Direct regulation of topoisomerase activity by a nucleoid-associated protein

The topological homeostasis of bacterial chromosomes is maintained by the balance between compaction and the topological organization of genomes. Two classes of proteins play major roles in chromosome organization: the nucleoid-associated proteins (NAPs) and topoisomerases. The NAPs bind DNA to compact the chromosome, whereas topoisomerases catalytically remove or introduce supercoils into the genome. We demonstrate that HU, a major NAP of Mycobacterium tuberculosis specifically stimulates the DNA relaxation ability of mycobacterial topoisomerase I (TopoI) at lower concentrations but interferes at higher concentrations. A direct physical interaction between M. tuberculosis HU (MtHU) and TopoI is necessary for enhancing enzyme activity both in vitro and in vivo. The interaction is between the amino terminal domain of MtHU and the carboxyl terminal domain of TopoI. Binding of MtHU did not affect the two catalytic trans-esterification steps but enhanced the DNA strand passage, requisite for the completion of DNA relaxation, a new mechanism for the regulation of topoisomerase activity. An interaction-deficient mutant of MtHU was compromised in enhancing the strand passage activity. The species-specific physical and functional cooperation between MtHU and TopoI may be the key to achieve the DNA relaxation levels needed to maintain the optimal superhelical density of mycobacterial genomes.

Noise Detected NMR Spectroscopy

Spin noise phenomenon was predicted way back in 1946. However, experimental investigations regarding spin noise became possible only recently with major technological improvements in NMR hardware. These experiments have several potential novel applications and also demand refinements in the existing theoretical framework to explain the phenomenon. Elegance of noise spectroscopy in gathering information about the properties of a system lies in the fact that it does not require external perturbation, and the system remains in thermal equilibrium. Spin noise is intrinsic magnetic fluctuations, and both longitudinal and transverse components have been detected independently in many systems. Detection of fluctuating longitudinal magnetization leads to field of Magnetic Resonance Force Microscopy (MRFM) that can efficiently probe very few spins even down to the level of single spin utilizing ultrasensitive cantilevers. Transverse component of spin noise, which can simultaneously monitor different resonances over a given frequency range enabling one to distinguish between different chemical environments, has also received considerable attention, and found many novel applications. These experiments demand a detailed understanding of the underlying spin noise phenomenon in order to perform perturbation-free magnetic resonance and widen the highly promising application area. Detailed investigations of noise magnetization have been performed recently using force microscopy on equilibrium ensemble of paramagnetic alkali atoms. It was observed that random fluctuations generate spontaneous spin coherences which has similar characteristics as generated by macroscopic magnetization of polarized ensemble in terms of precession and relaxation properties. Several other intrinsic properties like g-factors, isotope-abundance ratios, hyperfine splitting, spin coherence lifetimes etc. also have been achieved without having to excite the sample. In contrast to MRFM-approaches, detection of transverse spin noise also offers novel applications, attracting considerable attention. This has unique advantage as different resonances over a given frequency range enable one to distinguish between different chemical environments. Since these noise signatures scale inversely with sample size, these approaches lead to the possibility of non-perturbative magnetic resonance of small systems down to nano-scale. In this review, these different approaches will be highlighted with main emphasis on transverse spin noise investigations.

Photoluminescence, photocatalysis and Judd-Ofelt analysis of Eu3+-activated layered BiOCl phosphors

Eu3+-activated layered BiOCl phosphors were synthesized by the conventional solid-state method at relatively low temperature and shorter duration (400 degrees C for 1 h). All the samples were crystallized in the tetragonal structure with the space group P4/nmm (no. 129). Field emission scanning electron microscopy (FE-SEM) studies confirmed the plate-like morphology. Photoluminescence spectra exhibit characteristic luminescent D-5(0) -> F-7(J) (J = 0-4) intra-4f shell Eu3+ ion transitions. The electric dipole transition located at 620 nm (D-5(0) -> F-7(2)) was stronger than the magnetic dipole transition located at 594 nm (D-5(0) -> F-7(1)). The evaluated Commission International de l'Eclairage (CIE) color coordinates of Eu3+-activated BiOCl phosphors were close to the commercial Y2O3:Eu3+ and Y2O2S:Eu3+ red phosphors. Intensity parameters (Omega(2), Omega(4)) and various radiative properties such as transition probability (A(tot)), radiative lifetime (tau(rad)), stimulated emission cross-section (sigma(e)), gain bandwidth (sigma(e) x Delta lambda(eff)) and optical gain (sigma(e) x tau(rad)) were calculated using the Judd-Ofelt theory. The experimental decay curves of the D-5(0) level in Eu3+-activated BiOCl have a single exponential profile. In comparison with other Eu3+ doped materials, Eu3+-activated BiOCl phosphors have a long lifetime (tau(exp)), low non-radiative relaxation rate (W-NR), high quantum efficiency (eta) and better optical gain (sigma(e) x tau(rad)). The determined radiative properties revealed the usefulness of Eu3+-activated BiOCl in developing red lasers as well as optical display devices. Further, these samples showed efficient photocatalytic activity for the degradation of rhodamine B (RhB) dye under visible light irradiation. These photocatalysts are useful for the removal of toxic and non-biodegradable organic pollutants in water.

