Papers (including Reviews)

    Link to Google Scholar page
  1. Spontaneous Escherichia coli persisters with week-long survival dynamics and lasting memory of a short starvation pulse
    Mikkel Skjoldan Svenningsen, Michael A. Sørensen, Sine Lo Svenningsen, and Namiko Mitarai
    BioRxiv 2020.09.17.301598
  2. Distinct survival, growth lag, and ribosomal RNA degradation kinetics during long-term starvation for carbon or phosphate
    Yusuke Himeoka, Bertil Gummesson, Michael A. Sørensen, Sine Lo Svenningsen, and Namiko Mitarai
    BioRxiv 2020.09.04.284034
  3. When to wake up? The optimal waking-up strategies for starvation-induced persistence
    Yusuke Himeoka and Namiko Mitarai
  4. Scaling laws of multilevel selection: a striking difference between continuous-trait and binary-trait models
    Nobuto Takeuchi, Namiko Mitarai, Kunihiko Kaneko
  5. On phage adsorption to bacterial chains
    Rasmus Skytte Eriksen, Namiko Mitarai, Kim Snpeppen
    Biophysical Journal, Volume 119, Issue 9, 3 November 2020, Pages 1896-1904
    BioRxiv 2020.06.10.144675v1
  6. Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing
    ummesson Bertil, Shah Shiraz Ali, Borum Alexander Skov, Fessler Mathias, Mitarai Namiko, Sørensen Michael Askvad, Svenningsen Sine Lo
    Frontiers in Genetics 11, 144 (2020)
  7. Dynamics of bacterial populations under the feast-famine cycles
    Yusuke Himeoka and Namiko Mitarai
    Phys. Rev. Res. 2, 013372 (2000)
  8. Sustainability of spatially distributed bacteria-phage systems
    Rasmus Skytte Eriksen, Namiko Mitarai, Kim Snpeppen
    Sci. Rep. 10, 3154 (2000)
    BioRxiv 495671
  9. How pirate phage interferes with helper phage: Comparison of the two distinct strategies
    Namiko Mitarai
    J. Theor. Biol. 486, 110096 (2020).
    BioRxiv 576587
  10. Finite response time in stripe formation by bacteria with density-suppressed motility
    Xingyu Zhang and Namiko Mitarai
  11. Birth and Resuscitation of (p)ppGpp Induced Antibiotic Tolerant Persister Cells
    Mikkel S. Svenningsen, Alexandra Veress, Alexander Harms, Namiko Mitarai, Szabolcs Semsey.
    Scientific Reports vol. 9, 6056 (2019).
  12. Fast translation within the first 45 codons decreases mRNA stability and increases premature transcription termination in E. coli.
    Steen Pedersen, Thilde Terkelsen, Mette Eriksen, Magnus K Hauge, Casper C Lund, Kim Sneppen, and Namiko Mitarai.
    Journal of Molecular Biology vol. 431, pp. 1088-1097 (2019) (Special Issue: The future of microbiology).
  13. Gene expression changes with minor effects on the population average have major effects on the occurence of cells with extreme protein concentrations
    Mikkel S. Svenningsen, Szabolcs Semsey, Namiko Mitarai.
    mSpere 4, e00575-18 (2019); DOI: 10.1128/mSphere.00575-18.
  14. Modeling slow-processing of toxin messenger RNAs in type-I Toxin-Antitoxin systems: post-segregational killing and noise filtering
    Yusuke Himeoka, Namiko Mitarai
    Physical Biology vol. 16, 026001 (2019).
    BioRxiv 407288
  15. Dynamic modelling of indole glucosinolate hydrolysis and its impact on auxin signaling
    Daniel Vik, Namiko Mitarai, Nikolai Wulff, Barbara A. Halkier and Meike Burow
    Front. Plant Sci. | doi: 10.3389/fpls.2018.00550 (2018).
  16. Theory of invasion extinction dynamics in minimal food webs
    Jan O. Haerter, Namiko Mitarai, and Kim Sneppen
    Phys. Rev. E vol. 97, 022404 (2018).
  17. A Growing Microcolony can Survive and Support Persistent Propagation of Virulent Phages
    Rasmus Skytte Eriksen, Sine Lo Svenningsen, Kim Sneppen, Namiko Mitarai
    Proc. Nat. Acad. Sci. USA, vol. 115, pp.337-342 (2018).
