Efficient space-time codes from cyclic division algebras

An overview of space-time code construction based on cyclic division algebras (CDA) is presented. Applications of such space-time codes to the construction of codes optimal under the diversity-multiplexing gain (D-MG) tradeoff, to the construction of the so-called perfect space-time codes, to the construction of optimal space-time codes for the ARQ channel as well as to the construction of codes optimal for the cooperative relay network channel are discussed. We also present a construction of optimal codes based on CDA for a class of orthogonal amplify and forward (OAF) protocols for the cooperative relay network

Why Is Less Cationic Lipid Required To Prepare Lipoplexes from Plasmid DNA than Linear DNA in Gene Therapy?

The most important objective of the present study was to explain why cationic lipid (CL)-mediated delivery of plasmid DNA (pDNA) is better than that of linear DNA in gene therapy, a question that, until now, has remained unanswered. Herein for the first time we experimentally show that for different types of CLs, pDNA, in contrast to linear DNA, is compacted with a large amount of its counterions, yielding a lower effective negative charge. This feature has been confirmed through a number of physicochemical and biochemical investigations. This is significant for both in vitro and in vivo transfection studies. For an effective DNA transfection, the lower the amount of the CL, the lower is the cytotoxicity. The study also points out that it is absolutely necessary to consider both effective charge ratios between CL and pDNA and effective pDNA charges, which can be determined from physicochemical experiments.

Self-Assembling Peptides: From Molecules to Nanobiomaterials

Abstract | Molecular self-assembly plays a vital role in the construction of various nanostructures using the ‘bottom-up’ approach. Peptides have been considered important bio-molecular building blocks for different nanoscale structures as they are biocompatible, biodegradable, generally non-toxic and can be attuned to environmental responses like pH, temperature, salt concentration and others. Peptide based nanostructures can offer various wonderful biological applications in tissue engineering, cell culture, regenerative medicine and drug delivery. In this review, the construction of short peptide-based different nanostructures including nanotubes, nanovesicles and nanofibers, short peptide-based nanoporous materials, short peptide-based nanofibrous hydrogels and nanovesicles for various biological applications has been discussed. Moreover, morphological transformations from one nanoscopic structure to an other type of nanostructure (e.g., nanotubes to nanovesicles) are also clearly discussed in this review.

NMRof peptides

Developments and applications of NMR spectroscopy especially with biomolecules has taken big strides over the decades. This review gives a brief overview of peptide analysis by NMR as carried out in the author’s laboratory. A brief introduction to peptide biomolecules and NMR useful parameters are discussed in the beginning. This is followed by diagnostics features observed in NMR for identification of secondary structures. It further goes on to show how a three dimensional structure could be obtained by all-important NOE and hydrogen bond information. Use of heteronuclear experiments, which could be done at natural abundance is also highlighted in getting more details of peptide structures.Applications using Solid state NMR at natural abundance in connecting peptide solution and x-ray structures is demonstrated with couple of examples.

CNT loading into cationic cholesterol suspensions show improved DNA binding and serum stability and ability to internalize into cancer cells

Methods which disperse single-walled carbon nanotubes (SWNTs) in water as `debundled', while maintaining their unique physical properties are highly useful. We present here a family of cationic cholesterol compounds (Chol(+)) {Cholest-5en-3 beta-oxyethyl pyridinium bromide (Chol-PB+), Cholest-5en-3 beta-oxyethyl N-methyl pyrrolidinium bromide (Chol-MPB+), Cholest-5en-3 beta-oxyethyl N-methyl morpholinium bromide (Chol-MMB+) and Cholest-5en-3 beta-oxyethyl diazabicyclo octanium bromide (Chol-DOB+)}. Each of these could be easily dispersed in water. The resulting cationic cholesterol (Chol(+)) suspensions solubilized single-walled carbon nanotubes (SWCNTs) by the non-specific physical adsorption of Chol(+) to form stable, transparent, dark aqueous suspensions at room temperature. Electron microscopy reveals the existence of highly segregated CNTs in these samples. Zeta potential measurements showed an increase in potential of cationic cholesterol aggregates on addition of CNTs. The CNT-Chol(+) suspensions were capable of forming stable complexes with genes (DNA) efficiently. The release of double-helical DNA from such CNT-Chol(+) complexes could be induced upon the addition of anionic micellar solution of SDS. Furthermore, the CNT-based DNA complexes containing cationic cholesterol aggregates showed higher stability in fetal bovine serum media at physiological conditions. Confocal studies confirm that CNT-Chol(+) formulations adhere to HeLa cell surfaces and get internalized more efficiently than the cationic cholesterol suspensions alone (devoid of any CNTs). These cationic cholesterol-CNT suspensions therefore appear to be a promising system for further use in biological applications.