Wall-mode instability in plane shear flow of viscoelastic fluid over a deformable solid

The linear stability analysis of a plane Couette flow of an Oldroyd-B viscoelastic fluid past a flexible solid medium is carried out to investigate the role of polymer addition in the stability behavior. The system consists of a viscoelastic fluid layer of thickness R, density rho, viscosity eta, relaxation time lambda, and retardation time beta lambda flowing past a linear elastic solid medium of thickness HR, density rho, and shear modulus G. The emphasis is on the high-Reynolds-number wall-mode instability, which has recently been shown in experiments to destabilize the laminar flow of Newtonian fluids in soft-walled tubes and channels at a significantly lower Reynolds number than that for flows in rigid conduits. For Newtonian fluids, the linear stability studies have shown that the wall modes become unstable when flow Reynolds number exceeds a certain critical value Re c which scales as Sigma(3/4), where Reynolds number Re = rho VR/eta, V is the top-plate velocity, and dimensionless parameter Sigma = rho GR(2)/eta(2) characterizes the fluid-solid system. For high-Reynolds-number flow, the addition of polymer tends to decrease the critical Reynolds number in comparison to that for the Newtonian fluid, indicating a destabilizing role for fluid viscoelasticity. Numerical calculations show that the critical Reynolds number could be decreased by up to a factor of 10 by the addition of small amount of polymer. The critical Reynolds number follows the same scaling Re-c similar to Sigma(3/4) as the wall modes for a Newtonian fluid for very high Reynolds number. However, for moderate Reynolds number, there exists a narrow region in beta-H parametric space, corresponding to very dilute polymer solution (0.9 less than or similar to beta < 1) and thin solids (H less than or similar to 1.1), in which the addition of polymer tends to increase the critical Reynolds number in comparison to the Newtonian fluid. Thus, Reynolds number and polymer properties can be tailored to either increase or decrease the critical Reynolds number for unstable modes, thus providing an additional degree of control over the laminar-turbulent transition.

Single-ion magnet behaviour of heptacoordinated Fe(II) complexes: on the importance of supramolecular organization

Supramolecular organization of a metal complex may significantly contribute to the magnetization dynamics of mononuclear SMMs. This is illustrated for a heptacoordinated Fe(II) complex with rather moderate Ising-type anisotropy for which a slow magnetization relaxation with significant energy barrier was reached when this complex was properly organized in the crystal lattice. Incidentally, it is the first example of single-ion magnet behaviour of Fe(II) in a pentagonal bipyramid surrounding.

Controlling phase separation in La5/8-yPryCa3/8MnO3 (y=0.45) epitaxial thin films by strain disorder

Present study reveals that the length-scale of phase separation in La5/8-yPryCa3/8MnO3 thin films can be controlled by strain disorder invoked during the growth and relaxation process of film. Strain disorder provides an additional degree of freedom to tune colossal magnetoresistance. Magneto-transport measurements following cooling and heating in unequal fields protocol demonstrate that coherent strain stabilizes antiferromagnetic insulating phase, while strain disorder favors ferromagnetic metallic phase. Compared to bulk, antiferromagnetic-insulating phase freezes at lower temperatures in strain disordered films. Raman spectroscopy confirms the coexistence of charge-ordered-insulating and ferromagnetic-metallic phases which are structurally dissimilar and possess P2(1)/m and R-3C like symmetries, respectively. (C) 2015 AIP Publishing LLC.

Investigation on two magnon scattering processes in pulsed laser deposited epitaxial nickel zinc ferrite thin film

Ferromagnetic resonance (FMR) measurements are employed to evaluate the presence of the two magnon scattering contribution in the magnetic relaxation processes of the epitaxial nickel zinc ferrite thin films deposited using pulsed laser deposition (PLD) on the (0 0 1) MgAl2O4 substrate. Furthermore, the reciprocal space mapping reveals the presence of microstructural defects which acts as an origin for the two magnon scattering process in this thin film. The relevance of this scattering process is further discussed for understanding the higher FMR linewidth in the in-plane configuration compared to the out-of-plane configuration. FMR measurements also reveal the presence of competing uniaxial and cubic anisotropy in the studied films.

