Robust model-order reduction of complex biological processes

This paper addresses robust model-order reduction of a high dimensional nonlinear partial differential equation (PDE) model of a complex biological process. Based on a nonlinear, distributed parameter model of the same process which was validated against experimental data of an existing, pilot-scale BNR activated sludge plant, we developed a state-space model with 154 state variables in this work. A general algorithm for robustly reducing the nonlinear PDE model is presented and based on an investigation of five state-of-the-art model-order reduction techniques, we are able to reduce the original model to a model with only 30 states without incurring pronounced modelling errors. The Singular perturbation approximation balanced truncating technique is found to give the lowest modelling errors in low frequency ranges and hence is deemed most suitable for controller design and other real-time applications. (C) 2002 Elsevier Science Ltd. All rights reserved.

Genotyping of methicillin-resistant Staphylococcus aureus by assaying for the presence of variable elements associated with mecA

The region surrounding mecA in methicillin-resistant Staphylococcus aureus (MRSA) is highly variable. We describe an approach for the rapid genotyping of MRSA by assaying for the presence or absence of variable or mobile elements previously shown to be associated with the mecA region.

Existence of multiple solutions for finite difference approximations to second-order boundary value problems

Error condition detected We consider discrete two-point boundary value problems of the form D-2 y(k+1) = f (kh, y(k), D y(k)), for k = 1,...,n - 1, (0,0) = G((y(0),y(n));(Dy-1,Dy-n)), where Dy-k = (y(k) - Yk-I)/h and h = 1/n. This arises as a finite difference approximation to y" = f(x,y,y'), x is an element of [0,1], (0,0) = G((y(0),y(1));(y'(0),y'(1))). We assume that f and G = (g(0), g(1)) are continuous and fully nonlinear, that there exist pairs of strict lower and strict upper solutions for the continuous problem, and that f and G satisfy additional assumptions that are known to yield a priori bounds on, and to guarantee the existence of solutions of the continuous problem. Under these assumptions we show that there are at least three distinct solutions of the discrete approximation which approximate solutions to the continuous problem as the grid size, h, goes to 0. (C) 2003 Elsevier Science Ltd. All rights reserved.

Designing a 161-element Ku-band microstrip reflectarray of variable size patches using an equivalent unit cell waveguide approach

An equivalent unit cell waveguide approach (WGA) to designing 4 multilayer microstrip reflectarray of variable size patches is presented. In this approach, a normal incidence of a plane wave on an infinite periodic array of radiating elements is considered to obtain reflection coefficient phase curves for the reflectarray's elements. It is shown that this problem is equivalent to the problem of reflection of the dominant TEM mode in a waveguide with patches interleaved by layers of dielectric. This waveguide problem is solved using a field matching technique and a method of moments (MoM). Based on this solution, a fast computer algorithm is developed to generate reflection coefficient phase curves for a multilayer microstrip patch reflectarray. The validity of the developed algorithm is tested against alternative approaches and Agilent High Frequency Structure Simulator (HFSS). Having confirmed the validity of the WGA approach, a small offset feed two-layer microstrip patch array is designed and developed. This reflectarray is tested experimentally and shows good performance.

Large sets of large sets of Steiner triple systems of order 9

We describe a direct method of partitioning the 840 Steiner triple systems of order 9 into 120 large sets. The method produces partitions in which all of the large sets are isomorphic and we apply the method to each of the two non-isomorphic large sets of STS(9).

Dynamic stability of laminated FGM plates based on higher-order shear deformation theory

This paper conducts a dynamic stability analysis of symmetrically laminated FGM rectangular plates with general out-of-plane supporting conditions, subjected to a uniaxial periodic in-plane load and undergoing uniform temperature change. Theoretical formulations are based on Reddy's third-order shear deformation plate theory, and account for the temperature dependence of material properties. A semi-analytical Galerkin-differential quadrature approach is employed to convert the governing equations into a linear system of Mathieu-Hill equations from which the boundary points on the unstable regions are determined by Bolotin's method. Free vibration and bifurcation buckling are also discussed as subset problems. Numerical results are presented in both dimensionless tabular and graphical forms for laminated plates with FGM layers made of silicon nitride and stainless steel. The influences of various parameters such as material composition, layer thickness ratio, temperature change, static load level, boundary constraints on the dynamic stability, buckling and vibration frequencies are examined in detail through parametric studies.

Stokes-operator-squeezed continuous-variable polarization states

We investigate nonclassical Stokes-operator variances in continuous-wave polarization-squeezed laser light generated from one and two optical parametric amplifiers. A general expression of how Stokes-operator variances decompose into two-mode quadrature operator variances is given. Stokes parameter variance spectra for four different polarization-squeezed states have been measured and compared with a coherent state. Our measurement results are visualized by three-dimensional Stokes-operator noise volumes mapped on the quantum Poincare sphere. We quantitatively compare the channel capacity of the different continuous-variable polarization states for communication protocols. It is shown that squeezed polarization states provide 33% higher channel capacities than the optimum coherent beam protocol.

