Generalized Methods for Discovering Frequent Poly-Regions in DNA

The problem of discovering frequent poly-regions (i.e. regions of high occurrence of a set of items or patterns of a given alphabet) in a sequence is studied, and three efficient approaches are proposed to solve it. The first one is entropy-based and applies a recursive segmentation technique that produces a set of candidate segments which may potentially lead to a poly-region. The key idea of the second approach is the use of a set of sliding windows over the sequence. Each sliding window covers a sequence segment and keeps a set of statistics that mainly include the number of occurrences of each item or pattern in that segment. Combining these statistics efficiently yields the complete set of poly-regions in the given sequence. The third approach applies a technique based on the majority vote, achieving linear running time with a minimal number of false negatives. After identifying the poly-regions, the sequence is converted to a sequence of labeled intervals (each one corresponding to a poly-region). An efficient algorithm for mining frequent arrangements of intervals is applied to the converted sequence to discover frequently occurring arrangements of poly-regions in different parts of DNA, including coding regions. The proposed algorithms are tested on various DNA sequences producing results of significant biological meaning.

Discovering Frequent Poly-Regions in DNA Sequences

The problem of discovering frequent arrangements of regions of high occurrence of one or more items of a given alphabet in a sequence is studied, and two efficient approaches are proposed to solve it. The first approach is entropy-based and uses an existing recursive segmentation technique to split the input sequence into a set of homogeneous segments. The key idea of the second approach is to use a set of sliding windows over the sequence. Each sliding window keeps a set of statistics of a sequence segment that mainly includes the number of occurrences of each item in that segment. Combining these statistics efficiently yields the complete set of regions of high occurrence of the items of the given alphabet. After identifying these regions, the sequence is converted to a sequence of labeled intervals (each one corresponding to a region). An efficient algorithm for mining frequent arrangements of temporal intervals on a single sequence is applied on the converted sequence to discover frequently occurring arrangements of these regions. The proposed algorithms are tested on various DNA sequences producing results with significant biological meaning.

Interfacial Regions Governing Internal Cavities of Dendrimers. Studies of Poly(alkyl aryl ether) Dendrimers Constituted with Linkers of Varying Alkyl Chain Length

This report deals with a study of the properties of internal cavities of dendritic macromolecules that are capable Of encapsulating and mediating photoreactions of guest molecules. The internal cavity structures of dendrimers are determined by the interfacial regions between the aqueous exterior and hydrocarbon like interior constituted by the linkers that connect symmetrically sited branch points constituting the dendrimer and head groups that cap the dendrimers. Phloroglucinol-based poly(alkyl aryl ether) dendrimers constituted with a homologous series of alkyl linkers were undertaken for the current study. Twelve dendrimers within first, second, and third generations, having ethyl, n-propyl, n-butyl, and n-pentyl groups as the linkers and hydroxyl groups at peripheries in each generation, were synthesized. Encapsulation of pyrene and coumarins by aqueous basic solutions of dendrimers were monitored-by UV-vis and fluorescence spectroscopies, which showed that a lower generation dendrimer with an optimal alkyl linker presented better encapsulation abilities than a higher generation dendrimer. Norrish type I photoreaction of dibenzyl ketone was carried out within the above: series of dendrimers to probe their abilities to hold guests and reactive inthermediate radical pairs within themselves. The extent of cage effect from the series of third generation dendrimers was observed to be higher with dendrimers having an n-pentyl group as the linker.

Conformation of polypeptide-chains containing both l-residues and D-residues .2. Double-helical structures of poly-ld-peptides

Polypeptides with alternating L- and D-amino acid residues can take up stereochemically satisfactory coaxial double-helical structures, both antiparallel and parallel, which are stabilized by systematic interchain NH O hydrogen bonds. Semiempirical energy calculations over allowed regions of conformational space have yielded the characteristics of these double-helices. There are four possible types of antiparallel double-helices - A3, A4, A5 and A6, with n, the number of LD peptide units per turn, around 2.8, 3.6, 4.5 and 5.5 respectively, while for the parallel double-helices there are two types, P3 and P4, having similar helical parameters as in A3 and A4. The hydrogen-bonding scheme restricts the pitch in all the models to the narrow range of 10.0 to 11.5 Å. All these helices have large central cores whose radii increase proportionately with n. In this respect, A3 and A4 are suitable models for the structure of gramicidin A. In terms of their relative energies, antiparallel double-helices are marginally more stable than those with parallel strands. Our results indicate that the energy differences amongst the members in the antiparallel family are not significant and thus provide an explanation for the polymorphism reported for poly(γ-benzyl-LD-glutamate).

