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
# Membrane with curvature-inducing Proteins
H. Noguchi,
Two- or three-step assembly of banana-shaped proteins coupled with shape transformation of lipid membranes
EPL 108, 48001/1-6 (2014).
H. Noguchi,
Formation of polyhedral vesicles and polygonal membrane tubes induced by banana-shaped proteins
J. Chem. Phys. 143, 243109/1-7 (2015).
H. Noguchi,
Membrane tubule formation by banana-shaped proteins with or without transient network structure
Sci. Rep. 6, 20935/1-8 (2016).
H. Noguchi,
Shape deformation of lipid membranes by banana-shaped protein rods: Comparison with isotropic inclusions and membrane rupture
Phys. Rev. E 93, 052404/1-10 (2016).
H. Noguchi and J.-B. Fournier
Membrane structure formation induced by two types of banana-shaped proteins
Soft Matter, 13, 4099 (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. Noguchi
Shape transition from elliptical to cylindrical membrane tubes induced by chiral crescent-shaped protein rods
Sci. Rep. 9, 11721 (2019) DOI: 10.1038/s41598-019-48102-7
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) DOI: 10.1038/s41598-019-51202-z
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
N. Tamemoto and H. Noguchi,
Reaction-Diffusion Waves Coupled with Membrane Curvature
Soft Matter 17, 6589 - 6596 (2021).
https://doi.org/10.1039/d1sm00540e
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.
H. Noguchi,
Vesicle budding induced by binding of curvature-inducing proteins
Phys. Rev. E. ,104,, 014410 (2021).
https://doi.org/10.1103/PhysRevE.104.014410
H. Noguchi,
Binding of curvature-inducing proteins onto tethered vesicles
Soft Matter 17, 10469-10478 (2021) .
https://doi.org/10.1039/d1sm01360b
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
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
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
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
# Cyclic Potts Models
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
H. Noguchi,
Spatiotemporal Patterns in Active Four-State Potts Models
arXiv:2409.13962
# Liposome Shapes
A. Sakashita, M. Imai, and H. Noguchi,
Confinement-induced shape transitions in multilamellar vesicles
Phys. Rev. E 89, 040701(R) (4 pages) (2014).
H. Noguchi, A. Sakashita, and M. Imai,
Shape transformations of toroidal vesicles
Soft Matter, 11, 193-201 (2015).
H. Noguchi,
Shape transitions of high-genus fluid vesicles
EPL 112, 58004/1-6 (2015).
H. Noguchi,
Construction of nuclear envelope shape by a high-genus vesicle with pore-size constraint
Biophys. J. 111, 824-831 (2016).
B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl,
Limiting shapes of confined lipid vesicles
Soft Matter 15, 602-614 (2019), DOI: 10.1039/c8sm01956h.
# MD of Fluid
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. Asano, H. Watanabe, and H. Noguchi,
Finite-Size Effects on Karman Vortex in Molecular Dynamics Simulation
J. Phys. Soc. Jpn. 88, 075003 (2019),
DOI: 10.7566/JPSJ.88.075003
Y. Asano, H. Watanabe, and H. Noguchi,
Effects of Cavitation on Karman Vortex Behind Circular-Cylinder Arrays
J. Chem. Phys. 152, 034501 (2020).
https://doi.org/10.1063/1.5138212
Y. Asano, H. Watanabe, and H. Noguchi,
Molecular Dynamics Simulation of Soundwave Propagation in a Simple Fluid
J. Chem. Phys. 153, 124504 (2020).
https://doi.org/10.1063/5.0024150
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 (2021).
https://doi.org/10.1063/5.0056988
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
# Hydrodynamic methods
H. Noguchi, N. Kikuchi, and G. Gompper,
Particle-based mesoscale hydrodynamic techniques
Europhysics Letters 78, 10005 (5 pages) (2007).
H. Noguchi and G. Gompper,
Transport coefficients of dissipative particle dynamics with finite time step
Europhysics Letters 79, 36002 (6 pages) (2007).
I. O. Goetze, H. Noguchi, and G. Gompper,
Relevance of angular momentum conservation in mesoscale hydrodynamics simulations
Physical Review E 76, 046705 (9 pages) (2007).
H. Noguchi and G. Gompper,
Transport coefficients of off-lattice mesoscale-hydrodynamics simulation techniques
Physical Review E 78, 016706 (12 pages) (2008).
H. Noguchi
Angular-momentum conservation in discretization of Navier-Stokes equation for viscous fluids
Physical Review E 99, 023307 (2019),
DOI: 10.1103/PhysRevE.99.023307.