    Preprint: bioRxiv 149062; doi:
  18. Toxins, Targets, and Triggers: An Overvis of Toxin-Antitoxin Biology
    Alexander Harms, Ditlev Egeskov Brodersen, Namiko Mitarai, Kenn Gerdes
    (Review) Molecular Cell (2018),
  19. Existence and construction of large stable food webs
    Jan O. Haerter, Namiko Mitarai, Kim Sneppen.
    Phys. Rev. E, vol. 96, 032406 (2017).
    Preprint: biorXiv, doi:
  20. Synchronized switching of multiple Toxin-Antitoxin modules by (p)ppGpp fluctuation
    Chengzhe Tian, Szabolcs Semsey, Namiko Mitarai
    Nucleic Acids Research, Vol. 45, 8180-8189 (2017). doi: 10.1093/nar/gkx552
  21. Deterministic extinction by mixing in cyclically competing species
    Cilie W. Feldager, Namiko Mitarai, and Hiroki Ohta.
    Phys. Rev. E, vol. 95, 032318 (2017)
    Preprint: arXiv:1609.08297
  22. Occlusion of the ribosome binding site connects the translational initiation frequency, mRNA stability and premature transcription termination
    Mette Eriksen, Kim Sneppen, Steen Pedersen and Namiko Mitarai
    Frontiers in Microbiology, vol. 8, 362 (2017) .
  23. Characterization of phase transitions in a model ecosystem of sessile species
    Florian Uekermann, Joachim Mathiesen, and Namiko Mitarai.
    Phys. Rev. E, vol. 95, 032409 (2017)
    Preprint: arXiv:1611.00171
  24. Rapid Curtailing of The Stringent Response by Toxin-Antitoxin-Encoded mRNases
    Chengzhe Tian, Mohammad Roghanian, Mikkel Girke Jorgensen, Kim Sneppen, Michael A. Sorensen, Kenn Gerdes, Namiko Mitarai.
    Journal of Bacteriology vol. 198, no. 14, 1918-1926 (2016)
  25. Population dynamics of phage and bacteria in spatially structured habitats using Phage lambda and Escherichia coli
    Namiko Mitarai, Stanley Brown, and Kim Sneppen
    Journal of Bacteriology, vol. 198, no. 12, 1783-1793 (2016).
    Chosen for SPOTLIGHT
  26. Three is much more than two in coarsening dynamics of cyclic competitions
    Namiko Mitarai, Ivar Gunnarson, Buster Niels Pedersen, Christian Anker Rosiek, and Kim Sneppen
    Phys. Rev. E 93, 042408 (2016)
    preprint: arXiv:1512.00769
  27. Food web assembly rules for Generalized Lotka-Volterra Equations
    Jan O. Haerter, Namiko Mitarai, Kim Sneppen.
    Plos Computational Biology 12(2): e1004727 (2016)
    preprint: arXiv:1501.04497
  28. Bifurcation of Transition Paths Induced by Coupled Bistable Systems
    Chengzhe Tian and Namiko Mitarai
    J. Chem. Phys. vol 144, 215102 (2016)
    preprint: arXiv:1603.04477
  29. Dynamic competition between transcription initiation and repression: Role of non-equilibrium steps in cell-to-cell heterogeneity
    Namiko Mitarai, Szabolcs Semsey, Kim Sneppen.
    Phys. Rev. E 92, 022710 (2015).
    preprint: arXiv:1502.03011
  30. Coupled positive and negative feedbacks produce diverse expression patterns in bacterial colonies
    Namiko Mitarai, Mogens H. Jensen, and Szabolcs Semsey.
    mBio vol 6, no.2 e00059-15 (2015).
  31. Fixation in cyclically competing species on a directed graph with quenched disorder
    Hiroki Ohta and Namiko Mitarai.
    In revision.
    Preprint: arXiv:1402.6624
  32. Phage and bacteria support mutual diversity in a narrowing staircase of coexistence
    Jan O. Haerter, Namiko Mitarai, and Kim Sneppen.
    ISME J., 8, 2317-2326 (2014). doi:10.1038/ismej.2014.80
  33. Speciation, Diversification, and Coexistence of Sessile Species that Compete for Space
    Namiko Mitarai, Els Heinsalu, and Kim Sneppen.
    Plos One, vol 9, e96665 (2014).
  34. Modeling rises and falls in money addicted social hierarchies
    Bartlomiej Dybiec, Namiko Mitarai, and Kim Sneppen
    Physica Scripta, 89, 085002 (2014).
