Floquet generation of Majorana end modes and topological invariants

We show how Majorana end modes can be generated in a one-dimensional system by varying some of the parameters in the Hamiltonian periodically in time. The specific model we consider is a chain containing spinless electrons with a nearest-neighbor hopping amplitude, a p-wave superconducting term, and a chemical potential; this is equivalent to a spin-1/2 chain with anisotropic XY couplings between nearest neighbors and a magnetic field applied in the (z) over cap direction. We show that varying the chemical potential (or magnetic field) periodically in time can produce Majorana modes at the ends of a long chain. We discuss two kinds of periodic driving, periodic delta-function kicks, and a simple harmonic variation with time. We discuss some distinctive features of the end modes such as the inverse participation ratio of their wave functions and their Floquet eigenvalues which are always equal to +/- 1 for time-reversal-symmetric systems. For the case of periodic delta-function kicks, we use the effective Hamiltonian of a system with periodic boundary conditions to define two topological invariants. The first invariant is a well-known winding number, while the second invariant has not appeared in the literature before. The second invariant is more powerful in that it always correctly predicts the numbers of end modes with Floquet eigenvalues equal to + 1 and -1, while the first invariant does not. We find that the number of end modes can become very large as the driving frequency decreases. We show that periodic delta-function kicks in the hopping and superconducting terms can also produce end modes. Finally, we study the effect of electron-phonon interactions (which are relevant at finite temperatures) and a random noise in the chemical potential on the Majorana modes.

Protamine-Capped Mesoporous Silica Nanoparticles for Biologically Triggered Drug Release

The fabrication of a mesoporous silica nanoparticle (MSN)-protamine hybrid system (MSN-PRM) is reported that selectively releases drugs in the presence of specific enzyme triggers present in the proximity of cancer cells. The enzyme trigger involved is a protease called trypsin, which is overexpressed in certain specific pathological conditions, such as inflammation and cancer. Overexpression of trypsin is known to be associated with invasion, metastasis, and growth in several cancers, such as leukemia, colon cancer, and colorectal cancer. The current system (MSN-PRM) consists of an MSN support in which mesopores are capped with an FDA-approved peptide drug protamine, which effectively blocks the outward diffusion of the drug molecules from the mesopores of the MSNs. On exposure to the enzyme trigger, the protamine cap disintegrates, opening up the molecular gates and releasing the entrapped drug molecules. The system exhibits minimal premature release in the absence of the trigger and selectively releases the encapsulated drugs in the presence of the proteases secreted by colorectal cancer cells. The ability of the MSN-PRM particles to deliver anticancer drugs to colorectal cancer cells has also been demonstrated. The hydrophobic drug is released into cancer cells subsequent to disintegration of the protamine cap, resulting in cell death. Drug-induced cell death in colorectal cancer cells is significantly enhanced when the hydrophobic drug that is known to degrade in aqueous environments is encapsulated in the MSN-PRM system in comparison to the free drug (P < 0.05). The system, which shows good biocompatibility and selective drug release, is a promising platform for cancer specific drug delivery.

PROTEIN DISULFIDE ANALYSIS AND DESIGN

The significant contribution of naturally occurring disulfide bonds to protein stability has encouraged development of methods to engineer non-native disulfides in proteins. These have yielded mixed results. We summarize applications of the program MODIP for disulfide engineering. The program predicts sites in proteins where disulfides can be stably introduced. The program has also been used as an aid in conformational analysis of naturally occurring disulfides in a-helices, antiparallel and parallel beta-strands. Disulfides in a-helices occur only at N-termini, where the first cysteine residue is the N-cap residue of the helix. The disulfide occurs as a CXXC motif and can possess redox activity. In antiparallel beta-strands, disulfides occur exclusively at non-hydrogen bonded (NHB) registered pairs of antiparallel beta-sheets with only 1 known natural example occurring at a hydrogen bonded (HB) registered pair. Conformational analysis suggests that disulfides between HB residue pairs are under torsional strain. A similar analysis to characterize disulfides in parallel beta-strands was carried out. We observed that only 9 instances of cross-strand disulfides exist in a non-redundant dataset. Stereochemical analysis shows that while tbe chi(square) angles are similar to those of other disulfides, the chi(1) and chi(2) angles show more variation and that one of tbe strands is generally an edge strand.

