Increasing cleavage specificity and activity of restriction endonuclease KpnI

Restriction enzyme KpnI is a HNH superfamily endonuclease requiring divalent metal ions for DNA cleavage but not for binding. The active site of KpnI can accommodate metal ions of different atomic radii for DNA cleavage. Although Mg2+ ion higher than 500 mu M mediates promiscuous activity, Ca2+ suppresses the promiscuity and induces high cleavage fidelity. Here, we report that a conservative mutation of the metal-coordinating residue D148 to Glu results in the elimination of the Ca2+-mediated cleavage but imparting high cleavage fidelity with Mg2+. High cleavage fidelity of the mutant D148E is achieved through better discrimination of the target site at the binding and cleavage steps. Biochemical experiments and molecular dynamics simulations suggest that the mutation inhibits Ca2+-mediated cleavage activity by altering the geometry of the Ca2+-bound HNH active site. Although the D148E mutant reduces the specific activity of the enzyme, we identified a suppressor mutation that increases the turnover rate to restore the specific activity of the high fidelity mutant to the wild-type level. Our results show that active site plasticity in coordinating different metal ions is related to KpnI promiscuous activity, and tinkering the metal ion coordination is a plausible way to reduce promiscuous activity of metalloenzymes.

Simulations and experiments in punching spring-steel devices with sub-millimeter features

This work demonstrates the feasibility of mesoscale (100 μm to mm) punching of multiple holes of intricate shapes in metals. Analytical modeling, finite element (FE)simulation, and experimentations are used in this work. Two dimensional FE simulations in ABAQUS were done with an assumed material modeling and plane-strain condition. A known analytical model was used and compared with the ABAQUS simulation results to understand the effects of clearance between the punch and the die. FE simulation in ABAQUS was done for different clearances and corner radii at punch, die, and holder. A set of punches and dies were used to punch out a miniature spring-steel gripper. Comparison of compliant grippers manufactured by wire-cut electro discharge machining(EDM) and punching shows that realizing sharp interior and re-entrant corners by punching is not easy to achieve. Punching of circular holes with 5 mm and 2.5 mm diameter is achieved. The possibility of realizing meso-scale parts with complicated shapes through punching is demonstrated in this work; and some strategies are suggested for improvement.

Defect induced plasticity and failure mechanism of boron nitride nanotubes under tension

The effects of Stone-Wales (SW) and vacancy defects on the failure behavior of boron nitride nanotubes (BNNTs) under tension are investigated using molecular dynamics simulations. The Tersoff-Brenner potential is used to model the atomic interaction and the temperature is maintained close to 300 K. The effect of a SW defect is studied by determining the failure strength and failure mechanism of nanotubes with different radii. In the case of a vacancy defect, the effect of an N-vacancy and a B-vacancy is studied separately. Nanotubes with different chiralities but similar diameter is considered first to evaluate the chirality dependence. The variation of failure strength with the radius is then studied by considering nanotubes of different diameters but same chirality. It is observed that the armchair BNNTs are extremely sensitive to defects, whereas the zigzag configurations are the least sensitive. In the case of pristine BNNTs, both armchair and zigzag nanotubes undergo brittle failure, whereas in the case of defective BNNTs, only the zigzag ones undergo brittle failure. An interesting defect induced plastic behavior is observed in defective armchair BNNTs. For this nanotube, the presence of a defect triggers mechanical relaxation by bond breaking along the closest zigzag helical path, with the defect as the nucleus. This mechanism results in a plastic failure. (C) 2014 AIP Publishing LLC.

Stepwise Crystallization: Illustrative Examples of the Use of Metalloligands Cu-6(mna)(6)](6-) and (Ag-6(Hmna)(2)(mna)(4)](4-) (H(2)mna=2-Mercapto Nicotinic Acid) in the Formation of Heterometallic Two- and Three-Dimensional Assemblies with brucite, pcu, and sql Topologies

