Large-eddy simulation of flows past a flapping airfoil using immersed boundary method

The numerical simulation of flows past flapping foils at moderate Reynolds numbers presents two challenges to computational fluid dynamics: turbulent flows and moving boundaries. The direct forcing immersed boundary (IB) method has been developed to simulate laminar flows. However, its performance in simulating turbulent flows and transitional flows with moving boundaries has not been fully evaluated. In the present work, we use the IB method to simulate fully developed turbulent channel flows and transitional flows past a stationary/plunging SD7003 airfoil. To suppress the non-physical force oscillations in the plunging case, we use the smoothed discrete delta function for interpolation in the IB method. The results of the present work demonstrate that the IB method can be used to simulate turbulent flows and transitional flows with moving boundaries.

Enhancements of the simulation method on the edge effect in resin transfer molding processes

In resin transfer molding processes, small clearances exist between the fiber preform and the mold edges, which result in a preferential resin flow in the edge channel and then disrupt the flow patterns during the mold filling stage. A mathematical model including the effect of cavity thickness on resin flow was developed for flow behavior involving the interface between an edge channel and a porous medium. According to the mathematical analysis of momentum equations in a fully developed rectangular duct and formulations of the equivalent edge permeability, comparing with three-dimensional Navier-Stokes equations, the governing equations were modified in the edge channel. The volume of fluid (VOF) method was applied to track the flow front. A simple case is numerically simulated using the modified governing equations. The effects of edge channel width and cavity thickness on flow front and inlet pressure are analyzed, and the evolution characteristics of simulated results are in agreement with the experimental results. (c) 2007 Elsevier B.V. All rights reserved

Estimation of individual phases from the four-phase structure invariants in the single isomorphous replacement case

The probability distribution of the four-phase invariants in the case of single isomorphous replacement has been developed to estimate some individual phases. An example of its application to obtain the phases having special values of 0, pi or +/-pi /2 is given for a known protein structure in space group P2(1)2(1)2(1). The phasing procedure includes the determination of starting phases and an iterative calculation. The initial values of starting phases, which are required by the formula, can be obtained from the estimate of one-phase seminvariants and by specifying the origin and enantiomorph. In addition, the calculations lead to two sets of possible phases for each type of reflection by assigning arbitrarily an initial phase value. The present method provides a possibility for the multisolution technique to increase greatly the number of known phases while keeping the number of the trials quite small.

General expression for probabilistic estimation of multiphase structure invariants in the case of a native protein and multiple derivatives. Application to estimates of the three-phase structure invariants

Concise probabilistic formulae with definite crystallographic implications are obtained from the distribution for eight three-phase structure invariants (3PSIs) in the case of a native protein and a heavy-atom derivative [Hauptman (1982). Acta Cryst. A38, 289-294] and from the distribution for 27 3PSIs in the case of a native and two derivatives [Fortier, Weeks & Hauptman (1984). Acta Cryst. A40, 646-651]. The main results of the probabilistic formulae for the four-phase structure invariants are presented and compared with those for the 3PSIs. The analysis directly leads to a general formula of probabilistic estimation for the n-phase structure invariants in the case of a native and m derivatives. The factors affecting the estimated accuracy of the 3PSIs are examined using the diffraction data from a moderate-sized protein. A method to estimate a set of the large-modulus invariants, each corresponding to one of the eight 3PSIs, that has the largest \Delta\ values and relatively large structure-factor moduli between the native and derivative is suggested, which remarkably improves the accuracy, and thus a phasing procedure making full use of all eight 3PSIs is proposed.

ESTIMATION OF THE ONE-PHASE STRUCTURE SEMINVARIANTS IN THE SINGLE ISOMORPHOUS REPLACEMENT CASE - AN APPLICATION OF HAUPTMANS DISTRIBUTION

A method for estimating the one-phase structure seminvariants (OPSSs) having values of 0 or pi has been proposed on the basis of the probabilistic theory of the three-phase structure invariants for a pair of isomorphous structures [Hauptman (1982). Acta Cryst. A38, 289-294]. The test calculations using error-free diffraction data of protein cytochrome c(550) and its PtCl42- derivative show that reliable estimates of a number of the OPSSs can be obtained. The reliability of the estimation increases with the increase of the differences between diffraction intensities of the native protein and its heavy-atom derivative. A means to estimate the parameters of the distribution from the diffraction ratio is suggested.

Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin

Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.

Estimation of gas hydrate saturation using constrained sparse spike inversion: Case study from the northern South China Sea

Bottom-simulating reflectors (BSRs) were observed beneath the seafloor in the northern continental margin of the South China Sea (SCS). Acoustic impedance profile was derived by Constrained Sparse Spike Inversion (CSSI) method to provide information on rock properties and to estimate gas hydrate or free gas saturations in the sediments where BSRs are present. In general, gas hydrate-bearing sediments have positive impedance anomalies and free gas-bearing sediments have negative impedance anomalies. Based on well log data and Archie's equation, gas hydrate saturation can be estimated. But in regions where well log data is not available, a quantitative estimate of gas hydrate or free gas saturation is inferred by fitting the theoretical acoustic impedance to sediment impedance obtained by CSSI. Our study suggests that gas hydrate saturation in the Taixinan Basin is about 10 - 20% of the pore space, with the highest value of 50%, and free gas saturation below BSR is about 2 - 3% of the pore space, that can rise to 8 - 10% at a topographic high. The free gas is non-continuous and has low content in the southeastern slope of the Dongsha Islands. Moreover, BSR in the northern continental margin of the SCS is related to the presence of free gas. BSR is strong where free gas occurs.