Quenched Averages for Self-Avoiding Walks and Polygons on Deterministic Fractals

We study rooted self avoiding polygons and self avoiding walks on deterministic fractal lattices of finite ramification index. Different sites on such lattices are not equivalent, and the number of rooted open walks W _n (S), and rooted self-avoiding polygons P _n (S) of n steps depend on the root S. We use exact recursion equations on the fractal to determine the generating functions for P _n (S), and W _n(S) for an arbitrary point S on the lattice. These are used to compute the averages ,, and over different positions of S. We find that the connectivity constant μ, and the radius of gyration exponent are the same for the annealed and quenched averages. However, , and , where the exponents and , take values different from the annealed case. These are expressed as the Lyapunov exponents of random product of finite-dimensional matrices. For the 3-simplex lattice, our numerical estimation gives and , to be compared with the known annealed values and .     

Computation of triple differential cross-sections with the inclusion of exchange effects in atomic K-shell ionization by relativistic electrons for symmetric geometry

The triple differential cross-section for K-shell ionization of silver and copper atoms by relativistic electrons have been computed in the coplanar symmetric geometry with the inclusion of exchange effects following the multiple scattering theory of Das and Seal [1] multiplied by suitable spinors. Present computed results are marginally improved in some cases from the previous computed results [2]. Present results are compared with measured values [3] and with previous computation results [2]. Some other theoretical computational results are also presented here for comparison.      

Ternary copper complexes for photocleavage of DNA by red light: direct evidence for sulfur-to-copper charge transfer and d-d band involvement

A new class of ternary copper(II) complexes of formulation [Cu(L(n)B](ClO(4)) (1-4), where HL(n) is a NSO-donor Schiff base (HL(1), HL(2)) and B is a NN-donor heterocyclic base viz. 1,10-phenanthroline (phen) and 2,9-dimethyl-1,10-phenanthroline (dmp), are prepared, structurally characterized, and their DNA binding and photocleavage activities studied in the presence of red light. Ternary complex [Cu(L(3))(phen)](ClO(4)) (5) containing an ONO-donor Schiff base and a binary complex [Cu(L(2))(2)] (6) are also prepared and structurally characterized for mechanistic investigations of the DNA cleavage reactions. While 1-4 have a square pyramidal (4 + 1) CuN(3)OS coordination geometry with the Schiff base bonded at the equatorial sites, 5 has a square pyramidal (4 + 1) geometry with CuN(3)O(2) coordination with the alcoholic oxygen at the axial site, and 6 has a square planar trans-CuN(2)O(2) geometry. Binding of the complexes 1-4 to calf thymus DNA shows the relative order: phen > dmp. Mechanistic investigations using distamycin reveal minor groove binding for the complexes. The phen complexes containing the Schiff base with a thiomethyl or thiophenyl moiety show red light induced photocleavage. The dmp complexes are essentially photonuclease inactive. Complexes 5 and 6 are cleavage inactive under similar photolytic conditions. A 10 microM solution of 1 displays a 72% cleavage of SC DNA (0.5 microg) on an exposure of 30 min using a 603 nm Nd:YAG pulsed laser (60 mJ/P) in Tris-HCl buffer (pH 7.2). Significant cleavage of 1 is also observed at 694 nm using a Ruby laser. Complex 1 is cleavage inactive under argon or nitrogen atmosphere. It shows a more enhanced cleavage in pure oxygen than in air. Enhancement of cleavage in D(2)O and inhibition with sodium azide addition indicate the possibility of the formation of singlet oxygen as a reactive intermediate leading to DNA cleavage. The d-d band excitation with red light shows significant enhancement of cleavage yield. The results indicate that the phen ligand is necessary for DNA binding of the complex. Both the sulfur-to-copper charge transfer band and copper d-d band excitations helped the DNA cleavage. While the absorption of a red photon induces a metal d-d transition, excitation at shorter visible wavelengths leads to the sulfur-to-copper charge transfer band excitation at the initial step of photocleavage. The excitation energy is subsequently transferred to ground state oxygen molecules to produce singlet oxygen that cleaves the DNA.     

Arsenic(III) sorption on nanostructured cerium incorporated manganese oxide (NCMO): a physical insight into the mechanistic pathway

Arsenic(III) sorption was investigated with nanostructured cerium incorporated manganese oxide (NCMO). The pH between 6.0 and 8.0 was optimized for the arsenic(III) sorption. Kinetics and equilibrium data (pH=7.0±0.2, T=303±1.6 K, and I=0.01 M) of arsenic(III) sorption by NCMO described, respectively, the pseudo-second order and the Freundlich isotherm equations well. The sorption process was somewhat complicated in nature and divided into two different segments, initially very fast sorption followed by slow intraparticle diffusion process. Sorption reaction of arsenic(III) on NCMO was endothermic (ΔH°=+13.46 kJ mol(-1)) and spontaneous (ΔG°=-24.75 to -30.15 kJ mol(-1) at T=283-323 K), which took place with increasing entropy (ΔS°=+0.14 kJ mol(-1)K(-1)) at solid-liquid interface. Energy of arsenic(III) sorption estimated by analyzing the equilibrium data using the D-R isotherm model was 15.4 kJ mol(-1), indicating the ion-exchange type mechanism. Raman, FT-IR, pH effect, desorption, etc. studies indicated that arsenic(III) was oxidized to arsenic(V) during the sorption process.     

