Probing the Neutral Edge Modes in Transport across a Point Contact via Thermal Effects in the Read-Rezayi Non-Abelian Quantum Hall States

Non-Abelian quantum Hall states are characterized by the simultaneous appearance of charge and neutral gapless edge modes, with the structure of the latter being intricately related to the existence of bulk quasiparticle excitations obeying non-Abelian statistics. Here we propose a scenario for detecting the neutral modes by having two point contacts in series separated by a distance set by the thermal equilibration length of the charge mode. We show that by using the first point contact as a heating device, the excess charge noise measured at the second point contact carries a nontrivial signature of the presence of the neutral mode. We also obtain explicit expressions for the thermal conductance and corresponding Lorentz number for transport across a quantum point contact between two edges held at different temperatures and chemical potentials.

Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks

Background The genome of a wide variety of prokaryotes contains the luxS gene homologue, which encodes for the protein S-ribosylhomocysteinelyase (LuxS). This protein is responsible for the production of the quorum sensing molecule, AI-2 and has been implicated in a variety of functions such as flagellar motility, metabolic regulation, toxin production and even in pathogenicity. A high structural similarity is present in the LuxS structures determined from a few species. In this study, we have modelled the structures from several other species and have investigated their dimer interfaces. We have attempted to correlate the interface features of LuxS with the phenotypic nature of the organisms. Results The protein structure networks (PSN) are constructed and graph theoretical analysis is performed on the structures obtained from X-ray crystallography and on the modelled ones. The interfaces, which are known to contain the active site, are characterized from the PSNs of these homodimeric proteins. The key features presented by the protein interfaces are investigated for the classification of the proteins in relation to their function. From our analysis, structural interface motifs are identified for each class in our dataset, which showed distinctly different pattern at the interface of LuxS for the probiotics and some extremophiles. Our analysis also reveals potential sites of mutation and geometric patterns at the interface that was not evident from conventional sequence alignment studies. Conclusion The structure network approach employed in this study for the analysis of dimeric interfaces in LuxS has brought out certain structural details at the side-chain interaction level, which were elusive from the conventional structure comparison methods. The results from this study provide a better understanding of the relation between the luxS gene and its functional role in the prokaryotes. This study also makes it possible to explore the potential direction towards the design of inhibitors of LuxS and thus towards a wide range of antimicrobials.

Technicolor

The need for reexamination of the standard model of strong, weak, and electromagnetic interactions is discussed, especially with regard to 't Hooft's criterion of naturalness. It has been argued that theories with fundamental scalar fields tend to be unnatural at relatively low energies. There are two solutions to this problem: (i) a global supersymmetry, which ensures the absence of all the naturalness-violating effects associated with scalar fields, and (ii) composite structure of the scalar fields, which starts showing up at energy scales where unnatural effects would otherwise have appeared. With reference to the second solution, this article reviews the case for dynamical breaking of the gauge symmetry and the technicolor scheme for the composite Higgs boson. This new interaction, of the scaled-up quantum chromodynamic type, keeps the new set of fermions, the technifermions, together in the Higgs particles. It also provides masses for the electroweak gauge bosons W± and Z0 through technifermion condensate formation. In order to give masses to the ordinary fermions, a new interaction, the extended technicolor interaction, which would connect the ordinary fermions to the technifermions, is required. The extended technicolor group breaks down spontaneously to the technicolor group, possibly as a result of the "tumbling" mechanism, which is discussed here. In addition, the author presents schemes for the isospin breaking of mass matrices of ordinary quarks in the technicolor models. In generalized technicolor models with more than one doublet of technifermions or with more than one technicolor sector, we have additional low-lying degrees of freedom, the pseudo-Goldstone bosons. The pseudo-Goldstone bosons in the technicolor model of Dimopoulos are reviewed and their masses computed. In this context the vacuum alignment problem is also discussed. An effective Lagrangian is derived describing colorless low-lying degrees of freedom for models with two technicolor sectors in the combined limits of chiral symmetry and large number of colors and technicolors. Finally, the author discusses suppression of flavor-changing neutral currents in the extended technicolor models.

The effect of radiation on the electron pairing in a multiband system

The possible occurrence of a generalized (1-wave) nonequilibrium superconducting state in a multiband system under certain conditions is studied. In the model the radiation field causes interband mixing, and phonons of an appropriate mode (branch) are involved in the interband scattering of electrons of two conduction bands of the system. The strength of the generalized 1-wave pairing interaction between quasiparticles belonging to new radiation admixed states depends on the density (n o/V) of quanta in the system. The coupling constant has the form Xl= AiB(n o/V)/[C + B(no/V)], where A1, B, and C are parameters. For C > B(n0/V), the transition temperature T1* increases with (no/V) in the initial stages. It levels off with higher power. With further increase of power, the transition temperature is expected to drop sharply due to heating effects which cause pair breaking. Estimates show that p-wave (triplet state) pairing may be possible under radiation-induced nonequilibrium situations in appropriate systems. Estimates for lifetimes of various processes quasiparticle, phonon, pair relaxation, and photon-induced mixing) show that the coherence required for the mixing and pairing effects will be maintained for the temperature range and photon density considered.

