Quantum fidelity for one-dimensional Dirac fermions and two-dimensional Kitaev model in the thermodynamic limit

We study the scaling behavior of the fidelity (F) in the thermodynamic limit using the examples of a system of Dirac fermions in one dimension and the Kitaev model on a honeycomb lattice. We show that the thermodynamic fidelity inside the gapless as well as gapped phases follow power-law scalings, with the power given by some of the critical exponents of the system. The generic scaling forms of F for an anisotropic quantum critical point for both the thermodynamic and nonthermodynamic limits have been derived and verified for the Kitaev model. The interesting scaling behavior of F inside the gapless phase of the Kitaev model is also discussed. Finally, we consider a rotation of each spin in the Kitaev model around the z axis and calculate F through the overlap between the ground states for the angle of rotation eta and eta + d eta, respectively. We thereby show that the associated geometric phase vanishes. We have supplemented our analytical calculations with numerical simulations wherever necessary.

Quantum fidelity for one-dimensional Dirac fermions and two-dimensional Kitaev model in the thermodynamic limit

We study the scaling behavior of the fidelity (F) in the thermodynamic limit using the examples of a system of Dirac fermions in one dimension and the Kitaev model on a honeycomb lattice.We show that the thermodynamic fidelity inside the gapless as well as gapped phases follow power-law scalings, with the power given by some of the critical exponents of the system. The generic scaling forms of F for an anisotropic quantum critical point for both the thermodynamic and nonthermodynamic limits have been derived and verified for the Kitaev model. The interesting scaling behavior of F inside the gapless phase of the Kitaev model is also discussed. Finally, we consider a rotation of each spin in the Kitaev model around the z axis and calculate F through the overlap between the ground states for the angle of rotation η and η + dη, respectively. We thereby show that the associated geometric phase vanishes. We have supplemented our analytical calculations with numerical simulations wherever necessary

The Structure of the Thioredoxin−Triosephosphate Isomerase Complex Provides Insights into the Reversible Glutathione-Mediate Regulation of Triosephosphate Isomerase

Protein−protein interactions are crucial for many biological functions. The redox interactome encompasses numerous weak transient interactions in which thioredoxin plays a central role. Proteomic studies have shown that thioredoxin binds to numerous proteins belonging to various cellular processes, including energy metabolism. Thioredoxin has cross talk with other redox mechanisms involving glutathionylation and has functional overlap with glutaredoxin in deglutathionylation reactions. In this study, we have explored the structural and biochemical interactions of thioredoxin with the glycolytic enzyme, triosephosphate isomerase. Nuclear magnetic resonance chemical shift mapping methods and molecular dynamics-based docking have been applied in deriving a structural model of the thioredoxin−triosephosphate isomerase complex. The spatial proximity of active site cysteine residues of thioredoxin to reactive thiol groups on triosephosphate isomerase provides a direct link to the observed deglutathionylation of cysteine 217 in triosephosphate isomerase, thereby reversing the inhibitory effect of S-glutathionylation of triosephosphate isomerase.

Nonlinear cyclic load analysis for lateral response of batter piles in soft clay with a rigorous degradation model

Nonlinear analysis of batter piles in soft clay is performed using the finite element technique. As the batter piles are not only governed by lateral load but also axial load, the effect of P- Delta moment and geometric stiffness matrix is included in the analysis. For implementing the nonlinear soil behavior, reduction in soil strength (degradation), and formation of gap with number of load cycles, a numerical model is developed where a hyperbolic relation is adopted for the soil in static condition and hyperbolic relation considering degradation and gap for cyclic load condition. The numerical model is validated with published experimental results for cyclic lateral loading and the hysteresis loops are developed to predict the load-deflection behavior and soil resistance behavior during consecutive cycles of loading. This paper highlights the importance of a rigorous degradation model for subsequent cycles of loading on the pile-soil system by a hysteretic representation.

