A Numerical Scheme for Three-Dimensional Front Propagation and Control of Jordan Mode

As an example of a front propagation, we study the propagation of a three-dimensional nonlinear wavefront into a polytropic gas in a uniform state and at rest. The successive positions and geometry of the wavefront are obtained by solving the conservation form of equations of a weakly nonlinear ray theory. The proposed set of equations forms a weakly hyperbolic system of seven conservation laws with an additional vector constraint, each of whose components is a divergence-free condition. This constraint is an involution for the system of conservation laws, and it is termed a geometric solenoidal constraint. The analysis of a Cauchy problem for the linearized system shows that when this constraint is satisfied initially, the solution does not exhibit any Jordan mode. For the numerical simulation of the conservation laws we employ a high resolution central scheme. The second order accuracy of the scheme is achieved by using MUSCL-type reconstructions and Runge-Kutta time discretizations. A constrained transport-type technique is used to enforce the geometric solenoidal constraint. The results of several numerical experiments are presented, which confirm the efficiency and robustness of the proposed numerical method and the control of the Jordan mode.

Conversion between electromagnetically induced transparency and absorption in a three-level lambda system

We show that it is possible to change from a subnatural electromagnetically induced transparency (EIT) feature to a subnatural electromagnetically induced absorption (EIA) feature in a (degenerate) three-level. system. The change is effected by turning on a second control beam counter-propagating with respect to the first beam. We observe this change in the D-2 line of Rb in a room temperature vapor cell. The observations are supported by density-matrix analysis of the complete sublevel structure including the effect of Doppler averaging, but can be understood qualitatively as arising due to the formation of N-type systems with the two control beams. Since many of the applications of EIT and EIA rely on the anomalous dispersion near the resonances, this introduces a new ability to control the sign of the dispersion. Copyright (C) EPLA, 2012

How Do Glassy Domains Grow?

We construct equations for the growth kinetics of structural glass within mode-coupling theory, through a nonstationary variant of the three-density correlator defined by G. Biroli et al. Phys. Rev. Lett. 97, 195701 (2006)]. We solve a schematic form of the resulting equations to obtain the coarsening of the three-point correlator chi(3)(t, t(w)) as a function of waiting time tw. For a quench into the glass, we find that chi(3) attains a peak value similar to t(w)(0.5) at t - t(w) similar to t(w)(0.8), providing a theoretical basis for the numerical observations of Parisi J. Phys. Chem. B 103, 4128 (1999)] and Kob and Barrat Phys. Rev. Lett. 78, 4581 (1997)]. The aging is not ``simple'': the t(w) dependence cannot be attributed to an evolving effective temperature.

Model Pseudoconvex Domains and Bumping

The Levi geometry at weakly pseudoconvex boundary points of domains in C-n, n >= 3, is sufficiently complicated that there are no universal model domains with which to compare a general domain. Good models may be constructed by bumping outward a pseudoconvex, finite- type Omega subset of C-3 in such a way that: (i) pseudoconvexity is preserved, (ii) the (locally) larger domain has a simpler defining function, and (iii) the lowest possible orders of contact of the bumped domain with partial derivative Omega, at the site of the bumping, are realized. When Omega subset of C-n, n >= 3, it is, in general, hard to meet the last two requirements. Such well-controlled bumping is possible when Omega is h-extendible/semiregular. We examine a family of domains in C-3 that is strictly larger than the family of h-extendible/semiregular domains and construct explicit models for these domains by bumping.

NMR Analysis of Cross Strand Aromatic Interactions in an 8 Residue Hairpin and a 14 Residue Three Stranded beta-Sheet Peptide

Cross strand aromatic interactions between a facing pair of phenylalanine residues in antiparallel beta-sheet structures have been probed using two structurally defined model peptides. The octapeptide Boc-(LFVPPLFV)-P-D-P-L-OMe (peptide 1) favors the beta-hairpin conformation nucleated by the type II' beta-turn formed by the (D)Pro-(L)Pro segment, placing Phe2 and Phe7 side chains in proximity. Two centrally positioned (D)Pro-(L)Pro segments facilitate the three stranded beta-sheet formation in the 14 residue peptide Boc-LFV(D)P(L)PLFVA(D)P(L)PLFV-OMe (peptide 2) in which the Phe2/Phe7 orientations are similar to that in the octapeptide. The anticipated folded conformations of peptides 1 and 2 are established by the delineation of intramolecularly hydrogen bonded NH groups and by the observation of specific cross strand NOEs. The observation of ring current shifted aromatic protons is a diagnostic of close approach of the Phe2 and Phe7 side chains. Specific assignment of aromatic proton resonances using HSQC and HSQC-TOCSY methods allow an analysis of interproton NOEs between the spatially proximate aromatic rings. This approach facilitates specific assignments in systems containing multiple aromatic rings in spectra at natural abundance. Evidence is presented for a dynamic process which invokes a correlated conformational change about the C-alpha-C-beta(chi(1)) bond for the pair of interacting Phe residues. NMR results suggest that aromatic ring orientations observed in crystals are maintained in solution. Anomalous temperature dependence of ring current induced proton chemical shifts suggests that solvophobic effects may facilitate aromatic ring clustering in apolar solvents.