A conformational approach to the study of the dynamics of enzyme inhibition: studies on thermolysin

The preferred conformations of β-phenylpropionyl-Image -phenylalanine (β-PPP) and N-carbobenzoxy-L-phenylalanine (Cbz-Phe), two inhibitors of thermolysin, have been determined by computing potential energy using empirial potential energy functions. Of the 15 to 20 conformations that are favoured for each of these inhibitors only a few have the right conformation to reach the active site of the enzyme. The conformer of β-PPP that initiates binding with the enzyme is different from the bound one, while for Cbz-Phe the bound and initiating conformers are quite similar. Thus, β-PPP favours the ‘induced fit’ model while Cbz-Phe follows the ‘lock and key’ model of binding. The inhibitors differ in their alignment at the active site.

The modes of binding methyl-alpha (and beta)-D-glucopyranosides and some of their derivatives to concanavalin A--a theoretical approach

The probable modes of binding of Methyl--alpha (and beta)-D-glucopyranosides and some of their derivatives to concanavalin A have been proposed from theoretical studies. Theory predicts that beta-MeGlcP can bind to ConA in three different modes whereas alpha-MeGlcP can bind only in one mode. beta-MeGlcP in its most favourable mode of binding differs from alpha-MeGlcP in its alignment in the active-site of the lectin where it binds in a flipped or inverted orientation. Methyl substitution at the C-2 atom of the alpha-MeGlcP does not significantly affect the possible orientations of the sugar in the active-site of the lectin. Methyl substitution at C-3 or C-4, however, affects the allowed orientations drastically leading to the poor inhibiting power of Methyl-3-O-methyl-alpha-D-glucopyranoside and the inactivity of Methyl-4-O-methyl-alpha-D-glycopyranoside. These studies suggest that the increased activity of the alpha-MeGlcP over beta-MeGlcP may be due to the possibility of formation of better hydrogen bonds and to hydrophobic interactions rather than to steric factors as suggested by earlier workers. These models explain the available NMR and other binding studies.

Wrought aluminum-nickel alloys for high strength-high conductivity applications

Aluminum-Nickel alloys ranging from 0.06 pct to 6.1 pct (by wt) Ni have been developed for high strength-high conductivity applications. These alloys were produced by solidification in a permanent mold followed by homogenization, hot extrusion or hot rolling and cold drawing to wire form. This sequence of fabrication a) led to the production of fine fibrous dispersoids of NiAl3 as part of the Al-NiAl3 eutectic during the initial casting operation, b) permitted the retention of fine fibrous dispersiods of NiAl3 produced during casting without any significant coarsening during processing and c) led to uniform dispersion and general alignment of these fibrous dispersoids along a given direction in the product without any measurable fiber-matrix separation, extensive fiber-fragmentation or crack production in the matrix. These alloys can be processed to wire form as easily as aluminum and when processed by the above sequence, possess very attractive combination of high strength-high electrical conductivity. Tensile strengths range from 173 N/mm2 (at 0.6 pct Ni) to 241 N/mm2 (at 6.1 pct Ni) in combination with corresponding conductivity values between 62 pct IACS and 55.5 pct IACS. The wires also possess attractive yield strength; for instance, the 0.2 pct off-set strength of Al-6.1 pct Ni wire is 213 N/mm2. Using simple composite rules, the estimated strength and the conductivity of NiAl3 fibers were found to be 1380 N/mm2 and 18 pct IACS respectively, in these wires.

Automatic Path Planning and Control Design for Autonomous Landing of UAVs using Dynamic Inversion

In this paper a nonlinear control has been designed using the dynamic inversion approach for automatic landing of unmanned aerial vehicles (UAVs), along with associated path planning. This is a difficult problem because of light weight of UAVs and strong coupling between longitudinal and lateral modes. The landing maneuver of the UAV is divided into approach, glideslope and flare. In the approach UAV aligns with the centerline of the runway by heading angle correction. In glideslope and flare the UAV follows straight line and exponential curves respectively in the pitch plane with no lateral deviations. The glideslope and flare path are scheduled as a function of approach distance from runway. The trajectory parameters are calculated such that the sink rate at touchdown remains within specified bounds. It is also ensured that the transition from the glideslope to flare path is smooth by ensuring C-1 continuity at the transition. In the outer loop, the roll rate command is generated by assuring a coordinated turn in the alignment segment and by assuring zero bank angle in the glideslope and flare segments. The pitch rate command is generated from the error in altitude to control the deviations from the landing trajectory. The yaw rate command is generated from the required heading correction. In the inner loop, the aileron, elevator and rudder deflections are computed together to track the required body rate commands. Moreover, it is also ensured that the forward velocity of the UAV at the touch down remains close to a desired value by manipulating the thrust of the vehicle. A nonlinear six-DOF model, which has been developed from extensive wind-tunnel testing, is used both for control design as well as to validate it.