Main chain and segmental dynamics of semi interpenetrating based on polyisoprene and poly(methyl methacrylate)

Main chain and segmental dynamics of polyisoprene (PI) and poly(methyl methacrylate)(PMMA) chains in semi IPNs were systematically studied over a wide range of temperatures (above and below T-g of both polymers) as a function of composition, crosslink density, and molecular weight. The immiscible polymers retained most of its characteristic molecular motion; however, the semi IPN synthesis resulted in dramatic changes in the motional behavior of both polymers due to the molecular level interpenetration between two polymer chains. ESR spin probe method was found to be sensitive to the concentration changes of PMMA in semi IPNs. Low temperature spectra showed the characteristics of rigid limit spectra, and in the range of 293-373 K.complex spectra were obtained with the slow component mostly arisingout of the PMMA rich regions and fast component from the PI phase. We found that the rigid PMMA chains closely interpenetrated into thehighly mobile PI network imparts motional restriction in nearby PI chains, and the highly mobile PI chains induce some degree of flexibility in highly rigid PMMA chains. Molecular level interchain mixing was found to be more efficient at a PMMA concentration of 35 wt.%. Moreover, the strong interphase formed in the above mentionedsemi IPN contributed to the large slow component in the ESR spectra at higher temperature. The shape of the spectra along with the data obtained from the simulations of spectra was correlated to the morphology of the semi IPNs. The correlation time measurement detected the motional region associated with the glass transition of PI and PMMA, and these regions were found to follow the same pattern of shifts in a-relaxation of PI and PMMA observed in DMA analysis. Activation energies associated with the T-g regions were also calculated. T-50G was found to correlate with the T-g of PMMA, and the volume of polymer segments undergoing glass transitional motion was calculated to be 1.7 nm(3).C-13 T-1 rho measurements of PMMA carbons indicate that the molecular level interactions were strong in semi IPN irrespective of the immiscible nature of polymers. The motional characteristics of H atoms attached to carbon atoms in both polymers were analyzed using 2D WISE NMR. Main relaxations of both components shifted inward, and both SEM and TEM analysis showed the development of a nanometer sized morphology in the case of highly crosslinked semi IPN. (C) 2010 Elsevier Ltd. All rights reserved.

On the formation of poly(ethyleneoxide)-poly(vinylalcohol) blends

Poly(ethyleneoxide)-poly(vinylalcohol) blends were prepared and characterized using thermal, spectroscopic and structural methods, By all indications the blends appear to be microscopically inhomogeneous with no strong interpolymer bonding. The high degree of crystallinity in PEO regions induces a significant degree of ordering in neighbouring PVA regions, as evident from thermal properties. PVA obtained from solvent evaporation exhibits an irreversible endothermic transition which could be order-disorder type. Both IR and NMR spectroscopies also suggest the presence of subtle structural ordering influence of PEO on PVA. It is found to be possible to prepare self supporting films of the blends which consists of fine dispersion of PEO and PVA in each other. (C) 1999 Elsevier Science Ltd. All rights reserved.

Synthesis of poly(alkyl aryl ether) dendrimers

Poly(alkyl aryl ether) dendrimers of up to four generations composed of a phloroglucinol core, branching components, and pentamethylene spacers are synthesized by a divergent growth methodology. A repetitive synthetic sequence of phenolic O-alkylation and O-benzyl deprotection reactions are adopted for the synthesis of these dendrimers. The peripheries of the dendrimers contain 6, 12, 24, and 48 phenolic hydroxyl groups, either in the protected or unprotected form, for the first, second, third, and fourth generations, respectively. Because of the presence of hydrophilic exterior and relatively hydrophobic interior regions, alkaline aqueous solutions of these dendrimers are able to solubilize an otherwise insoluble pyrene molecule and these supramolecular complexes precipitate upon neutralization of the aqueous solutions.

