Glass Transition in the Density Functional Theory of Freezing

A mean-field description of the glass transition in the hard-sphere system is obtained by numerically locating "glassy" minima of a model free-energy functional. These minima, characterized by inhomogeneous but aperiodic density distributions, appear as the average density is increased above the value at which equilibrium crystallization takes place. Investigations of the density distribution and local bond-orientational order at these minima yield results similar to those obtained from simulations.

Diversity in Functional Organization of Class I and Class II Biotin Protein Ligase

The cell envelope of Mycobacterium tuberculosis (M. tuberculosis) is composed of a variety of lipids including mycolic acids, sulpholipids, lipoarabinomannans, etc., which impart rigidity crucial for its survival and pathogenesis. Acyl CoA carboxylase (ACC) provides malonyl-CoA and methylmalonyl-CoA, committed precursors for fatty acid and essential for mycolic acid synthesis respectively. Biotin Protein Ligase (BPL/BirA) activates apo-biotin carboxyl carrier protein (BCCP) by biotinylating it to an active holo-BCCP. A minimal peptide (Schatz), an efficient substrate for Escherichia coli BirA, failed to serve as substrate for M. tuberculosis Biotin Protein Ligase (MtBPL). MtBPL specifically biotinylates homologous BCCP domain, MtBCCP87, but not EcBCCP87. This is a unique feature of MtBPL as EcBirA lacks such a stringent substrate specificity. This feature is also reflected in the lack of self/promiscuous biotinylation by MtBPL. The N-terminus/HTH domain of EcBirA has the selfbiotinable lysine residue that is inhibited in the presence of Schatz peptide, a peptide designed to act as a universal acceptor for EcBirA. This suggests that when biotin is limiting, EcBirA preferentially catalyzes, biotinylation of BCCP over selfbiotinylation. R118G mutant of EcBirA showed enhanced self and promiscuous biotinylation but its homologue, R69A MtBPL did not exhibit these properties. The catalytic domain of MtBPL was characterized further by limited proteolysis. Holo-MtBPL is protected from proteolysis by biotinyl-59 AMP, an intermediate of MtBPL catalyzed reaction. In contrast, apo-MtBPL is completely digested by trypsin within 20 min of co-incubation. Substrate selectivity and inability to promote self biotinylation are exquisite features of MtBPL and are a consequence of the unique molecular mechanism of an enzyme adapted for the high turnover of fatty acid biosynthesis.

Electrooxidation of methanol in sulfuric-acid electrolyte on platized-carbon electrodes with several functional-group characteristics

The effect of acid/base functional-groups associated with platinized-carbon electrodes on their catalytic activity toward electro-oxidation of methanol in sulfuric acid electrolyte at 60-degrees-C is studied. Platinized-carbon electrodes with sm amounts of functional groups exhibit higher catalytic activity compared to those with large concentrations of acidic/basic surface functionalities. The overpotential for methanol oxidation is minimum on electrodes of platinized carbons with pHzpc values between 6 and 7. An x-ray photoelectron spectroscopic study of various platinized carbons suggests that the acid/base surface functional-groups produce ample amounts of surface Pt-oxides and a consequent decrease in activity toward methanol oxidation.

Exact free-surface flows for shallow-water equations .1. - the incompressible case

A comprehensive exact treatment of free surface flows governed by shallow water equations (in sigma variables) is given. Several new families of exact solutions of the governing PDEs are found and are shown to embed the well-known self-similar or traveling wave solutions which themselves are governed by reduced ODEs. The classes of solutions found here are explicit in contrast to those found earlier in an implicit form. The height of the free surface for each family of solutions is found explicitly. For the traveling or simple wave, the free surface is governed by a nonlinear wave equation, but is arbitrary otherwise. For other types of solutions, the height of the free surface is constant either on lines of constant acceleration or on lines of constant speed; in another case, the free surface is a horizontal plane while the flow underneath is a sine wave. The existence of simple waves on shear flows is analytically proved. The interaction of large amplitude progressive waves with shear flow is also studied.

