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Tokyo, Japan

Sophia University is a private Jesuit research university in Japan, with its main campus located near Yotsuya station, in an area of Tokyo's Chiyoda Ward. It is ranked as one of the top private universities in Japan with the most selective admission and is known for its international academic climate. It takes its name from the Greek Sophia meaning "wisdom". The Japanese name, Jōchi Daigaku literally means "University of Higher Wisdom". It has an exchange program with many universities throughout the world, including Yale University, Sogang University and the University of Hong Kong. The university was a men’s university in the past, but at present admits women; the proportion of men to women is now more or less equal. Sophia’s alumni are referred to as "Sophians"; they include the 79th Japanese Prime Minister of Japan, Morihiro Hosokawa, a number of politicians represented in the Diet of Japan and professors at institutions such as the University of Tokyo and Yale University. Wikipedia.

Takayanagi K.,Sophia University
Nuclear Physics A

The extended Krenciglowa-Kuo (EKK) method allows us to calculate the effective Hamiltonian in a non-degenerate model space. We show that the EKK method can be implemented numerically in two iterative schemes, which are explained in detail with emphasis on convergence conditions. Using test calculations in a simple model, we clarify how and on what conditions we can calculate the effective Hamiltonian. © 2011 Elsevier B.V. Source

Kondo J.,Sophia University | Westhof E.,University of Strasbourg
Nucleic Acids Research

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues. © The Author(s) 2011. Published by Oxford University Press. Source

Takayanagi K.,Sophia University
Annals of Physics

We present a unified description of the Bloch and Rayleigh-Schrödinger perturbation theories of the effective interaction in both algebraic and graphic representations. © 2015 Elsevier Inc. Source

Resistance explained: The crystal structures of the ribosomal decoding Asite with an A1408G antibiotic-resistance mutation were solved in the presence and absence of the aminoglycoside geneticin (see structure, geneticin carbon framework in yellow). These structures show how bacteria acquire high-level resistance against aminoglycosides by the mutation. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Takayanagi K.,Sophia University
Nuclear Physics A

The effective Hamiltonian in a model space has been derived from the decoupling equation. We present a rigorous proof of the proposition that the decoupling equation is a necessary and sufficient condition to give an effective Hamiltonian, establishing a robust one-to-one correspondence between a solution to the decoupling equation and an effective Hamiltonian. We then present discussions based on this result, emphasizing (i) that the current situation of the theory is far from being satisfactory, and (ii) that the proposition gives a rigorous mathematical foundation to any effort to improve the theory of the effective Hamiltonian on the basis of the decoupling equation. © 2013 Elsevier B.V. Source

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