Multiple Window and Cluster Size Scan Procedures

Researchers apply scan statistics to test for unusually large clusters of events within a time window of specified length w, or alternatively an unusually small window w that contains a specified number of events. In some cases, the researcher is interested in testing for a range of specified window lengths, or a set of several specified number of events k (cluster sizes). In this paper, we derive accurate approximations for the joint distributions of scan statistics for a range of values of w, or of k, that can be used to set an experiment-wide level of significance that takes into account the multiple comparisons involved. We use these methods to compare different ways of choosing the window sizes for the different cluster sizes. One special case is a multiple comparison procedure based on a generalized likelihood ratio test (GLRT) for a range of window sizes. We compare the power of the GLRT with another method for allocating the window sizes. We find that the GLRT is sensitive for very small window sizes at the expense of moderate and larger window sizes. We illustrate these results on two examples, one involving clustering of translocation breakpoints in DNA, and the other involving disease clusters.     

Reference values for drag and lift of a two‐dimensional time‐dependent flow around a cylinder

This paper presents a numerical study of a two‐dimensional time‐dependent flow around a cylinder. Its main objective is to provide accurate reference values for the maximal drag and lift coefficient at the cylinder and for the pressure difference between the front and the back of the cylinder at the final time. In addition, the accuracy of these values obtained with different time stepping schemes and different finite element methods is studied. Copyright © 2004 John Wiley & Sons, Ltd.     

High‐order accurate numerical solutions of incompressible flows with the artificial compressibility method

A high‐order accurate, finite‐difference method for the numerical solution of incompressible flows is presented. This method is based on the artificial compressibility formulation of the incompressible Navier–Stokes equations. Fourth‐ or sixth‐order accurate discretizations of the metric terms and the convective fluxes are obtained using compact, centred schemes. The viscous terms are also discretized using fourth‐order accurate, centred finite differences. Implicit time marching is performed for both steady‐state and time‐accurate numerical solutions. High‐order, spectral‐type, low‐pass, compact filters are used to regularize the numerical solution and remove spurious modes arising from unresolved scales, non‐linearities, and inaccuracies in the application of boundary conditions. The accuracy and efficiency of the proposed method is demonstrated for test problems. Copyright © 2004 John Wiley & Sons, Ltd.     

Robust handling of non‐linear constraints for GA optimization of aerodynamic shapes

A new approach to the robust handling of non‐linear constraints for GAs (genetic algorithms) optimization is proposed. A specific feature of the approach consists of the change in the conventional search strategy by employing search paths which pass through both feasible and infeasible points (contrary to the traditional approach where only feasible points may be included in a path). The method (driven by full Navier–Stokes computations) was applied to the problem of multiobjective optimization of aerodynamic shapes subject to various geometrical and aerodynamic constraints. The results demonstrated that the method retains high robustness of conventional GAs while keeping CFD computational volume to an acceptable level, which allowed the algorithm to be used in a demanding engineering environment. Copyright © 2004 John Wiley & Sons, Ltd.     

Least‐squares meshfree method for incompressible Navier–Stokes problems

A least‐squares meshfree method based on the first‐order velocity–pressure–vorticity formulation for two‐dimensional incompressible Navier–Stokes problem is presented. The convective term is linearized by successive substitution or Newton's method. The discretization of all governing equations is implemented by the least‐squares method. Equal‐order moving least‐squares approximation is employed with Gauss quadrature in the background cells. The boundary conditions are enforced by the penalty method. The matrix‐free element‐by‐element Jacobi preconditioned conjugate method is applied to solve the discretized linear systems. Cavity flow for steady Navier–Stokes problem and the flow over a square obstacle for time‐dependent Navier–Stokes problem are investigated for the presented least‐squares meshfree method. The effects of inaccurate integration on the accuracy of the solution are investigated. Copyright © 2004 John Wiley & Sons, Ltd.     