Three new inorganic coordination polymers, {Mn(H2O)(6)]-Mn-2(H2O)(6)](Cu-6(mna)(6)]center dot 6H(2)O}, 1, {Mn-4(OH)(2)(H2O)(10)] (Cu-6(mna)6]center dot 8H(2)O}, 2, and {Mn-2(H2O)(5)]Ag-6(Hmna)(2)(mna)(4)]center dot 20H(2)O}, 3, have been synthesized at room temperature through a sequential crystallization route. In addition, we have also prepared and characterized the molecular precursor Cu-6(Hmna)(6)]. Compounds 1 and 3 have a two-dimensional structure, whereas 2 has a three-dimensional structure. The formation of 2 has been achieved by minor modification in the synthetic composition, suggesting the subtle relationship between the reactant composition and the structure. The hexanudear copper and silver duster cores have Cu center dot center dot center dot Cu and Ag center dot center dot center dot Ag distances close to the sum of the van der Waals radii of Cu1+ and Ag1+, respectively. The connectivity between Cu-6(mna)(6)](6-) cluster units and Mn2+ ions gives rise to a brucite related layer in 1 and a pcu-net in 2. The Ag-6(Hmna)(2)(mna)(4)](4-) cluster in 3, on the other hand, forms a sql-net with Mn2+. Compound 1 exhibits an interesting and reversible hydrochromic behavior, changing from pale yellow to red, on heating at 70 degrees C or treatment under a vacuum. Electron paramagnetic resonance studies indicate no change in the valence states, suggesting the color change could be due to changes in the coordination environment only. The magnetic studies indicate weak antiferromagnetic behavior. Proton conductivity studies indicate moderate proton migrations in 1 and 3. The present study dearly establishes sequential crystallization as an important pathway for the synthesis of heterometallic coordination polymers.

Hydrogen bonding, halogen bonding and lithium bonding: an atoms in molecules and natural bond orbital perspective towards conservation of total bond order, inter- and intra-molecular bonding

One hundred complexes have been investigated exhibiting D-X center dot center dot center dot A interactions, where X = H, Cl or Li and DX is the `X bond' donor and A is the acceptor. The optimized structures of all these complexes have been used to propose a generalized `Legon-Millen rule' for the angular geometry in all these interactions. A detailed Atoms in Molecules (AIM) theoretical analysis confirms an important conclusion, known in the literature: there is a strong correlation between the electron density at the X center dot center dot center dot A bond critical point (BCP) and the interaction energy for all these interactions. In addition, we show that extrapolation of the fitted line leads to the ionic bond for Li-bonding (electrostatic) while for hydrogen and chlorine bonding, it leads to the covalent bond. Further, we observe a strong correlation between the change in electron density at the D-X BCP and that at the X center dot center dot center dot A BCP, suggesting conservation of the bond order. The correlation found between penetration and electron density at BCP can be very useful for crystal structure analysis, which relies on arbitrary van der Waals radii for estimating penetration. Various criteria proposed for shared-and closed-shell interactions based on electron density topology have been tested for H/Cl/Li bonded complexes. Finally, using the natural bond orbital (NBO) analysis it is shown that the D-X bond weakens upon X bond formation, whether it is ionic (DLi) or covalent (DH/DCl) and the respective indices such as ionicity or covalent bond order decrease. Clearly, one can think of conservation of bond order that includes ionic and covalent contributions to both D-X and X center dot center dot center dot A bonds, for not only X = H/Cl/Li investigated here but also any atom involved in intermolecular bonding.

Admissible fundamental operators(star)

Let F and G be two bounded operators on two Hilbert spaces. Let their numerical radii be no greater than one. This note investigates when there is a Gamma-contraction (S, P) such that F is the fundamental operator of (S, P) and G is the fundamental operator of (S*, P*). Theorem 1 puts a necessary condition on F and G for them to be the fundamental operators of (S, P) and (S*, P*) respectively. Theorem 2 shows that this necessary condition is also sufficient provided we restrict our attention to a certain special case. The general case is investigated in Theorem 3. Some of the results obtained for Gamma-contractions are then applied to tetrablock contractions to figure out when two pairs (F1, F2) and (G(1), G(2)) acting on two Hilbert spaces can be fundamental operators of a tetrablock contraction (A, B, P) and its adjoint (A*, B*, P*) respectively. This is the content of Theorem 3. (C) 2015 Elsevier Inc. All rights reserved.

Long way to go: how outflows from large galaxies propagate through the hot halo gas

Using hydrodynamic simulations, we study the mass-loss due to supernova-driven outflows from Milky Way type disc galaxies, paying particular attention to the effect of the extended hot halo gas. We find that the total mass-loss at inner radii scales roughly linearly with total mass of stars formed, and that the mass loading factor at the virial radius can be several times its value at inner radii because of the swept up hot halo gas. The temperature distribution of the outflowing material in the inner region (similar to 10 kpc) is bimodal in nature, peaking at 10(5) K and 10(6.5) K, responsible for optical and X-ray emission, respectively. The contribution of cold/warm gas with temperature <= 10(5.5) K to the outflow rate within 10 kpc is approximate to 0.3-0.5. The warm mass loading factor, eta(3e5) (T <= 3 x 10(5) K) is related to the mass loading factor at the virial radius (eta(v)) as eta(v) approximate to 25 eta(3e5) (SFR/M-circle dot yr(-1))(-0.15) for a baryon fraction of 0.1 and a starburst period of 50 Myr. We also discuss the effect of multiple bursts that are separated by both short and long periods. The outflow speed at the virial radius is close to the sound speed in the hot halo, less than or similar to 200 km s(-1). We identify two `sequences' of outflowing cold gas at small scales: a fast (approximate to 500 km s(-1)) sequence, driven by the unshocked free-wind; and a slow sequence (approximate to +/- 100 km s(-1)) at the conical interface of the superwind and the hot halo.