PVU and wave-particle splitting schemes for Euler equations of gas dynamics

A new way of flux-splitting, termed as the wave-particle splitting is presented for developing upwind methods for solving Euler equations of gas dynamics. Based on this splitting, two new upwind methods termed as Acoustic Flux Vector Splitting (AFVS) and Acoustic Flux Difference Splitting (AFDS) methods are developed. A new Boltzmann scheme, which closely resembles the wave-particle splitting, is developed using the kinetic theory of gases. This method, termed as Peculiar Velocity based Upwind (PVU) method, uses the concept of peculiar velocity for upwinding. A special feature of all these methods that the unidirectional and multidirectional parts of the flux vector are treated separately. Extensive computations done using these schemes demonstrate the soundness of the ideas.

Ionic conductivity, mechanical strength and Li-ion battery performance of mono-functional and bi-functional (''Janus'') ``soggy sand'' electrolytes

Influence of dispersion of uniformly sized mono-functional and bi-functional (''Janus'') particles on ionic conductivity of novel ``soggy sand'' electrolytes and its implications on mechanical strength and lithium-ion battery performance are discussed here.

A characteristic based numerical method with tracking for nonlinear wave equations

Many physical problems can be modeled by scalar, first-order, nonlinear, hyperbolic, partial differential equations (PDEs). The solutions to these PDEs often contain shock and rarefaction waves, where the solution becomes discontinuous or has a discontinuous derivative. One can encounter difficulties using traditional finite difference methods to solve these equations. In this paper, we introduce a numerical method for solving first-order scalar wave equations. The method involves solving ordinary differential equations (ODEs) to advance the solution along the characteristics and to propagate the characteristics in time. Shocks are created when characteristics cross, and the shocks are then propagated by applying analytical jump conditions. New characteristics are inserted in spreading rarefaction fans. New characteristics are also inserted when values on adjacent characteristics lie on opposite sides of an inflection point of a nonconvex flux function, Solutions along characteristics are propagated using a standard fourth-order Runge-Kutta ODE solver. Shocks waves are kept perfectly sharp. In addition, shock locations and velocities are determined without analyzing smeared profiles or taking numerical derivatives. In order to test the numerical method, we study analytically a particular class of nonlinear hyperbolic PDEs, deriving closed form solutions for certain special initial data. We also find bounded, smooth, self-similar solutions using group theoretic methods. The numerical method is validated against these analytical results. In addition, we compare the errors in our method with those using the Lax-Wendroff method for both convex and nonconvex flux functions. Finally, we apply the method to solve a PDE with a convex flux function describing the development of a thin liquid film on a horizontally rotating disk and a PDE with a nonconvex flux function, arising in a problem concerning flow in an underground reservoir.

A note on a class of singular integro-differential equations

A simplified analysis is employed to handle a class of singular integro-differential equations for their solutions

Effect of dynamical asymmetry on the viscosity of a random copolymer melt

The variation of the viscosity as a function of the sequence distribution in an A-B random copolymer melt is determined. The parameters that characterize the random copolymer are the fraction of A monomers f, the parameter lambda which determines the correlation in the monomer identities along a chain and the Flory chi parameter chi(F) which determines the strength of the enthalpic repulsion between monomers of type A and B. For lambda>0, there is a greater probability of finding like monomers at adjacent positions along the chain, and for lambda<0 unlike monomers are more likely to be adjacent to each other. The traditional Markov model for the random copolymer melt is altered to remove ultraviolet divergences in the equations for the renormalized viscosity, and the phase diagram for the modified model has a binary fluid type transition for lambda>0 and does not exhibit a phase transition for lambda<0. A mode coupling analysis is used to determine the renormalization of the viscosity due to the dependence of the bare viscosity on the local concentration field. Due to the dissipative nature of the coupling. there are nonlinearities both in the transport equation and in the noise correlation. The concentration dependence of the transport coefficient presents additional difficulties in the formulation due to the Ito-Stratonovich dilemma, and there is some ambiguity about the choice of the concentration to be used while calculating the noise correlation. In the Appendix, it is shown using a diagrammatic perturbation analysis that the Ito prescription for the calculation of the transport coefficient, when coupled with a causal discretization scheme, provides a consistent formulation that satisfies stationarity and the fluctuation dissipation theorem. This functional integral formalism is used in the present analysis, and consistency is verified for the present problem as well. The upper critical dimension for this type of renormaliaation is 2, and so there is no divergence in the viscosity in the vicinity of a critical point. The results indicate that there is a systematic dependence of the viscosity on lambda and chi(F). The fluctuations tend to increase the viscosity for lambda<0, and decrease the viscosity for lambda>0, and an increase in chi(F) tends to decrease the viscosity. (C) 1996 American Institute of Physics.

