Multi-Objective Genetic Algorithm for Pseudoknotted RNA Sequence Design

RNA inverse folding is a computational technology for designing RNA sequences which fold into a user-specified secondary structure. Although pseudoknots are functionally important motifs in RNA structures, less reports concerning the inverse folding of pseudoknotted RNAs have been done compared to those for pseudoknot-free RNA design. In this paper, we present a new version of our multi-objective genetic algorithm (MOGA), MODENA, which we have previously proposed for pseudoknot-free RNA inverse folding. In the new version of MODENA, (i) a new crossover operator is implemented and (ii) pseudoknot prediction methods, IPknot and HotKnots, are used to evaluate the designed RNA sequences, allowing us to perform the inverse folding of pseudoknotted RNAs. The new version of MODENA with the new crossover operator was benchmarked with a dataset composed of natural pseudoknotted RNA secondary structures, and we found that MODENA can successfully design more pseudoknotted RNAs compared to the other pseudoknot design algorithm. In addition, a sequence constraint function newly implemented in the new version of MODENA was tested by designing RNA sequences which fold into the pseudoknotted structure of a hepatitis delta virus ribozyme; as a result, we successfully designed eight RNA sequences. The new version of MODENA is downloadable from http://rna.eit.hirosaki-u.ac.jp/modena/

MODENA: a multi-objective RNA inverse folding

Artificially synthesized RNA molecules have recently come under study since such molecules have a potential for creating a variety of novel functional molecules. When designing artificial RNA sequences, secondary structure should be taken into account since functions of noncoding RNAs strongly depend on their structure. RNA inverse folding is a methodology for computationally exploring the RNA sequences folding into a user-given target structure. In the present study, we developed a multi-objective genetic algorithm, MODENA (Multi-Objective DEsign of Nucleic Acids), for RNA inverse folding. MODENA explores the approximate set of weak Pareto optimal solutions in the objective function space of 2 objective functions, a structure stability score and structure similarity score. MODENA can simultaneously design multiple different RNA sequences at 1 run, whose lowest free energies range from a very stable value to a higher value near those of natural counterparts. MODENA and previous RNA inverse folding programs were benchmarked with 29 target structures taken from the Rfam database, and we found that MODENA can successfully design 23 RNA sequences folding into the target structures; this result is better than those of the other benchmarked RNA inverse folding programs. The multi-objective genetic algorithm gives a useful framework for a functional biomolecular design. Executable files of MODENA can be obtained at http://rna.eit.hirosaki-u.ac.jp/modena/

Time-resolved carrier dynamics and electron-phonon coupling strength in proximized weak ferromagnet-superconductor nanobilayers

We present our femtosecond optical pump-probe studies of proximized ferromagnet-superconductor nanobilayers. The weak ferromagnetic nature of a thin NiCu film makes it possible to observe the dynamics of the nonequilibrium carriers through the near-surface optical reflectivity change measurements. The subpicosecond biexponential reflectivity decay has been identified as electron-phonon Debye and acoustic phonon relaxation times, and the decay of Debye phonons versus temperature dependence was used to evaluate the electron-phonon coupling constants for both the pure Nb and proximized Nb/NiCu heterostructures down to low temperatures. We have also demonstrated that the NiCu overlay on top of Nb dramatically reduced the slow, bolometric component of the photoresponse component, making such bilayers attractive for future radiation detector applications

Relationship between Microstructure and Magnetic Domain Structure of Nd-Fe-B Melt-Spun Ribbon Magnets

The relation between the microstructure, observed using an electron probe microanalyzer, and the domain structure, observed using a Kerr microscope, was established to evaluate the effects of hot rolling and the addition of Ti-C on the c-axis orientation and the magnetization process of hot-rolled Nd-Fe-B-Ti-C melt-spun ribbons. The addition of Ti-C promotes the c-axis orientation and high coercivity in the ribbons. Elemental mapping suggests a uniform elemental distribution; however, an uneven distribution of Ti was observed in an enlarged grain with Ti-enriched points inside the grain. The reversal domains that nucleated at the Ti-enriched point inside the grain cause low coercivity

The effect of a plasma sheath on hypersonic flight communications

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 1990.Includes bibliographical references (leaves 63-64).by Hiroshi Taneda.M.S