Non-neutral evolution in non-LEE-encoded type III effectors of attaching and effacing Escherichia coli

Attaching and effacing Escherichia coli (AEEC) employ type III secretion system (T3SS) to secrete effector proteins into host cells and regulate their function. Here we have investigated T3SS genes of AEEC for non-neutral evolution. Our analysis revealed non-neutral evolution in three genes (nleE1, nleB2 and nleD) which encode effector proteins. These genes are located outside the locus of enterocyte effacement (LEE). In general, non-LEE effector genes show greater deviation from neutral evolution than LEE effector genes. These results suggest that effector genes located outside LEE are under greater selection pressure than those present in LEE. (C) 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Identification of mycobacterial lectins from genomic data

Sixty-four sequences containing lectin domains with homologs of known three-dimensional structure were identified through a search of mycobacterial genomes. They appear to belong to the -prism II, the C-type, the Microcystis virdis (MV), and the -trefoil lectin folds. The first three always occur in conjunction with the LysM, the PI-PLC, and the -grasp domains, respectively while mycobacterial -trefoil lectins are unaccompanied by any other domain. Thirty heparin binding hemagglutinins (HBHA), already annotated, have also been included in the study although they have no homologs of known three-dimensional structure. The biological role of HBHA has been well characterized. A comparison between the sequences of the lectin from pathogenic and nonpathogenic mycobacteria provides insights into the carbohydrate binding region of the molecule, but the structure of the molecule is yet to be determined. A reasonable picture of the structural features of other mycobacterial proteins containing one or the other of the four lectin domains can be gleaned through the examination of homologs proteins, although the structure of none of them is available. Their biological role is also yet to be elucidated. The work presented here is among the first steps towards exploring the almost unexplored area of the structural biology of mycobacterial lectins. Proteins 2013. (c) 2012 Wiley Periodicals, Inc.

Designed three-stranded beta-sheet in an alpha/beta hybrid peptide

The incorporation of beta-amino acid residues into the antiparallel beta-strand segments of a multi-stranded beta-sheet peptide is demonstrated for a 19-residue peptide, Boc-LV(beta)FV(D)PGL(beta)FVVL(D)PGLVL(beta)FVV-OMe (BBH19). Two centrally positioned (D)Pro-Gly segments facilitate formation of a stable three-stranded beta-sheet, in which beta-phenylalanine ((beta)Phe) residues occur at facing positions 3, 8 and 17. Structure determination in methanol solution is accomplished by using NMR-derived restraints obtained from NOEs, temperature dependence of amide NH chemical shifts, rates of H/D exchange of amide protons and vicinal coupling constants. The data are consistent with a conformationally well-defined three-stranded beta-sheet structure in solution. Cross-strand interactions between (beta)Phe3/(beta)Phe17 and (beta)Phe3/Val15 residues define orientations of these side-chains. The observation of close contact distances between the side-chains on the N- and C-terminal strands of the three-stranded beta-sheet provides strong support for the designed structure. Evidence is presented for multiple side-chain conformations from an analysis of NOE data. An unusual observation of the disappearance of the Gly NH resonances upon prolonged storage in methanol is rationalised on the basis of a slow aggregation step, resulting in stacking of three-stranded beta-sheet structures, which in turn influences the conformational interconversion between type I' and type II' beta-turns at the two (D)Pro-Gly segments. Experimental evidence for these processes is presented. The decapeptide fragment Boc-LV(beta)FV(D)PGL(beta)FVV-OMe (BBH10), which has been previously characterized as a type I' beta-turn nucleated hairpin, is shown to favour a type II' beta-turn conformation in solution, supporting the occurrence of conformational interconversion at the turn segments in these hairpin and sheet structures.

Structural characterization and molecular order of rodlike mesogens with three- and four-ring core by XRD and C-13 NMR spectroscopy

Structural characterizations using XRD and C-13 NMR spectroscopy of two rodlike mesogens consisting of (i) three phenyl ring core with a polar cyano terminal and (ii) four phenyl ring core with flexible dodecyl terminal chain are presented. The three-ring-core mesogen with cyano terminal exhibits enantiotropic smectic A phase while the four-ring mesogen reveals polymesomorphism and shows enantiotropic nematic, smectic C, and tilted hexatic phases. The molecular organization in the three-ring mesogen is found to be partial bilayer smectic Ad type, and the interdigitation of the molecules in the neighboring layers is attributed to the presence of the polar terminal group. For the four-ring mesogen, the XRD results confirm the existence of the smectic C and the tilted hexatic mesophases. A thermal variation of the layer spacing across the smectic C phase followed by a discrete jump at the transition to the tilted hexatic phase is also observed. The tilt angles have been estimated to be about 45 degrees in the smectic C phase and about 40 degrees in tilted hexatic phase. C-13 NMR results indicate that in the mesophase the molecules are aligned parallel to the magnetic field. From the C-13-H-1 dipolar couplings determined from the 2D experiments, the overall order parameter for the three-ring mesogen in its smectic A phase has been estimated to be 0.72 while values ranging from 0.88 to 0.44 have been obtained for the four-ring mesogen as it passes from the tilted hexatic to the nematic phase. The orientations of the different rings of the core unit with respect to each other and also with respect to the long axis of the molecule have also been obtained.

