An ESR study of the radiolysis of semi-crystalline ethylene-propylene copolymers containing DOP mobilizer

The radiolysis of a poly(ethylene-co-propylene), Elpro, marketed by Thai Polypropylene Co. Ltd for the manufacture of medical goods has been investigated at 77 K. Calcium stearate was blended with the Elpro as a processing aid; and dioctyl phthalate, DOP, was added in various amounts as a radiation stabilizer. The ESR spectra of Elpro and Elpro+Ca were very similar and characterized principally by the presence of PP a-carbon radicals. The spectra of the samples containing DOP were similar to those for Elpro but with an additional narrow singlet arising from DOP radicals. On annealing the irradiated polymers to higher temperatures, the singlet was lost between 250 and 270 K, and at room temperature the principal radicals remaining were allyl radicals. The G-values for radical formation at 77 K for Elpro and Elpro+Ca at 77 K were 3.0 and 3.2, respectively, but incorporation of DOP resulted in lower G-values, ranging from 1.6 to 1.4 for 0.5 and 2.5 phr DOP, respectively.(c) 2005 Wiley Periodicals, Inc.

Discovery and characterization of a linear cyclotide from Viola odorata: Implications for the processing of circular proteins

Cyclotides are mini-proteins of 28-37 amino acid residues that have the unusual feature of a head-to-tail cyclic backbone surrounding a cystine knot. This molecular architecture gives the cyclotides heightened resistance to thermal, chemical and enzymatic degradation and has prompted investigations into their use as scaffolds in peptide therapeutics. There are now more than 80 reported cyclotide sequences from plants in the families Rubiaceae, Violaceae and Cucurbitaceae, with a wide variety of biological activities observed. However, potentially limiting the development of cyclotide-based therapeutics is a lack of understanding of the mechanism by which these peptides are cyclized in vivo. Until now, no linear versions of cyclotides have been reported, limiting our understanding of the cyclization mechanism. This study reports the discovery of a naturally occurring linear cyclotide, violacin A, from the plant Viola odorata and discusses the implications for in vivo cyclization of peptides. The elucidation of the cDNA clone of violacin A revealed a point mutation that introduces a stop codon, which inhibits the translation of a key Asn residue that is thought to be required for cyclization. The three-dimensional solution structure of violacin A was determined and found to adopt the cystine knot fold of native cyclotides. Enzymatic stability assays on violacin A indicate that despite an increase in the flexibility of the structure relative to cyclic counterparts, the cystine knot preserves the overall stability of the molecule. (c) 2006 Elsevier Ltd. All rights reserved.

A windows program for the derivation of steady-state equations in enzyme systems

Despite the number of computer-assisted methods described for the derivation of steady-state equations of enzyme systems, most of them are focused on strict steady-state conditions or are not able to solve complex reaction mechanisms. Moreover, many of them are based on computer programs that are either not readily available or have limitations. We present here a computer program called WinStes, which derives equations for both strict steady-state systems and those with the assumption of rapid equilibrium, for branched or unbranched mechanisms, containing both reversible and irreversible conversion steps. It solves reaction mechanisms involving up to 255 enzyme species, connected by up to 255 conversion steps. The program provides all the advantages of the Windows programs, such as a user-friendly graphical interface, and has a short computation time. WinStes is available free of charge on request from the authors. (c) 2006 Elsevier Inc. All rights reserved.

Gaussian process approximations of stochastic differential equations

Stochastic differential equations arise naturally in a range of contexts, from financial to environmental modeling. Current solution methods are limited in their representation of the posterior process in the presence of data. In this work, we present a novel Gaussian process approximation to the posterior measure over paths for a general class of stochastic differential equations in the presence of observations. The method is applied to two simple problems: the Ornstein-Uhlenbeck process, of which the exact solution is known and can be compared to, and the double-well system, for which standard approaches such as the ensemble Kalman smoother fail to provide a satisfactory result. Experiments show that our variational approximation is viable and that the results are very promising as the variational approximate solution outperforms standard Gaussian process regression for non-Gaussian Markov processes.