The generalized Onsager model for a binary gas mixture

The Onsager model for the secondary flow field in a high-speed rotating cylinder is extended to incorporate the difference in mass of the two species in a binary gas mixture. The base flow is an isothermal solid-body rotation in which there is a balance between the radial pressure gradient and the centrifugal force density for each species. Explicit expressions for the radial variation of the pressure, mass/mole fractions, and from these the radial variation of the viscosity, thermal conductivity and diffusion coefficient, are derived, and these are used in the computation of the secondary flow. For the secondary flow, the mass, momentum and energy equations in axisymmetric coordinates are expanded in an asymptotic series in a parameter epsilon = (Delta m/m(av)), where Delta m is the difference in the molecular masses of the two species, and the average molecular mass m(av) is defined as m(av) = (rho(w1)m(1) + rho(w2)m(2))/rho(w), where rho(w1) and rho(w2) are the mass densities of the two species at the wall, and rho(w) = rho(w1) + rho(w2). The equation for the master potential and the boundary conditions are derived correct to O(epsilon(2)). The leading-order equation for the master potential contains a self-adjoint sixth-order operator in the radial direction, which is different from the generalized Onsager model (Pradhan & Kumaran, J. Fluid Mech., vol. 686, 2011, pp. 109-159), since the species mass difference is included in the computation of the density, viscosity and thermal conductivity in the base state. This is solved, subject to boundary conditions, to obtain the leading approximation for the secondary flow, followed by a solution of the diffusion equation for the leading correction to the species mole fractions. The O(epsilon) and O(epsilon(2)) equations contain inhomogeneous terms that depend on the lower-order solutions, and these are solved in a hierarchical manner to obtain the O(epsilon) and O(epsilon(2)) corrections to the master potential. A similar hierarchical procedure is used for the Carrier-Maslen model for the end-cap secondary flow. The results of the Onsager hierarchy, up to O(epsilon(2)), are compared with the results of direct simulation Monte Carlo simulations for a binary hard-sphere gas mixture for secondary flow due to a wall temperature gradient, inflow/outflow of gas along the axis, as well as mass and momentum sources in the flow. There is excellent agreement between the solutions for the secondary flow correct to O(epsilon(2)) and the simulations, to within 15 %, even at a Reynolds number as low as 100, and length/diameter ratio as low as 2, for a low stratification parameter A of 0.707, and when the secondary flow velocity is as high as 0.2 times the maximum base flow velocity, and the ratio 2 Delta m/(m(1) + m(2)) is as high as 0.5. Here, the Reynolds number Re = rho(w)Omega R-2/mu, the stratification parameter A = root m Omega R-2(2)/(2k(B)T), R and Omega are the cylinder radius and angular velocity, m is the molecular mass, rho(w) is the wall density, mu is the viscosity and T is the temperature. The leading-order solutions do capture the qualitative trends, but are not in quantitative agreement.

Mesoporous silica-chondroitin sulphate hybrid nanoparticles for targeted and bio-responsive drug delivery

This work proposes the fabrication of a novel targeted drug delivery system based on mesoporous silica-biopolymer hybrids that can release drugs in response to biological stimuli present in cancer cells. The proposed system utilizes mesoporous silica nanoparticles as a carrier to host the drug molecules. A bio-polymer cap is attached onto these particles which serves the multiple functions of drug retention, targeting and bio-responsive drug release. The biopolymer chondroitin sulphate used here is a glycosaminoglycan that can specifically bind to receptors over-expressed in cancer cells. This molecule also possesses the property of disintegrating upon exposure to enzymes over-expressed in cancer cells. When these particles interact with cancer cells, the chondroitin sulphate present on the surface recognizes and attaches onto the CD44 receptors facilitating the uptake of these particles. The phagocytised particles are then exposed to the degradative enzymes, such as hyaluronidase present inside the cancer cells, which degrade the cap resulting in drug release. By utilizing a cervical cancer cell line we have demonstrated the targetability and intracellular delivery of hydrophobic drugs encapsulated in these particles. It was observed that the system was capable of enhancing the anticancer activity of the hydrophobic drug curcumin. Overall, we believe that this system might prove to be a valuable candidate for targeted and bioresponsive drug delivery.

The beta hairpin structure within ribosomal protein S5 mediates interplay between domains II and IV and regulates HCV IRES function

Translation initiation in Hepatitis C Virus (HCV) is mediated by Internal Ribosome Entry Site (IRES), which is independent of cap-structure and uses a limited number of canonical initiation factors. During translation initiation IRES-40S complex formation depends on high affinity interaction of IRES with ribosomal proteins. Earlier, it has been shown that ribosomal protein S5 (RPS5) interacts with HCV IRES. Here, we have extensively characterized the HCV IRES-RPS5 interaction and demonstrated its role in IRES function. Computational modelling and RNA-protein interaction studies demonstrated that the beta hairpin structure within RPS5 is critically required for the binding with domains II and IV. Mutations disrupting IRES-RPS5 interaction drastically reduced the 80S complex formation and the corresponding IRES activity. Computational analysis and UV cross-linking experiments using various IRES-mutants revealed interplay between domains II and IV mediated by RPS5. In addition, present study demonstrated that RPS5 interaction is unique to HCV IRES and is not involved in 40S-3 ` UTR interaction. Further, partial silencing of RPS5 resulted in preferential inhibition of HCV RNA translation. However, global translation was marginally affected by partial silencing of RPS5. Taken together, results provide novel molecular insights into IRES-RPS5 interaction and unravel its functional significance in mediating internal initiation of translation.