Maximum magnitude estimation considering the regional rupture character

The main objective of the paper is to develop a new method to estimate the maximum magnitude (M (max)) considering the regional rupture character. The proposed method has been explained in detail and examined for both intraplate and active regions. Seismotectonic data has been collected for both the regions, and seismic study area (SSA) map was generated for radii of 150, 300, and 500 km. The regional rupture character was established by considering percentage fault rupture (PFR), which is the ratio of subsurface rupture length (RLD) to total fault length (TFL). PFR is used to arrive RLD and is further used for the estimation of maximum magnitude for each seismic source. Maximum magnitude for both the regions was estimated and compared with the existing methods for determining M (max) values. The proposed method gives similar M (max) value irrespective of SSA radius and seismicity. Further seismicity parameters such as magnitude of completeness (M (c) ), ``a'' and ``aEuro parts per thousand b `` parameters and maximum observed magnitude (M (max) (obs) ) were determined for each SSA and used to estimate M (max) by considering all the existing methods. It is observed from the study that existing deterministic and probabilistic M (max) estimation methods are sensitive to SSA radius, M (c) , a and b parameters and M (max) (obs) values. However, M (max) determined from the proposed method is a function of rupture character instead of the seismicity parameters. It was also observed that intraplate region has less PFR when compared to active seismic region.

Bearing Capacity Factors for Ring Foundations

Bearing capacity factors because of the components of cohesion, surcharge, and unit weight, respectively, have been computed for smooth and rough ring footings for different combinations of r(i)= r(o) and. by using lower and upper bound theorems of the limit analysis in conjunction with finite elements and linear optimization, where r(i) and r(o) refer to the inner and outer radii of the ring, respectively. It is observed that for a smooth footing with a given value of r(o), the magnitude of the collapse load decreases continuously with an increase in r(i). Conversely, for a rough base, for a given value of r(o), hardly any reduction occurs in the magnitude of the collapse load up to r(i)= r(o) approximate to 0.2, whereas for r(i)= r(o) > 0.2, the magnitude of the collapse load, similar to that of a smooth footing, decreases continuously with an increase in r(i)= r(o). The results from the analysis compare reasonably well with available theoretical and experimental data from the literature. (C) 2015 American Society of Civil Engineers.

Electromagnetic analysis of novel class of multiple core/multiple clad step index single mode optical fiber by analytical means

General propagation properties and universal curves are given for double clad single mode fibers with inner cladding index higher or lower than the outer cladding index, using the parameter: inner cladding/core radii ratio. Mode cut-off conditions are also examined for the cases. It is shown that dispersion properties largely differ from the single clad single mode fiber case, leading to large new possibilities for extension of single mode operation for large wavelength tange. Paper demonstrates that how substantially we can extend the single mode operation range by using the raised inner cladding fiber. Throughout we have applied our own computations technique to find out the eigenvalue for a given modes. Detail derivations with all trivial mathematics for eigenmode equation are derived for each case. Paper also demonstrates that there is not much use of using depressed inner cladding fiber. We have also concluded that using the large inner cladding/inner core radius we can significantly increase the single mode operation range for the large wavelength region. (C) 2015 Elsevier GmbH. All rights reserved.

Numerical analysis of segmented-electrode Orbitraps

Simple geometries which are possible alternatives for the Orbitrap are studied in this paper. We have taken up for numerical investigation two segmented-electrode structures, ORB1 and ORB2, to mimic the electric field of the Orbitrap. In the ORB1, the inner spindle-like electrode and the outer barrel-like electrode of the Orbitrap have been replaced by 35 rings and 35 discs of fixed radii, respectively. In this structure two segmented end cap electrodes have been added. In this geometry, different potentials are applied to the different electrodes keeping top-bottom symmetry intact. In the second geometry, ORB2, the inner and outer electrodes of the Orbitrap were replaced by an approximate step structure which follows the profile of the Orbitrap electrodes. In the present study 45 steps have been used. In the ORB2, like the Orbitrap, the inner electrode is held at a negative potential and the outer electrode is at ground potential. For the purpose of comparing the performance of ORB1 and ORB2 with that of the Orbitrap, the following studies have been undertaken: (1) variation of electric potential, (2) computation of ion trajectories, (3) simulation of image currents. These studies have been carried out using both 2D and 3D Boundary Element Method (BEM), the 3D BEM was developed specifically for this study. It has been seen in these investigations that ORB1 and ORB2 have performance similar to that of the Orbitrap, with the performance of the ORB1 being seen to be marginally superior to that of the ORB2. It has been shown that with proper optimization, geometries containing far fewer electrodes can be used as mass analyzers. A novel technique of optimization of the electric field has been proposed with the objective of minimizing the dependence of axial frequency of ion motion on the initial position of an ion. The results on the optimization of 9 and 15 segmented-electrode traps having the same design as ORB1 show that it can provide accurate mass analysis. (C) 2015 Elsevier B.V. All rights reserved.