Effect of Ni-Zr codoping on dielectric and magnetic properties of SrFe12O19 via sol-gel route

Nanocrystalline strontium hexaferrites SrFe12-2x (Ni2+-Zr4+)(x)O-19] nanoparticles were successfully synthesized by sal gel process. For densification the powders were sintered at 950 degrees C/4 h. The sintered samples were characterized by X-ray diffraction (XRD), surface area measurement, and field emission scanning electron microscope (FESEM). The lattice parameter a is almost constant but c increased with x upto 0.8 and then decreased. The frequency dependent complex permittivity (epsilon and epsilon `' and permeability (mu' and mu `') and magnetic properties such as saturation magnetization (M-s), coercive field (H-c) were studied. If is observed that saturation magnetization increased gradually from 57.82 emuig to 67.2 emufg as x increased from 0.2 to 0.4 and then decreased from 672 emufg to 31.63 ernufg for x=1.0. In present study, x=0.4 shows high value of M-s 67.2 emu/g. The real part of permittivity (epsilon') remains constant upto a frequency 1 GHz and increases further with an increase of frequency, a resonance and anti resonance peak was observed above 1 GHz for all the samples. In real part of permeability (mu') the relaxation frequency is observed above 1 GHz for all the samples and it is attributed to the domain wall motion. It is well known that the permeability for polycrystalline ferrites can be described as the superposition of two different magnetizing mechanisms: spin rotation and domain wall motion. These low coercive strontium hexaferrites are suitable for magnetic recording applications in hard disks, floppy disks, video tapes, etc. (C) 2015 Elsevier B.V. All rights reserved.

Fracture in metallic glasses: mechanics and mechanisms

Significant progress in understanding the mechanical behavior of metallic glasses (MGs) was made over the past decade, particularly on mechanisms of plastic deformation. However, recent research thrust has been on exploring the mechanics and physics of fracture. MGs can be very brittle with K-Ic values similar to silicate glasses and ceramics or very tough with K-Ic akin to high toughness crystalline metals. Even the tough MGs can become brittle with structural relaxation following annealing at temperatures close to glass transition temperature (T-g). Detailed experimental studies coupled with complementary numerical simulations of the recent past have provided insights on the micromechanisms of failure as well as nature of crack tip fields, and established the governing fracture criteria for ductile and brittle glasses. In this paper, the above advances are reviewed and outstanding issues in the context of fracture of amorphous alloys that need to be resolved are identified.

Descending from infinity: Convergence of tailed distributions

We investigate the relaxation of long-tailed distributions under stochastic dynamics that do not support such tails. Linear relaxation is found to be a borderline case in which long tails are exponentially suppressed in time but not eliminated. Relaxation stronger than linear suppresses long tails immediately, but may lead to strong transient peaks in the probability distribution. We also find that a delta-function initial distribution under stronger than linear decay displays not one but two different regimes of diffusive spreading.

Optimal Linear Glauber Model

Contrary to the actual nonlinear Glauber model, the linear Glauber model (LGM) is exactly solvable, although the detailed balance condition is not generally satisfied. This motivates us to address the issue of writing the transition rate () in a best possible linear form such that the mean squared error in satisfying the detailed balance condition is least. The advantage of this work is that, by studying the LGM analytically, we will be able to anticipate how the kinetic properties of an arbitrary Ising system depend on the temperature and the coupling constants. The analytical expressions for the optimal values of the parameters involved in the linear are obtained using a simple Moore-Penrose pseudoinverse matrix. This approach is quite general, in principle applicable to any system and can reproduce the exact results for one dimensional Ising system. In the continuum limit, we get a linear time-dependent Ginzburg-Landau equation from the Glauber's microscopic model of non-conservative dynamics. We analyze the critical and dynamic properties of the model, and show that most of the important results obtained in different studies can be reproduced by our new mathematical approach. We will also show in this paper that the effect of magnetic field can easily be studied within our approach; in particular, we show that the inverse of relaxation time changes quadratically with (weak) magnetic field and that the fluctuation-dissipation theorem is valid for our model.

