Comparison of computational approaches for predicting the effects of missense mutations on p53 function

We applied our recently developed kinetic computational mutagenesis (KCM) approach [L.T. Chong, W.C. Swope, J.W. Pitera, V.S. Pande, Kinetic computational alanine scanning: application to p53 oligomerization, J. Mol. Biol. 357 (3) (2006) 1039–1049] along with the MM-GBSA approach [J. Srinivasan, T.E. Cheatham 3rd, P. Cieplak, P.A. Kollman, D.A. Case, Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices, J. Am. Chem. Soc. 120 (37) (1998) 9401–9409; P.A. Kollman, I. Massova, C.M. Reyes, B. Kuhn, S. Huo, L.T. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, T.E. Cheatham 3rd., Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models, Acc. Chem. Res. 33 (12) (2000) 889–897] to evaluate the effects of all possible missense mutations on dimerization of the oligomerization domain (residues 326–355) of tumor suppressor p53. The true positive and true negative rates for KCM are comparable (within 5%) to those of MM-GBSA, although MM-GBSA is much less computationally intensive when it is applied to a single energy-minimized configuration per mutant dimer. The potential advantage of KCM is that it can be used to directly examine the kinetic effects of mutations.     

Coupled cluster algorithms for networks of shared memory parallel processors

As the popularity of using SMP systems as the building blocks for high performance supercomputers increases, so too increases the need for applications that can utilize the multiple levels of parallelism available in clusters of SMPs. This paper presents a dual-layer distributed algorithm, using both shared-memory and distributed-memory techniques to parallelize a very important algorithm (often called the “gold standard”) used in computational chemistry, the single and double excitation coupled cluster method with perturbative triples, i.e. CCSD(T). The algorithm is presented within the framework of the GAMESS [M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.J. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S. Su, T.L. Windus, M. Dupuis, J.A. Montgomery, General atomic and molecular electronic structure system, J. Comput. Chem. 14 (1993) 1347–1363]. (General Atomic and Molecular Electronic Structure System) program suite and the Distributed Data Interface [M.W. Schmidt, G.D. Fletcher, B.M. Bode, M.S. Gordon, The distributed data interface in GAMESS, Comput. Phys. Comm. 128 (2000) 190]. (DDI), however, the essential features of the algorithm (data distribution, load-balancing and communication overhead) can be applied to more general computational problems. Timing and performance data for our dual-level algorithm is presented on several large-scale clusters of SMPs.     

A DAFT DL_POLY distributed memory adaptation of the Smoothed Particle Mesh Ewald method

The Smoothed Particle Mesh Ewald method [U. Essmann, L. Perera, M.L. Berkowtz, T. Darden, H. Lee, L.G. Pedersen, J. Chem. Phys. 103 (1995) 8577] for calculating long ranged forces in molecular simulation has been adapted for the parallel molecular dynamics code DL_POLY_3 [I.T. Todorov, W. Smith, Philos. Trans. Roy. Soc. London 362 (2004) 1835], making use of a novel 3D Fast Fourier Transform (DAFT) [I.J. Bush, The Daresbury Advanced Fourier transform, Daresbury Laboratory, 1999] that perfectly matches the Domain Decomposition (DD) parallelisation strategy [W. Smith, Comput. Phys. Comm. 62 (1991) 229; M.R.S. Pinches, D. Tildesley, W. Smith, Mol. Sim. 6 (1991) 51; D. Rapaport, Comput. Phys. Comm. 62 (1991) 217] of the DL_POLY_3 code. In this article we describe software adaptations undertaken to import this functionality and provide a review of its performance.     

Further results on iterative learning control with convergence conditions for linear time-variant discrete systems

This article is concerned with some further results on iterative learning control (ILC) algorithms with convergence conditions for linear time-variant discrete systems. By converting two-Dimensional (2-D) ILC process of the linear time-variant discrete systems into 1-D linear time-invariant discrete systems, this article presents convergent ILC algorithms with necessary and sufficient conditions for two classes of linear time-variant discrete systems. Main results in (Li, X.-D., Ho, J.K.L., and Chow, T.W.S. (2005), ‘Iterative Learning Control for Linear Time-variant Discrete Systems Based on 2-D System Theory’, IEE Proceedings, Control Theory and Applications, 152, 13–18 and Huang, S.N., Tan, K.K., and Lee, T.H. (2002), ‘Necessary and Sufficient Condition for Convergence of Iterative Learning Algorithm’, Automatica 38, 1257–1260) are extended and generalised.     