# Local Stress Field and Virtual Deformation Methods
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. Noguchi,
Virtual bending method to calculate bending rigidity, saddle-splay modulus, and
spontaneous curvature of thin fluid membranes
Phys. Rev. E 102, 053315 (2020).
https://doi.org/10.1103/PhysRevE.102.053315
# Surface Tension and Membrane Undulation
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).
H. Noguchi,
Anisotropic surface tension of buckled fluid membranes
Physical Review E 83, 061919 (6 pages) (2011).
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
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
# Explicit-Solvent Molecular Simulaiton of Membrane
K. M. Nakagawa and H. Noguchi,
Morphological changes of amphiphilic molecular assemblies induced by chemical reaction
Soft Matter 11, 1403-1411 (2015).
A. Khoshnood, H. Noguchi, and G. Gompper,
Lipid membranes with transmembrane proteins in shear flow
Journal of Chemical Physics 132, 025101 (10 pages) (2010).
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
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.
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
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
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
# Meshless Membrane Model
H. Noguchi and G. Gompper,
meshless membrane model based on the moving least-squares method
Physical Review E 73, 021903 (12 pages) (2006).
H. Noguchi and G. Gompper,
Dynamics of vesicle self-assembly and dissolution
Journal of Chemical Physics 125, 164908 (13 pages) (2006).
H. Shiba and H. Noguchi,
Estimation of the bending rigidity and spontaneous curvature of fluid membranes in simulations
Physical Review E 84, 031926 (13 pages) (2011).
H. Shiba, H. Noguchi, and G. Gompper
Structure formation of surfactant membranes under shear flow
Journal of Chemical Physics 139, 014702 (11 pages) (2013).
H. Noguchi,
Entropy-driven aggregation in multilamellar membranes
EPL 102, 68001 (6 pages) (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. Noguchi
Cup-to-vesicle transition of a fluid membrane with spontaneous curvature
J. Chem. Phys. 51, 094903 (2019) DOI: 10.1063/1.5113646
H. Noguchi
Detachment of fluid membrane from substrate and vesiculation
Soft Matter, 15, 8741 (2019) DOI: 10.1039/c9sm01622h
Solvent-Free Molecular Model: membrane fusion and fission
H. Noguchi and M. Takasu,
Self-assembly of amphiphiles into vesicles: A Brownian dynamics simulation
Phys. Rev. E 64, 041913 (7 pages) (2001).
H. Noguchi and M. Takasu,
Fusion pathways of vesicles: A Brownian dynamics simulation
Journal of Chemical Physics 115, 9547-9551 (2001).
H. Noguchi and M. Takasu,
Adhesion of nanoparticles to vesicles: A Brownian dynamics simulation
Biophysical Journal 83, 299-308 (2002)
H. Noguchi and M. Takasu,
Structural changes of pulled vesicles: A Brownian dynamics simulation
Phys. Rev. E 65, 051907 (7 pages) (2002).
H. Noguchi,
Fusion and toroidal formation of vesicles by mechanical forces: A Brownian dynamics simulation
Journal of Chemical Physics 117, 8130-8137 (2002).
H. Noguchi,
Polyhedral vesicles: A Brownian dynamics simulation
Physical Review E 67, 041901 (5 pages) (2003).
H. Noguchi,
Solvent-free coarse-grained lipid model for large-scale simulations
Journal of Chemical Physics 134, 055101 (12 pages) (2011).
Selected for Cover
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).
H. Noguchi,
Structure formation in binary mixtures of lipids and detergents: Self-assembly and vesicle division
Journal of Chemical Physics 138, 024907 (9 pages) (2013).
# Vesicle Dynamics in Flow
H. Noguchi and G. Gompper,
Fluid vesicles with viscous membranes in shear flow
Physical Review Letters 93, 258102 (4 pages) (2004).
H. Noguchi and G. Gompper,
Dynamics of fluid vesicles in shear flow: effect of membrane viscosity and thermal fluctuations
Physical Review E 72, 011901 (14 pages) (2005).
H. Noguchi and G. Gompper,
Shape Transitions of Fluid Vesicles and Red Blood Cells in Capillary Flows
Proceeding of the National Academy of Sciences in USA 102, 14159-14164 (2005).
H. Noguchi and G. Gompper,
Swinging and Tumbling of Fluid Vesicles in Shear Flow
Physical Review Letters 98, 128103 (4 pages) (2007).
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 (8 pages) (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 (12 pages) (2009).
H. Noguchi,
Dynamics of Fluid Vesicles in Oscillatory Shear Flow
J. Phys. Soc. Jpn. 79, 024801 (10 pages) (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 (6 pages) (2010).
H. Noguchi,
Dynamic modes of microcapsules in steady shear flow: Effects of bending and shear elasticities
Physical Review E 81, 056319 (10 pages) (2010).
H. Noguchi,
Dynamic modes of red blood cells in oscillatory shear flow
Physical Review E 81, 061920 (9 pages) (2010).