GLOBAL REGISTRATION OF MULTIPLE POINT CLOUDS USING SEMIDEFINITE PROGRAMMING

Consider N points in R-d and M local coordinate systems that are related through unknown rigid transforms. For each point, we are given (possibly noisy) measurements of its local coordinates in some of the coordinate systems. Alternatively, for each coordinate system, we observe the coordinates of a subset of the points. The problem of estimating the global coordinates of the N points (up to a rigid transform) from such measurements comes up in distributed approaches to molecular conformation and sensor network localization, and also in computer vision and graphics. The least-squares formulation of this problem, although nonconvex, has a well-known closed-form solution when M = 2 (based on the singular value decomposition (SVD)). However, no closed-form solution is known for M >= 3. In this paper, we demonstrate how the least-squares formulation can be relaxed into a convex program, namely, a semidefinite program (SDP). By setting up connections between the uniqueness of this SDP and results from rigidity theory, we prove conditions for exact and stable recovery for the SDP relaxation. In particular, we prove that the SDP relaxation can guarantee recovery under more adversarial conditions compared to earlier proposed spectral relaxations, and we derive error bounds for the registration error incurred by the SDP relaxation. We also present results of numerical experiments on simulated data to confirm the theoretical findings. We empirically demonstrate that (a) unlike the spectral relaxation, the relaxation gap is mostly zero for the SDP (i.e., we are able to solve the original nonconvex least-squares problem) up to a certain noise threshold, and (b) the SDP performs significantly better than spectral and manifold-optimization methods, particularly at large noise levels.

Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics

A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion diffusion, (ii) intermediate scattering function of the constituent ions, and (iii) ion solvation dynamics in electrolyte solution. Brownian dynamics with implicit water molecules and molecular dynamics method with explicit water are used to check the theoretical predictions. The time dependence of ionic self-diffusion coefficient and the corresponding intermediate scattering function evaluated from our MCT approach show quantitative agreement with early experimental and present Brownian dynamic simulation results. With increasing concentration, the dispersion of electrolyte friction is found to occur at increasingly higher frequency, due to the faster relaxation of the ion atmosphere. The wave number dependence of intermediate scattering function, F(k, t), exhibits markedly different relaxation dynamics at different length scales. At small wave numbers, we find the emergence of a step-like relaxation, indicating the presence of both fast and slow time scales in the system. Such behavior allows an intriguing analogy with temperature dependent relaxation dynamics of supercooled liquids. We find that solvation dynamics of a tagged ion exhibits a power law decay at long times-the decay can also be fitted to a stretched exponential form. The emergence of the power law in solvation dynamics has been tested by carrying out long Brownian dynamics simulations with varying ionic concentrations. The solvation time correlation and ion-ion intermediate scattering function indeed exhibit highly interesting, non-trivial dynamical behavior at intermediate to longer times that require further experimental and theoretical studies. (c) 2015 AIP Publishing LLC.

Targeting Mycobacterium tuberculosis Topoisomerase I by Small-Molecule Inhibitors

We describe inhibition of Mycobacterium tuberculosis topoisomerase I (MttopoI), an essential mycobacterial enzyme, by two related compounds, imipramine and norclomipramine, of which imipramine is clinically used as an antidepressant. These molecules showed growth inhibition of both Mycobacterium smegmatis and Mycobacterium tuberculosis cells. The mechanism of action of these two molecules was investigated by analyzing the individual steps of the topoisomerase I (topoI) reaction cycle. The compounds stimulated cleavage, thereby perturbing the cleavage-religation equilibrium. Consequently, these molecules inhibited the growth of the cells overexpressing topoI at a low MIC. Docking of the molecules on the MttopoI model suggested that they bind near the metal binding site of the enzyme. The DNA relaxation activity of the metal binding mutants harboring mutations in the DxDxE motif was differentially affected by the molecules, suggesting that the metal coordinating residues contribute to the interaction of the enzyme with the drug. Taken together, the results highlight the potential of these small molecules, which poison the Mycobacterium tuberculosis and Mycobacterium smegmatis topoisomerase I, as leads for the development of improved molecules to combat mycobacterial infections. Moreover, targeting metal coordination in topoisomerases might be a general strategy to develop new lead molecules.

Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide

Longitudinal relaxation due to cross-correlation between dipolar ((HN-1H alpha)-H-1) and amide-proton chemical shift anisotropy (H-1(N) CSA) has been measured in a model tripeptide Piv-(L)Pro-(L)Pro-(L)Phe-OMe. The peptide bond across diproline segment is known to undergo cis/trans isomerization and only in the cis form does the lone Phe amide-proton become involved in intramolecular hydrogen bonding. The strength of the cross correlated relaxation interference is found to be significantly different between cis and trans forms, and this difference is shown as an influence of intramolecular hydrogen bonding on the amide-proton CSA. (C) 2015 Elsevier B.V. All rights reserved.