An upwind discretization scheme for the finite volume lattice Boltzmann method

The fact that the classic lattice Boltzmann method is restricted to Cartesian Grids has inspired several researchers to apply Finite Volume [Nannelli F, Succi S. The lattice Boltzmann equation on irregular lattices. J Stat Phys 1992;68:401–7; Peng G, Xi H, Duncan C, Chou SH. Finite volume scheme for the lattice Boltzmann method on unstructured meshes. Phys Rev E 1999;59:4675–82; Chen H. Volumetric formulation of the lattice Boltzmann method for fluid dynamics: basic concept. Phys Rev E 1998;58:3955–63] or Finite Element [Lee T, Lin CL. A characteristic Galerkin method for discrete Boltzmann equation. J Comp Phys 2001;171:336–56; Shi X, Lin J, Yu Z. Discontinuous Galerkin spectral element lattice Boltzmann method on triangular element. Int J Numer Methods Fluids 2003;42:1249–61] methods to the Discrete Boltzmann equation. The finite volume method proposed by Peng et al. works on unstructured grids, thus allowing an increased geometrical flexibility. However, the method suffers from substantial numerical instability compared to the standard LBE models. The computational efficiency of the scheme is not competitive with standard methods.We propose an alternative way of discretizing the convection operator using an upwind scheme, as opposed to the central scheme described by Peng et al. We apply our method to some test problems in two spatial dimensions to demonstrate the improved stability of the new scheme and the significant improvement in computational efficiency. Comparisons with a lattice Boltzmann solver working on a hierarchical grid were done and we found that currently finite volume methods for the discrete Boltzmann equation are not yet competitive as stand alone fluid solvers.     

Numerical analysis of Horvath-Kawazoe equation.

A new Determining Horvath-Kawazoe (DHK) program for the evaluation of pore-size distribution curve based on the HK method (J. Chem. Eng. Jpn. 16 (1983) 470) is described. The standard bisection procedure (Gerald, C.F., 1977. Applied Numerical Analysis, 2nd ed. Addison-Wesley, CA) is used as a kernel in the proposed algorithm. The calculation of the effective pore-size distribution and the comparative analysis with the previous data published by Horvath and co-workers (J. Chem. Eng. Jpn. 16 (1983) 470; Fraissard, J., Conner, C.W., 1997. Physical Adsorption: Experiment, Theory and Applications. Kluwer Academic, London) and recalculated by Do (Do, D.D., 1998. Adsorption Analysis: Equilibria and Kinetics. Imperial College Press, London) were done.     

A quantum chemical study of the mechanism of action of Vitamin K epoxide reductase (VKOR) II. Transition states

A reaction path including transition states is generated for the Silverman mechanism [R.B. Silverman, Chemical model studies for the mechanism of Vitamin K epoxide reductase, J. Am. Chem. Soc. 103 (1981) 5939-5941] of action for Vitamin K epoxide reductase (VKOR) using quantum mechanical methods (B3LYP/6-311G**). VKOR, an essential enzyme in mammalian systems, acts to convert Vitamin K epoxide, formed by Vitamin K carboxylase, to its (initial) quinone form for cellular reuse. This study elaborates on a prior work that focused on the thermodynamics of VKOR [D.W. Deerfield II, C.H. Davis, T. Wymore, D.W. Stafford, L.G. Pedersen, Int. J. Quant. Chem. 106 (2006) 2944-2952]. The geometries of proposed model intermediates and transition states in the mechanism are energy optimized. We find that once a key disulfide bond is broken, the reaction proceeds largely downhill. An important step in the conversion of the epoxide back to the quinone form involves initial protonation of the epoxide oxygen. We find that the source of this proton is likely a free mercapto group rather than a water molecule. The results are consistent with the current view that the widely used drug Warfarin likely acts by blocking binding of Vitamin K at the VKOR active site and thereby effectively blocking the initiating step. These results will be useful for designing more complete QM/MM studies of the enzymatic pathway once three-dimensional structural data is determined and available for VKOR.     

