Differential Reaction Kinetics, Cleavage Complex Formation, and Nonamer Binding Domain Dependence Dictate the Structure-Specific and Sequence-Specific Nuclease Activity of RAGs

During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the ``nonamer binding region,'' which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease. (C) 2011 Elsevier Ltd. All rights reserved.

Observation of pseudo-gap and Kondo behaviour in Al70Pd30−xMnx quasicrystals

We report here the electrical and magnetic properties of Al70Pd30−xMnx quasicrystals (x=9 and 11), from resistivity and point contact spectroscopy measurements. Electrical resistivity shows a resistivity maximum for both of these compositions. The positive TCR at lower temperature is attributed to spin–orbit scattering. For x=11, we observe an upturn in the resistivity below 20 K, which follows a lnT dependence indicating Kondo-like behaviour. In the point contact spectroscopy studies we observe two regimes showing a V2 dependence at low bias voltages (for V<10 meV) crossing over to the V0.5 dependence at higher voltages. This is attributed to the signature of a pseudo-gap in the density of states at zero bias. We suggest that this V2 dependence can also arise due to magnetic scattering effects, which are signatures of the Kondo-like behaviour.

Contact instabilities of anisotropic and inhomogeneous soft elastic films

Anisotropy plays important roles in various biological phenomena such as adhesion of geckos and grasshoppers enabled by the attachment pods having hierarchical structures like thin longitudinal setae connected with threads mimicked by anisotropic films. We study the contact instability of a transversely isotropic thin elastic film when it comes in contact proximity of another surface. In the present study we investigate the contact stability of a thin incompressible transversely isotropic film by performing linear stability analysis. Based on the linear stability analysis, we show that an approaching contactor renders the film unstable. The critical wavelength of the instability is a function of the total film thickness and the ratio of the Young's modulus in the longitudinal direction and the shear modulus in the plane containing the longitudinal axis. We also analyze the stability of a thin gradient film that is elastically inhomogeneous across its thickness. Compared to a homogeneous elastic film, it becomes unstable with a longer wavelength when the film becomes softer in going from the surface to the substrate.

Unusual dependence of raman mode frequency on excitation wavelength in graphite and single walled carbon nanotubes

In this paper we report resonance Raman scattering from graphite covering excitation energies in the range 2.4 eV to 6 eV. The Raman excitation profile shows a maximum at 4.94 eV (lambda = 251nm) for the G - band (1582 cm(-1)). The D-band at similar to 1350 cm(-1), attributed to disorder activated Raman scattering, does not show up in Raman spectra recorded with excitation wavelengths smaller than 257.3 nm, revealing that the resonance enhancements of the G and D-modes are widely different. Earlier Raman measurements in carbon materials have also revealed a very large and unusual dependence of the D - mode frequency on excitation laser wavelength. This phenomenon is also observed in carbon nanotubes. In this paper we show for the first time that the above unusual dependence arises from the disorder - induced double resonance mechanism.

Influence of the Methane-Zeolite A Interaction Potential on the Concentration Dependence of Self-diffusivity

Studies on the diffusion of methane in a zeolite structure type LTA (as per IZA nomenclature) have indicated that different types of methane zeolite potentials exist in the literature in which methane is treated within the united-atom model. One set of potentials, referred to as model A, has a methane oxygen diameter of 3.14 angstrom, while another set of potential parameters, model B, employs a larger value of 3.46 angstrom. Fritzsche and co-workers (1993) have shown that these two potentials lead to two distinctly different energetic barriers for the passage of methane through the eight-ring window in the cation-free form of zeolite A. Here, we compute the variation of the self-diffusivity (D) with loading (c) for these two types of potentials and show that this slight variation in the diameter changes the concentration dependence qualitatively: thus, D decreases monotonically with c for model A, while D increases and goes through a maximum before finally decreasing for model B. This effect and the surprising congruence of the diffusion coefficients for both models at high loadings is examined in detail at the molecular level. Simulations for different temperatures reveal the Arrhenius behaviour of the self-diffusion coefficient. The apparent activation energy is found to vary with the loading. We conclude that beside the cage-to-cage jumps, which are essential for the migration of the guest molecules, at high concentrations migration within the cage and guest guest interactions with other molecules become increasingly dominant influences on the diffusion coefficient and make the guest zeolite interaction less important for both model A and model B.