Reduced graphene oxide induced phase miscibility in polystyrene-poly(vinyl methyl ether) blends

Graphene oxide and reduced graphene oxide (r-GO) were synthesized by wet chemistry and the effect of r-GO in PS-PVME blends was investigated here with respect to phase miscibility, intermolecular cooperativity in the glass transition region and concentration fluctuation variance by shear rheology and dielectric spectroscopy. The spinodal decomposition temperature (T-s) and correlation length were evaluated from isochronal temperature scans in shear rheology. The r-GO is shown to induce miscibility in the blends, which may lead to increased local heterogeneity in the blends, though the length of cooperatively re-arranged regions (xi) at T-g is more or less unaltered. The evolution of the phase morphology as a function of temperature was assessed using polarized optical microscopy (POM). In the case of the 60/40 PS-PVME blends with 0.25 wt% r-GO, apart from significant refinement in the morphology, retention of the interconnected ligaments of PVME was observed, even in the late stages of phase separation suggesting that the coarsening of the phase morphology has been slowed down in the presence of r-GO. This phenomenon was also supported by AFM. Surface enrichment of PVME, owing to its lower surface tension, in the demixed samples was supported by XPS scans. The interconnected network of PVME has resulted in significantly higher permittivity in the bi-phasic blends, although the concentration of r-GO is below the percolation threshold.

Ordering-induced micro-bands in thin films of a main-chain liquid crystalline chloro-poly(aryl ether ketone)

Micro-banded textures developed from thin films of a main-chain thermotropic liquid crystalline chloro-poly(aryl ether ketone) in the melt were investigated using transmission electron microscopy (TEM). selective area electron diffraction, and atomic force microscopy techniques. The micro-banded textures were formed in the copolymer thin films after annealing at temperatures between 320 and 330degreesC, where a highly ordered smectic crystalline phase is formed without mechanical shearing. The micro-banded textures displayed a sinusoidal-like periodicity with a spacing of 150 nm and an amplitude of 2 rim. The long axis of the banded texture was parallel to the b-axis of an orthorhombic unit cell. In the convex regions, the molecular chains exhibited a homeotropic alignment, i.e. the chain direction was parallel to the film normal. In the concave re-ions, the molecular chains possessed a tilted alignment. In addition to the effects of annealing temperatures and times, the thickness of the film played a vital role in the formation of the banded texture. A possible formation mechanism of this banded texture vas also suggested and discussed. It was suggested that the micro-bands were formed during cooling.

Formation of a unique crystal morphology for the poly(ethylene glycol)-poly(epsilon-caprolactone) diblock copolymer

The crystallization behaviors of the poly(ethylene glycol)-poly(epsilon-caprolactone) diblock copolymer with the PEG weight fraction of 0.50 (PEG(50)-PCL50) was studied by DSC, WAXD, SAXS, and FTIR. A superposed melting point at 58.5 degrees C and a superposed crystallization temperature at 35.4 degrees C were obtained from the DSC profiles running at 10 degrees C/min, whereas the temperature-dependent FTIR measurements during cooling from the melt at 0.2 degrees C/min showed that the PCL crystals formed starting at 48 degrees C while the PEG crystals started at 45 degrees C. The PEG and PCL blocks of the copolymer crystallized separately and formed alternating lamella regions according to the WAXD and SAXS results. The crystal growth of the diblock copolymer was observed by polarized optical microscope (POM). An interesting morphology of the concentric spherulites developed through a unique crystallization behavior. The concentric spherulites were analyzed by in situ microbeam FTIR, and it was determined that the morphologies of the inner and outer portions were mainly determined by the PCL and PEG spherulites, respectively. However, the compositions of the inner and outer portions were equal in the analysis by microbeam FTIR.

