227 resultados para DOUBLE BARRIER STRUCTURES


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Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation ill each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA ar rd RNA duplex structures.

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We describe an investigation of (Ba3MMWO9)-M-II-W-IV oxides for M-II = Ca, Zn, and other divalent metals and M-IV = Ti, Zr. In general, a 1:2-ordered 6H (hexagonal, P6(3)/mmc) perovskite structure is stabilized at high temperatures (1300 degrees C) for all of the (Ba3MTiWO9)-Ti-II oxides investigated. An intermediate phase possessing a partially ordered 1:1 double perovskite (3C) structure with the cation distribution, Ba-2(Zn2/3Ti1/3)(W2/3Ti1/3)O-6, is obtained at 1200 degrees C for Ba3ZnTiWO9. Sr substitution for Ba in the latter stabilizes the cubic 3C structure instead of the 6H structure. A metastable Ba3CaZrWO9 that adopts the 3C (cubic, Fm (3) over barm) structure has also been synthesized by a low-temperature metathesis route. Besides yielding several new perovskite oxides that may be useful as dielectric ceramics, the present investigation provides new insights into the complex interplay of crystal chemistry (tolerance factor) and chemical bonding (anion polarization and d(0)-induced distortion of metal-oxygen octahedra) in the stabilization of 6H versus 3C perovskite structures for the (Ba3MMWO9)-M-II-W-IV series.

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We describe an investigation of (Ba3MMWO9)-M-II-W-IV oxides for M-II = Ca, Zn, and other divalent metals and M-IV = Ti, Zr. In general, a 1:2-ordered 6H (hexagonal, P6(3)/mmc) perovskite structure is stabilized at high temperatures (1300 degrees C) for all of the (Ba3MTiWO9)-Ti-II oxides investigated. An intermediate phase possessing a partially ordered 1:1 double perovskite (3C) structure with the cation distribution, Ba-2(Zn2/3Ti1/3)(W2/3Ti1/3)O-6, is obtained at 1200 degrees C for Ba3ZnTiWO9. Sr substitution for Ba in the latter stabilizes the cubic 3C structure instead of the 6H structure. A metastable Ba3CaZrWO9 that adopts the 3C (cubic, Fm (3) over barm) structure has also been synthesized by a low-temperature metathesis route. Besides yielding several new perovskite oxides that may be useful as dielectric ceramics, the present investigation provides new insights into the complex interplay of crystal chemistry (tolerance factor) and chemical bonding (anion polarization and d(0)-induced distortion of metal-oxygen octahedra) in the stabilization of 6H versus 3C perovskite structures for the (Ba3MMWO9)-M-II-W-IV series.

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The sequence specificity of the recombination activating gene (RAG) complex during V(D)J recombination has been well studied. RAGs can also act as structure-specific nuclease; however, little is known about the mechanism of its action. Here, we show that in addition to DNA structure, sequence dictates the pattern and efficiency of RAG cleavage on altered DNA structures. Cytosine nucleotides are preferentially nicked by RAGs when present at single-stranded regions of heteroduplex DNA. Although unpaired thymine nucleotides are also nicked, the efficiency is many fold weaker. Induction of single- or double-strand breaks by RAGs depends on the position of cytosines and whether it is present on one or both of the strands. Interestingly, RAGs are unable to induce breaks when adenine or guanine nucleotides are present at single-strand regions. The nucleotide present immediately next to the bubble sequence could also affect RAG cleavage. Hence, we propose “C(d)C(S)C(S)” (d, double-stranded; s, single-stranded) as a consensus sequence for RAG-induced breaks at single-/double-strand DNA transitions. Such a consensus sequence motif is useful for explaining RAG cleavage on other types of DNA structures described in the literature. Therefore, the mechanism of RAG cleavage described here could explain facets of chromosomal rearrangements specific to lymphoid tissues leading to genomic instability.

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L-Lysine D-glutamate crystallizes in the monoclinic space group P2(1) with a = 4.902, b = 30.719, c = 9.679 A, beta = 90 degrees and Z = 4. The crystals of L-lysine D-aspartate monohydrate belong to the orthorhombic space group P2(1)2(1)2(1) with a = 5.458, b = 7.152, c = 36.022 A and Z = 4. The structures were solved by the direct methods and refined to R values of 0.125 and 0.040 respectively for 1412 and 1503 observed reflections. The glutamate complex is highly pseudosymmetric. The lysine molecules in it assume a conformation with the side chain staggered between the alpha-amino and the alpha-carboxylate groups. The interactions of the side chain amino groups of lysine in the two complexes are such that they form infinite sequences containing alternating amino and carboxylate groups. The molecular aggregation in the glutamate complex is very similar to that observed in L-arginine D-aspartate and L-arginine D-glutamate trihydrate, with the formation of double layers consisting of both types of molecules. In contrast to the situation in the other three LD complexes, the unlike molecules in L-lysine D-aspartate monohydrate aggregate into alternating layers as in the case of most LL complexes. The arrangement of molecules in the lysine layer is nearly the same as in L-lysine L-aspartate, with head-to-tail sequences as the central feature. The arrangement of aspartate ions in the layers containing them is, however, somewhat unusual. Thus the comparison between the LL and the LD complexes analyzed so far indicates that the reversal of chirality of one of the components in a complex leads to profound changes in molecular aggregation, but these changes could be of more than one type.

