野口研究室論文

野口研の論文リスト

Review article

H. Noguchi
Membrane Simulation Models from Nanometer to Micrometer Scale
J. Phys. Soc. Jpn. 78, 041007/1-9 (2009). https://doi.org/10.1143/JPSJ.78.041007
free download

D. A. Fedosov, H. Noguchi, and G. Gompper
Multiscale modeling of blood flow: from single cells to blood rheology
Biomech. Model. Mechanobiol. 13, 239-258 (2014).
https://doi.org/10.1007/s10237-013-0497-9

H. Noguchi
Binding of Curvature-Inducing Proteins onto Biomembranes
Int. J. Mod. Phys. B 36, 2230002/1-29 (2022).
https://doi.org/10.1142/S021797922230002X
(arXiv:2203.14514).

H. Noguchi
Nonequilibrium Membrane Dynamics Induced by Active Protein Interactions and Chemical Reactions: A Review
ChemSystemsChem DOI:10.1002/syst.202400042
https://doi.org/10.1002/syst.202400042
(arXiv:2407.15371).

Original papers、和文解説

2024

H. Noguchi,
Curvature sensing of curvature-inducing proteins with internal structure
Phys. Rev. E 109, 024403/1-10 (2024).
https://doi.org/10.1103/PhysRevE.109.024403

H. Noguchi, F. van Wijland, and J.-B. Fournier,
Cycling and spiral-wave modes in an active cyclic Potts model
J. Chem. Phys. 161, 025101/1-7 (2024).
https://doi.org/10.1063/5.0221050

H. Noguchi and J.-B. Fournier,
Spatiotemporal patterns in the active cyclic Potts model
New J. Phys.26, 093043 (2024).
https://doi.org/10.1088/1367-2630/ad7dac

A. S. Sorokina, R. A. Gumerov, H. Noguchi, and I. I. Potemkin,
Computer Simulations of Responsive Nanogels at Lipid Membrane
Macromol. Rapid Commun. DOI:10.1002/marc.202400406
https://doi.org/10.1002/marc.202400406

H. Noguchi and Jens Elgeti,
Growth and shrinkage of tissue sheets on substrates: buds, buckles, and pores
New J. Phys. 26, 103027 (2024).
https://doi.org/10.1088/1367-2630/ad86e8

H. Noguchi,
Spatiotemporal Patterns in Active Four-State Potts Models
arXiv:2409.13962

H. Noguchi,
Spatiotemporal pattern formation of membranes induced by surface molecular binding/unbinding
arXiv:2410.23635

2023

H. Noguchi,
Membrane domain formation induced by binding/unbinding of curvature-inducing molecules on both membrane surfaces
Soft Matter 19, 679-688 (2023).
https://doi.org/10.1039/d2sm01536f

H. Noguchi,
Disappearance, division, and route change of excitable reaction-diffusion waves in deformable membranes
Sci. Rep. 13, 6207 (2023).
https://doi.org/10.1038/s41598-023-33376-9

H. Noguchi, N. Walani, and M. Arroyo,
Estimation of anisotropic bending rigidities and spontaneous curvatures of crescent curvature-inducing proteins from tethered-vesicle experimental data
Soft Matter, 19, 5300-5310 (2023).
https://doi.org/10.1039/D3SM00340J

M. Kobayashi, H. Noguchi, G. Sato, C. Watanabe, K. Fujiwara, and M. Yanagisawa,
Phase-separated giant liposomes for stable elevation of α-hemolysin concentration in lipid membranes
Langmuir 39, 11481-11489 (2023).
https://doi.org/10.1021/acs.langmuir.3c02019

2022

Y. Asano, H. Watanabe, and H. Noguchi,
Effects of vapor-liquid phase transitions on soundwave propagation: A molecular dynamics study
Phys. Rev. Fluids 7, 064302/1-21 (2022).
https://doi.org/10.1103/PhysRevFluids.7.064302

Rie Wakabayashi, Rino Imatani, Mutsuhiro Katsuya, Yuji Higuchi, Hiroshi Noguchi, Noriho Kamiya, and Masahiro Goto,
Hydrophobic immiscibility controls self-sorting or co-assembly of peptide amphiphiles
Chem. Commun. 58, 585-588 (2022).
https://doi.org/10.1039/D1CC05560G

H. Noguchi, C. Tozzi, and M. Arroyo,
Binding of anisotropic curvature-inducing proteins onto membrane tubes
Soft Matter 18, 3384-3394 (2022).
https://doi.org/10.1039/D2SM00274D

N. Tamemoto and H. Noguchi,
Excitable reaction-diffusion waves of curvature-inducing proteins on deformable membrane tubes
Phys. Rev. E 106, 024403 (2022).
https://doi.org/10.1103/PhysRevE.106.024403

K. Fukushima, K. Matsuzaki, M. Oji, Y. Higuchi, G. Watanabe, Y. Suzuki, M. Kikuchi, N. Fujimura, N. Shimokawa, H. Ito, T. Kato, S. Kawaguchi and M. Tanaka,
Anisotropic, degradable polymer assemblies driven by a rigid hydrogen-bonding motif that induce shape-specific cell responses
Macromolecules 55, 15-25 (2022).
https://doi.org/10.1021/acs.macromol.1c01894

H. Noguchi,
Membrane shape deformation induced by curvature-inducing proteins consisting of chiral crescent binding and intrinsically disordered domains
J. Chem. Phys. 157, 034901/1-8 (2022).
https://doi.org/10.1063/5.0098249
Featured in Scilight 2022, 381108 (2022); https://doi.org/10.1063/10.0013779

K. Kawaguchi, H. Nagao, H. Shindou, and H. Noguchi,
Conformations of three types of ultra-long-chain fatty acids in multi-component lipid bilayers
J. Phys. Chem. B 126, 9316-9324 (2022).
https://doi.org/10.1021/acs.jpcb.2c06189
Selected for Cover

野口博司，爲本尚樹,
曲率誘導タンパク質の反応拡散による生体膜のパターン形成
生物物理 62, 338-340 (2022).
https://doi.org/10.2142/biophys.62.338

2021

H. Noguchi and O. Pierre-Louis,
Undulation of a moving fluid membrane pushed by filament growth
Sci. Rep. 11, 7985 (2021).
https://doi.org/10.1038/s41598-021-87073-6

Q. Goutaland, F. van Wijland, J.-B. Fournier, and H. Noguchi,
Binding of thermalized and active membrane curvature-inducing proteins
Soft Matter 17, 5560-5573 (2021).
https://doi.org/10.1039/d1sm00027f.

Y. Higuchi,
Coarse-grained molecular dynamics simulations of void generation and growth processes in the fracture of the lamellar structure of polyethylene
Phys. Rev. E 103, 042502/1-6 (2021).
https://doi.org/10.1103/PhysRevE.103.042502

Y. Higuchi, Y. Asano, T. Kuwahara, and M. Hishida,
Rotational Dynamics of Water at the Phospholipid Bilayer Depending on the Head Groups Studied by Molecular Dynamics Simulations
Langmuir 37, 5329-5338 (2021).
https://doi.org/10.1021/acs.langmuir.1c00417

N. Tamemoto and H. Noguchi,
Reaction-Diffusion Waves Coupled with Membrane Curvature
Soft Matter 17, 6589 - 6596 (2021).
https://doi.org/10.1039/d1sm00540e

H. Noguchi,
Vesicle budding induced by binding of curvature-inducing proteins
Phys. Rev. E. 104, 014410/1-13 (2021).
https://doi.org/10.1103/PhysRevE.104.014410

Y. Asano, H. Watanabe, and H. Noguchi,
Effects of polymers on the cavitating flow around a cylinder: A Large-scale molecular dynamics analysis
J. Chem. Phys. 155, 014905/1-9 (2021).
https://doi.org/10.1063/5.0056988

H. Noguchi,
Binding of curvature-inducing proteins onto tethered vesicles
Soft Matter 17, 10469-10478 (2021) .
https://doi.org/10.1039/d1sm01360b

2020

Y. Asano, H. Watanabe, and H. Noguchi,
Effects of Cavitation on Karman Vortex Behind Circular-Cylinder Arrays: A Molecular Dynamics Study
J. Chem. Phys. 152, 034501 (2020).
https://doi.org/10.1063/1.5138212

N.Tamemoto, M. Akishiba, K. Sakamoto, K. Kawano, H. Noguchi, S. Futaki,
Rational Design Principles of Attenuated Cationic Lytic Peptides for Intracellular Delivery of Biomacromolecules
Mol. Pharmaceutics 17, 2175-2185 (2020).
https://doi.org/10.1021/acs.molpharmaceut.0c00312

N. Tamemoto and H. Noguchi,
Pattern Formation in Reaction-Diffusion System on Membrane with Mechanochemical Feedback
Sci. Rep. 10, 19582/1-10 (2020).
https://doi.org/10.1038/s41598-020-76695-x

Y. Asano, H. Watanabe, and H. Noguchi,
Molecular Dynamics Simulation of Soundwave Propagation in a Simple Fluid
J. Chem. Phys. 153, 124504/1-8 (2020).
https://doi.org/10.1063/5.0024150

K. Kawaguchi, K. M. Nakagawa, S. Nakagawa, H. Shindou, H. Nagao, and H. Noguchi,
Conformation of ultra-long-chain fatty acid in lipid bilayer: Molecular dynamics study
J. Chem. Phys. 153, 165101/1-7 (2020).
https://doi.org/10.1063/5.0026030

H. Noguchi,
Virtual bending method to calculate bending rigidity, saddle-splay modulus, and spontaneous curvature of thin fluid membranes
Phys. Rev. E 102, 053315/1-10 (2020).
https://doi.org/10.1103/PhysRevE.102.053315

H. Tsuchiya, G. Sinawang, T.-A. Asoh, M. Osaki, Y. Ikemoto, Y. Higuchi, H. Yamaguchi, A. Harada, H. Uyama and Y. Takashima,
Supramolecular Biocomposite Hydrogels Formed by Cellulose and Host-Guest Polymers Assisted by Calcium Ion Complexes
Biomacromolecules21, 3936-3944 (2020).
https://doi.org/10.1021/acs.biomac.0c01095

浅野優太, 渡辺宙志, 野口博司
分子動力学計算による複雑流体中のカルマン渦の解析
分子シミュレーション研究会会誌 “アンサンブル” 22(2), 157-162 (2020).

樋口祐次
高分子材料の破壊に関する粗視化分子シミュレーション
分子シミュレーション研究会会誌 “アンサンブル” 22(3), 216-221 (2020).

2019

H. Watanabe, and K. M. Nakagawa,
SIMD Vectorization for the Lennard-Jones Potential with AVX2 and AVX-512 instructions
Computer Physics Communications 237, 1-7 (2019).
https://doi.org/10.1016/j.cpc.2018.10.028

B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl,
Limiting shapes of confined lipid vesicles
Soft Matter 15, 602-614 (2019).
https://doi.org/10.1039/c8sm01956h.

H. Noguchi
Angular-momentum conservation in discretization of Navier-Stokes equation for viscous fluids
Physical Review E 99, 023307 (2019).
https://doi.org/10.1103/PhysRevE.99.023307

Y. Asano, H. Watanabe, and H. Noguchi,
Finite-Size Effects on Karman Vortex in Molecular Dynamics Simulation
J. Phys. Soc. Jpn. 88, 075003 (2019).
https://doi.org/10.7566/JPSJ.88.075003

H. Noguchi
Shape transition from elliptical to cylindrical membrane tubes induced by chiral crescent-shaped protein rods
Sci. Rep. 9, 11721 (2019).
https://doi.org/10.1038/s41598-019-48102-7

H. Noguchi
Cup-to-vesicle transition of a fluid membrane with spontaneous curvature
J. Chem. Phys. 51, 094903 (2019).
https://doi.org/10.1063/1.5113646

H. Noguchi
Detachment of fluid membrane from substrate and vesiculation
Soft Matter, 15, 8741 (2019).
https://doi.org/10.1039/c9sm01622h

M. I. Mahmood, H. Noguchi, and K. Okazaki
Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations
Sci. Rep. 9, 14557 (2019).
https://doi.org/10.1038/s41598-019-51202-z

N. Shimokawa, H. Ito, and Y. Higuchi
Coarse-grained molecular dynamics simulation for uptake of nanoparticles into a charged lipid vesicle dominated by electrostatic interactions
Phys. Rev. E 100, 012407 (2019).
https://doi.org/10.1103/PhysRevE.100.012407

Y. Higuchi
Stress Transmitters at the Molecular Level in the Deformation and Fracture Processes of the Lamellar Structure of Polyethylene via Coarse-Grained Molecular Dynamics Simulations
Macromolecules 52, 6201 (2019).
https://doi.org/10.1021/acs.macromol.9b00636

2018

K. M. Nakagawa and H. Noguchi,
Bilayer sheet protrusions and budding from bilayer membranes induced by hydrolysis and condensation reactions
Soft Matter 14, 1397-1407 (2018), DOI: 10.1039/C7SM02326J.

Y. Asano, H. Watanabe, and H. Noguchi,
Polymer effects on Karman Vortex: Molecular Dynamics Study
Journal of Chemical Physics 148, 144901/1-9 (2018),
DOI: 10.1063/1.5024010

Y. Higuchi, K. Saito, T. Sakai, J. P. Gong and M. Kubo,
Fracture Process of Double-Network Gels by Coarse-Grained Molecular Dynamics Simulation
Macromolecules 51, 3075 (2018),
DOI: 10.1021/acs.macromol.8b00124

Y. Higuchi,
Fracture processes of crystalline polymers using coarse-grained molecular dynamics simulations
Polym. J. 50, 579 (2018), DOI: 10.1038/s41428-018-0067-1

中川恒
短距離古典分子動力学シミュレーションコードのGPGPU化（２）
分子シミュレーション研究会会誌 “アンサンブル” 20(1), 40-45 (2018).

2017

H. Noguchi and J.-B. Fournier
Membrane structure formation induced by two types of banana-shaped proteins
Soft Matter 13, 4099-4111 (2017), DOI: 10.1039/C7SM00305F.

H. Noguchi
Acceleration and suppression of banana-shaped-protein-induced tubulation by addition of small membrane inclusions of isotropic spontaneous curvatures
Soft Matter 13, 7771-7779 (2017), DOI: 10.1039/C7SM01375B.

H. Shindou, H. Koso, J. Sasaki, H. Nakanishi, H. Sagara, K. M. Nakagawa, Y. Takahashi, D. Hishikawa, Y. Iizuka-Hishikawa, F. Tokumasu, H. Noguchi, S. Watanabe, T. Sasaki, and T. Shimizu
Docosahexaenoic acid preserves visual function by maintaining correct disc morphology in retinal photoreceptor cells
J. Bio. Chem. 292, 12054-12064 (2017)
DOI: 10.1074/jbc.M117.790568

中川恒
分子シミュレーションにおける三体ポテンシャルを含んだ系の局所応力テンソルの非一意性
分子シミュレーション研究会会誌 “アンサンブル” 19(1), 69 (2017).

中川恒
短距離古典分子動力学シミュレーションコードのGPGPU化（１）
分子シミュレーション研究会会誌 “アンサンブル” 19(4), 267-273 (2017).

2016

H. Noguchi,
Membrane tubule formation by banana-shaped proteins with or without transient network structure
Scientific Reports 6, 20935/1-8 (2016).

H. Shiba, H. Noguchi, and J.-B. Fournier,
Monte Carlo study of the frame, fluctuation and internal tensions of fluctuating membranes with fixed area
Soft Matter 12, 2373-2380 (2016).

J. J. Molina, K. Otomura, H. Shiba, H. Kobayashi, M. Sano, and R. Yamamoto,
Rheological evaluation of colloidal dispersions using smoothed profile method - formulation and applications
Journal of Fluid Mechanics 792, 590-619 (2016).

H. Noguchi,
Shape deformation of lipid membranes by banana-shaped protein rods: Comparison with isotropic inclusions and membrane rupture
Physical Review E 93, 052404/1-10 (2016).

H. Noguchi,
Construction of nuclear envelope shape by a high-genus vesicle with pore-size constraint
Biophysical Journal 111, 824-831 (2016).

K. M. Nakagawa and H. Noguchi,
Nonuniqueness of local stress of three-body potentials in molecular simulations
Physical Review E 94, 053304/1-11 (2016).

H. Shiba, Y. Yamada, T. Kawasaki, and K. Kim,
Unveiling Dimensionality Dependence of Glassy Dynamics: 2D Infinite Fluctuation Eclipses Inherent Structural Relaxation
Physical Review Letters 117, 245701/1-6 (2016).

2015

H. Noguchi, A. Sakashita, and M. Imai,
Shape transformations of toroidal vesicles
Soft Matter, 11, 193-201 (2015).

K. M. Nakagawa and H. Noguchi,
Morphological changes of amphiphilic molecular assemblies induced by chemical reaction
Soft Matter 11, 1403-1411 (2015).

H. Noguchi,
Formation of polyhedral vesicles and polygonal membrane tubes induced by banana-shaped proteins
Journal of Chemical Physics 143, 243109/1-7 (2015).

H. Noguchi,
Shape transitions of high-genus fluid vesicles
EPL 112, 58004/1-6 (2015).

2014

A. Sakashita, M. Imai, and H. Noguchi,
Morphological variation of lipid vesicle confined in spherical vesicle
Physical Review E 89, 040701(R)/1-4 (2014).

H. Noguchi,
Two- or three-step assembly of banana-shaped proteins coupled with shape transformation of lipid membranes
EPL 108, 48001/1-6 (2014).

M. Tarama, Y. Itino, A.M. Menzel, and T. Ohta,
Individual and collective dynamics of self-propelled soft particles
Eur. Phys. J. Special Topics 223, 121-139 (2014).

M. Tarama, A.M. Menzel, and H. Loewen,
A deformable microswimmer in a swirl: capturing and scattering dynamics
Physical Review E 90, 032907/1-11 (2014).

M. Tarama, P. Cremer, D. Y. Borin, S. Odenbach, H. Loewen, and A.M. Menzel,
Tunable dynamic response of magnetic gels: Impact of structural properties and magnetic fields
Physical Review E 90, 042311/1-9 (2014).

芝隼人, 野口博司
界面活性剤系の構造形成の粗視化分子シミュレーション
分子シミュレーション研究会会誌 “アンサンブル” 16(1), 59-65 (2014).

野口博司
粒子描像の流体力学計算手法 II
分子シミュレーション研究会会誌 “アンサンブル” 16(2), 118-121 (2014).

野口博司
粒子描像の流体力学計算手法 III
分子シミュレーション研究会会誌 “アンサンブル” 16(3), 211-214 (2014).

野口博司
粒子描像の流体力学計算手法 IV
分子シミュレーション研究会会誌 “アンサンブル” 16(4), 252-254 (2014).

2013

H. Noguchi,
Structure formation in binary mixtures of lipids and detergents: Self-assembly and vesicle division
Journal of Chemical Physics 138, 024907/1-9 (2013).

H. Shiba, H. Noguchi, and G. Gompper
Structure formation of surfactant membranes under shear flow
Journal of Chemical Physics 139, 014702/1-11 (2013).

H. Noguchi,
Entropy-driven aggregation in multilamellar membranes
EPL 102, 68001/1-6 (2013).

H. Wu, H. Shiba, and H. Noguchi,
Mechanical properties and microdomain separation of fluid membranes with anchored polymers
Soft Matter 9 , 9907-9917 (2013).

H. Shiba and T. Kawasaki,
Spatiotemporal heterogeneity of local free volumes in highly supercooled liquid
Journal of Chemical Physics 139, 184502/1-8 (2013).

M. Tarama, A. M. Menzel, B. ten Hagen, R. Wittkowski, T. Ohta, and H. Loewen,
Dynamics of a deformable active particle under shear flow
Journal of Chemical Physics 139, 104906/1-12 (2013).

M. Tarama, and T. Ohta,
Oscillatory motions of an active deformable particle
Physical Review E87, 062912/1-8 (2013).

野口博司
脂質膜の構造形成の粗視化シミュレーション
生物物理 53(1), 11-14 (2013).

野口博司
粒子描像の流体力学計算手法 I
分子シミュレーション研究会会誌 “アンサンブル” 15(4), 265-268 (2013).

2012

H. Noguchi,
Line tension of branching junctions of bilayer membranes
Soft Matter 8, 3146-3153 (2012).

H. Noguchi,
Structure formation in binary mixtures of surfactants: vesicle opening-up to bicelles and octopus-like micelles
Soft Matter 8, 8926-8935 (2012).

J. Liam McWhirter, H. Noguchi, and G. Gompper,
Ordering and arrangement of deformed red blood cells in flow through microcapillaries
New Journal of Physics 14, 085026/1-23 (2012).

H. Shiba, T. Kawasaki, and A. Onuki,
Relationship between bond-breakage correlations and four-point correlations in heterogeneous glassy dynamics: Configuration changes and vibration modes
Phys. Rev. E 86, 041501/1-14 (2012).

野口博司
生体膜の粗視化シミュレーション
分子シミュレーション研究会会誌 “アンサンブル” 14(1), 1-4 (2012).

2011

H. Noguchi,
Solvent-free coarse-grained lipid model for large-scale simulations
Journal of Chemical Physics 134, 055101/1-12 (2011).
Selected for Cover

H. Noguchi,
Anisotropic surface tension of buckled fluid membranes
Physical Review E 83, 061919/1-6 (2011).

H. Shiba and H. Noguchi,
Estimation of the bending rigidity and spontaneous curvature of fluid membranes in simulations
Physical Review E 84, 031926/1-13 (2011).

J. Liam McWhirter, H. Noguchi, and G. Gompper,
Deformation and clustering of red blood cells in microcapillary flows
Soft Matter 7, 10967-10977 (2011).

2010

H. Noguchi,
Dynamics of Fluid Vesicles in Oscillatory Shear Flow
J. Phys. Soc. Jpn. 79, 024801/1-10 (2010). free download

H. Noguchi, G. Gompper, L. Schmid, A. Wixforth, and T. Franke
Dynamics of Fluid Vesicles in Flow through Structured Microchannels
EPL 89, 28002/1-6 (2010).

H. Noguchi,
Dynamic modes of microcapsules in steady shear flow: Effects of bending and shear elasticities
Physical Review E 81, 056319/1-10 (2010).

H. Noguchi,
Dynamic modes of red blood cells in oscillatory shear flow
Physical Review E 81, 061920/1-9 (2010).

A. Khoshnood, H. Noguchi, and G. Gompper,
Lipid membranes with transmembrane proteins in shear flow
Journal of Chemical Physics 132, 025101/1-10 (2010).

H. Shiba and A. Onuki,
Plastic deformations in crystal, polycrystal, and glass in binary mixtures under shear: Collective yielding
Phys. Rev. E 81, 051501/1-15 (2010).

野口博司
赤血球、脂質小胞の流動ダイナミクス
日本物理学会誌 65(6), 429 (2010). （表紙の図）

2009

J. Liam McWhirter, H. Noguchi, and G. Gompper,
Flow-induced clustering and alignment of vesicles and red blood cells in microcapillaries
Proceeding of the National Academy of Sciences in USA 106, 6039-6043 (2009). Cover image of PNAS

H. Noguchi,
Swinging and synchronized rotations of red blood cells in simple shear flow
Physical Review E 80, 021902/1-8 (2009).

S. Messlinger, B. Schmidt, H. Noguchi, and G. Gompper,
Dynamical regimes and hydrodynamic lift of viscous vesicles under shear
Physical Review E 80, 011901/1-12 (2009).

Publication list of H. Noguchi

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野口研の論文リスト

Review article

Original papers、和文解説

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009