Dynamic mechanical and thermal properties of plasticized poly(lactic acid)

The blends of low molecular weight triacetin (TAC) and oligomeric poly(1,3-butylene glycol adipate) (PBGA) were used as multiple plasticizers to lubricate poly(lactic acid) (PLA) in this study. The thermal and mechanical properties of plasticized polymers were investigated by means of dynamic mechanical analysis and differential scanning calorimetry. Atomic force microscopy (AFM) was used to analyze the morphologies of the blends. Multiple plasticizers were effective in lowering the glass transition temperature (T-g) and the melting temperature (T-m) of PLA. Moreover, crystallinity of PLA increased with increasing the con-tent of multiple plasticizers. Tensile strength of the blends decreased following the increasing of the plasticizers, but increased in elongation at break. AFM topographic images showed that the multiple plasticizers dispersed between interfibrillar regions. Moreover, the fibrillar crystallite formed the quasicrosslinkings, which is another cause for the increase in elongation at break.

Isothermal melt and cold crystallization kinetics of poly(aryl ether ketone ether ketone ketone)

The isothermal melt and cold crystallization kinetics of poly(aryl ether ketone ether ketone ketone) are investigated by differential scanning calorimetry over two temperature regions. The Avrami equation describes the primary stage of isothermal crystallization kinetics with the exponent n approximate to 2 for both melt and cold crystallization. With the Hoffman-Weeks method, the equilibrium melting point is estimated to be 406 degrees C. From the spherulitic growth equation proposed by Hoffman and Lauritzen, the nucleation parameter (K-g) of the isothermal melt and cold crystallization is estimated. In addition, the K-g value of the isothermal melt crystallization is compared to those of the other poly(aryl ether ketone)s. (C) 2000 John Wiley & Sons, Inc.

The single crystal-like banded textures in the films of a thermotropic liquid crystalline poly(aryl ether ketone) containing a lateral chloro group

The banded textures in the films of a thermotropic liquid crystalline poly(aryl ether ketone) containing a lateral chloro group have been studied by means of transmission electron microscopy(TEM), electron diffraction(ED) and atomic force microscopy (AFM). The crystallization-induced Landed texture without external shear can be formed when the thin films were annealed at the temperature range(320-330 degrees C) of the liquid crystalline state from the melt, The results show that the banded regions have high orientation of single crystal based on the orthorhombic packing and the growing direction of the Lands is along the b axis of the crystals, This kind of single crystal-like bands is due to the different orientation of the packing molecular chains, The molecular chains of the dark bands in the bright field electron micrograph are perpendicular to the film plane, while the ones of the bright Lands are tilt along the b axis with the tilt angle upto +/-20 degrees.

Influence of intermolecular entanglements on the glass transition and structural relaxation behaviors of macromolecules. 2. Polystyrene and phenolphthalein poly(ether sulfone)

The effect of entanglements on the glass transition and structural relaxation behaviors has been studied for polystyrene (PS) and phenolphthalein poly(ether sulfone) (PES-C) samples by fast evaporation of the solution of concentrations varying from above the overlapping concentration to far below it, and compared to the results we have studied previously in PC. It has been found that for all the polymers we have studied, in the concentrated solution region, the T-g of the samples obtained from solution are independent of the change of concentration and are very close to that of normal bulk samples, whereas in the dilute solution region the T-g of the samples decrease with the logarithm of decreasing concentration. The critical concentrations that divide the two distinct regions for the three polymers are 0.9% g/mL for PC, 0.1% g/mL for PS, and 1% g/mL for PES-C. The decrease of T-g of the samples is interpreted by the decrease of intermolecular entanglements as the isolation of polymer chains, and the entanglement of polymer chains restrained the mobility of the segments. The structural relaxation behavior of the polymers is also found to be different from that of normal bulk samples. The enthalpies of single-chain samples are lower than that of the bulk ones, which correspond to the lower glass transition temperature; the peaks are lower and broader, and the relaxed enthalpy is much lower as compared to that of bulk samples. In the three polymers we have studied, the influence of change of entanglements on both the decrease in glass transition temperature and relaxed enthalpy is the most significant for PS and the least for PES-C. It is indicated that the interactions in the flexible polymers are weak; thus, the restraint of the entanglements on the mobility of the segments plays a more important role in the flexible polymers, and the change of entanglement in the flexible polymers has a more significant influence on the physical properties.