Free energy perturbation study on a Trp-binding mutant (Ser88 ->Cys) of the trp-repressor

The Ser⁸⁸Cys mutant of the trp-repressor showed a lower affinityfor the corepressor than the wild-type repressor [G = 1.7 ±0.3 kcal/mol, Chou and Matthews (1989) J. Biol. Chem., 264,18314–18319].A molecular dynamics/free energy cycle perturbation study wasperformed to understand the origin of the decreased affinity.A value (G = 1.58 ± 0.28 kcal/mol) comparable with theexperimental value was obtained by the simulation. Free energycomponent analysis revealed that destabilization of the vander Waals interaction between Ser⁸⁸ and Trp¹⁰⁹ (corepressor)mainly contributed to the decreased affinity of the mutant.The rotational transition of the hydroxyl (sulfhydryl) groupof Ser⁸⁸ (Cys⁸⁸) during the simulations affected the contributionsof Arg⁸⁴ and water to the free energy change in the aporepressorand those of Arg⁸⁴ and Trp ¹⁰⁹ to that in the holorepressor.However, the contributions from different residues compensatedeach other, and the total free energy changes were almost invariablein the various simulations.     

Morphology,thermal, and mechanical properties of vinylester resin nanocomposites with various organo‐modified montmorillonites

New nanocomposites based on a vinylester resin (VER) and the organo‐montmorillonites (ODA‐M, BHL‐M, DEM‐M, BHLV‐M) modified with octadecylammonium, bis(2‐hydroxyethyl)lauryl ammonium, diethyl[2‐(methacryloyloxyl)ethyl]ammonium, and bis(2‐hydroxyethyl)lauryl(vinylbenzyl)‐ammonium chlorides, respectively, were prepared by dispersing the organoclays in VER, and subsequent crosslinking at finally 120°C. X‐ray diffraction studies and morphological studies using transmission electron microscopy revealed that exfoliation occurs for the VER/ODA‐M and BHL‐M composites, intercalation occurs for the VER/BHLV‐M composite, and neither intercalation nor exfoliation occur for the VER/DEM‐M and unmodified montmorillonite composites. On the whole, although the enhancement in flexural modulus was observed for the exfoliated ODA‐M and BHL‐M composites, the flexural strength was rather lowered. Dynamic viscoelastic measurement revealed that the ODA‐M, BHL‐M, and BHLV‐M nanocomposites have significantly higher storage modulus at the rubbery state than the other composites. Polym. Eng. Sci. 44:2041–2046, 2004. © 2004 Society of Plastics Engineers.     

Three-dimensional medical image recognition of cancer of the liver by a revised radial basis function (RBF) neural network algorithm

In this study, we propose a revised radial basis function (RBF) neural network algorithm and apply this algorithm to computer-aided diagnosis (CAD) of the liver. First, the revised RBF neural network algorithm is applied to recognition of the liver regions, and the recognition results are compared with those obtained using the conventional RBF neural network and the conventional multilayered neural network trained using the back-propagation algorithm. It is shown that the revised RBF neural network is accurate, and is a useful method because the parameters are automatically determined. Then, the revised RBF neural network is applied to CAD of the liver cancer called hepatocellular carcinoma (HCC).     

Data-driven dual-rate cascade control and application to pitch angle control of UAV

A data-driven design method for a cascade control system is proposed. The cascade control system consists of inner and outer loops, where the control interval of the outer loop is an integer multiple of the inner loop; hence, the system is a dual-rate system. In the proposed method, controllers in the inner and outer loops are designed based on one-shot data. In such a dual-rate cascade system, since the controllers are designed using different data-rate signals, the lifting technique is applied to align the dual-rate data. To show its effectiveness, the proposed method is compared with a conventional single-rate cascade control method, and numerical simulations and experiments are presented to examine servo and regulation performance.     

3D block-based medial axis transform and chessboard distance transform based on dominance

Traditionally, the block-based medial axis transform (BB-MAT) and the chessboard distance transform (CDT) were usually viewed as two completely different image computation problems, especially for three dimensional (3D) space. In fact, there exist some equivalent properties between them. The relationship between both of them is first derived and proved in this paper. One of the significant properties is that CDT for 3D binary image V is equal to BB-MAT for image V' where it denotes the inverse image of V. In a parallel algorithm, a cost is defined as the product of the time complexity and the number of processors used. The main contribution of this work is to reduce the costs of 3D BB-MAT and 3D CDT problems proposed by Wang [65]. Based on the reverse-dominance technique which is redefined from dominance concept, we achieve the computation of the 3D CDT problem by implementing the 3D BB-MAT algorithm first. For a 3D binary image of size N³, our parallel algorithm can be run in O(logN) time using N³ processors on the concurrent read exclusive write (CREW) parallel random access machine (PRAM) model to solve both 3D BB-MAT and 3D CDT problems, respectively. The presented results for the cost are reduced in comparison with those of Wang's. To the best of our knowledge, this work is the lowest costs for the 3D BB-MAT and 3D CDT algorithms known. In parallel algorithms, the running time can be divided into computation time and communication time. The experimental results of the running, communication and computation times for the different problem sizes are implemented in an HP Superdome with SMP/CC-NUMA (symmetric multiprocessor/cache coherent non-uniform memory access) architecture. We conclude that the parallel computer (i.e., SMP/CC-NUMA architecture or cluster system) is more suitable for solving problems with a large amount of input size.     

Bottom-up pyramid cellular acceptors with three-dimensional layers

In 1997, C.R. Dyer and A. Rosenfeld introduced an acceptor on a two-dimensional pattern (or tape), called the pyramid cellular acceptor, and demonstrated that many useful recognition tasks are executed by pyramid cellular acceptors in time proportional to the logarithm of the diameter of the input. They also introduced a bottom-up pyramid cellular acceptor which is a restricted version of the pyramid cellular acceptor, and proposed some interesting open problems of the bottom-up pyramid cellular acceptors. On the other hand, we think that the study of threedimensional automata has been meaningful as the computational model of three-dimensional information processing such as computer vision, robotics, and so forth. In this paper, we investigate about bottom-up pyramid cellular acceptors with three-dimensional layers, and show their some accepting powers. This work was presented in part at the 13th International Symposium on Artificial Life and Robotics, Oita, Japan, January 31–February 2, 2008     

Effects of 4He impurities on 3He nuclear spin-lattice relaxation in hcp solid 3He

Nuclear spin-lattice relaxation properties of hcp solid ³He with ⁴He impurities have been studied. At temperatures below the exchange plateau region, three kinds of relaxation time were observed. To analyze the data, a phenomenological four-bath model was developed, the four baths being the Zeeman bath, the phonon bath, an X-bath, and a Y-bath. The X-bath consists of the exchange bath and a part of the ⁴He-⁴He elastic interaction bath. The Y-bath is the main part of the elastic interaction bath. We measured the concentration dependence of the energy constants of all the baths, as well as the temperature and concentration dependences of the three kinds of relaxation time. The relaxation behavior corresponding to the process between the X-bath and the Y-bath could not be expressed by a single exponential function of time and the relaxation rate was strongly dependent on the concentration. This process may be related to the internal thermal equilibrium process within the elastic interaction bath. The impurity-dependent relaxation time between the X-bath and the phonon bath had a temperature dependence of T ^–n with n = 7.4±0.3.     

Logic circuit synthesis using Prolog

This paper briefly reviews the current use of CAD in logic design, and then describes an expert system used to synthesize logic circuits. Specialized knowledge dealing with standard TTL ICs is written in Prolog and AGE, and the results are compared.