Stereological simulations of asymmetric polymerization in channels of bile acid inclusion compounds: A detailed analysis of the monomer arrangements in the channels

We studied simulations by computer graphics to estimate the steric mechanism of the asymmetric polymerization of prochiral diene monomers in channels of inclusion compounds of steroidal bile acids, such as deoxycholic acid (DCA) and cholic acid. We applied a hierarchization method to interpret the crystal structures of bile acids, clarifying that the chiral host molecules associated to form characteristic 2₁-helical assemblies with uneven surfaces. A detailed analysis of the uneven channels in a close-packing state indicated that there were many possible arrangements of the monomers in the channels. The plausible arrangements in the channel could explain a previous study, which showed that the polymerization in the DCA channel yielded chiral polymers with a predominant configuration from prochiral diene monomers, such as 2-methyl-trans-1,3-pentadiene. On the basis of such simulation studies of the arrangements of guest monomers in the channel, we examined a plausible steric mechanism for asymmetric inclusion polymerization. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4648–4655, 2004     

Pseudo-Isotherms Using a Second Order Kinetic Expression Constant

The kinetics of four sorption systems, Cu/tree fern, Pb/tree fern, AB9/activated clay and BR18/activated clay have been studied based on the assumption of a pseudo-second order rate law. Pseudo-isotherms using the pseudo-second order kinetic expression constant have been developed to describe the four liquid-solid sorption systems. The experimental results have been analyzed using a pseudo-Langmuir and a pseudo-Redlich-Peterson isotherm. Both isotherms were found to represent the measured sorption data well. According to the evaluation using the pseudo-Langmuir equation, the monolayer sorption capacities were obtained to be 13.9, 46.6, 124 and 105 mg g^–1 for copper, lead, AB9 and BR18 respectively.     

Multiphysical modeling and meshless simulation of electric‐sensitive hydrogels

According to a multiphase mixture theory, we have mathematically developed a multiphysical model with chemoelectromechanical coupling considerations, termed the multieffect‐coupling electric‐stimulus (MECe) model, to simulate the responsive behavior of electric‐sensitive hydrogels immersed in a bath solution under an externally applied electric field. For solutions of the MECe model consisting of coupled nonlinear partial differential governing equations, a meshless Hermite–Cloud method with a hierarchical iteration technique has been used for a one‐dimensional steady‐state analysis of a hydrogel strip. The computed results are compared with the experimental data, and there is very good agreement. Simulations within the domains of both hydrogels and surrounding solutions also present distributions of the ionic concentrations and electric potential as well as the hydrogel displacement. The effects of various physical parameters on the response behavior of electric‐stimulus responsive hydrogels are discussed in detail. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 1514–1531, 2004     

Addition–fragmentation chain transfer: Molecular weight distributions and retardation in the system methyl methacrylate/methyl α‐(bromomethyl)acrylate

A detailed investigation of addition–fragmentation chain transfer (AFCT) in the free‐radical polymerization of methyl methacrylate (MMA) in the presence of methyl α‐(bromomethyl)acrylate (MBMA) was carried out to elucidate mechanistic details with efficient macromonomer synthesis as an underlying goal. Advanced modeling techniques were used in connection with the experimental work. Curve fitting of simulated and experimental molecular weight distributions with respect to the rate coefficient for addition of propagating radicals to MBMA (k_add) over 60–120 °C resulted in E_add = 21.7 kJ mol^?1 and A_add = 2.18 × 10⁶ M^?1 s^?1 and a very weak temperature dependence of the chain‐transfer constant (E_add ≈ E_p). The rate coefficient for fragmentation of adduct radicals at 60 °C was estimated as k_f ≈ 39 s^?1 on the basis of experimental data of the MMA conversion and the concentration of 2‐carbomethoxy‐2‐propenyl end groups. The approach developed is generic and can be applied to any AFCT system in which copolymerization does not occur and in which the resulting unsaturated end groups do not undergo further reactions. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2640–2650, 2004     

有源光放大器链路中交叉相位调制的不稳定性

利用两种方法研究了有源放大器波分复用系统光纤链路中交叉 相位调制的不稳定性．首先利用非线性薛定谔耦合方程，在小幅度扰动下，研究了正常色散 和反常色散光纤中的交叉相位调制不稳定性. 由于相位噪声涨落，利用分裂步长傅里叶 变换法与Monte-Carlo法，模拟了有源放大器链路中反常色散和正常色散情况下的调制不稳定性. 两种方法得到的结论基本一致. 关键词： 调制不稳定性 交叉相位调制 斯托克斯带 反斯托克斯 带