ENROUTE: An Entropy Aware Routing Scheme for Information-Centric Networks (ICN)

With the exponential growth of end users and web data, the internet is undergoing the change of paradigm from a user-centric model to a content-centric one, popularly known as information-centric networks (ICN). Current ICN research evolves around three key-issues namely (i) content request searching, (ii) content routing, and (iii) in-network caching scheme to deliver the requested content to the end user. This would improve the user experience to obtain requested content because it lowers the download delay and provides higher throughput. Existing researches have mainly focused on on-path congestion or expected delivery time of a content to determine the optimized path towards custodian. However, it ignores the cumulative effect of the link-state parameters and the state of the cache, and consequently it leads to degrade the delay performance. In order to overcome this shortfall, we consider both the congestion of a link and the state of on-path caches to determine the best possible routes. We introduce a generic term entropy to quantify the effects of link congestion and state of on-path caches. Thereafter, we develop a novel entropy dependent algorithm namely ENROUTE for searching of content request triggered by any user, routing of this content, and caching for the delivery this requested content to the user. The entropy value of an intra-domain node indicates how many popular contents are already cached in the node, which, in turn, signifies the degree of enrichment of that node with the popular contents. On the other hand, the entropy for a link indicates how much the link is congested with the traversal of contents. In order to have reduced delay, we enhance the entropy of caches in nodes, and also use path with low entropy for downloading contents. We evaluate the performance of our proposed ENROUTE algorithm against state-of-the-art schemes for various network parameters and observe an improvement of 29–52% in delay, 12–39% in hit rate, and 4–39% in throughput.

     

Pose scoring by NMR

Recently, we have developed a fast approach to calculate NMR chemical shifts using the divide and conquer method at the semiempirical level. To demonstrate the utility of this approach for characterizing protein-ligand interactions, we used the deviation of calculated chemical shift perturbations from experiment to determine the orientation of a ligand (GPI-1046) in the binding pocket of the FK506 binding protein (FKBP12). Moreover, we were able to select the native state of the ligand from a collection of decoy poses. A key hydrogen bond between O1 and HN in Ile56 was also identified. Our results suggest that ligand-induced chemical shift perturbations can be used to refine protein/ligand structures.     

Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction

Pairwise decomposition of the interaction energy between molecules is shown to be a powerful tool that can increase our understanding of macromolecular recognition processes. Herein we calculate the pairwise decomposition of the interaction energy between the protein human carbonic anhydrase II (HCAII) and the fluorine-substituted ligand N-(4-sulfamylbenzoyl)benzylamine (SBB) using semiempirical quantum mechanics based methods. We dissect the interaction between the ligand and the protein by dividing the ligand and the protein into subsystems to understand the structure-activity relationships as a result of fluorine substitution. In particular, the off-diagonal elements of the Fock matrix that is composed of the interaction between the ionic core and the valence electrons and the exchange energy between the subsystems or atoms of interest is examined in detail. Our analysis reveals that the fluorine-substituted benzylamine group of SBB does not directly affect the binding energy. Rather, we find that the strength of the interaction between Thr199 of HCAII and the sulfamylbenzoyl group of SBB affects the binding affinity between the protein and the ligand. These observations underline the importance of the sulfonamide group in binding affinity as shown by previous experiments (Maren, T. H.; Wiley: C. E. J. Med. Chem. 1968, 11, 228-232). Moreover, our calculations qualitatively agree with the structural aspects of these protein-ligand complexes as determined by X-ray crystallography.     

Mutagenesis Mediated by Triple Helix–Forming Oligonucleotides Conjugated to Psoralen: Effects of Linker Arm Length and Sequence Context

Targeted mutagenesis and gene knock-out can be mediated by triple helix-forming oligonucleotides (TFO) linked to mutagenic agents, such as psoralen. However, this strategy is limited by the availability of homopurine/ homopyrimidine stretches at or near the target site because such sequences are required for high-affinity triplex formation. To overcome this limitation, we have tested TFO conjugated to psoralen via linker arms of lengths varying from 2 to 86 bonds, thereby designed to deliver the psoralen at varying distances from the third strand binding site present at the 3'end of the supFG1 mutation reporter gene. Following triplex formation and UVA irradiation, mutations were detected using an SV40-based shuttle vector assay in human cells. The frequency and distribution of mutations depended on the length of the linker arm. Precise targeting was observed only for linker arms of length 2 and 6, which also yielded the highest mutation frequencies (3 and 14%, respectively). Psoralen–TFO with longer tethers yielded mutations at multiple sites, with the maximum distance from the triplex site limited by the linker length but with the distribution within that range influenced by the propensity for psoralen intercalation at A:T base-pair-rich sites. Thus, gene modification can be extended beyond the site of third strand binding but with a decrease in the precision of the targeting.     