On pseudoknot-bordered words and their properties

We study a generalization of the classical notions of bordered and unbordered words, motivated by biomolecular computing. DNA strands can be viewed as finite strings over the alphabet {A, G, C, T}, and are used in biomolecular computing to encode information. Due to the fact that A is Watson–Crick complementary to T and G to C, DNA single strands that are Watson–Crick complementary can bind to each other or to themselves forming so-called secondary structures. Most of these secondary structures are undesirable for biomolecular computational purposes since the strands they involve cannot further interact with other strands. This paper studies pseudoknot-bordered words, a mathematical formalization of pseudoknot-like inter- and intra-molecular structures. In this context, pseudoknot-unbordered words model DNA or RNA strands that will be free of such secondary structures. We obtain several properties of pseudoknot-bordered and -unbordered words. We also address following problem: Given a pseudoknot-unbordered word u, does ${\{u\}}^{+}$ consist of pseudoknot-unbordered words only? We show that this is not generally true. We find that a sufficient condition for ${\{u\}}^{+}$ to consist of pseudoknot-unbordered words only is that u be not primitive. All of our results hold for arbitrary antimorphic involutions, of which the DNA Watson–Crick complementarity function is a particular case.     

A unified least-squares formulation for fluid–structure interaction problems

In this exploratory article a new least squares formulation for the solution of fluid structure interaction problems consisting of the Navier–Stokes equations and the equations of linear elastodynamics will be analysed. It is an extension of the ideas presented in [Cai Z, Starke G. First-order system least squares for the stress–displacement formulation: linear elasticity. SIAM J Numer Anal 2003;41:715–30, Cai Z, Lee B, Wang P. Least-squares methods for incompressible newtonian fluid flow: linear stationary problem. SIAM J Numer Anal 2004;42(2):843–59] for the equations of linear elasticity and the Stokes equations. In those papers a mixed first order least squares formulation which includes the stresses as additional unknowns is proposed. As the stress field has to be approximated by discrete subspaces of H_div, the usual compatibility of the normal traction will automatically be satisfied on any element edge. Therefore the strongly coupled problem can be formulated in an almost uniform manner. After introducing the basic ideas and the general formulation, a computational error analysis is presented which confirms optimal convergence rates in all problem unknowns. Then the formulation is applied to test cases which come closer to real life applications. Also for these cases the formulation achieves a convincing accuracy.     

An improved smart card based password authentication scheme with provable security

Password authentication has been adopted as one of the most commonly used solutions in network environment to protect resources from unauthorized access. Recently, Lee–Kim–Yoo [S.W. Lee, H.S. Kim, K.Y. Yoo, Improvement of Chien et al.'s remote user authentication scheme using smart cards, Computer Standards & Interfaces 27 (2) (2005) 181–183] and Lee-Chiu [N.Y. Lee, Y.C. Chiu, Improved remote authentication scheme with smart card, Computer Standards & Interfaces 27 (2) (2005) 177–180] respectively proposed a smart card based password authentication scheme. We show that these two schemes are both subject to forgery attacks provided that the information stored in the smart card is disclosed by the adversary. We also propose an improved scheme with formal security proof.     

Robust H∞ control for Van de Vusse reactor via T–S fuzzy bilinear scheme

This paper proposes a fuzzy bilinear scheme including a fuzzy modeling method and a fuzzy controller for a class of uncertain nonlinear systems with an additive disturbance input. Firstly, this procedure of modeling describes how to transform a nonlinear system into a fuzzy bilinear system (FBS). For controller design problem, the parallel distributed compensation (PDC) method is adopted to design a fuzzy controller which ensures the robust asymptotic stability of the uncertain T–S FBS with an additive disturbance input and guarantees an H_∞ norm bound constraint on disturbance attenuation. Besides, some sufficient conditions are derived to guarantee the robust stabilization of the overall fuzzy control system via linear matrix inequalities (LMIs). Finally, the Van de Vusse reactor (Chen, Lin, Lin, & Tong, 2008; Chong & Zak, 1996; Kashiwagi & Rong, 2002; Li, Tsai, Lee, Hsiao, & Chao, 2008; Perez, Ogunnaike, & Devasia, 2000) with additive disturbance input is utilized to demonstrate the validity and feasibility of the proposed control scheme.     

