Computational and mutagenesis studies of the streptavidin native dimer interface

Wt streptavidin forms a domain swapped tetramer consisting of two native dimers. The role of tetramerization has been studied previously and is known to contribute to biotin binding by allowing the exchange of W120 between adjacent subunits. However, the role of dimer formation in streptavidin folding and function has been largely overlooked to date, although native dimers are necessary for tetramer formation and thus for high affinity biotin binding. To understand how the side chain interactions at the dimer interface stabilize the subunit association, we studied the structural and functional consequences of introducing interfacial mutations by a combination of molecular dynamics (MD) simulation and biochemical characterization. In particular, we introduced rational mutations at the dimer interface to engineer new side chain interactions and measured the stability and function of the resulting mutants. We focused on two residues that form a "knob" and a "hole" pair, G74 and T76, since steric complementarity plays an important role at these positions. We introduced mutations that would change the polarity and side chain packing to test if the interface can be rationally redesigned. Both energy calculation and geometric parameterization were used to interpret the simulated structures and predict how the mutations affect the dimer stability. In this regard, obtaining precise energy estimates was difficult because the simulated structures have large stochastic variations and some mutants did not reach an equilibrium by the end of the simulation. In contrast, comparing the wt and mutants to one another and parameterizing the simulation using a geometric parameter, i.e. the degree of solvation of the buried interface, resulted in a testable prediction regarding which mutations would result in a stable dimer. We present experimental data (denaturation and binding measurements) to show that an intuitive parameter based on physical reasoning can be useful for characterizing simulations that are difficult to analyze quantitatively.     

A centrality analysis of the transaction relationships in Panasonic

Panasonic initiated a reform strategy called “Value Creation 21” in 2001. This strategy had a strong impact on its transaction relationships. This research covers one of the important issues in analyzing how the transaction network in Panasonic has changed during the period of “Value Creation 21.” In order to make Panasonic’s transaction relationships visible and countable, we have introduced graph theory and a measure centrality index from the viewpoints of degree, closeness, and betweenness by using data collected in 2002 and 2005. Our findings are reported here. First, the number of firms in Panasonic’s transaction network in 2005 was smaller than in 2002. Second, not only the degree, but also the closeness and betweenness, of the main firms in the Panasonic Group and their suppliers decreased a little more in 2005. Third, the number of in-degree firms declined, whereas the relative importance of Panasonic in the transaction network was more significant. Fourth, Panasonic’s affiliated firms in components & devices and the digital AVC network domain ranked higher than other firms in the transaction network. Last, its out-degree suppliers dropped more in 2005 than in 2002. With these findings, we finally concluded how Panasonic arranged its transaction relationships during the turnaround.     

Improving traversability of quadruped walking robots using body movement in 3D rough terrains

This paper presents a study on improving the traversability of a quadruped walking robot in 3D rough terrains. The key idea is to exploit body movement of the robot. The position and orientation of the robot are systematically adjusted and the possibility of finding a valid foothold for the next swing is maximized, which makes the robot have more chances to overcome the rough terrains. In addition, a foothold search algorithm that provides the valid foothold while maintaining a high traversability of the robot, is investigated and a gait selection algorithm is developed to help the robot avoid deadlock situations. To explain the algorithms, new concepts such as reachable area, stable area, potential search direction, and complementary kinematic margin are introduced, and the effectiveness of the algorithms is validated via simulations and experiments.     

The election problem in asynchronous distributed systems with bounded faulty processes

Determining the “weakest” failure detectors is a central topic in solving many agreement problems such as Consensus, Non-Blocking Atomic Commit and Election in asynchronous distributed systems. So far, this has been studied extensively for several such fundamental problems. It is stated that Perfect Failure Detector P is the weakest failure detector to solve the Election problem with any number of faulty processes. In this paper, we introduce Modal failure detector M and show that to solve Election, M is the weakest failure detector to solve election when the number of faulty processes is less than ⌈n/2⌉. We also show that it is strictly weaker than P.

