Search Results - "Fujisaki, Hiroshi"

Multiscale Aspects of Molecular Motions: From Molecular Vibrations, Conformational Changes of Biomolecules to Cellular Dynamics by Fujisaki, Hiroshi

“…Molecular aspects of living systems are important because it is the most basic aspects of life as exemplified in biochemistry and structural biology. Since…”
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Path Ensembles for Pin1-Catalyzed Cis–Trans Isomerization of a Substrate Calculated by Weighted Ensemble Simulations by Moritsugu, Kei, Yamamoto, Norifumi, Yonezawa, Yasushige, Tate, Shin-ichi, Fujisaki, Hiroshi

“…Pin1 enzyme protein recognizes specifically phosphorylated serine/threonine (pSer/pThr) and catalyzes the slow interconversion of the peptidyl-prolyl bond…”
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Minimum free energy path of ligand-induced transition in adenylate kinase by Matsunaga, Yasuhiro, Fujisaki, Hiroshi, Terada, Tohru, Furuta, Tadaomi, Moritsugu, Kei, Kidera, Akinori

“…Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare…”
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Mathematical model for promotion of wound closure with ATP release by Odagiri, Kenta, Fujisaki, Hiroshi, Takada, Hiroya, Ogawa, Rei

“…To computationally investigate the recent experimental finding such that extracellular ATP release caused by exogeneous mechanical forces promote wound…”
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Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature by Fujisaki, Hiroshi, Suetani, Hiromichi, Maragliano, Luca, Mitsutake, Ayori

“…We apply the non-Markov-type analysis of state-to-state transitions to nearly microsecond molecular dynamics (MD) simulation data at a folding temperature of a…”
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Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques-Searching for Mechanism and Kinetics of Biomolecular Functions by Fujisaki, Hiroshi, Moritsugu, Kei, Matsunaga, Yasuhiro

“…To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics need to be characterized, but its…”
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Multiscale enhanced path sampling based on the Onsager-Machlup action: application to a model polymer by Fujisaki, Hiroshi, Shiga, Motoyuki, Moritsugu, Kei, Kidera, Akinori

“…We propose a novel path sampling method based on the Onsager-Machlup (OM) action by generalizing the multiscale enhanced sampling technique suggested by…”
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Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB by Matsunaga, Yasuhiro, Yamane, Tsutomu, Terada, Tohru, Moritsugu, Kei, Fujisaki, Hiroshi, Murakami, Satoshi, Ikeguchi, Mitsunori, Kidera, Akinori

“…The multidrug transporter AcrB transports a broad range of drugs out of the cell by means of the proton-motive force. The asymmetric crystal structure of…”
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Exploring Reaction Pathways for Peptidylprolyl-Isomerase by Fujisaki, Hiroshi, Yonezawa, Yasushige, Shiga, Motoyuki, Maragliano, Luca, Tate, Shin-ichi

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Vibrational Energy Relaxation in Proteins by Fujisaki, Hiroshi, Straub, John E., Berne, Bruce J.

“…An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied by using two…”
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A quantum generalization of intrinsic reaction coordinate using path integral centroid coordinates by Shiga, Motoyuki, Fujisaki, Hiroshi

“…We propose a generalization of the intrinsic reaction coordinate (IRC) for quantum many-body systems described in terms of the mass-weighted ring polymer…”
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Mode-Specific Vibrational Energy Relaxation of Amide I′ and II′ Modes in N-Methylacetamide/Water Clusters: Intra- and Intermolecular Energy Transfer Mechanisms by Zhang, Yong, Fujisaki, Hiroshi, Straub, John E

“…The mode-specific vibrational energy relaxation of the amide I′ and amide II′ modes in NMA-d 1/(D2O) n (n = 0−3) clusters were studied using the time-dependent…”
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Molecular Dynamics Study on the Solvent Dependent Heme Cooling Following Ligand Photolysis in Carbonmonoxy Myoglobin by Zhang, Yong, Fujisaki, Hiroshi, Straub, John E

“…The time scale and mechanism of vibrational energy relaxation of the heme moiety in myoglobin was studied using molecular dynamics simulation. Five different…”
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Quantum dynamics of N-methylacetamide studied by the vibrational configuration interaction method by Fujisaki, Hiroshi, Yagi, Kiyoshi, Hirao, Kimihiko, Straub, John E.

“…Dominant vibrational energy relaxation pathways from the amide I mode of N-methylacetamide calculated by the vibrational configuration interaction method…”
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Vibrational Energy Relaxation of Isotopically Labeled Amide I Modes in Cytochrome c:  Theoretical Investigation of Vibrational Energy Relaxation Rates and Pathways by Fujisaki, Hiroshi, Straub, John E.

“…With use of a time-dependent perturbation theory, vibrational energy relaxation (VER) of isotopically labeled amide I modes in cytochrome c solvated with water…”
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Different inhibitory potency of febuxostat towards mammalian and bacterial xanthine oxidoreductases: insight from molecular dynamics by Kikuchi, Hiroto, Fujisaki, Hiroshi, Furuta, Tadaomi, Okamoto, Ken, Leimkühler, Silke, Nishino, Takeshi

“…Febuxostat, a drug recently approved in the US, European Union and Japan for treatment of gout, inhibits xanthine oxidoreductase (XOR)-mediated generation of…”
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Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins by Fujisaki, Hiroshi, Zhang, Yong, Straub, John E

“…Without invoking the Markov approximation, we derive formulas for vibrational energy relaxation (VER) and dephasing for an anharmonic system oscillator using a…”
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Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model by Zhang, Yong, Fujisaki, Hiroshi, Straub, John E

“…The time scales and mechanisms of mode-specific vibrational energy relaxation in imidazole ligated ferrous iron porphine were studied using a non-Markovian…”
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Quantum and classical vibrational relaxation dynamics of N-methylacetamide on ab initio potential energy surfaces by Fujisaki, Hiroshi, Yagi, Kiyoshi, Straub, John E., Stock, Gerhard

“…Employing extensive quantum‐chemical calculations at the DFT/B3LYP and MP2 level, quartic force fields of isolated N‐methylacetamide are constructed. Taking…”
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Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review by Fujisaki, Hiroshi, Moritsugu, Kei, Matsunaga, Yasuhiro, Morishita, Tetsuya, Maragliano, Luca

“…Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA…”
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