Evolution of Jahn-Teller distortion, transport and dielectric properties with doping in perovskite NdFe1-xMnxO3 (0 <= x <= 1) compounds

We have carried out dielectric and transport measurements in NdFe1-xMnxO3 (0 <= x <= 1) series of compounds and studied the variation of activation energy due to a change in Mn concentration. Despite similar ionic radii in Mn3+ and Fe3+, large variation is observed in the lattice parameters and a crossover from dynamic to static Jahn-Teller distortion is discernible. The Fe/Mn-O-Fe/Mn bond angle on the ab plane shows an anomalous change with doping. With an increase in the Mn content, the bond angle decreases until x = 0.6; beyond this, it starts rising until x = 0.8 and again falls after that. A similar trend is observed in activation energies estimated from both transport and dielectric relaxation by assuming a small polaron hopping (SPH) model. Impedance spectroscopy measurements delineate grain and grain boundary contributions separately both of which follow the SPH model. Frequency variation of the dielectric constant is in agreement with the modified Debye law from which relaxation dispersion is estimated.

Numerical analysis of segmented-electrode Orbitraps

Simple geometries which are possible alternatives for the Orbitrap are studied in this paper. We have taken up for numerical investigation two segmented-electrode structures, ORB1 and ORB2, to mimic the electric field of the Orbitrap. In the ORB1, the inner spindle-like electrode and the outer barrel-like electrode of the Orbitrap have been replaced by 35 rings and 35 discs of fixed radii, respectively. In this structure two segmented end cap electrodes have been added. In this geometry, different potentials are applied to the different electrodes keeping top-bottom symmetry intact. In the second geometry, ORB2, the inner and outer electrodes of the Orbitrap were replaced by an approximate step structure which follows the profile of the Orbitrap electrodes. In the present study 45 steps have been used. In the ORB2, like the Orbitrap, the inner electrode is held at a negative potential and the outer electrode is at ground potential. For the purpose of comparing the performance of ORB1 and ORB2 with that of the Orbitrap, the following studies have been undertaken: (1) variation of electric potential, (2) computation of ion trajectories, (3) simulation of image currents. These studies have been carried out using both 2D and 3D Boundary Element Method (BEM), the 3D BEM was developed specifically for this study. It has been seen in these investigations that ORB1 and ORB2 have performance similar to that of the Orbitrap, with the performance of the ORB1 being seen to be marginally superior to that of the ORB2. It has been shown that with proper optimization, geometries containing far fewer electrodes can be used as mass analyzers. A novel technique of optimization of the electric field has been proposed with the objective of minimizing the dependence of axial frequency of ion motion on the initial position of an ion. The results on the optimization of 9 and 15 segmented-electrode traps having the same design as ORB1 show that it can provide accurate mass analysis. (C) 2015 Elsevier B.V. All rights reserved.

Stabilization of Collective Motion in Synchronized, Balanced and Splay Phase Arrangements on a Desired Circle

This paper proposes a design methodology to stabilize collective circular motion of a group of N-identical agents moving at unit speed around individual circles of different radii and different centers. The collective circular motion studied in this paper is characterized by the clockwise rotation of all agents around a common circle of desired radius as well as center, which is fixed. Our interest is to achieve those collective circular motions in which the phases of the agents are arranged either in synchronized, in balanced or in splay formation. In synchronized formation, the agents and their centroid move in a common direction while in balanced formation, the movement of the agents ensures a fixed location of the centroid. The splay state is a special case of balanced formation, in which the phases are separated by multiples of 2 pi/N. We derive the feedback controls and prove the asymptotic stability of the desired collective circular motion by using Lyapunov theory and the LaSalle's Invariance principle.

Thermocapillary flow in an annular liquid layer painted on a moving fiber

In the present paper, a theoretical model is studied on the flow in the liquid annular film, which is ejected from a vessel with relatively higher temperature and painted on the moving solid fiber. A temperature gradient, driving a thermocapillary flow, is formed on the free surface because of the heat transfer from the liquid with relatively higher temperature to the environmental gas with relatively lower temperature. The thermocapillary flow may change the radii profile of the liquid film. This process analyzed is based on the approximations of lubrication theory and perturbation theory, and the equation of the liquid layer radii and the process of thermal hydrodynamics in the liquid layer are solved for a temperature distribution on the solid fiber.