Cryptanalysis of a password authentication scheme over insecure networks

The security of a password authentication scheme using smart cards proposed by Liao et al. [I.-E. Liao, C.-C. Lee, M.-S. Hwang, A password authentication scheme over insecure networks, J. Comput. System Sci. 72 (2006) 727–740] is analyzed. Three kinds of attacks are presented in different scenarios.     

Computer‐assisted school information systems: Back to the future

Adrie J. Visscher, P. Wild, & A.C.W. Fung. (Eds.). (2001). Information Technology in Educational Management: Synthesis of Experience, Research and Future Perspectives on Computer‐Assisted School Information Systems. Boston: Kluwer Academic Publishers. ISBN 0–7923–7074–0     

A novel algorithm and its parallelization for solving nearly penta-diagonal linear systems

In the current paper, a new serial algorithm for solving nearly penta-diagonal linear systems is presented. The computational cost of the algorithm is less than or almost equal to those of recent successful algorithms [J. Jia, Q. Kong, and T. Sogabe, A fast numerical algorithm for solving nearly penta-diagonal linear systems, Int. J. Comput. Math. 89 (2012), pp. 851–860; X.G. Lv and J. Le, A note on solving nearly penta-diagonal linear systems, Appl. Math. Comput. 204 (2008), pp. 707–712; S.N. Neossi Nguetchue and S. Abelman, A computational algorithm for solving nearly penta-diagonal linear systems, Appl. Math. Comput. 203 (2008), pp. 629–634]. Moreover, it is suitable for developing its parallel algorithms. One of the parallel algorithms is given and is shown to be promising. The implementation of the algorithms using Computer Algebra Systems such as MATLAB and MAPLE is straightforward. Two numerical examples are given in order to illustrate the validity and efficiency of our algorithms.     

Approximating common fixed points of asymptotically nonexpansive maps in uniformly convex Banach spaces

We introduce three-step iterative schemes with errors for two and three nonexpansive maps and establish weak and strong convergence theorems for these schemes. Mann-type and Ishikawa-type convergence results are included in the analysis of these new iteration schemes. The results presented in this paper substantially improve and extend the results due to [S.H. Khan, H. Fukhar-ud-din, Weak and strong convergence of a scheme with errors for two nonexpansive mappings, Nonlinear Anal. 8 (2005) 1295–1301], [N. Shahzad, Approximating fixed points of non-self nonexpansive mappings in Banach spaces, Nonlinear Anal. 61 (2005) 1031–1039], [W. Takahashi, T. Tamura, Convergence theorems for a pair of nonexpansive mappings, J. Convex Anal. 5 (1995) 45–58], [K.K. Tan, H.K. Xu, Approximating fixed points of nonexpansive mappings by the Ishikawa iteration process, J. Math. Anal. Appl. 178 (1993) 301–308] and [H.F. Senter, W.G. Dotson, Approximating fixed points of nonexpansive mappings, Proc. Amer. Math. Soc. 44 (1974) 375–380].     

A fractional variational iteration method for solving fractional nonlinear differential equations

Recently, fractional differential equations have been investigated by employing the famous variational iteration method. However, all the previous works avoid the fractional order term and only handle it as a restricted variation. A fractional variational iteration method was first proposed in [G.C. Wu, E.W.M. Lee, Fractional variational iteration method and its application, Phys. Lett. A 374 (2010) 2506–2509] and gave a generalized Lagrange multiplier. In this paper, two fractional differential equations are approximately solved with the fractional variational iteration method.     

一种处理部分遮挡表情图像的方法

针对目前表情识别中眼部因头发、帽子等物体而存在部分遮挡的问题,提出了一种基于对称变换的眼部遮挡处理方法。方法针对二值化的人脸表情图像,参照人脸几何特征对眼部区域进行垂直积分投影;通过中心线检测算法,确定人脸的中心线并判断是否存在遮挡。对于不可容忍的遮挡,进行对称变换处理以修复表情图像。实验表明,在相同的特征提取方法和分类器选择情况下,该方法可有效提高部分遮挡人脸表情的识别效果,并可容忍头部一定范围内的偏转。