Direct selective detection of genomic DNA from coliform using a fiber optic biosensor

Fiber optic biosensors operated in a total internal reflection format were prepared based on covalent immobilization of 25mer lacZ single-stranded nucleic acid probe. Genomic DNA from Escherichia coli was extracted and then sheared by sonication to prepare fragments of approximately 300mer length. Other targets included a 25mer fully complementary lacZ sequence, 100mer polymerase chain reaction (PCR) products containing the lacZ sequence at various locations, and non-complementary DNA including genomic samples from salmon sperm. Non-selective adsorption of non-complementary oligonucleotides (ncDNA) was found to occur at a significantly faster rate than hybridization of complementary oligomers (cDNA) in all cases. The presence of ncDNA oligonucleotides did not inhibit selective interactions between immobilized DNA and cDNA in solution. The presence of high concentrations of non-complementary genomic DNA had little effect on extent or speed of hybridization of complementary oligonucleotides. Detection of genomic fragments containing the lacZ sequence was possible in as little as 20 s by observation of the steady-state fluorescence intensity increase or by time-dependent rate of fluorescence intensity changes.     

Studies on the thermal decomposition of N-2,4,6 tetranitro-N-methyl aniline

The kinetics of the initial stage of thermal decomposition of N-2,4,6 tetranitro-N-methyl aniline (tetryl) in condensed state has been investigated by high temperature infrared spectroscopy (IR) in conjunction with pyrolysis gas analysis and thermogravimetry (TG). The decomposition in KBr matrix in the temperature range of 131 to 145 °C shows rapid decrease in the N-NO₂ band intensity as compared to the C-NO₂ band. Decomposition products in the initial stage show mainly NO₂ gas and picric acid. The studies show that the initial stage of decomposition of tetryl occurs by the rupture of the N-NO₂ bond and the energy of activation for this process is 177 kJ/mol.

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Zusammenfassung Mittels Hochtemperatur-IR-Spektroskopie wurde in Verbindung mit Pyrolysengasanalyse und Thermogravimetrie (TG) die Kinetik des einleitenden Schrittes der thermischen Zersetzung von N-2,4,6-Tetranitro-N-Methylanilin (Tetryl) im kondensierten Zustand untersucht. Die Zersetzung in einer KBr-Matrix im Temperaturbereich von 131–145 °C äußert sich in einem schnellen Abnehmen der Intensität der N-NO₂ Bande bezogen auf die der C-NO₂ Bande. Zersetzungsprodukte des einleitenden Schrittes sind hauptsächlich NO₂ Gas und Pikrinsäure. Die Untersuchungen zeigten, daß der einleitende Schritt der Zersetzung von Tetryl die Spaltung der N-NO₂ Bindung ist. Die Aktivierungsenergie für diesen Prozess beträgt 177 kJ/mol.

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N-2,4,6-N- () , . 131–145 °C N-NO₂ C-NO₂. . , N-NO₂, 177 /.

     

Thermal study of an array of inline horizontal cylinders below a nearly adiabatic ceiling

Steady state two-dimensional free convection heat transfer from a horizontal, isothermal cylinder in a horizontal array of cylinders consists of three isothermal cylinders, located underneath a nearly adiabatic ceiling is studied experimentally. A Mach–Zehnder interferometer is used to determine thermal field and smoke test is made to visualize flow field. Effects of the cylinders spacing to its diameter (S/D), and cylinder distance from ceiling to its diameter (L/D) on heat transfer from the centered cylinder are investigated for Rayleigh numbers from 1500 to 6000. Experiments are performed for an inline array configuration of horizontal cylinders of diameters D = 13 mm. Results indicate that due to the nearly adiabatic ceiling and neighboring cylinders, thermal plume resulted from the centered cylinder separates from cylinder surface even for high L/D values and forming recirculation regions. By decreasing the space ratio S/D, the recirculation flow strength increases. Also, by decreasing S/D, boundary layers of neighboring cylinders combine and form a developing flow between cylinders. The strength of developing flow depends on the cylinders Rayleigh number and S/D ratio. Due to the developing flow between cylinders, the vortex flow on the top of the centered cylinder appears for all L/D ratios and this vortex influences the value of local Nusselt number distribution around the cylinder.Variation of average Nusselt number of the centered cylinder depends highly on L/D and the trend with S/D depends on the value of Rayleigh number.     

Surfactant mediated oxygen reuptake in water for green aerobic oxidation: mass-spectrometric determination of discrete intermediates to correlate oxygen uptake with oxidation efficiency

A novel strategy of catalytic green aerobic oxidation by surfactant-mediated oxygen reuptake in water offers a new dimension to the applications of surfactants to look beyond as solubility aids and a conceptual advancement in understanding the role of surfactants in aquatic organic reactions through mass spectrometry guided identification of discrete intermediates.