  35. Disturbance accelerates the transition from low- to high-diversity state in a model ecosystem
    Filippo Botta and Namiko Mitarai
    Physical Review E vol 89, 022704 (2014).
    Preprint: arXiv:1312.3445
  36. Experimental observation of shear thickening oscillation
    Shin-ichiro Nagahiro, Hiizu Nakanishi, Namiko Mitarai
    EPL (Europhysics Leters), 104, 28002 (2013).
    Preprint: arXiv:1211.2886
  37. Control of ribosome traffic by position-dependent choice of synonymous codons.
    Namiko Mitarai and Steen Pedersen
    Phys. Biol. 10, 056011 (2013)
    preprint: arXiv:1309.0936
  38. Conditional cooperativity of Toxin-Antitoxin regulation can mediate bistability between growth and dormancy
    Ilaria Cataudella, Kim Sneppen, Kenn Gerdes, and Namiko Mitarai
    Plos Comput. Biol. 8, e1003174 (2013)
    PDF, Supporting Text 1, and Supporting Text 2
  39. Entrainment of noise-induced and limit cycle oscillators under weak noise
    Namiko Mitarai, Uri Alon, Mogens H. Jensen
    Chaos 23, 023125 (2013).
    Preprint: arXiv:1301.2440
  40. Circuit architecture explains functional similarity of bacterial heat shock responses
    Masayo Inoue, Namiko Mitarai, and Ala Trusina.
    Phys. Biol. 9, 066003 (2012)
  41. Multistability with a Metastable Mixed State
    Kim Sneppen and Namiko Mitarai
    Phys. Rev. Lett. 109, 100602 (2012)
  42. Emergence of diversity in a model ecosystem
    Namiko Mitarai, Joachim Mathiesen, Kim Sneppen
    Phys. Rev. E 86, 011929 (2012)
  43. Axelrod model: accepting or discussing
    Bartlomiej Dybiec, Namiko Mitarai, Kim Sneppen
    Eur. Phys. J. B, 85, 357 (2012)
  44. Information spreading and development of cultural centers
    Bartlomiej Dybiec, Namiko Mitarai, Kim Sneppen
    Phys. Rev. E 85, 056116 (2012).
  45. Switching between oscillations and homeostasis in competing negative and positive feedback motifs
    Weihan Li, Sandeep Krishna, Simone Pigolotti, Namiko Mitarai, and Mogens H. Jensen.
    J. Thor. Biol. 307, 205-210 (2012).
  46. Conditional Cooperativity in Toxin-Antitoxin Regulation Prevents Random Toxin Activation and Promotes Fast Translational Recovery
    Ilaria Cataudella, Ala Trusina, Kim Sneppen, Kenn Gerdes, and Namiko Mitarai
    Nucl. Acids Res. (2012) 40, 6424-6434.
    PDF and Supplement
  47. Granular flow: Dry and wet
    Namiko Mitarai and Hiizu Nakanishi
    Eur. Phys. J. Special Topics 204, 5-17 (2012)
  48. Fluid dynamics of dilatant fluid
    Hiizu Nakanishi, Shin-ichiro Nagahiro, and Namiko Mitarai.
    Phys. Rev. E 85, 011401 (2012)
  49. Protein localization with flexible DNA or RNA
    Sebastian Bernhardsson, Namiko Mitarai, and Kim Sneppen.
    Plos One, Vol. 7, e29218 (2012)
    PDF and Supporting Material
  50. Ecosystems with mutually exclusive interactions self-organize to a state of high diversity
    Joachim Mathiesen, Namiko Mitarai, Kim Sneppen, and Ala Trusina
    Phys. Rev. Lett. 107, 188101 (2011)
  51. Modelling the Spatial Dynamics of Culture Spreading in the Presence of Cultural Strongholds
    Ludvig Lizana, Namiko Mitarai, Hiizu Nakanishi, and Kim Sneppen
    Phys. Rev. E 83, 066116 (2011)
  52. Shear Thickening Oscillation in a Dilatant Fluid
    Hiizu Nakanishi and Namiko Mitarai
    J. Phys. Soc. Jpn., Vol.80, No.3, p.033801 (2011)
  53. The functional half-life of an mRNA depends on the ribosome spacing in an early coding region
    Margit Pedersen, Soren Nissen, Namiko Mitarai, Sine Lo Svenningsen, Kim Sneppen, and Steen Pedersen
    J. Mol. Biol. 407, 35-44 (2011)
  54. Theory for stability and regulation of epigenetic landscapes
    Mille A. Micheelsen, Namiko Mitarai, Kim Sneppen, and Ian. B. Dodd
    Phys. Biol. 7, 026010 (2010)
  55. Simple Model for Wet Granular Materials with Liquid Clusters
    Namiko Mitarai and Hiizu Nakanishi
    Europhys. Lett. 88, 64001 (2009)
  56. Non-ideal behavior of intramolecular structure factor of dilute polymers in a theta solvent
    Kenji Shimomura, Hiizu Nakanishi, and Namiko Mitarai
    Phys. Rev. E 80, 051804 (2009)
  57. Loewner driving functions for off-critical percolation clusters
    Yoichiro Kondo, Namiko Mitarai, and Hiizu Nakanishi
    Phys. Rev. E 80, 050102R (2009)