J. Liam McWhirter, H. Noguchi, and G. Gompper,
Deformation and clustering of red blood cells in microcapillary flows
Soft Matter 7, 10967-10977 (2011).
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).
# Folding of Semiflexible Polymer
H. Noguchi, S. Saito, S. Kidoaki, and K. Yoshikawa,
Self-organized nanostructures constructed with a single polymer chain
Chemical Physics Letters 261, 527-533 (1996).
H. Noguchi and K. Yoshikawa,
First-order phase transition in a stiff polymer chain
Chemical Physics Letters 278, 184-188 (1997).
H. Noguchi and K. Yoshikawa,
Morphological variation in a collapsed single homopolymer chain
Journal of Chemical Physics 109, 5070-5077 (1998).
H. Noguchi and K. Yoshikawa,
Folding path in a semiflexible homopolymer chain: A Brownian dynamics simulation
Journal of Chemical Physics 113, 854-862 (2000).
# DNA Electrophoresis
H. Noguchi,
Dynamics of DNA electrophoresis in dilute and entangled polymer solutions
Journal of Chemical Physics 112, 9671-9678 (2000).
H. Noguchi and M. Takasu,
Linear-shaped motion of DNA in concentrated polymer solutions under a steady field
Journal of Physical Society of Japan 69, 3792-3795 (2000).
H. Noguchi and M. Takasu,
Dynamics of DNA in entangled polymer solutions: An anisotropic friction model
Journal of Chemical Physics 114, 7260-7266 (2001).
H. Noguchi, M. Ueda, Y. Baba, and M. Takasu,
Anisotropic Friction Model of DNA Electrophoresis in Polymer Solutions: Comparison with Direct Observations
Journal of Polymer Science: Part B: Polymer Physics 41, 1316-1322 (2003).
# Others
B. A. Berg, H. Noguchi, and Y. Okamoto,
Multioverlap simulations for transitions between reference configurations
Physical Review E 68, 036126 (11 pages) (2003).
K. Yoshikawa and, H. Noguchi,
A working hypothesis on the mechanism of molecular machinery
Chemical Physics Letters 303, 10-14 (1999).
A. Sugimura, M. Asai, T. Matsunaga, Y. Akagi, T. Sakai, H. Noguchi and M. Shibayama,
Mechanical properties of a polymer network of Tetra-PEG gel
Polym J. 45, 300-306 (2013).
K. Nishi, M. Chijiishi, Y. Katsumoto, T. Nakao, K. Fujii, U.-I. Chung, H. Noguchi, T. Sakai and M. Shibayama,
Rubber elasticity for incomplete polymer networks
J. Chem. Phys. 137, 224903/1-7 (2012).
K. Nishi, H. Noguchi, T. Sakai, and M. Shibayama,
Rubber elasticity for percolation network consisting of Gaussian chains
J. Chem. Phys. 143, 184905/1-9 (2015).
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 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
Proceedings
K. Yoshikawa, H. Noguchi, and Y. Yoshikawa,
Folding transition in single long duplex DNA chain
Progress in Colloid and Polymer Science 106, 204-208 (1997).
H. Noguchi,
Various morphology with collapse transition in a homopolymer chain
Progress of Theoretical Physics Supplement 138, 392-393 (2000).
H. Noguchi,
Electrophoretic Behavior of Polyelectrolytes in Gel and Polymer Solutions
Trans.MRS-J 26, 687-690 (2001).
H. Noguchi,
Folding dynamics in a semiflexible polymer as a model of DNA
International Journal of Bifurcation and Chaos 12, 2003-2008 (2002).
H. Noguchi and G. Gompper,
Vesicle dynamics in shear and capillary flows: A multi-particle collision dynamics simulation
Journal of Physics: condensed-matter 17, S3439-S3444 (2005).
H. Noguchi,
Dynamical Modes of Deformed Red Blood Cells
and Lipid Vesicles in Flows
Progress of Theoretical Physics Supplement 184, 364-368 (2010).
H. Noguchi,
Structure formation of lipid membranes: Membrane self-assembly and vesicle opening-up to octopus-like micelles
AIP Conference Proceedings 1518, 566-570 (2013).
H. Wu and H. Noguchi,
Effects of anchored flexible polymers on mechanical properties of model biomembranes
AIP Conference Proceedings 1518, 649-653 (2013).
H. Noguchi and N. Tamemoto,
Nonequilibrium dynamics of a fluid vesicle: Turing patterns and traveling waves
J. Phys.: Conf. Ser. 2207, 012017 (2022).
News and Comments
H. Noguchi,
Red Blood Cell Flow Along Four Corners of Square Tube
JPSJ News and Comments 19, 14 (2022).