Dependence of climate forcing and response on the altitude of black carbon aerosols

Black carbon aerosols absorb solar radiation and decrease planetary albedo, and thus can contribute to climate warming. In this paper, the dependence of equilibrium climate response on the altitude of black carbon is explored using an atmospheric general circulation model coupled to a mixed layer ocean model. The simulations model aerosol direct and semi-direct effects, but not indirect effects. Aerosol concentrations are prescribed and not interactive. It is shown that climate response of black carbon is highly dependent on the altitude of the aerosol. As the altitude of black carbon increases, surface temperatures decrease; black carbon near the surface causes surface warming, whereas black carbon near the tropopause and in the stratosphere causes surface cooling. This cooling occurs despite increasing planetary absorption of sunlight (i.e. decreasing planetary albedo). We find that the trend in surface air temperature response versus the altitude of black carbon is consistent with our calculations of radiative forcing after the troposphere, stratosphere, and land surface have undergone rapid adjustment, calculated as ``regressed'' radiative forcing. The variation in climate response from black carbon at different altitudes occurs largely from different fast climate responses; temperature dependent feedbacks are not statistically distinguishable. Impacts of black carbon at various altitudes on the hydrological cycle are also discussed; black carbon in the lowest atmospheric layer increases precipitation despite reductions in solar radiation reaching the surface, whereas black carbon at higher altitudes decreases precipitation.

Dependence of diffusivity on density and solute diameter in liquid phase: A molecular dynamics study of Lennard-Jones system

Investigations into the variation of self-diffusivity with solute radius, density, and degree of disorder of the host medium is explored. The system consists of a binary mixture of a relatively smaller sized solute, whose size is varied and a larger sized solvent interacting via Lennard-Jones potential. Calculations have been performed at three different reduced densities of 0.7, 0.8, and 0.933. These simulations show that diffusivity exhibits a maximum for some intermediate size of the solute when the solute diameter is varied. The maximum is found at the same size of the solute at all densities which is at variance with the prediction of the levitation effect. In order to understand this anomaly, additional simulations were carried out in which the degree of disorder has been varied while keeping the density constant. The results show that the diffusivity maximum gradually disappears with increase in disorder. Disorder has been characterized by means of the minimal spanning tree. Simulations have also been carried out in which the degree of disorder is constant and only the density is altered. The results from these simulations show that the maximum in diffusivity now shifts to larger distances with decrease in density. This is in agreement with the changes in void and neck distribution with density of the host medium. These results are in excellent agreement with the predictions of the levitation effect. They suggest that the effect of disorder is to shift the maximum in diffusivity towards smaller solute radius while that of the decrease in density is to shift it towards larger solute radius. Thus, in real systems where the degree of disorder is lower at higher density and vice versa, the effect due to density and disorder have opposing influences. These are confirmed by the changes seen in the velocity autocorrelation function, self part of the intermediate scattering function and activation energy. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.3701619]

Quenching across quantum critical points in periodic systems: Dependence of scaling laws on periodicity

We study the quenching dynamics of a many-body system in one dimension described by a Hamiltonian that has spatial periodicity. Specifically, we consider a spin-1/2 chain with equal xx and yy couplings and subject to a periodically varying magnetic field in the (z) over cap direction or, equivalently, a tight-binding model of spinless fermions with a periodic local chemical potential, having period 2q, where q is a positive integer. For a linear quench of the strength of the magnetic field (or chemical potential) at a rate 1/tau across a quantum critical point, we find that the density of defects thereby produced scales as 1/tau(q/(q+1)), deviating from the 1/root tau scaling that is ubiquitous in a range of systems. We analyze this behavior by mapping the low-energy physics of the system to a set of fermionic two-level systems labeled by the lattice momentum k undergoing a nonlinear quench as well as by performing numerical simulations. We also show that if the magnetic field is a superposition of different periods, the power law depends only on the smallest period for very large values of tau, although it may exhibit a crossover at intermediate values of tau. Finally, for the case where a zz coupling is also present in the spin chain, or equivalently, where interactions are present in the fermionic system, we argue that the power associated with the scaling law depends on a combination of q and the interaction strength.

Evidence for the ``Amphoteric'' Nature of Fluorine in Halogen Bonds: An Instance of Cl center dot center dot center dot F Contact

This study presents unambiguous experimental evidence in support of the highly debated ``halogen bond donor'' character of organic fluorine. Two examples of intermolecular Cl center dot center dot center dot F contacts, with F-atom as halogen bond acceptor and donor, have been analyzed by in situ cryocrystallography and theoretical charge density studies.

