in a restricted sense. This has the consequence that in the even case one is led to several equally good definitions of the Wigner distributions as opposed to the odd case where the choice turns out to be unique.

A new open-framework zinc arsenate [C4N3H16](2)[Zn-5(AsO4)(4)(HAsO4)(2)]

A three-dimensional zinc arsenate with an interrupted zeolitic framework (-IIO), [C4N3H16](2)[Zn-5(AsO4)(4)(HAsO4)(2)], I has been synthesized solvothermally. The structure is built up from ZnO4, AsO4 and HAsO4 tetrahedral units connected alternatively through their vertices forming the 3-D structure possessing one-dimensional channels bound by 10 T-atoms (T = Zn, As), The framework density of the structure is 10.4 T-atoms which indicates considerable openness in its structure. (C) 2009 Elsevier B.V. All rights reserved.

An analytical model for performance evaluation of multimedia applications over EDCA in an IEEE 802.11e WLAN

We extend the modeling heuristic of (Harsha et al. 2006. In IEEE IWQoS 06, pp 178 - 187) to evaluate the performance of an IEEE 802.11e infrastructure network carrying packet telephone calls, streaming video sessions and TCP controlled file downloads, using Enhanced Distributed Channel Access (EDCA). We identify the time boundaries of activities on the channel (called channel slot boundaries) and derive a Markov Renewal Process of the contending nodes on these epochs. This is achieved by the use of attempt probabilities of the contending nodes as those obtained from the saturation fixed point analysis of (Ramaiyan et al. 2005. In Proceedings ACM Sigmetrics, `05. Journal version accepted for publication in IEEE TON). Regenerative analysis on this MRP yields the desired steady state performance measures. We then use the MRP model to develop an effective bandwidth approach for obtaining a bound on the size of the buffer required at the video queue of the AP, such that the streaming video packet loss probability is kept to less than 1%. The results obtained match well with simulations using the network simulator, ns-2. We find that, with the default IEEE 802.11e EDCA parameters for access categories AC 1, AC 2 and AC 3, the voice call capacity decreases if even one streaming video session and one TCP file download are initiated by some wireless station. Subsequently, reducing the voice calls increases the video downlink stream throughput by 0.38 Mbps and file download capacity by 0.14 Mbps, for every voice call (for the 11 Mbps PHY). We find that a buffer size of 75KB is sufficient to ensure that the video packet loss probability at the QAP is within 1%.

Influence of spatial variability of permeability property on steady state seepage flow and slope stability analysis

In recent years, spatial variability modeling of soil parameters using random field theory has gained distinct importance in geotechnical analysis. In the present Study, commercially available finite difference numerical code FLAC 5.0 is used for modeling the permeability parameter as spatially correlated log-normally distributed random variable and its influence on the steady state seepage flow and on the slope stability analysis are studied. Considering the case of a 5.0 m high cohesive-frictional soil slope of 30 degrees, a range of coefficients of variation (CoV%) from 60 to 90% in the permeability Values, and taking different values of correlation distance in the range of 0.5-15 m, parametric studies, using Monte Carlo simulations, are performed to study the following three aspects, i.e., (i) effect ostochastic soil permeability on the statistics of seepage flow in comparison to the analytic (Dupuit's) solution available for the uniformly constant permeability property; (ii) strain and deformation pattern, and (iii) stability of the given slope assessed in terms of factor of safety (FS). The results obtained in this study are useful to understand the role of permeability variations in slope stability analysis under different slope conditions and material properties. (C) 2009 Elsevier B.V. All rights reserved.

Buckled nano rod - a two state system: quantum effects on its dynamics

We consider a suspended elastic rod under longitudinal compression. The compression can be used to adjust potential energy for transverse displacements from the harmonic to the double well regime. The two minima in potential energy curve describe two possible buckled states. Using transition state theory (TST) we have calculated the rate of conversion from one state to other. If the strain epsilon = 4 epsilon c the simple TST rate diverges. We suggest a method to correct this divergence for quantum calculations. We also find that zero point energy contributions can be quite large so that single mode calculations can lead to large errors in the rate.

Critical lattice size limit for synchronized chaotic state in one- and two-dimensional diffusively coupled map lattices

We consider diffusively coupled map lattices with P neighbors (where P is arbitrary) and study the stability of the synchronized state. We show that there exists a critical lattice size beyond which the synchronized state is unstable. This generalizes earlier results for nearest neighbor coupling. We confirm the analytical results by performing numerical simulations on coupled map lattices with logistic map at each node. The above analysis is also extended to two-dimensional P-neighbor diffusively coupled map lattices.

Identification and thermodynamic characterization of molten globule states of periplasmic binding proteins

Molten globule-like intermediates have been shown to occur during protein folding and are thought to be involved in protein translocation and membrane insertion. However, the determinants of molten globule stability and the extent of specific packing in molten globules is currently unclear. Using far- and near-UV CD and intrinsic and ANS fluorescence, we show that four periplasmic binding proteins (LBP, LIVBP, MBP, and RBP) form molten globules at acidic pH values ranging from 3.0 to 3.4. Only two of these (LBP and LIVBP) have similar sequences, but all four proteins adopt similar three-dimensional structures. We found that each of the four molten globules binds to its corresponding ligand without conversion to the native state. Ligand binding affinity measured by isothermal titration calorimetry for the molten globule state of LIVBP was found to be comparable to that of the corresponding native state, whereas for LBP, MBP, and RBP, the molten globules bound ligand with approximately 5-30-fold lower affinity than the corresponding native states. All four molten globule states exhibited cooperative thermal unfolding assayed by DSC. Estimated values of Delta C-p of unfolding show that these molten globule states contain 28-67% of buried surface area relative to the native states. The data suggest that molten globules of these periplasmic binding proteins retain a considerable degree of long range order. The ability of these sequentially unrelated proteins to form highly ordered molten globules may be related to their large size as well as an intrinsic property of periplasmic binding protein folds.