Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Conditional Response to Stress in Yeast

All living cells respond to sudden, adverse changes in their environment by evoking a stress response. Here we focus mainly on the response of the model eukaryotic organism Saccharomyces cerevisiae (bakers yeast) to an increase in external osmolarity. We summarize data demonstrating that stress responses largely depend on the existing environmental growth conditions. Nutrients and other medium parameters such as external pH determine how yeast cells sense osmotic stress circumstances and subsequently elicit adaptive responses. It is likely that the composition of cell wall and plasma membrane plays an important role in this process.     

An evaluation of the accuracy of shallow water matched field inversion results

In this article the accuracy of geo-acoustic and geometric parameter estimates obtained through matched field inversion (MFI) was assessed. Multi-frequency MFI was applied to multi-tone data (200-600 Hz) received at a 2-km source/receiver range. The acoustic source was fixed and the signals were received at a vertical array. Simultaneously with the acoustic transmissions, a CTD (conductivity, temperature and depth)-chain was towed along the acoustic track. A genetic algorithm was used for the global optimization, whereas a normal mode model was applied for the forward acoustic calculations. Acoustic data received at consecutive times were inverted and the stability of the inverted parameters was determined. Also, the parameter estimates were compared with independent measurements, such as multi-channel seismic surveys (for geo-acoustic parameters). The obtained uncertainty in the inversion results was assumed to have two distinct origins. The first origin is the inversion method itself, since each optimization will come up with some solution close to the exact optimum. Parameter coupling and the fact that some parameters hardly influence the acoustic propagation further contribute to this uncertainty. The second is due to oceanographic variability. Both contributions were evaluated through simulation. The contribution of oceanographic variability was evaluated through synthetic inversions that account for the actual sound speed variations as measured by the towed CTD-chain.     

Extension of the Steele 10-4-3 potential for adsorption calculations in cylindrical, spherical, and other pore geometries

Simplified fluid-substrate interaction models derived from the Lennard-Jones potential are widely used in the simulation of gas physisorption phenomena. In this paper, we reinterpret the well known Steele 10-4-3 potential for a gas molecule interacting with a planar surface, and use the resultant scheme to derive new potentials for cylindrical and spherical pore geometries. These new potentials correctly recover the Steele result in the limit of infinite pore radius, a useful improvement over existing models. We demonstrate the new cylindrical Steele 10-4-3 potential in calculations of argon adsorption via fluid density functional theory. This potential yields markedly different adsorption behavior than existing cylindrical potentials, which follow from small but significant differences in both the strength and the shape of the fluid-surface interaction. These differences cannot be fully reconciled simply by reparameterizing (scaling) the existing models; the new potential is more realistic in design, and is especially to be preferred in studies where comparison with planar substrates is made. Finally, we discuss extensions of this approach to more complicated pore geometries, yielding a family of Steele-like potentials that all satisfy the correct planar limit.     

Computable error bounds for pointwise derivatives of a Neumann problem

In this paper we discuss the recovery of derivatives and thecomputation of rigorous and useful upper bounds for the pointwiseerror in the recovered derivatives, for finite element approximationsof the Laplace equation with Neumann boundary conditions, especiallyat points close to or on a smooth, curved boundary. We analyzethe dipole image technique for the case of curved boundaries,and show how to compute reliable recovered derivatives and errorbounds even in the limiting case of points lying on the curvedboundary. Numerical experiments show reasonably tight errorbounds for points both close to and away from a curved boundary.     

Effects of ocean thermocline variability on noncoherent underwater acoustic communications

The performance of acoustic modems in the ocean is strongly affected by the ocean environment. A storm can drive up the ambient noise levels, eliminate a thermocline by wind mixing, and whip up violent waves and thereby break up the acoustic mirror formed by the ocean surface. The combined effects of these and other processes on modem performance are not well understood. The authors have been conducting experiments to study these environmental effects on various modulation schemes. Here the focus is on the role of the thermocline on a widely used modulation scheme (frequency-shift keying). Using data from a recent experiment conducted in 100-m-deep water off the coast of Kauai, HI, frequency-shift-key modulation performance is shown to be strongly affected by diurnal cycles in the thermocline. There is dramatic variation in performance (measured by bit error rates) between receivers in the surface duct and receivers in the thermocline. To interpret the performance variations in a quantitative way, a precise metric is introduced based on a signal-to-interference-noise ratio that encompasses both the ambient noise and intersymbol interference. Further, it will be shown that differences in the fading statistics for receivers in and out of the thermocline explain the differences in modem performance.     

Bayesian geoacoustic inversion using wind-driven ambient noise

This paper applies Bayesian inversion to bottom-loss data derived from wind-driven ambient noise measurements from a vertical line array to quantify the information content constraining seabed geoacoustic parameters. The inversion utilizes a previously proposed ray-based representation of the ambient noise field as a forward model for fast computations of bottom loss data for a layered seabed. This model considers the effect of the array's finite aperture in the estimation of bottom loss and is extended to include the wind speed as the driving mechanism for the ambient noise field. The strength of this field relative to other unwanted noise mechanisms defines a signal-to-noise ratio, which is included in the inversion as a frequency-dependent parameter. The wind speed is found to have a strong impact on the resolution of seabed geoacoustic parameters as quantified by marginal probability distributions from Bayesian inversion of simulated data. The inversion method is also applied to experimental data collected at a moored vertical array during the MAPEX 2000 experiment, and the results are compared to those from previous active-source inversions and to core measurements at a nearby site.     

On the use of multiple interpolation functions in scaled particle theory to improve the predictions of the properties of the hard-sphere fluid

We present a modification to a previously proposed method of adapting scaled particle theory (SPT) to an arbitrary hard-sphere equation of state that satisfies a large number of exact SPT conditions, including thermodynamic consistency. By introducing a set of functions to interpolate the density of hard-spheres centers at the cavity surface, a broad range of hard-sphere properties, in particular the planar surface tension and related properties, are predicted with high accuracy as compared to simulation data. Similarly accurate results are obtained when this modified interpolation scheme is incorporated into a self-consistent version of SPT, i.e., an equation of state is a predicted output of the method. Hence, SPT is now able to closely match the surface thermodynamic properties of the hard-sphere fluid either without using any adjustable parameters or by simply setting the pressure and chemical potential via a reliable equation of state. We also consider other interpolation schemes, some of which better represent certain exact relations that can be derived within SPT. The limited success of these more rigorous approaches provides insights into the various trade-offs between the simplicity and rigor of the chosen interpolation method, as well as the accuracy of the results, that arise in any (inexact) version of SPT.