Establishment of the functional importance of thiamin carrier protein in pregnant rats by using monoclonal antibodies

Monoclonal antibodies (mAbs) to chicken thiamin carrier protein (TCP) have been produced by hybridoma technology to identify the crucial epitopes involved in bioneutralization of the vitamin carrier. The monoclonality of these mAbs (A4C4, F3H6, H8H3, C8C1 and G7H10) was sought to be confirmed by sub-class isotyping; they all belong to IgG1, k type. The epitopes recognized by all the five mAbs are conserved in TCP from the chicken to the rat as assessed by liquid phase RIA and immunoprecipitation of I-125-labelled proteins from pregnant rat serum. Among these mAbs, passive immunization of pregnant rats with the mAb C8C1 only on three consecutive days (day 10, 11 and 12) resulted in embryonic resorption. These results demonstrate the importance of epitopic structure specified by the mAb C8C1 on TCP during pregnancy in rats.

Functional analysis of conserved motifs in EcoP15I DNA methyltransferase

EcoP15I DNA methyltransferase recognizes the sequence 5'-CAGCAG-3' and transfers a methyl group to N-6 of the second adenine residue in the recognition sequence. All N-6 adenine methyltransferases contain two highly conserved sequences, FxGxG (motif I), postulated to form part of the S-adenosyl-L-methionine binding site and (D/N/S)PP(Y/F) (motif IV) involved in catalysis. We have altered the second glycine residue in motif I to arginine and serine, and substituted tyrosine in motif IV with tryptophan in EcoP15I DNA methyltransferase, using site-directed mutagenesis. The mutant enzymes were overexpressed, purified and characterized by biochemical methods. The mutations in motif I completely abolished AdoMet binding but left target DNA recognition unaltered. Although the mutation in motif IV resulted in loss of enzyme activity, we observed enhanced crosslinking of S-adenosyl-L-methionine and DNA. This implies that DNA and AdoMet binding sites are close to motif IV. Taken together, these results reinforce the importance of motif I in AdoMet binding and motif IV in catalysis. Additionally, limited proteolysis and UV crosslinking experiments with EcoP15I DNA methyltransferase imply that DNA binds in a cleft formed by two domains in the protein. Methylation protection analysis provides evidence for the fact that EcoP15I DNA MTase makes contacts in the major groove of its substrate DNA. Interestingly, hypermethylation of the guanine residue next to the target adenine residue indicates that the protein probably flips out the target adenine residue. (C) 1996 Academic Press Limited

Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms

Molybdenum-cofactor (Moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. Two proteins, MogA and MoeA, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. Here, three crystal structures of the Moco-biosynthesis protein MogA from the two thermophilic organisms Thermus thermophilus (TtMogA; 1.64 angstrom resolution, space group P2(1)) and Aquifex aeolicus (AaMogA; 1.70 angstrom resolution, space group P2(1) and 1.90 angstrom resolution, space group P1) have been determined. The functional roles and the residues involved in oligomerization of the protein molecules have been identified based on a comparative analysis of these structures with those of homologous proteins. Furthermore, functional roles have been proposed for the N- and C-terminal residues. In addition, a possible protein-protein complex of MogA and MoeA has been proposed and the residues involved in protein-protein interactions are discussed. Several invariant water molecules and those present at the subunit interfaces have been identified and their possible structural and/or functional roles are described in brief. In addition, molecular-dynamics and docking studies with several small molecules (including the substrate and the product) have been carried out in order to estimate their binding affinities towards AaMogA and TtMogA. The results obtained are further compared with those obtained for homologous eukaryotic proteins.