Interactions at the head-tape interface of a linear tape system

Many of the recent improvements in the capacity of data cartridge systems have been achieved through the use of narrower tracks, higher linear densities and continuous servo tracking with multi-channel heads. These changes have produced new tribological problems at the head/tape interface. It is crucial that the tribology of such systems is understood and this will continue since increasing storage capacities and faster transfer rates are constantly being sought. Chemical changes in the surface of single and dual layer MP tape have been correlated to signal performance. An accelerated tape tester, consisting of a custom made cycler ("loop tester"), was used to ascertain if results could be produced that were representative of a real tape drive system. A second set of experiments used a modified tape drive (Georgens cycler), which allowed the effects of the tape transport system on the tape surface to be studied. To isolate any effects on the tape surface due to the head/tape interface, read/write heads were not fitted to the cycler. Two further sets of experiments were conducted which included a head in the tape path. This allowed the effects of the head/tape interface on the physical and chemical properties of the head and tape surfaces to be investigated. It was during the final set of experiments that the effect on the head/tape interface, of an energised MR element, was investigated. The effect of operating each cycler at extreme relative humidity and temperature was investigated through the use of an environmental chamber. Extensive use was made of surface specific analytical techniques such as XPS, AFM, AES, and SEM to study the physical and chemical changes that occur at the head/tape interface. Results showed that cycling improved the signal performance of all the tapes tested. The data cartridge drive belt had an effect on the chemical properties of the tape surface on which it was in contact. Also binder degradation occurred for each tape and appeared to be greater at higher humidity. Lubricant was generally seen to migrate to the tape surface with cycling. Any surface changes likely to affect signal output occurred at the head surface rather than the tape.

Variational Markov Chain Monte Carlo for Bayesian smoothing of non-linear niffusions

In this paper we develop set of novel Markov chain Monte Carlo algorithms for Bayesian smoothing of partially observed non-linear diffusion processes. The sampling algorithms developed herein use a deterministic approximation to the posterior distribution over paths as the proposal distribution for a mixture of an independence and a random walk sampler. The approximating distribution is sampled by simulating an optimized time-dependent linear diffusion process derived from the recently developed variational Gaussian process approximation method. Flexible blocking strategies are introduced to further improve mixing, and thus the efficiency, of the sampling algorithms. The algorithms are tested on two diffusion processes: one with double-well potential drift and another with SINE drift. The new algorithm's accuracy and efficiency is compared with state-of-the-art hybrid Monte Carlo based path sampling. It is shown that in practical, finite sample, applications the algorithm is accurate except in the presence of large observation errors and low observation densities, which lead to a multi-modal structure in the posterior distribution over paths. More importantly, the variational approximation assisted sampling algorithm outperforms hybrid Monte Carlo in terms of computational efficiency, except when the diffusion process is densely observed with small errors in which case both algorithms are equally efficient.

Study of epitaxial silicon layers with reference to the technology of semi-conductor devices

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Variational mean-field algorithm for efficient inference in large systems of stochastic differential equations

This work introduces a Gaussian variational mean-field approximation for inference in dynamical systems which can be modeled by ordinary stochastic differential equations. This new approach allows one to express the variational free energy as a functional of the marginal moments of the approximating Gaussian process. A restriction of the moment equations to piecewise polynomial functions, over time, dramatically reduces the complexity of approximate inference for stochastic differential equation models and makes it comparable to that of discrete time hidden Markov models. The algorithm is demonstrated on state and parameter estimation for nonlinear problems with up to 1000 dimensional state vectors and compares the results empirically with various well-known inference methodologies.

Computing and Visualizing Solution Sets of Interval Linear Systems

The paper has been presented at the 12th International Conference on Applications of Computer Algebra, Varna, Bulgaria, June, 2006

A Computer Algebra Application to Determination of Lie Symmetries of Partial Differential Equations

The paper has been presented at the 12th International Conference on Applications of Computer Algebra, Varna, Bulgaria, June, 2006

Necessary and Sufficient Conditions for the Extendability of Ternary Linear Codes

We give the necessary and sufficient conditions for the extendability of ternary linear codes of dimension k ≥ 5 with minimum distance d ≡ 1 or 2 (mod 3) from a geometrical point of view.