  58. Dynamics of the recovery from sRNA-mediated gene silencing.
    Szabolcs Semsey, Julie-Anna M. Bemjamin, Namiko Mitarai, Sandeep Krishna, Zsolt Csiszovszki, Kim Sneppen, and Eric Masse.
    Cell Cycle. vol. 8(18):2863-4 (2009)
  59. Dynamic features of gene expression control by small regulatory RNAs
    Namiko Mitarai, Julie-Anna M. Bemjamin, Sandeep Krishna, Szabolcs Semsey, Zsolt Csiszovszki, Eric Masse, and Kim Sneppen.
    Proc. Nat. Acad. Sci. USA 106, 10655-10659(2009) doi:10.1073/pnas.0901466106 PDF and Supplement
  60. Dynamical Analysis on Gene Activity in the Presence of Repressors and an Interfering Promoter
    Hiizu Nakanishi, Namiko Mitarai, and Kim Sneppen
    Biophys. J. 95: 4228-4240 (2008)
  61. Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization
    Namiko Mitarai, Kim Sneppen, and Steen Pedersen
    J. Mol. Biol. 382: 236 (2008)
  62. The generation of promoter-mediated transcriptional noise in bacteria
    Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, and Kim Sneppen
    Plos. Comp. Biol. 4(7): e1000109 (2008).
  63. Anomalous fluctuations in sliding motion of cytoskeletal filament driven by molecular motors: Model simulations
    Yasuhiro Imafuku, Namiko Mitarai, Katsuhisa Tawada, and Hiizu Nakanishi
    J. Phys. Chem. B, 112 (5), 1487 -1493 (2008)
  64. Velocity correlations in the dense granular shear flows: Effects on energy dissipation and normal stress
    Namiko Mitarai and Hiizu Nakanishi
    Phys. Rev. E vol. 75, 031305 (2007).
  65. Efficient degradation and expression prioritization with small RNAs
    Namiko Mitarai, Anna M.C. Andersson, Sandeep Krishna, Szabolcs Semsey, and Kim Sneppen
    Phys. Biol. vol. 4, 164-171 (2007)
  66. Lattice Model of Sweeping Interface for Drying Process in Water-Granule Mixture
    Hiizu Nakanishi, Ryo Yamamoto, Yumino Hayase, Namiko Mitarai
    J. Phys. Soc. Jpn. vol. 76, No. 2, 024003 (7pages) (2007)
  67. Broad distribution of stick-slip events in Slowly Sheared Granular Media: Table-top production of a Gutenberg-Richter-like distribution
    Michael Bretz, Russell Zaretzki, Stuart B. Field, Namiko Mitarai and Franco Nori
    Europhys. Lett., Vol. 74, pp. 1116-1122 (2006)
    cond-mat/ arXiv:0706.3136
  68. Wet granular materials
    Namiko MITARAI and Franco NORI
    Adv. Phys. Vol. 55, No. 01-02, pp.1-45 (2006)
  69. Bagnold scaling, density plateau, and kinetic theory analysis of dense granular flow
    Namiko MITARAI and Hiizu NAKANISHI
    Phys. Rev. Lett. Vol. 94, 128001 (2005)
  70. Linear stability analysis of rapid granular flow down a slope and density wave formation
    Namiko MITARAI and Hiizu NAKANISHI
    J. Fluid Mech. Vol. 507, pp. 309-334 (2004) cond-mat/0303543
  71. Hard-sphere Limit of Soft-sphere Model for Granular Materials:
    Stiffness Dependence of Steady Granular Flow
    Namiko MITARAI and Hiizu NAKANISHI
    Phys. Rev. E 67, 021301 (2003) cond-mat/0210630
  72. Collisional Granular Flow as a Micropolar Fluid
