The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study. (c) 2005 Wiley Periodicals, Inc.

Modelling conditional probability distributions for periodic variables

Most of the common techniques for estimating conditional probability densities are inappropriate for applications involving periodic variables. In this paper we introduce two novel techniques for tackling such problems, and investigate their performance using synthetic data. We then apply these techniques to the problem of extracting the distribution of wind vector directions from radar scatterometer data gathered by a remote-sensing satellite.

Modelling conditional probability distributions for periodic variables

Most of the common techniques for estimating conditional probability densities are inappropriate for applications involving periodic variables. In this paper we apply two novel techniques to the problem of extracting the distribution of wind vector directions from radar catterometer data gathered by a remote-sensing satellite.

Modelling conditional probability distributions for periodic variables

Most conventional techniques for estimating conditional probability densities are inappropriate for applications involving periodic variables. In this paper we introduce three related techniques for tackling such problems, and investigate their performance using synthetic data. We then apply these techniques to the problem of extracting the distribution of wind vector directions from radar scatterometer data gathered by a remote-sensing satellite.

Estimating conditional probability densities for periodic variables

Most of the common techniques for estimating conditional probability densities are inappropriate for applications involving periodic variables. In this paper we introduce three novel techniques for tackling such problems, and investigate their performance using synthetic data. We then apply these techniques to the problem of extracting the distribution of wind vector directions from radar scatterometer data gathered by a remote-sensing satellite.

Towards a semiology of the periodic review of UK regulated utilities

This note explores the regulatory process of UK privatised utilities through the periodic review of prices. It provides a brief history of the privatisation programme in the UK and the theoretical arguments for the price-cap regulation that has been used. It argues that regulatory process appears to involve a covert dialogue and exchange of information between the regulator and regulated and also a second separate review process that consists of an overt dialogue. Using a semiotic analysis the authors suggest that the unfolding of each of these overt reviews follows a very similar pattern that is constantly being re-enacted. It is concluded that further research is required into the relative importance of the two separate review processes in the setting of the price-cap.

Regulation - the movie:a semiotic study of the periodic review of UK regulated industry

This paper explores the regulatory process of UK privatised utilities as manifest in the periodic review of prices. Two separate review processes are identified, operating concurrently - a covert dialogue between the regulator and the regulated and an overt dialogue taking place in the public arena. Using a semiotic analysis of the review the authors argue that the overt event is the real review. Furthermore they argue that the unfolding of each review is so similar that it can be likened to a film script which is constantly re-enacted. The purpose of the review as a legitimating vehicle for the regulator and regulated, who exist in a symbiotic relationship, is explored in terms of the semiotics involved and the myth creation role of legitimation in order to explain the significance of the regulatory process.

Stable propagation of solitons with increased energy through the combined action of dispersion management and periodic saturable absorption

It is shown, through numerical simulations, that by using a combination of dispersion management and periodic saturable absorption it is possible to transmit solitonlike pulses with greatly increased energy near to the zero net dispersion wavelength. This system is shown to support the stable propagation of solitons over transoceanic distances for a wide range of input powers.

Modulational instabilities in fibres with periodic dispersion

We analytically and numerically analyze the occurrence of modulational instability in fibers with periodic changes in the group-velocity dispersion. For small variations, a set of resonances occurs in the gain spectrum. However, large dispersion variations eliminate these resonances and restrict the bandwidth of the fundamental gain spectrum. This research has been motivated by the adoption of dispersion management techniques in long-haul optical communications.

SAS/OWA:ordered weighted averaging in SAS optimization

This paper explores the use of the optimization procedures in SAS/OR software with application to the ordered weight averaging (OWA) operators of decision-making units (DMUs). OWA was originally introduced by Yager (IEEE Trans Syst Man Cybern 18(1):183-190, 1988) has gained much interest among researchers, hence many applications such as in the areas of decision making, expert systems, data mining, approximate reasoning, fuzzy system and control have been proposed. On the other hand, the SAS is powerful software and it is capable of running various optimization tools such as linear and non-linear programming with all type of constraints. To facilitate the use of OWA operator by SAS users, a code was implemented. The SAS macro developed in this paper selects the criteria and alternatives from a SAS dataset and calculates a set of OWA weights. An example is given to illustrate the features of SAS/OWA software. © Springer-Verlag 2009.

Optical data transmission using periodic in-line all-optical format conversion

We introduce a novel transmission technique of periodic in-line all-optical format conversion between return-to-zero and non-return-to-zero-like aimed at delaying the accumulation of format-specific impairments. A particular realization of this approach using in-line normal dispersion fibre-enhanced nonlinear optical loop mirrors at 40Gbit/s data rate is presented. © 2004 Optical Society of America.

Localized waves in optical systems with periodic dispersion and nonlinearity management

We overview our recent developments in the theory of dispersion-managed (DM) solitons within the context of optical applications. First, we present a class of localized solutions with a period multiple to that of the standard DM soliton in the nonlinear Schrödinger equation with periodic variations of the dispersion. In the framework of a reduced ordinary differential equation-based model, we discuss the key features of these structures, such as a smaller energy compared to traditional DM solitons with the same temporal width. Next, we present new results on dissipative DM solitons, which occur in the context of mode-locked lasers. By means of numerical simulations and a reduced variational model of the complex Ginzburg-Landau equation, we analyze the influence of the different dissipative processes that take place in a laser.