Performance analysis of UDP with energy efficient link layer on Markov fading channels

In this paper, we analyze the throughput and energy efficiency performance of user datagram protocol (UDP) using linear, binary exponential, and geometric backoff algorithms at the link layer (LL) on point-to-point wireless fading links. Using a first-order Markov chain representation of the packet success/failure process on fading channels, we derive analytical expressions for throughput and energy efficiency of UDP/LL with and without LL backoff. The analytical results are verified through simulations. We also evaluate the mean delay and delay variation of voice packets and energy efficiency performance over a wireless link that uses UDP for transport of voice packets and the proposed backoff algorithms at the LL. We show that the proposed LL backoff algorithms achieve energy efficiency improvement of the order of 2-3 dB compared to LL with no backoff, without compromising much on the throughput and delay performance at the UDP layer. Such energy savings through protocol means will improve the battery life in wireless mobile terminals.

Some Aspects of the Kobayashi and Carath,odory Metrics on Pseudoconvex Domains

The purpose of this article is to consider two themes, both of which emanate from and involve the Kobayashi and the Carath,odory metric. First, we study the biholomorphic invariant introduced by B. Fridman on strongly pseudoconvex domains, on weakly pseudoconvex domains of finite type in C (2), and on convex finite type domains in C (n) using the scaling method. Applications include an alternate proof of the Wong-Rosay theorem, a characterization of analytic polyhedra with noncompact automorphism group when the orbit accumulates at a singular boundary point, and a description of the Kobayashi balls on weakly pseudoconvex domains of finite type in C (2) and convex finite type domains in C (n) in terms of Euclidean parameters. Second, a version of Vitushkin's theorem about the uniform extendability of a compact subgroup of automorphisms of a real analytic strongly pseudoconvex domain is proved for C (1)-isometries of the Kobayashi and Carath,odory metrics on a smoothly bounded strongly pseudoconvex domain.

Dynamic Internal Cavities of Dendrimers as Constrained Media. A Study of Photochemical Isomerizations of Stilbene and Azobenzene Using Poly(alkyl aryl ether) Dendrimers

Dendritic rnicroenvironments defined by dynamic internal cavities of a dendrimer were probed through geometric isomerization of stilbene and azobenzene. A third-generation poly(alkyl aryl ether) dendrimer with hydrophilic exterior and hydrophobic interior was used as a reaction cavity in aqueous medium. The dynamic inner cavity sizes were varied by utilizing alkyl linkers that connect the branch junctures from ethyl to n-pentyl moiety (C(2)G(3)-C(5)G(3)). Dendrimers constituted with n-pentyl linker were found to afford higher solubilities of stilbene and azobenzene. Direct irradiation of trans-stilbene showed that C(5)G(3) and C(4)G(3) dendrimers afforded considerable phenanthrene formation, in addition to cis-stilbene, whereas C(3)G(3) and C(2)G(3) gave only cis-stilbene. An electron-transfer sensitized trans-cis isomerization, using cresyl violet perchlorate as the sensitizer, also led to similar results. Thermal isomerization of cis-azobenzene to trans-azobenzene within dendritic microenvironments revealed that the activation energy of the cis- to trans-isomer was increasing in the series C(5)G(3) < C(4)G(3) < C(3)G(3)

PAMAM Dendrimer-Drug Interactions: Effect of pH on the Binding and Release Pattern

Understanding the dendrimer-drug interaction is of great importance to design and optimize the dendrimer-based drug delivery system. Using atomistic molecular dynamics (MD) simulations, we have analyzed the release pattern of four ligands (two soluble drugs, namely, salicylic acid (Sal), L-alanine (Ala), and two insoluble drugs, namely, phenylbutazone (Pbz) and primidone (Prim)), which were initially encapsulated inside the ethylenediamine (EDA) cored polyamidoamine (PAMAM) dendrimer using the docking method. We have computed the potential of mean force (PMF) variation with generation 5 (G5)-PAMAM dendrimer complexed with drug molecules using umbrella sampling. From our calculated PMF values, we observe that soluble drugs (Sal and Ala) have lower energy barriers than insoluble drugs (Pbz and Prim). The order of ease of release pattern for these drugs from G5 protonated PAMAM dendrimer was found to be Ala > Sal > Prim > Pbz. In the case of insoluble drugs (Prim and Pbz), because of larger size, we observe much nonpolar contribution, and thus, their larger energy barriers can be reasoned to van der Waals contribution. From the hydrogen bonding analysis of the four PAMAM drug complexes under study, we found intermolecular hydrogen bonding to show less significant contribution to the free energy barrier. Another interesting feature appears while calculating the PMF profile of G5NP (nonprotonated)-PAMAM Pbz and G5NP (nonprotonated)-PAMAM-Sal complex. The PMF was found to be less when the drug is bound to nonprotonated dendrimer compared to the protonated dendrimer. Our results suggest that encapsulation of the drug molecule into the host PAMAM dendrimer should be carried out at higher pH values (near pH 10). When such complex enters the human body, the pH is around 7.4 and at that physiological pH, the dendrimer holds the drug tightly. Hence the release of drug can occur at a controlled rate into the bloodstream. Thus, our findings provide a microscopic picture of the encapsulation and controlled release of drugs in the case of dendrimer-based host-guest systems.

