Researcher Database

TOGASHI YUICHI

Department / Course College of Life Sciences Department of Bioinformatics

Title / Position Professor

Papers
1.	2022/08/23	Molecular dynamics analysis of biomolecular systems including nucleic acids │ Biophysics and Physicobiology │ 19,pp.e190027 (Co-authored)
2.	2022/04/08	Translational recoding by chemical modification of non-AUG start codon ribonucleotide bases │ Science Advances │ 8 (14),pp.eabm8501 (Co-authored)
3.	2022	Multiscale Modeling of Chromatin Considering the State and Shape of Molecules │ Lecture Notes in Mechanical Engineering │ ,pp.171-175 (Sole-authored)
4.	2021/06	Free energy landscape of RNA binding dynamics in start codon recognition by eukaryotic ribosomal pre-initiation complex │ PLoS Computational Biology │ 17 (6),pp.e1009068 (Co-authored)
5.	2021/01/11	Structural dynamics of DNA depending on methylation pattern │ Physical Review E │ (Co-authored)
6.	2020/03	PHi-C: deciphering Hi-C data into polymer dynamics │ NAR Genomics and Bioinformatics │ 2 (2),pp.lqaa020 (Co-authored)
7.	2019/11/28	Histone Tail Dynamics in Partially Disassembled Nucleosomes During Chromatin Remodeling │ FRONTIERS IN MOLECULAR BIOSCIENCES │ ,pp.133 (Co-authored)
8.	2019/09	Analyzing fluctuation properties in protein elastic networks with sequence specific and distance dependent interactions │ Biomolecules │ 9 (10),pp.549 (Co-authored)
9.	2019/02/21	Modeling of Nanomachine/Micromachine Crowds: Interplay between the Internal State and Surroundings │ JOURNAL OF PHYSICAL CHEMISTRY B │ ,pp.1481-1490 (Sole-authored)
10.	2018/12/05	Coarse-Grained Protein Dynamics Studies Using Elastic Network Models │ INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES │ ,pp.3899 (Co-authored)
11.	2018/10/13	Designed Elastic Networks: Models of Complex Protein Machinery │ INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES │ ,pp.3152 (Co-authored)
12.	2018/09/18	Single-molecule diffusion-based estimation of ligand effects on G protein-coupled receptors. │ Science signaling │ 11 (548),pp.eaao1917 (Co-authored)
13.	2017/11	Small Numbers and Individuality of Molecules │ Experimental Medicine │ ,pp.3190-3196 (Co-authored)
14.	2017/03	The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry │ FRONTIERS IN PHYSIOLOGY │ 8,pp.103 (Co-authored)
15.	2017	Bridging the dynamics and organization of chromatin domains by mathematical modeling │ NUCLEUS │ 8 (4),pp.353-359 (Co-authored)
16.	2017	VARYING THE RESOLUTION OF THE ROUSE MODEL ON TEMPORAL AND SPATIAL SCALES: APPLICATION TO MULTISCALE MODELING OF DNA DYNAMICS │ MULTISCALE MODELING&SIMULATION │ 15 (4),pp.1672-1693 (Co-authored)
17.	2016/11/29	Book Review: CELL BIOLOGY by the numbers │ Seibutsu Butsuri │ ,pp.352-352 (Sole-authored)
18.	2016/11	Non-RVD mutations that enhance the dynamics of the TAL repeat array along the superhelical axis improve TALEN genome editing efficacy │ SCIENTIFIC REPORTS │ 6,pp.37887 (Co-authored)
19.	2016/10	Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells │ PLOS COMPUTATIONAL BIOLOGY │ 12 (10),pp.e1005136 (Co-authored)
20.	2016/04/01	Screening for mechanical responses of proteins using coarse-grained elastic network models │ IEICE NONLINEAR THEORY AND ITS APPLICATIONS │ ,pp.190-201 (Sole-authored)
21.	2016/03	An Analytical Framework for Studying Small-Number Effects in Catalytic Reaction Networks: A Probability Generating Function Approach to Chemical Master Equations │ FRONTIERS IN PHYSIOLOGY │ 7,pp.89 (Co-authored)