Orientational ordering in sheared inelastic dumbbells

Using even driven simulations, we show that homogeneously sheared inelastic dumbbells in two dimensions are randomly orientated in the limit of low density. As the packing fraction is increased, particles first tend to orient along the extensional axis, and then as the packing fraction is further increased, the alignment shifts closer to the flow axis. The orientational order parameter displays a continuous increase with packing fraction and does not appear to exhibit a universal scaling with elongation. Except at the highest packing fractions, the orientational distribution function can be reconstructed with only the first coefficient of the Fourier expansion.

Primary structure of a Thomsen-Friedenreich-antigen-specific lectin, jacalin [Artocarpus integrifolia (jack fruit) agglutinin]. Evidence for the presence of an internal repeat

Jacalin [Artocarpus integrifolia (jack fruit) agglutinin] is made up of two types of chains, heavy and light, with M(r) values of 16,200 +/- 1200 and 2090 +/- 300 respectively (on the basis of gel-permeation chromatography under denaturing conditions). Its complete amino acid sequence was determined by manual degradation using a 4-dimethylaminoazobenzene 4'-isothiocyanate double-coupling method. Peptide fragments for sequence analysis were obtained by chemical cleavages of the heavy chain with CNBr, hydroxylamine hydrochloride and iodosobenzoic acid and enzymic cleavage with Staphylococcus aureus proteinase. The peptides were purified by a combination gel-permeation and reverse-phase chromatography. The light chains, being only 20 residues long, could be sequenced without fragmentation. Amino acid analyses and carboxypeptidase-Y-digestion C-terminal analyses of the subunits provided supportive evidence for their sequence. Computer-assisted alignment of the jacalin heavy-chain sequence failed to show sequence similarity to that of any lectin for which the complete sequence is known. Analyses of the sequence showed the presence of an internal repeat spanning residues 7-64 and 76-130. The internal repeat was found to be statistically significant.

A Search for Energy Minimized Sequences of Proteins

In this paper, we present numerical evidence that supports the notion of minimization in the sequence space of proteins for a target conformation. We use the conformations of the real proteins in the Protein Data Bank (PDB) and present computationally efficient methods to identify the sequences with minimum energy. We use edge-weighted connectivity graph for ranking the residue sites with reduced amino acid alphabet and then use continuous optimization to obtain the energy-minimizing sequences. Our methods enable the computation of a lower bound as well as a tight upper bound for the energy of a given conformation. We validate our results by using three different inter-residue energy matrices for five proteins from protein data bank (PDB), and by comparing our energy-minimizing sequences with 80 million diverse sequences that are generated based on different considerations in each case. When we submitted some of our chosen energy-minimizing sequences to Basic Local Alignment Search Tool (BLAST), we obtained some sequences from non-redundant protein sequence database that are similar to ours with an E-value of the order of 10(-7). In summary, we conclude that proteins show a trend towards minimizing energy in the sequence space but do not seem to adopt the global energy-minimizing sequence. The reason for this could be either that the existing energy matrices are not able to accurately represent the inter-residue interactions in the context of the protein environment or that Nature does not push the optimization in the sequence space, once it is able to perform the function.

Mutational analysis of active-site residues in the Mycobacterium leprae RecA intein, a LAGLIDADG homing endonuclease: Asp(122) and Asp(193) are crucial to the double-stranded DNA cleavage activity whereas Asp(218) is not