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.

Understanding the role of domain-domain linkers in the spatial orientation of domains in multi-domain proteins

Inter-domain linkers (IDLs)' bridge flanking domains and support inter-domain communication in multi-domain proteins. Their sequence and conformational preferences enable them to carry out varied functions. They also provide sufficient flexibility to facilitate domain motions and, in conjunction with the interacting interfaces, they also regulate the inter-domain geometry (IDG). In spite of the basic intuitive understanding of the inter-domain orientations with respect to linker conformations and interfaces, we still do not entirely understand the precise relationship among the three. We show that IDG is evolutionarily well conserved and is constrained by the domain-domain interface interactions. The IDLs modulate the interactions by varying their lengths, conformations and local structure, thereby affecting the overall IDG. Results of our analysis provide guidelines in modelling of multi-domain proteins from the tertiary structures of constituent domain components.

Effects of a Delocalizable Cation on the Headgroup of Gemini Lipids on the Lipoplex-Type Nanoaggregates Directly Formed from Plasmid DNA

Lipoplex-type nanoaggregates prepared from pEGFP-C3 plasmid DNA (pDNA) and mixed liposomes, with a gemini cationic lipid (CL) 1,2-bis(hexadecyl imidazolium) alkanes], referred as (C(16)Im)(2)C-n (where C-n is the alkane spacer length, n = 2, 3, 5, or 12, between the imidazolium heads) and DOPE zwitterionic lipid, have been analyzed by zeta potential, gel electrophoresis, SAXS, cryo-TEM, fluorescence anisotropy, transfection efficiency, fluorescence confocal microscopy, and cell viability/cytotoxicity experiments to establish a structure-biological activity relationship. The study, carried out at several mixed liposome compositions, alpha, and effective charge ratios, rho(eff), of the lipoplex, demonstrates that the transfection of pDNA using CLs initially requires the determination of the effective charge of both. The electrochemical study confirms that CLs with a delocalizable positive charge in their headgroups yield an effective positive charge that is 90% of their expected nominal one, while pDNA is compacted yielding an effective negative charge which is only 10-25% than that of the linear DNA. SAXS diffractograms show that lipoplexes formed by CLs with shorter spacer (n = 2, 3, or 5) present three lamellar structures, two of them in coexistence, while those formed by CL with longest spacer (n = 12) present two additional inverted hexagonal structures. Cryo-TEM micrographs show nanoaggregates with two multilamellar structures, a cluster-type (at low alpha value) and a fingerprint-type, that coexist with the cluster-type at moderate alpha composition. The optimized transfection efficiency (TE) of pDNA, in HEK293T, HeLa, and H1299 cells was higher using lipoplexes containing gemini CLs with shorter spacers at low a value. Each lipid formulation did not show any significant levels of toxicity, the reported lipoplexes being adequate DNA vectors for gene therapy and considerably better than both Lipofectamine 2000 and CLs of the 1,2-bis(hexadecyl ammnoniun) alkane series, recently reported.

Hypersonic interference heating on flat plate with short three-dimensional protuberances

Experiments were conducted to measure the heat flux in the vicinity of a three-dimensional protuberance placed on a flat plate facing a hypersonic flow at zero angle of attack. The effects of flow enthalpy and height of the protuberance on the interference heating in its vicinity were studied. Evidence of disturbed flow with highly three-dimensional characteristics and heightened vorticity was observed near the protrusion. A parametric study by changing the deflection angle of the protuberance was also made. Correlations exist in the open literature for enthalpy values lower than 2  MJ/kg. This effort has yielded a new correlation that is valid for enthalpies up to 6  MJ/kg. The Z-type schlieren technique was used to visualize the flow features qualitatively for one of the flow conditions studied.

Optimal trajectory planning for path convergence in three-dimensional space

This article addresses the problem of determining the shortest path that connects a given initial configuration (position, heading angle, and flight path angle) to a given rectilinear or a circular path in three-dimensional space for a constant speed and turn-rate constrained aerial vehicle. The final path is assumed to be located relatively far from the starting point. Due to its simplicity and low computational requirements the algorithm can be implemented on a fixed-wing type unmanned air vehicle in real time in missions where the final path may change dynamically. As wind has a very significant effect on the flight of small aerial vehicles, the method of optimal path planning is extended to meet the same objective in the presence of wind comparable to the speed of the aerial vehicles. But, if the path to be followed is closer to the initial point, an off-line method based on multiple shooting, in combination with a direct transcription technique, is used to obtain the optimal solution. Optimal paths are generated for a variety of cases to show the efficiency of the algorithm. Simulations are presented to demonstrate tracking results using a 6-degrees-of-freedom model of an unmanned air vehicle.

Model domains in C-3 with abelian automorphism group

It is shown that every hyperbolic rigid polynomial domain in C-3 of finite-type, with abelian automorphism group is equivalent to a domain that is balanced with respect to some weight.