Periodically Grafted Amphiphilic Copolymers: Nonionic Analogues of Ionenes

We describe a novel class of periodically grafted amphiphilic copolymers (PGACs) that could serve as nonionic functional mimics of ionenes, the primary difference being that the periodically occurring charged units along the backbone of ionenes are replaced by hydrophilic oligoethylene glycol segments. The synthesis and properties of this new class of segmented polymers that carry a hydrophobic alkylene polyester backone with periodically placed hydrophilic oligo(oxyethylene) pendant units are presented. When the length of the intervening alkylene segment is adequately long, 22-carbons in this case, and the pendant unit is a hexaethylene glycol monomethyl ether (HEG) segment, the polymer chain appears to adopt a folded zigzag conformation, reminiscent of the accordion-type structure formed by cationic ionenes. This transformation is driven by the intrinsic immiscibility of the alkylene and HEG segments and is reinforced by the strong tendency for long chain alkylene segments to crystallize in a paraffinic lattice. Evidence of the formation of such structures comes from the AFM images, which reveal the formation of remarkably flat pancake-like aggregates that are formed by the lateral aggregation of individually collapsed polymer chains; importantly, the heights of these structures match well with the lamellar layer-spacing obtained from SAXS studies of bulk samples. DSC studies further confirm the crystallization of the intervening alkylene segments, especially when they are long (C22), suggesting the formation of the folded zigzag structures. In a suitably designed PGAC that carries diacetylene units symmetrically placed within the alkylene segment, attempts were made to cross-polymerize the diacetylene units and generate PEGylated nanoparticles. However, these attempts were unsuccessful demonstrating the very stringent geometric requirements for the topotactic polymerization of diacetylenes.

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.

Guided Wave based Damage Detection in a Composite T-joint using 3D Scanning Laser Doppler Vibrometer

Composite T-joints are commonly used in modern composite airframe, pressure vessels and piping structures, mainly to increase the bending strength of the joint and prevents buckling of plates and shells, and in multi-cell thin-walled structures. Here we report a detailed study on the propagation of guided ultrasonic wave modes in a composite T-joint and their interactions with delamination in the co-cured co-bonded flange. A well designed guiding path is employed wherein the waves undergo a two step mode conversion process, one is due to the web and joint filler on the back face of the flange and the other is due to the delamination edges close to underneath the accessible surface of the flange. A 3D Laser Doppler Vibrometer is used to obtain the three components of surface displacements/velocities of the accessible face of the flange of the T-joint. The waves are launched by a piezo ceramic wafer bonded on to the back surface of the flange. What is novel in the proposed method is that the location of any change in material/geometric properties can be traced by computing a frequency domain power flow along a scan line. The scan line can be chosen over a grid either during scan or during post-processing of the scan data off-line. The proposed technique eliminates the necessity of baseline data and disassembly of structure for structural interrogation.

Regioselective synthesis and antimicrobial studies of ester linked 1,4-disubstituted 1,2,3-bistriazoles

A series of 1,4-disubstituted 1,2,3-bistriazoles was synthesized via click chemistry by cycloaddition of various bisalkynes with benzyl/2-phenylethyl azide. Synthesized triazoles were characterized by IR, H-1 NMR, C-13 NMR and mass spectral techniques. All the compounds were evaluated for antibacterial/antifungal activities and found to possess moderate to good antimicrobial activities. Further the docking study for the most active compound against DNA Gyrase was also carried out. (C) 2012 Elsevier Ltd. All rights reserved.