Experimental investigation of criteria for continuous variable entanglement

We generate a pair of entangled beams from the interference of two amplitude squeezed beams. The entanglement is quantified in terms of EPR paradox and inseparability criteria, with both results clearly beating the standard quantum limit. We experimentally analyze the effect of decoherence on each criterion and demonstrate qualitative differences. We also characterize the number of required and excess photons present in the entangled beams and provide contour plots of the efficacy of quantum information protocols in terms of these variables.

Experimental investigation of continuous-variable quantum teleportation

We report the experimental demonstration of quantum teleportation of the quadrature amplitudes of a light field. Our experiment was stably locked for long periods, and was analyzed in terms of fidelity F and with signal transfer T-q=T++T- and noise correlation V-q=Vinparallel to out+Vinparallel to out-. We observed an optimum fidelity of 0.64+/-0.02, T-q=1.06+/-0.02, and V-q=0.96+/-0.10. We discuss the significance of both T-q>1 and V-q

Continuous variable polarization entanglement, experiment and analysis

We generate and characterize continuous variable polarization entanglement between two optical beams. We first produce quadrature entanglement, and by performing local operations we transform it into a polarization basis. We extend two entanglement criteria, the inseparability criteria proposed by Duan et al (2000 Phys. Rev. Lett. 84 2722) and the Einstein–Podolsky–Rosen (EPR) paradox criteria proposed by Reid and Drummond (1988 Phys. Rev. Lett. 60 2731), to Stokes operators; and use them to characterize the entanglement. Our results for the EPR paradox criteria are visualized in terms of uncertainty balls on the Poincaré sphere. We demonstrate theoretically that using two quadrature entangled pairs it is possible to entangle three orthogonal Stokes operators between a pair of beams, although with a bound √3 times more stringent than for the quadrature entanglement.

Genetic characterization of pilin glycosylation and phase variation in Neisseria meningitidis

Pili of Neisseria meningitidis are a key virulence factor, being the major adhesin of this capsulate organism and contributing to specificity for the human host. Pili are post-translationally modified by addition of either an O-linked trisaccharide, Gal (beta1-4) Gal (alpha1-3) 2,4-diacetamido-2,4,6-trideoxyhexose or an O-linked disaccharide Gal (alpha1,3) GlcNAc. The role of these structures in meningococcal pathogenesis has not been resolved. In previous studies we identified two separate genetic loci, pglA and pglBCD, involved in pilin glycosylation. Putative functions have been allocated to these genes; however, there are not enough genes to account for the complete biosynthesis of the described structures, suggesting additional genes remain to be identified. In addition, it is not known why some strains express the trisaccharide structure and some the disaccharide structure. In order to find additional genes involved in the biosynthesis. of these structures, we used the recently published group A strain Z2491 and group B strain MC58 Neisseria meningitidis genomes and the unfinished Neisseria meningitidis group C strain FAM18 and Neisseria gonorrhoeae strain FA1090 genomes to identify novel genes involved in pilin glycosylation, based on homology to known oligosaccharide biosynthetic genes. We identified a new gene involved in pilin glycosylation designated pglE and examined four additional genes pgIB/B2, pglF, pglG and pglH. A strain survey revealed that pglE and pglF were present in each strain examined. The pglG, pglH and pgIB2 polymorphisms were not found in strain C311#3 but were present in a large number of clinical isolates. Insertional mutations were constructed in pglE and pglF in N. meningitidis strain C311#3, a strain with well-defined lipopolysaccharide (LPS) and pilin-linked glycan structures. Increased gel migration of the pilin subunit molecules of pglE and pglF mutants was observed by Western analysis, indicating truncation of the trisaccharide structure. Antisera specific for the C311#3 trisaccharide failed to react with pilin from these pglE and pglF mutants. GC-MS analysis of the sugar composition of the pglE mutant showed a reduction in galactose compared with C311#3 wild type. Analysis of amino acid sequence homologies has suggested specific roles for pglE and pglF in the biosynthesis of the trisaccharide structure. Further, we present evidence that pglE, which contains heptanucleotide repeats, is responsible for the phase variation between trisaccharide and disaccharide structures in strain C311#3 and other strains. We also present evidence that pglG, pglH and pgIB2 are potentially phase variable.

Identification and characterization of pptA: a gene involved in the phase-variable expression of phosphorylcholine on pili of Neisseria meningitidis

Pili of pathogenic Neisseria are major virulence factors associated with adhesion, cytotoxicity, twitching motility, autoaggregation, and DNA transformation. Pili are modified posttranslationally by the addition of phosphorylcholine. However, no genes involved in either the biosynthesis or the transfer of phosphorylcholine in Neisseria meningitidis have been identified. In this study, we identified five candidate open reading frames (ORFs) potentially involved in the biosynthesis or transfer of phosphorylcholine to pilin in N. meningitidis. Insertional mutants were constructed for each ORF in N. meningitidis strain C311#3 to determine their effect on phosphorylcholine expression. The effect of the mutant ORFs on the modification by phosphorylcholine was analyzed by Western analysis with phosphorylcholine-specific monoclonal antibody TEPC-15. Analysis of the mutants showed that ORF NMB0415, now defined as pptA (pilin phosphorylcholine transferase A), is involved in the addition of phosphorylcholine to pilin in N. meningitidis. Additionally, the phase variation (high frequency on-off switching of expression) of phosphorylcholine on pilin is due to changes in a homopolymeric guanosine tract in pptA.