Tetrahydrofuran amino acid-containing gramicidin S analogues with improved biological profiles

Gramicidin S (GS) is a cyclic cationic antimicrobial peptide (CAP) with a wide spectrum of antibiotic activities whose usage has been limited to topical applications owing to its cytotoxic side effects. We have synthesized tetrahydrofuran amino acid (Taa)-containing GS analogues, and we have carried out conformational analysis and explored their structure activity relationships by evaluating their antitubercular, antibacterial and cytotoxic properties. Two of these analogues showed impressive as well as selective activity against Mycobacterium tuberculosis (MTB) without toxicity towards mammalian Vero cells or human RBCs, and are promising as potential leads.

New symmetrical dinucleating ligand based assembly of bridged dicopper(II) and dizinc(II) centers: Synthesis, structure, spectroscopy, magnetic properties and glycoside hydrolysis

Two dinuclear copper(II) complexes Li(H2O)(3)(CH3OH)](4)Cu2Br4]Cu-2(cpdp)(mu-O2CCH3)](4)(OH)(2) (1), Cu (H2O)(4)]Cu-2(cpdp)(mu-O2CC6H5)](2)Cl-2 center dot 5H(2)O (2), and a dinuclear zinc(II) complex Zn-2(cpdp)(mu-O2CCH3)] (3) have been synthesized using pyridine and benzoate functionality based new symmetrical dinucleating ligand, N, N'-Bis2-carboxybenzomethyl]-N, N'-Bis2-pyridylmethyl]-1,3-diaminopropan-2-ol (H(3)cpdp). Complexes 1, 2 and 3 have been synthesized by carrying out reaction of the ligand H3cpdp with stoichiometric amounts of Cu-2(O2CCH3)(4)(H2O)(2)], CuCl2 center dot 2H(2)O/C6H5COONa, and Zn(CH3COO)(2)center dot 2H(2)O, respectively, in methanol in the presence of NaOH at ambient temperature. Characterizations of the complexes have been done using various analytical techniques including single crystal X-ray structure determination. The X-ray crystal structure analyses reveal that the copper(II) ions in complexes 1 and 2 are in a distorted square pyramidal geometry with Cu-Cu separation of 3.455(8) angstrom and 3.492(1)angstrom, respectively. The DFT optimized structure of complex 3 indicates that two zinc(II) ions are in a distorted square pyramidal geometry with Zn-Zn separation of 3.492(8)angstrom. UV-Vis and mass spectrometric analyses of the complexes confirm their dimeric nature in solution. Furthermore, H-1 and C-13 NMR spectroscopic investigations authenticate the integrity of complex 3 in solution. Variable-temperature (2-300 K) magnetic susceptibility measurements show the presence of antiferromagnetic interactions between the copper centers, with J = -26.0 cm(-1) and -23.9 cm(-1) ((H) over cap = -2JS(1)S(2)) in complexes 1 and 2, respectively. In addition, glycosidase-like activity of the complexes has been investigated in aqueous solution at pH similar to 10.5 by UV-Vis spectrophotometric technique using p-nitrophenyl-alpha-D-glucopyranoside (4) and p-nitrophenyl-beta-D-glucopyranoside (5) as model substrates. (C) 2015 Elsevier B.V. All rights reserved.

Behavior of Brick-Mortar Interfaces in FRP-Strengthened Masonry Assemblages under Normal Loading and Shear Loading