22.	2015/08	Integrin LFA-1 regulates cell adhesion via transient clutch formation │ BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS │ 464 (2),pp.459-466 (Co-authored)
23.	2015/03	DNA Structural Dynamics (Team 5) │ Dagstuhl Reports │ 4,pp.191-194 (Co-authored)
24.	2015/03	Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes │ NEW JOURNAL OF PHYSICS │ 17,pp.033024 (Co-authored)
25.	2015/03	Spying “Minorities” in the Cell │ Dagstuhl Reports │ 4,pp.165-166 (Sole-authored)
26.	2014/02	Energetics of single active diffusion trajectories │ EPL │ 105 (3),pp.30002 (Co-authored)
27.	2014	Theoretical Studies of Reaction Networks Involving Small Numbers of Molecules │ Seitai no Kagaku │ ,pp.450-451 (Sole-authored)
28.	2012/11	Spontaneous Structural Changes in Actin Regulate G-F Transformation │ PLOS ONE │ 7 (11),pp.e45864 (Co-authored)
29.	2012/10	Complex Intramolecular Mechanics of G-actin - An Elastic Network Study │ PLOS ONE │ 7 (10),pp.e45859 (Co-authored)
30.	2012/02	Myosin-V as a Mechanical Sensor: An Elastic Network Study │ BIOPHYSICAL JOURNAL │ 102 (3),pp.542-551 (Co-authored)
31.	2011	A mesoscopic model for protein enzymatic dynamics in solution │ PHYSICAL CHEMISTRY CHEMICAL PHYSICS │ 13 (22),pp.10527-10537 (Co-authored)
32.	2011	Modeling bio-molecular machinery in the complex environment inside the cell │ Proceedings - 11th IEEE/IPSJ International Symposium on Applications and the Internet, SAINT 2011 │ ,pp.266-266 (Sole-authored)
33.	2010/09/23	2004 Nonlinearity of Mechanical Motions in Biomolecular Machines │ The Computational Mechanics Conference │ ,pp.7-9 (Co-authored)
34.	2010/06	Nonlinearity of Mechanochemical Motions in Motor Proteins │ PLOS COMPUTATIONAL BIOLOGY │ 6 (6),pp.e1000814 (Co-authored)
35.	2010/01	Multiple Structural Forms of Actin in the Filamentous State │ BIOPHYSICAL JOURNAL │ 98 (3),pp.154A-154A (Co-authored)
36.	2008/05	Mesoscale modeling of molecular machines: Cyclic dynamics and hydrodynamical fluctuations │ PHYSICAL REVIEW E │ 77 (5),pp.050901 (Co-authored)
37.	2008/03	Dynamical Features and Design Principles of Protein Machines: Elastic Network Studies │ Seibutsu Butsuri │ ,pp.114-118 (Sole-authored)
38.	2008	745 Dynamical Features of Bio-molecular Machines : A Comparative Study Using Coarse-Grained Molecular Dynamics Simulations │ (Co-authored)
39.	2007/07	Molecular synchronization waves in arrays of allosterically regulated enzymes │ PHYSICAL REVIEW LETTERS │ 99 (4),pp.048301 (Co-authored)
40.	2007/05	Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines │ PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA │ 104 (21),pp.8697-8702 (Co-authored)
41.	2007/01	Switching Dynamics in Reaction Networks Induced by Molecular Discreteness │ Journal of Physics: Condensed Matter │ 19 (6),pp.065150 (Co-authored)
42.	2005/02	Discreteness-induced Stochastic Steady State in Reaction Diffusion Systems: Self-consistent Analysis and Stochastic Simulations │ Physica D │ 205 (1-4),pp.87-99 (Co-authored)
43.	2004/08	Molecular discreteness in reaction-diffusion systems yields steady states not seen in the continuum limit │ PHYSICAL REVIEW E │ 70 (2),pp.020901 (Co-authored)
44.	2003/01	Alteration of chemical concentrations through discreteness-induced transitions in small autocatalytic systems │ JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN │ 72 (1),pp.62-68 (Co-authored)
45.	2002	TINAMI - Trial of Intelligent Image Search System │ Proc. of JSAI │ ,pp.212 (Co-authored)
46.	2001/03	Transitions induced by the discreteness of molecules in a small autocatalytic system │ PHYSICAL REVIEW LETTERS │ 86 (11),pp.2459-2462 (Co-authored)