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X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

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The right-handed double-helical Watson-Crick model for B-form DNA is the most commonly known DNA structure. In addition to this classic structure, several other forms of DNA have been observed and it is clear that the DNA molecule can assume different structures depending on the base sequence and environment. The various forms of DNA have been identified as A, B, C etc. In fact, a detailed inspection of the literature reveals that only the letters F, Q, U, V and Y are now available to describe any new DNA structure that may appear in the future. It is also apparent that it may be more relevant to talk about the A, B or C type dinucleotide steps, since several recent structures show mixtures of various different geometries and a careful analysis is essential before identifying it as a 'new structure'. This review provides a glossary of currently identified DNA structures and is quite timely as it outlines the present understanding of DNA structure exactly 50 years after the original discovery of DNA structure by Watson and Crick

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The present work explores the temperature dependent transport behavior of n-InN nanodot/p-Si(100) heterojunction diodes. InN nanodot (ND) structures were grown on a 20 nm InN buffer layer on p-Si(100) substrates. These dots were found to be single crystalline and grown along 001] direction. The junction between these two materials exhibits a strong rectifying behavior at low temperatures. The average barrier height (BH) was determined to be 0.7 eV from current-voltage-temperature, capacitance-voltage, and flat band considerations. The band offsets derived from built-in potential were found to be Delta E-C=1.8 eV and Delta E-V=1.3 eV and are in close agreement with Anderson's model. (C) 2010 American Institute of Physics. doi:10.1063/1.3517489]

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The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

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The reactions of As-chlorocyclotriphosphazane [EtNPCl], with phenols or trifluoroethanol yield the respective aryloxy- or trifluoroethoxy-containingX 3-cyclotriphosphazanes [EtNP(OR)]3 (R = C6H4Br-4 (2),C 6H5 (3C,6 H3-Mez-3,5 (4), C6H3Mez-2,6 (5), CH2CF3 (6)) as their cis-transisomericmixtures. The products have beencharacterized by IRand NMRspectroscopy. Thecrystalstructuresofboth thecis (2a) and trans(2b) isomer_softhep-bromophenoxy derivative have been determined by X-ray diffraction. Crystal data for 2a: triclinic, P1, a = 9.872(4) A, b = 13.438(6) A, c = 13.548(8) A, CY = 117.02(5)', 0 = 96.00(6)', y = 105.38(4)O, Z = 2, final R = 0.080. Crystal data for 2b: monoclinic, P21/n, a = 12.721(6) A, b = 13.468(7) A, c = 17.882(5) A, /3 = 101.62(3)O, Z = 4, final R = 0.066. The cis isomer exhibits a chair-triaxial conformation and the trans isomer a boat-triaxial conformation. Conformational preferences of X3-cyclotriphosphazanes have been probed by both MNDO and ab initio calculations on model systems [HNPXIp (X = H, F). In addition to vicinal lone pair repulsions, negative hyperconjugative interactions involving the nitrogen lone pairs and adjacent P-X Q* orbitals are found to be important (especially when X is an electronegative substituent) in determining the conformational preferences of X3-cyclotriphosphazanes. The calculations also show that the axial - equatorial conversion at phosphorus has a large activation barrier in these systems

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We consider the Kramers problem for a long chain polymer trapped in a biased double-well potential. Initially the polymer is in the less stable well and it can escape from this well to the other well by the motion of its N beads across the barrier to attain the configuration having lower free energy. In one dimension we simulate the crossing and show that the results are in agreement with the kink mechanism suggested earlier. In three dimensions, it has not been possible to get an analytical `kink solution' for an arbitrary potential; however, one can assume the form of the solution of the nonlinear equation as a kink solution and then find a double-well potential in three dimensions. To verify the kink mechanism, simulations of the dynamics of a discrete Rouse polymer model in a double well in three dimensions are carried out. We find that the time of crossing is proportional to the chain length, which is in agreement with the results for the kink mechanism. The shape of the kink solution is also in agreement with the analytical solution in both one and three dimensions.

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A new method based on analysis of a single diffraction pattern is proposed to measure deflections in micro-cantilever (MC) based sensor probes, achieving typical deflection resolutions of 1nm and surface stress changes of 50 mu N/m. The proposed method employs a double MC structure where the deflection of one of the micro-cantilevers relative to the other due to surface stress changes results in a linear shift of intensity maxima of the Fraunhofer diffraction pattern of the transilluminated MC. Measurement of such shifts in the intensity maxima of a particular order along the length of the structure can be done to an accuracy of 0.01mm leading to the proposed sensitivity of deflection measurement in a typical microcantilever. This method can overcome the fundamental measurement sensitivity limit set by diffraction and pointing stability of laser beam in the widely used Optical Beam Deflection method (OBDM).

