The development of “Ultimate Rudder” for EEDI

EEDI (Energy Efficiency Design Index) came into effect mandatory in Jan. 2013, and the ship owners definitely required a higher efficiency propulsion system than ever before. Hence, the shipyards have been conducting an optimization of ESD (Energy Saving Device) system in self-propulsion test for each project. As the results, the shipyards have installed a rudder bulb as an effective ESD. The rudder bulb is a popular ESD system from a long time ago. Mewis1) described that the rudder bulb was developed by Costa in 1952 and the efficiency improve by the rudder bulb for a container vessel was 1% on average. Fujii et al.2) developed “MIPB (Mitsui Integrated Propeller Boss)” as an advanced rudder bulb. The feature of MIPB was a streamlined profile from propeller cap to rudder. According to their paper, the efficiency improve by installing MIPB was 2-4%. Recently, NAKASHIMA PROPELLER Co., Ltd. developed ECO-Cap (economical propeller cap)3) as a new ESD with FRP (Fiber Reinforced Plastics). The strength of FRP is higher than that of NAB (Nickel Aluminium Bronze), therefore ECO-Cap was able to adopt thin fins on propeller caps for low resistance. Although the material used for the energy- saving propeller cap was generally NAB, the research results on FRP showed that FRP could be used as ESD due to their properties such as lightweight and flexibility. As explained above, the authors thought that there was a possibility to evolve the rudder bulb profile using the easily moldable FRP compared with NAB. This paper described about the development of “Ultimate Rudder” of new design concept by FRP. The authors optimized the profile of “Ultimate Rudder” by CFD and confirmed the efficiency increase from 4.9 to 5.4% in self-propulsion test

Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome

In order to understand an overview of promoter activities intrinsic to primary DNA sequences in the human genome within a particular cell type, we carried out systematic quantitative luciferase assays of DNA fragments corresponding to putative promoters for 472 human genes which are expressed in HEK (human embryonic kidney epithelial) 293 cells. We observed the promoter activities of them were distributed in a bimodal manner; putative promoters belonging to the first group (with strong promoter activities) were designated as P1 and the latter (with weak promoter activities) as P2. The frequencies of the TATA-boxes, the CpG islands, and the overall G + C-contents were significantly different between these two populations, indicating there are two separate groups of promoters. Interestingly, similar analysis using 251 randomly isolated genomic DNA fragments showed that P2-type promoter occasionally occurs within the human genome. Furthermore, 35 DNA fragments corresponding to putative promoters of non-protein-coding transcripts (ncRNAs) shared similar features with the P2 in both promoter activities and sequence compositions. At least, a part of ncRNAs, which have been massively identified by full-length cDNA projects with no functional relevance inferred, may have originated from those sporadic promoter activities of primary DNA sequences inherent to the human genome

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme