[PS2] Poster 2 | 34th IUPAP Conference on Computational Physics（CCP2023）

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Poster 2

Mon. Aug 7, 2023 4:00 PM - 6:00 PM JST
Mon. Aug 7, 2023 7:00 AM - 9:00 AM UTC

Reception Hall 3F

[PS2-01]Symmetry of two point spatial correlators in 2+1-flavor QCD at high temperature

*David Ward¹ (1. Osaka University (Japan))

[PS2-03]Cayley transformation for unitary matrix model in Numerical Stochastic Perturbation Theory

*Hironori Takei¹, Ken-Ichi Ishikawa¹, Yingbo Ji¹ (1. Hiroshima Univ. (Japan))

[PS2-04]QCD thermodynamics with Möbius domain wall fermions near physical point

*Yasumichi Aoki¹, Sinya Aoki², Hidenori Fukaya³, Jishnu Goswami¹, Shoji Hashimoto^4,5, Issaku Kanamori¹, Takashi Kaneko^4,5,6, Yoshifumi Nakamura¹, Yu Zhang¹ (1. RIKEN (Japan), 2. YITP (Japan), 3. Osaka Univ. (Japan), 4. KEK (Japan), 5. SOKENDAI (Japan), 6. KMI (Japan))

[PS2-05]Axial U(1) symmetry at low and high temperatures in Nf=2+1 lattice QCD with chiral fermions

*Kei Suzuki¹, Sinya Aoki², Yasumichi Aoki³, Hidenori Fukaya⁴, Shoji Hashimoto^5,6, Issaku Kanamori³, Takashi Kaneko^5,6,7, Yoshifumi Nakamura³, Christian Rohrhofer⁴, David Ward⁴ (1. Advanced Science Research Center, Japan Atomic Energy Agency (JAEA) (Japan), 2. Yukawa Institute for Theoretical Physics, Kyoto University (Japan), 3. RIKEN Center for Computational Science (Japan), 4. Department of Physics, Osaka University (Japan), 5. KEK Theory Center, High Energy Accelerator Research Organization (KEK) (Japan), 6. School of High Energy Accelerator Science, The Graduate University for Advanced Studies (Sokendai) (Japan), 7. Kobayashi Maskawa Institute (KMI) for the Origin of Particles and the Universe, Nagoya University (Japan))

[PS2-06]Vibronic excitations in RIXS spectra of spin-orbit Mott insulators

*Naoya Iwahara¹, Shouta Shikano¹, Wataru Furukawa¹ (1. Chiba University (Japan))

[PS2-07]Molecular dynamics study of Fe-Light-Element mixtures under high pressure using DFT and neural network interatomic potential

*Satoshi Ohmura¹, Kohei Shimamura², Fuyuki Shimojo² (1. Hiroshima Inst. of Tech. (Japan), 2. Kumamoto Univ. (Japan))

[PS2-08]Electronic Properties and Spin Polarization of B-N Doped Triangulene

*Shoichi Sakamoto¹, Tadashi Kon¹ (1. Seikei University (Japan))

[PS2-09]Evaluating the interaction of hydrogen boride sheets and water

*Kurt Irvin Medina Rojas¹, Yoshitada Morikawa^1,2,3, Ikutaro Hamada¹ (1. Department of Precision Engineering, Graduate School of Engineering, Osaka University (Japan), 2. Element Strategy Initiative for Catalyst and Batteries, Kyoto University (Japan), 3. Research Center for Precision Engineering, Graduate School of Engineering, Osaka University (Japan))

[PS2-12]Doping dependence of superconducting transition temperature T_c of SrTiO₃ in the over-doped regime based on the first-principles calculations.

*Riku Ikaida¹, Kazuhiro Sano², Yoshimi Masuda², Takuya Sekikawa¹, Yoshiaki Ōno¹ (1. Niigata Univ. (Japan), 2. Mie Univ. (Japan))

[PS2-13]Computational acceleration of the density functional approach
code with using GPU

*Chandro Pardede¹, Masao Obata¹, Rinku Majumder¹, Tatsuki Oda¹ (1. Grad. Sch. Nat. Sci. & Tech., Kanazawa Univ. (Japan))

[PS2-14]Migration of the twin boundary in a modulated martensite phase
of magnetic shape memory alloy Ni₂MnGa

*Rinku Majumder^1,2, Masao Obata¹, Chandro Pardede¹, Jakub Luštinec^1,3, Ladislav Kalvoda³, Tatsuki Oda¹ (1. Grad. Sch. Nat. Sci. & Tech., Kanazawa Univ. (Japan), 2. Phys. Discipline, Khulana Univ. (Bangladesh), 3. Dep. Solid State Eng., Czech Tech. Univ. (Czech Republic))

[PS2-16]Temperature Induced Electronic Structure and Phonon Thermal Properties in Bilayer Silicene

*Sapta Sindhu Paul Chowdhury¹, Santosh Mogurampelly¹ (1. Indian Institute of Technology Jodhpur (India))

[PS2-17]Phase-field simulation of mechanical transition of polar skyrmion lattice

*Kohta Kasai¹, Toya Itano¹, Susumu Minami¹, Takahiro Shimada¹ (1. Kyoto Univercity (Japan))

[PS2-18]Oxygen evolution reaction at the rhombohedral boron mono-sulfide electrode/alkaline medium interface

*Satoshi Hagiwara¹, Fumiaki Kuroda¹, Linghui Li², Takahiro Kondo^2,3, Minoru Otani^1,2 (1. Center for Computational Sciences, University of Tsukuba (Japan), 2. Department of Materials Science and Tsukuba Research Center for Energy Materials Science, Institute of Pure and Applied Sciences and R&D Center for Zero CO2 Emission with Functional (Japan), 3. Advanced Institute for Materials Research, Tohoku University (Japan))

[PS2-19]On the Stability and Electron-phonon Coupling of Hole-doped KMgH3

*Shaocong Lu¹, Ryosuke Akashi², Shinji Tsuneyuki¹ (1. Department of Physics, Graduate School of Science, The University of Tokyo (Japan), 2. National Institutes for Quantum Science and Technology (Japan))

[PS2-20]Electronic Structure Calculations Using Machine Learning

*Yunjae Kim¹, Wonseok Ryu¹, Suklyun Hong¹ (1. Sejong University (Korea))

[PS2-22]Large-scale simulation of L1₀ FePt nanoparticles toward magnetic recording

*Hung Ba Tran^1,2, Yu-ichiro Matsushita^1,2,3 (1. Tokyo Tech. (Japan), 2. Quemix Inc. (Japan), 3. National Institutes for Quantum Science and Technology (Japan))

[PS2-23]Development of a combined simulation of SC-AFIR and ESM-RISM methods toward the systematic exploration of elementary reactions and the construction of a reaction path network at solid-liquid interface

*Taisuke Hasegawa¹, Satoshi Hagiwara¹, Minoru Otani¹, Satoshi Maeda² (1. University of Tsukuba (Japan), 2. Hokkaido University (Japan))

[PS2-24]Temperature-driven Graphitization of the Diamond (111) and (100) Surfaces Studied by Graph Neural Network Molecular Dynamics

*John Isaac Guinto Enriquez¹, Harry Handoko Halim¹, Takahiro Yamasaki², Masato Michiuchi², Kouji Inagaki¹, Masaaki Geshi³, Ikutaro Hamada¹, Yoshitada Morikawa^1,4 (1. Graduate School of Engineering, Osaka University (Japan), 2. Advanced Materials Laboratory, Sumitomo Electric Industries Ltd (Japan), 3. R^3 Institute for Newly-Emerging Science Design, Osaka University (Japan), 4. Research Center for Ultra-Precision Science and Technology, Graduate School of Engineering, Osaka University (Japan))

[PS2-25]Three-Dimensional Molecular Dynamics Method for Vortex Dynamics in a Superconductor with Columnar Defects

*Masaru Kato¹ (1. Department of Physics and Electronics, Osaka Metropolitan University (Japan))

[PS2-27]Vortex solution to Bose-Einstein condensation with the iterative method

*Songvudhi Chimchinda¹, Sarun Phibanchon², Nupan Kheaomaingam³ (1. Department of Physics, Faculty of Science, Burapha University (Thailand), 2. Faculty of Education, Burapha University (Thailand), 3. Department of Physics, Faculty of Science, Burapha University (Thailand))

[PS2-28]Semiempirical Non-Local Pseudopotential Method for Low-dimensional Materials

*Raj Kumar Paudel^1,2,5, Chung Yuan Ren⁴, Yia Chung Chang^2,3 (1. National Central University (Taiwan), 2. Research Center for Applied Sciences (Taiwan), 3. National Cheng-Kung University (Taiwan), 4. National Kaohsiung Normal University (Taiwan), 5. Molecular Science and Technology, Taiwan International Graduate Program, Academia Sinica (Taiwan))

[PS2-30]Cutoff-induced layer structure of dipolar spins on the spin-ice lattice

*Yoshiteru Yonetani¹ (1. National Institutes for Quantum Science and Technology (Japan))

[PS2-31]Karman Vortex around Obstacle with Active Brownian Particles

*Koji Iwase¹, Masaharu Isobe¹ (1. Nagoya Institute of Technology (Japan))

[PS2-32]Simple and efficient method on free volume estimation in dense poly-disperse hard disk systems

*Daigo Mugita¹, Kazuyoshi Souno¹, Hiromasa Koyoma¹, Masaharu Isobe¹ (1. Nagoya Institute of Technology (Japan))

[PS2-34]Estimating miscibility of the long-chain polymer mixtures using all-atom model

*Kazuo Yamada^1,2, Nobuyuki Matubayasi² (1. Fukui Institute For Fundamental Chemistry, Kyoto University (Japan), 2. Osaka University (Japan))

[PS2-35]Spatiotemporal Dynamics and Directed Transport of Atomic Layers in an Interfacial System

*Takaaki Kawaguchi¹ (1. Department of Physics, Toho University (Japan))

[PS2-36]Elliptical chase and escape

*Sota Yoshihara¹ (1. Graduate School of Mathematics, Nagoya University (Japan))

[PS2-37]Bond-Orientational Order Parameters for Classifying Solid-like Clusters in a Lennard-Jones System

*Ten-Ming Wu¹, Sheng-Yuan Zeng¹, Chih-Hao Hsu¹ (1. Institute of Physics, National Yang Ming Chiao Tung University (Taiwan))

[PS2-38]Structure and superfluidity of helium clusters doped with an OCS molecule

*Koki Kyushi¹, Sinichi Miura¹ (1. Kanazawa University (Japan))

[PS2-39]An efficient replica exchange method based on the gaussian ensemble for first-order transitions

*Syunsuke Daimon¹, Shinichi Miura¹ (1. Kanazawa university (Japan))

[PS2-40]Analysis of Hydrogen Bonds inside Reverse Micelles
by Molecular Dynamics Simulations

*Yuri Ono¹, Tomoko Mizuguchi, Mao Fukuyama (1. Kyoto Institute of Technology (Japan))

[PS2-41]Thermal conduction of tripod molecular thin films with molecular rotators

*Naoyuki Karasawa¹, Tetsuya Morishita¹, Eiji Tsuchida¹, Hisao Nakamura¹ (1. National Institute of Advanced Industrial Science and Technology (AIST) (Japan))

[PS2-42]Vapor-Liquid equilibrium of d-limonene/1-pentanol solution using molecular dynamics simulation

*Suguru Nishikawa¹, Hitoshi Washizu¹ (1. Graduate school of Information Science, University of Hyogo (Japan))

[PS2-43]Large Scale Molecular Dynamics Simulations of Impinging Droplets on Solid Surfaces

*Takahiro Koishi¹, Kenji Yasuoka², Xiao Cheng Zeng³ (1. University of Fukui (Japan), 2. Keio University (Japan), 3. City University of Hong Kong (China))

[PS2-48]Molecular theory of diffusion based on the energy representation: Application to solvation dynamics

*Kazuya Okita¹, Kento Kasahara¹, Nobuyuki Matubayasi¹ (1. Osaka University (Japan))

[PS2-49]Development of Coarse-Grained Models in Molecular Dynamics Software GENESIS and Applications to Biomolecular Condensation Simulations

*Cheng Tan¹, Yuji Sugita^1,2,3 (1. RIKEN Center for Computational Science (Japan), 2. RIKEN Cluster for Pioneering Research (Japan), 3. RIKEN Center for Biosystems Dynamics Research (Japan))

[PS2-50]Computational study of the Ring Opening Process in Nonenzymatic Peptide Bond Cleavage at the C-Terminal Side of an Asparagine Residue

*Koichi Kato^1,2,3, Tomoki Nakayoshi^3,4, Eiji Kurimoto³, Akifumi Oda^3,5, Yoshinobu Ishikawa¹ (1. Facul. of Pharm. Sci., Shonan Univ. of Med. Sci. (Japan), 2. Coll. of pharm., Kinjo Gakuin Univ. (Japan), 3. Facul. of Pharm., Meijo Univ. (Japan), 4. Grad. Inf. Sci., Hiroshima City Univ. (Japan), 5. Inst. Prot. Res., Osaka Univ. (Japan))

[PS2-51]Molecular dynamics of autophagosomal lipid transfer Atg2

*Yuji Sakai^1,2, Nobuo N Noda³, Yuji Sugita⁴ (1. Kyoto Univ. (Japan), 2. Univ. Tokyo (Japan), 3. Hokkaido Univ. (Japan), 4. RIKEN (Japan))

[PS2-52]Allosteric regulation of β-reaction stage I in tryptophan synthase

*Shingo Ito¹, Kiyoshi Yagi¹, Yuji Sugita¹ (1. RIKEN, Cluster for Pioneering Research, Theoretical Molecular Science Laboratory (Japan))

[PS2-53]Analysis of structural changes of multi-chain/multi-domain proteins by coarse-grained description.

*Chigusa Kobayashi¹, Hisham M Dokainish², Suyong Re³, Takaharu Mori², Jaewoon Jung^1,2, Yuji Sugita^1,2,4 (1. RIKEN Center for Computational Science (Japan), 2. RIKEN Cluster for Pioneering Research (Japan), 3. National Institutes of Biomedical Innovation, Health and Nutrition (Japan), 4. RIKEN Center for Biosystems Dynamics Research (Japan))

[PS2-54]Energy Spectrum Analysis on a Red Blood Cell Model

*Tetsuya Yamamoto¹, Hiroshi Watanabe¹ (1. Graduate School of Science and Technology, Keio University (Japan))

[PS2-55]Coarse-grained molecular dynamics study of transmembrane proteins in multicomponent lipid bilayers

*Diego Ugarte¹, Shoji Takada², Yuji Sugita^1,3,4 (1. RIKEN CCS (Japan), 2. Kyoto Univ. (Japan), 3. RIKEN CPR (Japan), 4. RIKEN BDR (Japan))

[PS2-56]Prediction of hydration structures of protein by convolutional neural network optimized using experimental data

*Kochi Sato^1,2, Mao Oide^3,4, Masayoshi Nakasako^1,2 (1. Keio Univ. (Japan), 2. RIKEN RSC (Japan), 3. RIKEN CPR (Japan), 4. JST PRESTO (Japan))

[PS2-57]Molecular Dynamics Simulations of Computationally Predicted Protein-Ligand Complex Structures to Evaluate the Structural Validity

Koichi Kato^1,2,3, Tomoki Nakayoshi^1,4, Yuna Moritsuki¹, Saki Makino¹, Eiji Kurimoto¹, *Akifumi Oda^1,5 (1. Meijo Univ. (Japan), 2. Shonan Univ. Med. Sci. (Japan), 3. Kinjo Gakuin Univ. (Japan), 4. Hiroshima City Univ. (Japan), 5. Osaka Univ. (Japan))

[PS2-58]Potential energy landscape and thermodynamic folding transition of a miniprotein

*yuuto yamada¹, Daisuke Suzuki¹, Shinichi Miura¹ (1. Kanazawa University (Japan))

[PS2-59]Machine-learned constitutive relations of entangled polymer melts for multi-scale flow simulations

*Souta Miyamoto¹, John J Molina¹, Takashi Taniguchi¹ (1. Kyoto Univ. (Japan))

[PS2-60]Molecular-dynamics study on the stress-thermal rule of polymeric liquids under shear flows

*Kotaro Oda¹, Shugo Yasuda¹ (1. Graduate School of Information Science, University of Hyogo (Japan))

[PS2-61]Development of a coarse-grained model for nucleotide-binding protein

*Kazutomo Kawaguchi¹, Hidemi Nagao¹ (1. Kanazawa University (Japan))

[PS2-63]Estimation of Free-Energy Landscape by Molecular Simulations using Interpolation with Higher Order Terms

*Shohei Toyama^1,2, Yuji Higuchi³, Hiroshi Noguchi² (1. Dept. of Phys., Univ. Tokyo., Japan (Japan), 2. ISSP., Univ. Tokyo., Japan (Japan), 3. RIIT., Kyushu Univ., Japan (Japan))

[PS2-65]Structural changes due to hydrogen bonds in the LIM2 domain of FHL1

*Motokuni Nakajima¹, Yoh Noguchi^1,3, Hironao Yamada^2,3, Ryota Morikawa¹, masako Takasu¹, Yukiko K. Hayashi⁴ (1. Tokyo University of Pharmacy and Life Sciences (Japan), 2. Sch. of Pharm., Tokyo Univ. of Pharm. and Life Sci. (Japan), 3. The Institute of Statistical Mathematics (Japan), 4. TokyoMed. Univ. (Japan))

[PS2-66]Effect of surfactants on the elasticity of the liquid–liquid interface

*Shunta Kikuchi¹, Hiroshi Watanabe¹ (1. Keio University (Japan))

[PS2-67]Structure analysis of fhl1 protein from zebrafish using MD simulation.

Mami Sekine¹, Motokuni Nakajima¹, *Yoh Noguchi^1,2, Ryota Morikawa¹, Masako Takasu¹, Genri Kawahara³, Yukiko K. Hayashi³ (1. School of Life Sciences, Tokyo University of Pharmacy and Life Sciences (Japan), 2. The Institute of Statistical Mathematics (Japan), 3. Department of Medicine, Tokyo Medical University (Japan))

[PS2-68]All-atom molecular dynamics simulations of Taste receptor type 1

*Kazuma Okada¹, Yasuhiro Matsunaga¹ (1. Saitama Univ. (Japan))

[PS2-70]Revealing the hidden dynamics of confined water in acrylate polymers: Insights from hydrogen-bond lifetime analysis

*Kokoro Shikata¹, Takuma Kikutsuji¹, Nobuhiro Yasoshima^1,2, Kang Kim¹, Nobuyuki Matubayasi¹ (1. Graduate School of Engineering Science, Osaka University (Japan), 2. Department of Information and Computer Engineering, National Institute of Technology, Toyota College (Japan))

[PS2-71]Concentration dependency analysis of fibril-forming peptides in the initial stage of the aggregation process

*Yoshitake Sakae^1,2, Takeshi Kawasaki², Yuko Okamoto² (1. RIST (Japan), 2. Nagoya Univ. (Japan))

[PS2-73]Free energetics of the ATP effects on peptide aggregation and dissolution by all-atom molecular dynamics

*Tuan Minh Do^1,2, Dominik Horinek², Nobuyuki Matubayasi¹ (1. Osaka University (Japan), 2. University of Regensburg (Germany))

[PS2-75]Computational Insight into Dynamics and Intermediate State in OX2R Activation

*Shun Yokoi^1,2, Ayori Mitsutake¹ (1. Meiji University (Japan), 2. Stanford University (United States of America))

[PS2-76]Dimer formation process of amyloid-β peptides studied by the generalized-ensemble algorithms

*Satoru G. Itoh^1,2,3, Hisashi Okumura^1,2,3 (1. IMS (Japan), 2. ExCELLS (Japan), 3. SOKENDAI (Japan))

[PS2-77]Investigating Protein Dynamics and Stability using Relaxation Mode Analysis and Reference Interaction Site Model Theory

*Ayori Mitsutake¹ (1. Meiji University (Japan))

[PS2-78]3D structural determination of biomolecules using spatial correlations in X-ray free-electron laser data

*Wenyang Zhao¹, Osamu Miyashita¹, Miki Nakano¹, Florence Tama^1,2,3 (1. RIKEN Center for Computational Science (Japan), 2. Institute of Transformative Bio-Molecules, Nagoya University (Japan), 3. Department of Physics, Nagoya University (Japan))

[PS2-79]Proton conduction mechanism in water channels of ATP synthase studied by molecular dynamics simulation

*Yukinari Kamiyama¹, Dan Parkin², Junichi Ono², Yoshifumi Nishimura², Hiromi Nakai^1,2, Mitsunori Takano^1,2 (1. Grad. Sch. Adv. Sci. & Eng., Waseda Univ. (Japan), 2. Waseda Res. Inst. for Sci. & Eng. (Japan))

[PS2-80]Morphing method that introduced the time scale and its application to the dynamics of monoamine oxidase B (MAO-B).

*Shota Shimogochi¹, Yoshitaka Tadokoro¹, Ryota Kiyooka¹, Naoyuki Miyashita^1,2 (1. Grad. sch. BOST, KINDAI Univ. (Japan), 2. BOST, KINDAI Univ. (Japan))

[PS2-81]Coarse-grained model molecular dynamics simulations of gamma-secretase and APP / Notch system.

*Naoyuki Miyashita^1,2, Chika Minami² (1. Dept. Comp. Sys. Biol., BOST, KINDAI Univ. (Japan), 2. Dept. Biol. Sys. Eng., Grad. Sch. BOST, KNDAI Univ. (Japan))

[PS2-82]An effect of antigen-antibody interaction upon inherent dynamics of SARS-CoV-2 spike

*Mao Oide¹, Yuji Sugita^1,2,3 (1. Cluster for Pioneering Research, RIKEN (Japan), 2. Center for Computational Science, RIKEN (Japan), 3. Center for Biosystems Dynamics Research, RIKEN (Japan))

[PS2-83]Automated Density Extraction of Isomorphous Difference map and Occupancy-estimation for Conformer Fitting

*Sriram srinivasa raghavan¹, Florence Tama^1,2,3, Osamu Miyashita¹ (1. RIKEN Center for Computational Science (Japan), 2. Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, (Japan), 3. Department of Physics, Graduate School of Science, Nagoya University (Japan))

[PS2-84]The rational design of 2-(1H-benzo[d]imidazol-2-yl)-2-cyanovinyl derivatives as potent GyrB inhibitors against tuberculosis based on fragment molecular orbital calculations

*Naruedon Phusi¹, Yoshinobu Nagura², Bundit Kamsri¹, Bongkochawan Pakamwong¹, Paptawan Thongdee¹, Pharit Kamsri³, Auradee Punkvang³, Khomson Suttisintong⁴, Noriyuki Kurita², Pornpan Pungpo¹ (1. Ubon Ratchathani University (Thailand), 2. Toyohashi University of Technology (Japan), 3. Nakhon Phanom University (Thailand), 4. Thailand Science Park (Thailand))

[PS2-85]Concentration dependence of protein diffusion coefficients in crowded systems studied by Brownian dynamics simulations

*Yoshiharu Mori¹, Shigenori Tanaka¹ (1. Kobe Univ. (Japan))

[PS2-86]Insight into specific interactions of Pyrrolamide Derivatives as highly potential potent GyrB inhibitors using fragment molecular orbital (FMO) calculations

*Paptawan - Thongdee¹, Bongkochawan - Pakamwong¹, Bundit - Kamsri¹, Naruedon - Phusi¹, Jidapa - Sangswan², Pharit - Kamsri³, Auradee - Punkvang³, Khomson - Suttisintong⁴, Kyohei - Imai⁵, Noriyuki - Kurita⁵, Pornpan - Pungpo¹ (1. Department of Chemistry, Ubon Ratchathani Univ. (Thailand), 2. Department of Biological Science, Ubon Ratchathani Univ. (Thailand), 3. Division of Chemistry, Nakhon Phanom Univ. (Thailand), 4. National Nanotechnology Center, NSTDA (Thailand), 5. Department of Computer Science and Engineering, TUT (Japan))

[PS2-87]A Gradient-Based Approach for Optimizing Molecular Structures using Atomic Force Microscopy Images and Normal Mode Analysis

*Xuan Wu¹, Osamu Miyashita², Florence Tama^1,2,3 (1. Nagoya University (Japan), 2. RIKEN Center for Computational Science (Japan), 3. Institute of Transformative Bio-Molecules, Nagoya University (Japan))