Biofouling control by quorum sensing inhibition and its dependence on membrane surface

Biofouling control by quorum sensing (QS) inhibition and the influence of membrane surface characteristics on biofilm formation and QS inhibition were investigated. Pseudomonas putida isolated from the bio-fouled reverse osmosis (RO) membranes in a real plant was used. Acylase was chosen as a model QS inhibitor. Bacteria on the membrane coupons were quantified with the heterotrophic plate count method. Cell distribution was imaged by a confocal laser scanning microscope. Results showed that biofilm formation on the membrane was reduced by acylase as it inhibits the activity of N-acylhomoserine lactone (AHL) which is a signal molecule of QS. It was also shown that membrane surface characteristics were influential factors affecting bacterial adhesion, biofilm formation, and QS inhibition.     

Heuristics for determining a patrol path of an unmanned combat vehicle

We consider a problem of finding a path of an unmanned combat vehicle that patrols a given area by visiting a given set of checkpoints with the objective of minimizing possibility of enemy’s infiltration. In this study, we focus on a situation in which the possibility of enemy’s infiltration at (through) each checkpoint is increased nonlinearly as time passes and the checkpoint may be patrolled multiple times during a planning horizon. We develop two-phase heuristics in which an initial path is constructed in the first phase and then it is improved in the second phase. For evaluation of the performance of the proposed heuristics, computational experiments are performed on randomly generated problem instances, and results show that the heuristics give good solutions in a reasonably short time.     

Proactive Human Search for the Designated Person with Prior Context Information in an Undiscovered Environments

This paper describes a scheme for proactive human search for a designated person in an undiscovered indoor environment without human operation or intervention. In designing and developing human identification with prior information a new approach that is robust to illumination and distance variations in the indoor environment is proposed. In addition, a substantial exploration method with an octree structure, suitable for path planning in an office configuration, is employed. All these functionalities are integrated in a message- and component-based architecture for the efficient integration and control of the system. This approach is demonstrated by succeeding human search in the challenging robot mission of the 2009 Robot Grand Challenge Contest.     

Analysis of the unloading performance considering dimple–flexure behavior in HDD

Currently, almost all hard disk drives (HDDs) have adopted a loading/unloading mechanism that increases their recording capacity and improves their reliability. However, these mechanisms still create a few scratches or defects in the loading/unloading zone. Slipping at the dimple–flexure interface was recently reported as one of the causes. In this research, we first analyzed the relative behavior of dimple–flexure based on fretting wear marks. We determined that the dimple–flexure behavior included both slipping and rotating motion simultaneously. We then verified the distinct slipping and rolling phenomenon at the moment of ramp contact using finite-element method (FEM) analysis. An experimental setup was constructed, and an unloading experiment was carried out to obtain the ramp contact characteristics corresponding to various unloading velocities. Based on the verified FEM, the characteristics of dimple–flexure relative behavior were investigated for various suspension design parameters, ramp contact characteristics, and unloading velocities. A higher ramp contact force and shorter contact duration resulted in larger slip displacements and roll angles between the dimple and the flexure. Finally, we analyzed the unloading performance of an HDD for various design parameters using quasi-static approximation while considering the relative behavior between the dimple and flexure. The quasi-static analysis indicated a change of approximately 15?% in the flying height at an unloading velocity of 40?in. per second when the relative motion between the dimple and flexure was considered during the unloading process. Even, slider–disk contact occurred at an unloading velocity of 50 ISP.     

Improvement in the volume efficiency of multilayered ceramic capacitors (MLCCs)

An attempt was made to improve the conventional lamination process in the multilayered ceramic capacitors (MLCCs) fabrication by adapting a solvent treatment on the BaTiO₃ green sheets. During the lamination process, additional particle rearrangement in the BaTiO₃ green block was stimulated by solvent treatment. This rearrangement resulted in a more compact structure of the BaTiO₃ green sheets compared to that obtained through the conventional lamination process. The overall thickness of BaTiO₃/Ni/BaTiO₃ laminates was also reduced after solvent treatment. It is suggested that miniaturization in the fabrication of MLCCs can be improved by adapting a solvent treatment during the lamination process.