    Namiko MITARAI, Hisao HAYAKAWA, and Hiizu NAKANISHI
    Phys. Rev. Lett. 88, 174301 (2002) cond-mat/0108192
  73. Instability of dilute granular flow on rough slope
    Namiko MITARAI and Hiizu NAKANISHI
    J. Phys. Soc. Jpn. Vol. 70, No. 10, pp. 2809-2812 (2001) cond-mat/0104571
  74. Convective Instability and Structure Formation in Traffic Flow
    Namiko MITARAI and Hiizu NAKANISHI
    J. Phys. Soc. Jpn. Vol. 69,No. 11, pp. 3752-3761 (2000) PDF FILE
  75. Spatiotemporal Structure of Traffic Flow in a System with an Open Boundary
    Namiko MITARAI and Hiizu NAKANISHI
    Phys. Rev. Lett. Vol. 85, pp. 1766-1769 (2000) cond-mat/0004294
  76. Stability Analysis of Optimal Velocity Model for Traffic and Granular Flow under Open Boundary Condition
    Namiko MITARAI and Hiizu NAKANISHI
    J. Phys. Soc. Jpn. Vol. 68, No. 8, pp. 2475-2478 (1999) cond-mat/9905315

Reviews in Japanese

  1. 流れる粉体の動力学--バグノルド則をめぐって-- (解説)
    日本物理学会誌、vol. 62, pp. 676- 684 (2007年9月号)

Conference Proceedings (with review)

  1. Simple Interaction Model for Particlly Wet Granular Materials"
    Namiko MITARAI and Hiizu NAKANISHI
    Proceedings of IUTAM-ISIMM symposium on mathematical modeling and physical instances of granular flows.
    AIP Conf. Proc. Vol. 1227, pp. 214-220 (2010).
  2. Stability analysis of collisional granular flow on a slope
    Namiko MITARAI and Hiizu NAKANISHI
    Proceedings of DDAP2
    Int. J. Mod. Phys. B Vol. 17, pp.4290 (2003)
  3. Collisional Granular Flow on a Rough Slope and its Instability
    Namiko MITARAI, Hiizu NAKANISHI, and Hisao HAYAKAWA
    Traffic and Granular Flow '01 pp. 485-490.
    (M. Fukui, Y. Sugiyama, M. Schreckenberg, and D. E. Wolf ed., Springer, 2003)

Other publications

  1. 流れる粉体
    御手洗菜美子、物性研究Vol.91 No.4 (2009年1月号)p.371-401
  2. Essay "Physics: see how the world works" (in Japanese)
    Namiko Mitarai
    in booklet published to steer girls towards scientific careers, Kyushu University, Japan (2007).
  3. 粉体せん断流における速度相関
    御手洗菜美子,中西 秀; 数理解析研究所講究録, 1472 (2006) 101.108.
  4. 高密度な粉体斜面流の密度プロファイル
    御手洗菜美子、中西秀、数理解析研究所講究録1413 (2005)「複雑流体の構造形成と 崩解の数理」p.60.
  5. 分子モーターによるフィラメントの滑べり運動の揺らぎのフィラメント長依存性
    御手洗菜美子、中西秀、京大基研研究会「ソフトマターの物理学2003 −普遍性と 多様性」研究会報告、物性研究Vol. 81 No. 2 pp.268-269.
  6. Instability of Granular Flow on Rough Inclined Plane
    Namiko MITARAI and Hiizu NAKANISHI
    Proceedings of Powders and Grains 2001, p.455 (2001).
  7. Particle diffusion in the cooling process of granular gas
    Hiizu NAKANISHI and Namiko MITARAI
    Proceedings of Powders and Grains 2001, p.581 (2001).
  8. 極性流体としての粉体斜面流
    京大基研研究会 「非平衡系の新局面 -- 運動、機能、構造 --」 研究会報告:物性研究2001年11月号(Vol. 17)、p.260.
  9. 斜面上の粉体流とその安定性
    研究集会報告13ME-S4 「非線形波動現象の理論と応用」 p. 107 (九州大学応用力学研究所、2002年4月)


  • Doctor Thesis "Stdady Flow and its Instability of Gravitational Granular Fllow"
    Namiko Mitarai, 2003. PDF file
  • Master Thesis "Dynamics of Traffic Flow and Granular Pipe Flow" (In Japanese)
    Namiko Mitarai, 2000. PDF file