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Diastereomers (SRu,Sc)-1a and (RRu,Sc)-1b, in a ratio of 85: 15 and formulated as [Ru(η-MeC6H4Pri-p)Cl(L*)], have been prepared by treating [{Ru(η-MeC6H4Pri-p)Cl2}2] with the sodium salt of (S)-α-methylbenzylsalicylaldimine (HL*) in tetrahydrofuran at –70 °C. The reaction of 1(1a+1b) with AgClO4 in acetone followed by an addition of PPh3 or 4-methylpyridine (4Me-py) leads to the formation of adducts [Ru(η-MeC6H4Pri-p)(PPh3)(L*)]ClO42[(SRu,Sc)2a, (FRu,Sc)2b] and [Ru(η-MeC6H4Pri-p)(4Me-py)(L*)]ClO43[(SRu,Sc)3a, (RRu,Sc)3b] in the diastereomeric ratios (SRu,Sc) : (RRu,Sc) of 2 : 98 and 76 : 24, respectively. Complex 1 crystallises with equal numbers of 1a and 1b molecules in an asymmetric unit of monoclinic space group P21 with a= 10.854(1), b= 17.090(1), c= 12.808(4)Å, β= 110.51(1)°, and Z= 4. The structure was refined to R= 0.0552 and R′= 0.0530 with 2893 reflections having I[gt-or-equal] 1.5σ(I). The absolute configurations of the chiral centres in the optically pure single crystal of the PPh3 adduct have been obtained from an X-ray study. Crystals of formulation [Ru(η-MeC6H4Pri-p)-(PPh3)(L*)]2[ClO4][PF6]·1.5 CHCl3, obtained in presence of both ClO4 and PF6 anions, belong to the non-centric triclinic space group P1 with a= 10.852(2), b= 14.028(1), c= 15.950(2)Å, α= 91.51(1), β= 105.97(1), γ= 106.11(1)°, and Z= 2. The final residuals were R= 0.0713, R′= 0.0752 with 7283 reflections having I[gt-or-equal] 2.5σ(I). The crystal structures of 1a,1b, and the PPh3 adduct (2b,2b′) consist of a ruthenium(II) centre bonded to a η-p-cymene, a bidentate chelating Schiff base, and a unidentate ligand (Cl or PPh3). The chirooptical properties of the complexes have been studied using 1H NMR and CD spectral data. The presence of a low-energy barrier for the intermediate involved in these reactions, showing both retention as well as inversion of the metal configuration, is discussed.

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Theoretical approaches are of fundamental importance to predict the potential impact of waste disposal facilities on ground water contamination. Appropriate design parameters are, in general, estimated by fitting the theoretical models to a field monitoring or laboratory experimental data. Double-reservoir diffusion (Transient Through-Diffusion) experiments are generally conducted in the laboratory to estimate the mass transport parameters of the proposed barrier material. These design parameters are estimated by manual parameter adjusting techniques (also called eye-fitting) like Pollute. In this work an automated inverse model is developed to estimate the mass transport parameters from transient through-diffusion experimental data. The proposed inverse model uses particle swarm optimization (PSO) algorithm which is based on the social behaviour of animals for finding their food sources. Finite difference numerical solution of the transient through-diffusion mathematical model is integrated with the PSO algorithm to solve the inverse problem of parameter estimation.The working principle of the new solver is demonstrated by estimating mass transport parameters from the published transient through-diffusion experimental data. The estimated values are compared with the values obtained by existing procedure. The present technique is robust and efficient. The mass transport parameters are obtained with a very good precision in less time

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The electrical transport behavior of n-n indium nitride nanodot-silicon (InN ND-Si) heterostructure Schottky diodes is reported here, which have been fabricated by plasma-assisted molecular beam epitaxy. InN ND structures were grown on a 20 nm InN buffer layer on Si substrates. These dots were found to be single crystalline and grown along [0 0 0 1] direction. Temperature-dependent current density-voltage plots (J-V-T) reveal that the ideality factor (eta) and Schottky barrier height (SBH) (Phi(B)) are temperature dependent. The incorrect values of the Richardson constant (A**) produced suggest an inhomogeneous barrier. Descriptions of the experimental results were explained by using two models. First one is barrier height inhomogeneities (BHIs) model, in which considering an effective area of the inhomogeneous contact provided a procedure for a correct determination of A**. The Richardson constant is extracted similar to 110 A cm(-2) K(-2) using the BHI model and that is in very good agreement with the theoretical value of 112 A cm(-2) K(-2). The second model uses Gaussian statistics and by this, mean barrier height Phi(0) and A** were found to be 0.69 eV and 113 A cm(-2) K(-2), respectively.