Mycobacterium leprae recA harbors an in-frame insertion sequence that encodes an intein homing endonuclease (PI-MleI). Most inteins (intein endonucleases) possess two conserved LAGLIDADG (DOD) motifs at their ctive center. A common feature of LAGLIDADG-type homing endonucleases is that they recognize and cleave the same or very similar DNA sequences. However, PI-MleI is distinctive from other members of the family of LAGLIDADG-type HEases for its modular structure with functionally separable domains for DNA-binding and cleavage, each with distinct sequence preferences. Sequence alignment analyses of PI-MleI revealed three putative LAGLIDADG motifs; however, there is conflicting bioinformatics data in regard to their identity and specific location within the intein polypeptide. To resolve this conflict and to determine the active-site residues essential for DNA target site recognition and double-stranded DNA cleavage, we performed site-directed mutagenesis of presumptive catalytic residues in the LAGLIDADG motifs. Analysis of target DNA recognition and kinetic parameters of the wild-type PI-MleI and its variants disclosed that the two amino acid residues, Asp(122) (in Block C) and Asp(193) (in functional Block E), are crucial to the double-stranded DNA endonuclease activity, whereas Asp(218) (in pseudo-Block E) is not. However, despite the reduced catalytic activity, the PI-MleI variants, like the wild-type PI-MleI, generated a footprint of the same length around the insertion site. The D122T variant showed significantly reduced catalytic activity, and D122A and D193A mutations although failed to affect their DNA-binding affinities, but abolished the double-stranded DNA cleavage activity. On the other hand, D122C variant showed approximately twofold higher double-stranded DNA cleavage activity, compared with the wild-type PI-MleI. These results provide compelling evidence that Asp(122) and Asp(193) in DOD motif I and II, respectively, are bona fide active-site residues essential for DNA cleavage activity. The implications of these results are discussed in this report.

Use of structure-directed DNA ligands to probe the binding of recA protein to narrow and wide grooves of DNA and on its ability to promote homologous pairing

We have used circular dichroism and structure-directed drugs to identify the role of structural features, wide and narrow grooves in particular, required for the cooperative polymerization, recognition of homologous sequences, and the formation of joint molecules promoted by recA protein. The path of cooperative polymerization of recA protein was deduced by its ability to cause quantitative displacement of distamycin from the narrow groove of duplex DNA. By contrast, methyl green bound to the wide groove was retained by the nucleoprotein filaments comprised of recA protein-DNA. Further, the mode of binding of these ligands and recA protein to DNA was confirmed by DNaseI digestion. More importantly, the formation of joint molecules was prevented by distamycin in the narrow groove while methyl green in the wide groove had no adverse effect. Intriguingly, distamycin interfered with the production of coaggregates between nucleoprotein filaments of recA protein-M13 ssDNA and naked linear M13 duplex DNA, but not with linear phi X174 duplex DNA. Thus, these data, in conjunction with molecular modeling, suggest that the narrow grooves of duplex DNA provide the fundamental framework required for the cooperative polymerization of recA protein and alignment of homologous sequences. These findings and their significance are discussed in relation to models of homologous pairing between two intertwined DNA molecules.

DNA-induced conformational changes in RecA protein. Evidence for structural heterogeneity among nucleoprotein filaments and implications for homologous pairing

We have used circular dichroism as a probe to characterize the solution conformational changes in RecA protein upon binding to DNA. This approach revealed that RecA protein acquires significant amounts of alpha-helix upon interaction with DNA. These observations, consistent with the data from crystal structure (Story, R. M., Weber, I., and Steitz, T. (1992) Nature 355, 318-325), support the notion that some basic domains including the DNA binding motifs of RecA protein are unstructured and might contribute to the formation of alpha-helix. A comparison of nucleoprotein filaments comprised of RecA protein and a variety of DNA substrates revealed important structural heterogeneity. The most significant difference was observed with poly(dG). poly(dC) and related polymers, rich in GC sequences, which induced minimal amounts of alpha-helix in RecA protein. The magnitude of induction of alpha-helix in RecA protein, which occurred concomitant with the production of ternary complexes, was 2-fold higher with homologous than heterologous duplex DNA. Most importantly, the stimulation of ATP hydrolysis by high salt coincided with that of the induction of alpha-helix in RecA protein. These conformational differences provide a basis for thinking about the biochemical and structural transitions that RecA protein experiences during the formal steps of presynapsis, recognition, and alignment of homologous sequences.

SIR Analysis and Interference Cancellation in Uplink OFDMA with Large Carrier Frequency/Timing Offsets

In uplink OFDMA, carrier frequency offsets (CFO) and/or timing offsets (TO) of other users with respect to a desired user can cause multiuser interference (MUI). In practical uplink OFDMA systems (e.g., IEEE 802.16e standard), effect of this MUI is made acceptably small by requiring that frequency/timing alignment be achieved at the receiver with high precision (e.g., CFO must be within 1 % of the subcarrier spacing and TO must be within 1/8th of the cyclic prefix duration in IEEE 802.16e), which is realized using complex closed-loop frequency/timing correction between the transmitter and the receiver. An alternate open-loop approach to handle the MUI induced by large CFOs and TOs is to employ interference cancellation techniques at the receiver. In this paper, we first analytically characterize the degradation in the average output signal-to-interference ratio (SIR) due to the combined effect of large CFOs and TOs in uplink OFDMA. We then propose a parallel interference canceller (PIC) for the mitigation of interference due to CFOs and TOs in this system. We show that the proposed PIC effectively mitigates the performance loss due to CFO/TO induced interference in uplink OFDMA.