Bromodimethylsulfonium bromide (BDMS): a useful reagent for conversion of aldoximes and primary amides to nitriles

An operationally simple and high yielding procedure has been developed for the preparation of nitriles from aldoximes and primary amides using bromodimethylsulfonium bromide (BDMS) as a novel and efficient reagent in the absence of any added base or catalyst. The optimal protocol is applicable to access a wide range of cyano compounds including aromatic, heterocyclic, and aliphatic species. The conversion of aldoximes to nitriles takes place at room temperature in acetonitrile, whereas acetonitrile at reflux temperature is required for rapid conversion in the case of primary amides.     

Population model with diffusion and supplementary forest resource in a two-patch habitat

A mathematical model is proposed to study the role of supplementary self-renewable resource on species population in a two-patch habitat. It is assumed that the density of forest resource biomass is governed by the logistic equation in both the regions but with the different intrinsic growth rate but the same carrying capacity in the entire habitat. It is further assumed that the densities of species population is also governed by the generalized logistic equations in both the regions but with different growth rates and carrying capacities. It is shown that the steady state solutions are positive, monotonic and continuous under both reservoir and no-flux boundary conditions. The linear and non-linear asymptotic stability conditions of non-uniform steady state are compared with the case of the model with and without diffusion in a homogeneous habitat.     

Population Genetic Structure and Marker Trait Associations Using Morphological,Phytochemical and Molecular Parameters in <Emphasis Type="Italic">Habenaria edgeworthii</Emphasis>—a Threatened Medicinal Orchid of West Himalaya,India

Habenaria edgeworthii Hook. f. ex Collett is an important terrestrial orchid used in different Ayurvedic formulations. In the present study, variations among morphological, phytochemical and molecular markers were assessed. A significant difference was observed among populations using morphological traits. Inter-simple sequence repeat (ISSR) data revealed lower genetic diversity at population level (He = 0.207) as compared to species level (He = 0.334). Analysis of molecular variance (AMOVA) indicates 74 % variation among populations and 26 % within population. Tuber extracts showed significantly (p < 0.05) higher total phenolics and flavonoids among the populations. Antioxidant activity determined by 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging and ferric reducing antioxidant power (FRAP) assays exhibited considerable antioxidant potential. Furthermore, the associations between molecular and morphological and phytochemical attributes were studied using multiple regression analysis (MRA). Several ISSR fragments were associated with some morphological and phytochemical traits. These ISSR fragments can be useful for breeding programme of the species when no other genetic information, such as linkage maps and quantitative trait loci, is available.     

Context-dependent effects of asparagine glycosylation on Pin WW folding kinetics and thermodynamics

Asparagine glycosylation is one of the most common and important post-translational modifications of proteins in eukaryotic cells. N-glycosylation occurs when a triantennary glycan precursor is transferred en bloc to a nascent polypeptide (harboring the N-X-T/S sequon) as the peptide is cotranslationally translocated into the endoplasmic reticulum (ER). In addition to facilitating binding interactions with components of the ER proteostasis network, N-glycans can also have intrinsic effects on protein folding by directly altering the folding energy landscape. Previous work from our laboratories (Hanson et al. Proc. Natl. Acad. Sci. U.S.A. 2009, 109, 3131-3136; Shental-Bechor, D.; Levy, Y. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 8256-8261) suggested that the three sugar residues closest to the protein are sufficient for accelerating protein folding and stabilizing the resulting structure in vitro; even a monosaccharide can have a dramatic effect. The highly conserved nature of these three proximal sugars in N-glycans led us to speculate that introducing an N-glycosylation site into a protein that is not normally glycosylated would stabilize the protein and increase its folding rate in a manner that does not depend on the presence of specific stabilizing protein-saccharide interactions. Here, we test this hypothesis experimentally and computationally by incorporating an N-linked GlcNAc residue at various positions within the Pin WW domain, a small β-sheet-rich protein. The results show that an increased folding rate and enhanced thermodynamic stability are not general, context-independent consequences of N-glycosylation. Comparison between computational predictions and experimental observations suggests that generic glycan-based excluded volume effects are responsible for the destabilizing effect of glycosylation at highly structured positions. However, this reasoning does not adequately explain the observed destabilizing effect of glycosylation within flexible loops. Our data are consistent with the hypothesis that specific, evolved protein-glycan contacts must also play an important role in mediating the beneficial energetic effects on protein folding that glycosylation can confer.     

Breaking away: violation of distortion emission phase-frequency invariance at low frequencies

The phase versus frequency function of the distortion product otoacoustic emission (DPOAE) at 2f(1) - f(2) is approximately invariant at frequencies above 1.5 kHz in human subjects when recorded with a constant f(2)/f(1). However, a secular break from this invariance has been observed at lower frequencies where the phase-gradient becomes markedly steeper. Apical DPOAEs, such as 2f(1)?- f(2), are known to contain contributions from multiple sources. This experiment asked whether the phase behavior of the ear canal DPOAE at low frequencies is driven by the phase of the component from the distortion product (DP) region at 2f(1)?- f(2), which exhibits rapid phase accumulation. Placing a suppressor tone close in the frequency to 2f(1)?- f(2) reduced the contribution of this component to the ear canal DPOAE in normal-hearing adult human ears. When the contribution of this component was reduced, the phase behavior of the ear canal DPOAE was not altered, suggesting that the breaking from DPOAE phase invariance at low frequencies is an outcome of apical-basal differences in cochlear mechanics. The deviation from DPOAE phase invariance appears to be a manifestation of the breaking from approximate scaling symmetry in the human cochlear apex.