Rationalizing perhydrolase activity of aryl-esterase and subtilisin Carlsberg mutants by molecular dynamics simulations of the second tetrahedral intermediate state

The perhydrolysis reaction in hydrolases is an important example of catalytic promiscuity and has many potential industrial applications. The mechanisms of perhydrolase activity of a subtilisin Carlsberg mutant and of an aryl-esterase mutant have been investigated using classical molecular dynamics simulations of the second tetrahedral intermediate (TI) state. The simulations demonstrated that hydrogen bonding between the second TI of the perhydrolysis reaction is possible in the mutants but not wild type. The stabilization by hydrogen bonds was specific for the perhydrolysis intermediate and either no hydrogen bonding or only weakened hydrogen bonding to the second TI state of the hydrolysis reaction was observed. Furthermore, a significant hindrance to the formation of the catalytically important hydrogen bond between His64 and Ser221 in the catalytic triad by competing hydrogen bonds was found for the subtilisin mutant but not wild type enzyme in case of the hydrolysis intermediate. The opposite was observed in case of the perhydrolysis intermediate. The result offers a qualitative explanation for the overall reduced hydrolysis activity of the subtilisin mutant. In addition, the simulations also explain qualitatively the perhydrolysis activity of the enzyme variants and may be helpful for designing enzyme mutants with further improved perhydrolysis activity.     

Comment on "Long time evolution of phase oscillator systems" [Chaos 19, 023117 (2009)

In a recent paper by Ott and Antonsen [Chaos 19, 023117 (2009)], it was shown for the case of Lorentzian distributions of oscillator frequencies that the dynamics of a very general class of large systems of coupled phase oscillators time-asymptotes to a particular simplified form given by Ott and Antonsen [Chaos 18, 037113 (2008)]. This comment extends this previous result to a broad class of oscillator distribution functions.     

Magnetic layered structure for the production of polarized neutron microbeams

A neutron waveguide is a three-layer structure in which a guiding layer with low optical potential is placed between two cladding layers with high optical potential. Under proper operation conditions, the neutron density is resonantly enhanced inside the guiding layer. In our experimental scheme, the neutron beam enters through the surface of the top layer at glancing angle and goes out from the edge of the guiding layer, with an angular distribution corresponding to Fraunhofer diffraction from a narrow slit. The incident neutron beam is relatively wide (0.1 mm) and highly collimated (0.01°). The outgoing sub-micron beam is extremely narrow at the outlet (0.1 μm) and more divergent (0.1°). So far only the production of unpolarized sub-micron neutron beams has been reported. Here we present first experiments on polarized sub-micron neutron beams. For these studies a polarized incident beam was used and two types of magnetic waveguides were investigated: a polarizing magnetic waveguide Fe(20 nm)/Cu(140 nm)/Fe(50 nm)//glass and a non-polarizing magnetic waveguide Py(10 nm)/Al(140 nm)/Py(50 nm)//glass (Py is permalloy). The waveguide samples were characterized by polarized neutron reflectometry.     

Theoretical analysis of an optimal control problem of conductive–convective–radiative heat transfer

The problem of optimal heat removal from a three-dimensional domain is considered. The specific of the study consist in accounting for the radiative heat transfer. The so-called P₁ approximation of the radiative heat transfer equation is used, which reduces the model to a nonlinear elliptic system. A problem of optimal boundary control of this system is considered. The solvability of the control problem is proved, and necessary optimality conditions of first order are derived. Examples of non-singularity of these conditions are given.     

A Capped Optimal Stopping Problem for the Maximum Process

This paper concerns an optimal stopping problem driven by the running maximum of a spectrally negative Lévy process X. More precisely, we are interested in capped versions of the American lookback optimal stopping problem (Gapeev in J. Appl. Probab. 44:713–731, 2007; Guo and Shepp in J. Appl. Probab. 38:647–658, 2001; Pedersen in J. Appl. Probab. 37:972–983, 2000), which has its origins in mathematical finance, and provide semi-explicit solutions in terms of scale functions. The optimal stopping boundary is characterised by an ordinary first-order differential equation involving scale functions and, in particular, changes according to the path variation of X. Furthermore, we will link these capped problems to Peskir’s maximality principle (Peskir in Ann. Probab. 26:1614–1640, 1998).     

Usefulness of Transgenic Luminescent Bacteria in Direct Bioautographic Investigation of Chamomile Extracts

JPC – Journal of Planar Chromatography – Modern TLC - Direct bioautography performed with luminescence gene-tagged bacteria enables almost real-time detection of antimicrobial compounds...     

Adsorption of hydrogen and of oxygen on an open metal surface-HREELS investigation at Ni(311)

The adsorption behavior of hydrogen and oxygen on the stepped Ni(311) surface has been investigated by HREELS. A series of metastable phases was found for hydrogen adsorption at low temperatures with a succession of different adsorption sites indicated by the following loss peaks: 55 and 149 meV for the threefold site, shifting with higher coverage to 65 and 155 meV, respectively; 40 and 90 meV for the fourfold site, shifting to 35 and 85 meV with coverage; and 110 and 124 meV for an additional site between close packed rows. Room temperature adsorption of hydrogen leads to the reconstruction of the surface with occupation of three- and fourfold sites, represented by loss peaks at 60 and 145 meV for the threefold site and 74 meV for the fourfold site. This phase is the thermodynamically stable one. Oxygen is most likely initially adsorbed on a bridge site (loss peak at 66 meV). The stepped surface is already oxidized at very low exposures to oxygen, as seen by the characteristic vibration for oxide islands at 55 meV and later by the Fuchs-Kliewer mode of NiO at 68 meV.     

Separable routing: A scheme for state-dependent routing of circuit switched telephone traffic

Separable routing is the first of a number of routing schemes for circuit switched telephone traffic invented at Bellcore. These routing schemes are state dependent, in the sense that, for each call attempt, a routing decision is made on the basis of the state of the network (defined in terms of the numbers of busy and idle trunks in the various trunk groups at the moment of the call attempt). In this paper, we describe separable routing and its mathematical background. Simulation results we have presented elsewhere show that the family of state-dependent routing schemes, of which separable routing is a member, is very attractive in terms of blocking rate, built-in network management features, and behavior in the presence of traffic forecast error.