Compositional dependence optical properties study of As40Se60-xSbx thin films

Thin films were thermally evaporated from the bulk glasses of As40Se60-xSbx (with x = 0, 5, 10, 15 at.%) under high vacuum. We have characterized the deposited films by Fourier Transform Infrared spectroscopy. The relationship between the structural and optical properties and the compositional variation has been investigated. Increasing Sb content was found to affect the thermal and optical properties of these films. Non-direct electronic transition was found to be responsible for the photon absorption inside the investigated films. It was found that, the optical band gap E-o decreases while the width of localized states (Urbach energy) E-e increases. (C) 2011 Elsevier B.V. All rights reserved.

Micromechanisms of damage nucleation during contact deformation of columnar multilayer nitride coatings

In order to resolve some missing micromechanistic details regarding contact deformation in nitride multilayer coatings we report here observations from cross-sectional transmission electron microscopy and focused ion beam studies of the Vickers indentations on TiN/TiAlN multilayer films of various total thicknesses as well as bilayer periods. The study of damage induced by contact deformation in a nitride multilayer coating is complemented by stress calculated using an analytical model. Kinked boundaries of sliding columns give rise to cracks which propagate at an angle to the indentation axis under a combination of compressive and shear stresses. It is seen that multilayers provide more distributed columnar sliding, thereby reducing the stress intensity factor for shear cracking, while interfacial dislocations provide a stress relief mechanism by enabling lateral movement of material. (C) 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Carrier concentration dependence of donor activation energy in n-type GaN epilayers grown on Si (111) by plasma-assisted MBE

The n-type GaN layers were grown by plasma-assisted MBE and either intentionally doped with Si or unintentionally doped. The optical characteristics of a donor level in Si-doped, GaN were studied in terms of photoluminescence (PL) spectroscopy as a function of electron concentration. Temperature dependent PL measurements allowed us to estimate the activation energy of a Si-related donor from temperature-induced decay of PL intensity. PL peak positions, full width at half maximum of PL and activation energies are found to be proportional to the cube root of carrier density. The involvement of donor levels is supported by the temperature-dependent electron concentration measurements. (C) 2012 Elsevier Ltd. All rights reserved.

Mechanical properties of ZnS nanowires and thin films: Microscopic origin of the dependence on size and growth direction

Mechanical properties of ZnS nanowires and thin films are studied as a function of size and growth direction using all-atom molecular dynamics simulations. Using the stress-strain relationship we extract Young's moduli of nanowires and thin films at room temperature. Our results show that Young's modulus of 0001] nanowires has strong size dependence. On the other hand, 01 (1) over bar0] nanowires do not exhibit a strong size dependence of Young's modulus in the size range we have investigated. We provide a microscopic understanding of this behavior on the basis of bond stretching and contraction due to the rearrangement of atoms in the surface layers. The ultimate tensile strengths of the nanowires do not show much size dependence. To investigate the mechanical behavior of ZnS in two dimensions, we calculate Young's modulus of thin films under tensile strain along the 0001] direction. Young's modulus of thin films converges to the bulk value more rapidly than that of the 0001] nanowire.

Mechanical and electrical contact resistance characteristics of a cellular assembly of carbon nanotubes

We employ nanoindentation coupled with electrical contact resistance measurements for simultaneous characterization of the electrical and mechanical behaviors of a cellular assembly of carbon nanotubes (CNTs). Experimental results reveal two different responses that correspond to relatively dense and porous regions of the cellular structure. Distinct nonlinear electron transport characteristics are observed, which mainly originate from diffusive conductance in the CNT structure. In the denser region, differential conductance shows asymmetric minima at lower bias, implying that conductivity mainly results from bulk tunneling. However, the porous regions show insignificant differential conduction as opposed to the denser region.

Temperature dependence of spin lifetime of conduction electrons in bulk germanium

Optically generated spin polarized electrons in bulk n-type Ge samples have been detected by using a radio-frequency modulation technique. Using the Hanle effect in an external magnetic field, the spin lifetime was measured as a function of temperature in the range 90 K to 180 K. The lifetime decreases with increasing temperature from similar to 5 ns at 100 K to similar to 2 ns at 180 K. We show that the temperature dependence is consistent with the Elliott-Yafet spin relaxation mechanism R. J. Elliot, Phys. Rev. 96, 266 (1954)]. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4772500]