Gap model of one-way cyclic lateral load on vertical files in soft clay

For the analysis and design of pile foundation used for coastal structures the prediction of cyclic response, which is influenced by the nonlinear behavior, gap (pile soil separation) and degradation (reduction in strength) of soil becomes necessary. To study the effect of the above parameters a nonlinear cyclic load analysis program using finite element method is developed, incorporating the proposed gap and degradation model and adopting an incremental-iterative procedure. The pile is idealized using beam elements and the soil by number of elastoplastic sub-element springs at each node. The effect of gap and degradation on the load-deflection behavior. elasto-plastic sub-element and resistance of the soil at ground-line have been clearly depicted in this paper.

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.

Designed Cyclic Permutants of HIV-1 gp120: Implications for Envelope Trimer Structure and Immunogen Design

Most HIV-1 broadly neutralizing antibodies are directed against the gp120 subunit of the env surface protein. Native env consists of a trimer of gp120-gp41 heterodimers, and in contrast to monomeric gp120, preferentially binds CD4 binding site (CD4bs)-directed neutralizing antibodies over non-neutralizing ones. Some cryo-electron tomography studies have suggested that the V1V2 loop regions of gp120 are located close to the trimer interface. We have therefore designed cyclically permuted variants of gp120 with and without the h-CMP and SUMO2a trimerization domains inserted into the V1V2 loop. h-CMP-V1cyc is one such variant in which residues 153 and 142 are the N- and C-terminal residues, respectively, of cyclically permuted gp120 and h-CMP is fused to the N-terminus. This molecule forms a trimer under native conditions and binds CD4 and the neutralizing CD4bs antibodies b12 with significantly higher affinity than wild-type gp120. It binds non-neutralizing CD4bs antibody F105 with lower affinity than gp120. A similar derivative, h-CMP-V1cycl, bound the V1V2 loop-directed broadly neutralizing antibodies PG9 and PG16 with similar to 20-fold higher affinity than wild-type JRCSF gp120. These cyclic permutants of gp120 are properly folded and are potential immunogens. The data also support env models in which the V1V2 loops are proximal to the trimer interface.

Adsorption of cationic dyes on poly(acrylic acid-co-sodium acrylate-co-acrylamide) superabsorbents

Inverse suspension polymerization was carried out to synthesize poly(acrylic acid-co-sodium acrylate-co-acrylamide) superabsorbent polymers (SAPs) crosslinked with ethylene glycol dimethacrylate (EGDMA). The equilibrium swelling capacities of the SAPs, determined by swelling them in DI water, were found to vary with the acrylamide (AM) content. The SAPs were used to adsorb four cationic dyes (Acriflavine, Auramine-O, Azure-I and Pyronin-Y). The effect of AM content in the SAPs on the adsorption of the cationic dyes was investigated. Different initial concentrations of Azure-I were used with the same amount of the SAP to explore the effect of initial dye concentration on the adsorption. The effect of the adsorbent amount was investigated by taking different amounts of SAP with a fixed initial concentration of Acriflavine. The kinetics of the dye adsorption was modeled by a first order model and the equilibrium amount of the dye adsorbed, adsorption rate coefficients, removal efficiency and partition coefficients were determined. (C) 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012

Thermal Management of Electronics Using PCM-Based Heat Sink Subjected to Cyclic Heat Load