Determination of shear strength of brick-mortar bed joint is critical to overcome the sliding-shear or joint-shear failure in masonry. In the recent past, researchers have attempted to enhance the shear strength and deformation capacity of brick-mortar bed joints by gluing fiber-reinforced polymer (FRP) composite across the bed joint. FRP composites offer several advantages like high strength-to-weight ratio, and ease of application in terms of labor, time, and reduced curing period. Furthermore, FRP composites are desirable for strengthening old masonry buildings having heritage value because of its minimal interference with the existing architecture. A majority of earlier studies on shear strengthening of masonry available in the literature adopted masonry having the ratio of modulus of elasticity of masonry unit (Emu) to modulus of elasticity of mortar (Em) greater than one. Information related to shear behavior of FRP glued masonry composed of masonry units having Young's modulus lower than mortar is limited. Hence the present study is focused on characterizing the interfacial behavior of brick-mortar bed joint of masonry assemblages composed of solid burnt clay bricks and cement-sand mortar (E-mu/E-m ratio less than one), strengthened with FRP composites. Masonry triplets and prisms with bed joint inclined to loading axis (0 degrees, 30 degrees, 45 degrees, 60 degrees and 90 degrees) are employed in this study. Glass and carbon FRP composites composed of bidirectional FRP fabric with equal density in both directions are used for strengthening masonry. Masonry triplets are glued with glass and carbon FRP composites in two configurations: (1) both faces of the triplet specimens are fully glued with GFRP composites; and (2) both faces of the triplet specimens are glued with GFRP and CFRP composites in strip form. The performance of masonry assemblages strengthened with FRP composites is assessed in terms of gain in shear strength, shear displacement, and postpeak behavior for various configurations and types of FRP composites considered. A semianalytical model is proposed for the prediction of shear strength of masonry bed joints glued with FRP composites. A composite failure envelope consisting of a Coulomb friction model and a compression cap is obtained for unreinforced masonry and GFRP-strengthened masonry based on the test results of masonry triplets and masonry prisms with bed joints having various inclinations to the loading (C) 2015 American Society of Civil Engineers.

Numerical analysis of segmented-electrode Orbitraps

Simple geometries which are possible alternatives for the Orbitrap are studied in this paper. We have taken up for numerical investigation two segmented-electrode structures, ORB1 and ORB2, to mimic the electric field of the Orbitrap. In the ORB1, the inner spindle-like electrode and the outer barrel-like electrode of the Orbitrap have been replaced by 35 rings and 35 discs of fixed radii, respectively. In this structure two segmented end cap electrodes have been added. In this geometry, different potentials are applied to the different electrodes keeping top-bottom symmetry intact. In the second geometry, ORB2, the inner and outer electrodes of the Orbitrap were replaced by an approximate step structure which follows the profile of the Orbitrap electrodes. In the present study 45 steps have been used. In the ORB2, like the Orbitrap, the inner electrode is held at a negative potential and the outer electrode is at ground potential. For the purpose of comparing the performance of ORB1 and ORB2 with that of the Orbitrap, the following studies have been undertaken: (1) variation of electric potential, (2) computation of ion trajectories, (3) simulation of image currents. These studies have been carried out using both 2D and 3D Boundary Element Method (BEM), the 3D BEM was developed specifically for this study. It has been seen in these investigations that ORB1 and ORB2 have performance similar to that of the Orbitrap, with the performance of the ORB1 being seen to be marginally superior to that of the ORB2. It has been shown that with proper optimization, geometries containing far fewer electrodes can be used as mass analyzers. A novel technique of optimization of the electric field has been proposed with the objective of minimizing the dependence of axial frequency of ion motion on the initial position of an ion. The results on the optimization of 9 and 15 segmented-electrode traps having the same design as ORB1 show that it can provide accurate mass analysis. (C) 2015 Elsevier B.V. All rights reserved.

Numerical analysis of segmented-electrode Orbitraps

Simple geometries which are possible alternatives for the Orbitrap are studied in this paper. We have taken up for numerical investigation two segmented-electrode structures, ORB1 and ORB2, to mimic the electric field of the Orbitrap. In the ORB1, the inner spindle-like electrode and the outer barrel-like electrode of the Orbitrap have been replaced by 35 rings and 35 discs of fixed radii, respectively. In this structure two segmented end cap electrodes have been added. In this geometry, different potentials are applied to the different electrodes keeping top-bottom symmetry intact. In the second geometry, ORB2, the inner and outer electrodes of the Orbitrap were replaced by an approximate step structure which follows the profile of the Orbitrap electrodes. In the present study 45 steps have been used. In the ORB2, like the Orbitrap, the inner electrode is held at a negative potential and the outer electrode is at ground potential. For the purpose of comparing the performance of ORB1 and ORB2 with that of the Orbitrap, the following studies have been undertaken: (1) variation of electric potential, (2) computation of ion trajectories, (3) simulation of image currents. These studies have been carried out using both 2D and 3D Boundary Element Method (BEM), the 3D BEM was developed specifically for this study. It has been seen in these investigations that ORB1 and ORB2 have performance similar to that of the Orbitrap, with the performance of the ORB1 being seen to be marginally superior to that of the ORB2. It has been shown that with proper optimization, geometries containing far fewer electrodes can be used as mass analyzers. A novel technique of optimization of the electric field has been proposed with the objective of minimizing the dependence of axial frequency of ion motion on the initial position of an ion. The results on the optimization of 9 and 15 segmented-electrode traps having the same design as ORB1 show that it can provide accurate mass analysis. (C) 2015 Elsevier B.V. All rights reserved.