A variant peptide of buffalo colostrum beta-lactoglobulin inhibits angiotensin I-converting enzyme activity

beta-lactoglobulin is a rich source of bioactive peptides. The LC-MS separated tryptic peptides of buffalo colostrum beta-lactoglobulin (BLG-col) were computed based on MS-MS fragmentation for de novo sequencing. Among the selected peptides (P1-P8), a variant was detected with methionine at position 74 instead of glutamate. The sequences of two peptides were identical to hypocholesterolemic peptides whereas the remaining peptides were in accordance with buffalo milk beta-lactoglobulin. Comparative sequence analysis of BLG-col to milk beta-lactoglobulin was carried out using CLUSTALW2 and a molecular model for BLG-col was constructed (PMDB ID-PM0076812). The synthesized variant pentapeptide (IIAMK, m/z-576 Da) was found to inhibit angiotensin I-converting enzyme (ACE) with an IC50 of 498 +/- 2 mu M, which was rationalized through docking simulations using Molgrow virtual docker. (C) 2012 Elsevier Masson SAS. All rights reserved.

A Rhodanine Derivative CCR-11 Inhibits Bacterial Proliferation by Inhibiting the Assembly and GTPase Activity of FtsZ

A perturbation of FtsZ assembly dynamics has been shown to inhibit bacterial cytokinesis. In this study, the antibacterial activity of 151 rhodanine compounds was assayed using Bacillus subtilis cells. Of 151 compounds, eight strongly inhibited bacterial proliferation at 2 mu M. Subsequently, we used the elongation of B. subtilis cells as a secondary screen to identify potential FtsZ-targeted antibacterial agents. We found that three compounds significantly increased bacterial cell length. One of the three compounds, namely, CCR-11 (E)-2-thioxo-5-({3-(trifluoromethyl)phenyl]furan-2-yl}methylene) thiazolidin-4-one], inhibited the assembly and GTPase activity of FtsZ in vitro. CCR-11 bound to FtsZ with a dissociation constant of 1.5 +/- 0.3 mu M. A docking analysis indicated that CCR-11 may bind to FtsZ in a cavity adjacent to the T7 loop and that short halogen oxygen, H-bonding, and hydrophobic interactions might be important for the binding of CCR-11 with FtsZ. CCR-11 inhibited the proliferation of B. subtilis cells with a half-maximal inhibitory concentration (IC50) of 1.2 +/- 0.2 mu M and a minimal inhibitory concentration of 3 mu M. It also potently inhibited proliferation of Mycobacterium smegmatis cells. Further, CCR-11 perturbed Z-ring formation in B. subtilis cells; however, it neither visibly affected nucleoid segregation nor altered the membrane integrity of the cells. CCR-11 inhibited HeLa cell proliferation with an IC50 value of 18.1 +/- 0.2,mu M (similar to 15 x IC50 of B. subtilis cell proliferation). The results suggested that CCR-11 inhibits bacterial cytokinesis by inhibiting FtsZ assembly, and it can be used as a lead molecule to develop FtsZ-targeted antibacterial agents.

Evolution of quantum discord and its stability in two-qubit NMR systems

We investigate evolution of quantum correlations in ensembles of two-qubit nuclear spin systems via nuclear magnetic resonance techniques. We use discord as a measure of quantum correlations and the Werner state as an explicit example. We, first, introduce different ways of measuring discord and geometric discord in two-qubit systems and then describe the following experimental studies: (a) We quantitatively measure discord for Werner-like states prepared using an entangling pulse sequence. An initial thermal state with zero discord is gradually and periodically transformed into a mixed state with maximum discord. The experimental and simulated behavior of rise and fall of discord agree fairly well. (b) We examine the efficiency of dynamical decoupling sequences in preserving quantum correlations. In our experimental setup, the dynamical decoupling sequences preserved the traceless parts of the density matrices at high fidelity. But they could not maintain the purity of the quantum states and so were unable to keep the discord from decaying. (c) We observe the evolution of discord for a singlet-triplet mixed state during a radio-frequency spin-lock. A simple relaxation model describes the evolution of discord, and the accompanying evolution of fidelity of the long-lived singlet state, reasonably well.