Designing a heat sink based on a phase change material (PCM) under cyclic loading is a critical issue. For cyclic operation, it is required that the fraction of the PCM melting during the heating cycle should completely resolidify during the cooling period, so that that thermal storage unit can be operated for an unlimited number of cycles. Accordingly, studies are carried out to find the parameters influencing the behavior of a PCM under cyclic loading. A number of parameters are identified in the process, the most important ones being the duty cycle and heat transfer coefficient (h) for cooling. The required h or the required cooling period for complete resolidification for infinite cyclic operation of a conventional PCM-based heat sink is found to be very high and unrealistic with air cooling from the surface. To overcome this problem, the conventional design is modified where h and the area exposed to heat transfer can be independently controlled. With this arrangement, the enhanced area provided for cooling keeps h within realistic limits. Analytical investigation is carried out to evaluate the thermal performance of this modified PCM-based heat sink in comparison to those with conventional designs. Experiments are also performed on both the conventional and the modified PCM-based heat sinks to validate the new findings.

Chain Length Effects on Helix-Hairpin Distribution in Short Peptides with Aib-(D)Ala and Aib-Aib Segments

The Aib-(D)Ala dipeptide segment has a tendency to form both type-I'/III' and type-I/III beta-turns. The occurrence of prime turns facilitates the formation of beta-hairpin conformations, while type-I/III turns can nucleate helix formation. The octapeptide Boc-Leu-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-OMe (1) has been previously shown to form a beta-hairpin in the crystalline state and in solution. The effects of sequence truncation have been examined using the model peptides Boc-Phe-Val-Aib-Xxx-Leu-Phe-NHMe (2, 6), Boc-Val-Aib-Xxx-Leu-NHMe (3, 7), and Boc-Aib-Xxx-NHMe (4, 8), where Xxx = (D)Ala, Aib. For peptides with central Aib-Aib segments, Boc-Phe-Val-Aib-Aib-Leu-Phe-NHMe (6), Boc-Val-Aib-Aib-Leu-NHMe (7), and Boc-Aib-Aib-NHMe (8) helical conformations have been established by NMR studies in both hydrogen bonding (CD(3)OH) and non-hydrogen bonding (CDCl(3)) solvents. In contrast, the corresponding hexapeptide Boc-Phe-Val-Aib-(D)Ala-Leu-Phe-Val-NHMe (2) favors helical conformations in CDCl(3) and beta-hairpin conformations in CD(3)OH. The beta-turn conformations (type-I'/III) stabilized by intramolecular 4 -> 1 hydrogen bonds are observed for the peptide Boc-Aib-(D)Ala-NHMe (4) and Boc-Aib-Aib-NIiMe (8) in crystals. The tetrapeptide Boc-Val-Aib-Aib-Leu-NHMe (7) adopts an incipient 3(10)-helical conformation stabilized by three 4 -> 1 hydrogen bonds. The peptide Boc-Val-Aib-(D)Ala-Leu-NHMe (3) adopts a novel et-turn conformation, stabilized by three intramolecular hydrogen bonds (two 4 -> 1 and one 5 -> 1). The Aib-L(D)Ala segment adopts a type-I' beta-turn conformation. The observation of an NOE between Val (1) NH <-> HNCH(3) (5) in CD(3)OH suggests, that the solid state conformation is maintained in methanol solutions. (C) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 744-756, 2011.

Spontaneous self-assembly of designed cyclic dipeptide (Phg-Phg) into two-dimensional nano- and mesosheets

In this study, we present the spontaneous self-assembly of designed simplest aromatic cyclic dipeptides of (L-Phg-L-Phg) and (D-Phg-L-Phg) to form highly stable two-dimensional (2D) nano- and mesosheets with large lateral surface area. Various microscopy data revealed that the morphology of 2D mesosheets resembles the hierarchical natural materials with layered structure. Solution and solid-state NMR studies on cyclo(L-Phg-L-Phg) revealed the presence of strong (N-H-O) hydrogen-bonded molecular chains supported by aromatic pi-pi interactions to form 2D mesosheets. Interestingly, cyclo(D-Phg-L-Phg) self-assembles to form single-crystalline as well as non-crystalline 2D rhomboid sheets with large lateral dimension. X-ray diffraction analysis revealed the stacking of (N-H-O) hydrogen-bonded molecular layers along c-axis supported by aromatic pi-pi interactions. The thermogravimetric analysis shows two transitions with overall high thermal stability attributed to layered hierarchy found in 2D mesosheets.