Namiko Mitarai

Namiko Mitarai

Associate Professor

ORCID: 0000-0003-0116-7606

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  1. Published

    When to wake up? The optimal waking-up strategies for starvation-induced persistence

    Himeoka, Y. & Mitarai, Namiko, 11 Feb 2021, In: PLoS Computational Biology. 17, 2, 21 p., 1008655.

    Research output: Contribution to journal › Journal article › Research › peer-review

  2. Published

    Wet granular materials

    Mitarai, Namiko & Nori, F., 30 Jun 2006, In: Advances in Physics. 55, 1-2, p. 1-45 45 p.

    Research output: Contribution to journal › Review › Research › peer-review

  3. Published

    Velocity correlations in dense granular shear flows: Effects on energy dissipation and normal stress

    Mitarai, Namiko & Nakanishi, H., 2007, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). 75, 3, p. 031305

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing

    Gummesson, Bertil, Shah, S. A., Borum, A. S., Fessler, M., Mitarai, Namiko, Sørensen, Michael Askvad & Svenningsen, Sine Lo, 2020, In: Frontiers in Genetics. 11, 17 p., 144.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology

    Harms, A., Brodersen, D. E., Mitarai, Namiko & Gerdes, K., 7 Jun 2018, In: Molecular Cell. 70, 5, p. 768-784 17 p.

    Research output: Contribution to journal › Review › Research › peer-review

  6. Published

    Three is much more than two in coarsening dynamics of cyclic competitions

    Mitarai, Namiko, Gunnarson, I., Pedersen, B. N., Rosiek, C. A. & Sneppen, Kim, Apr 2016, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). 93, 042408.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    Theory of invasion extinction dynamics in minimal food webs

    Härter, Jan Olaf Mirko, Mitarai, Namiko & Sneppen, Kim, 12 Feb 2018, In: Physical Review E. 97, 2, 10 p., 022404.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Theory for the stability and regulation of epigenetic landscapes

    Micheelsen, M. A., Mitarai, Namiko, Sneppen, Kim & Dodd, I. B., 4 Jun 2010, In: Physical Biology. 7, 2, p. 026010 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    The generation of promoter-mediated transcriptional noise in bacteria

    Mitarai, Namiko, Dodd, I. B., Crooks, M. T. & Sneppen, Kim, 11 Jul 2008, In: PLoS Computational Biology. 4, 7, p. e 10000109

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. Published

    The functional half-life of an mRNA depends on the ribosome spacing in an early coding region

    Pedersen, M., Nissen, S., Mitarai, Namiko, Svenningsen, Sine Lo, Sneppen, Kim & Pedersen, Steen, 2011, In: Journal of Molecular Biology. 407, 1, p. 35-44 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    The dynamics of phage predation on a microcolony

    Eriksen, R. S., Larsen, Frej Andreas Nøhr, Svenningsen, Sine Lo, Sneppen, Kim & Mitarai, Namiko, 2024, In: Biophysical Journal. 123, 2, p. 147-156 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    The Gompertz Law emerges naturally from the inter-dependencies between sub-components in complex organisms

    Yde, Pernille, Jensen, Majken Karoline, Mitarai, Namiko & Bhatt, Samir, 2024, In: Scientific Reports. 14, 1, 11 p., 1196.

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    Synchronized switching of multiple toxin-antitoxin modules by (p)ppGpp fluctuation

    Tian, C., Semsey, S. & Mitarai, Namiko, 21 Aug 2017, In: Nucleic Acids Research. 45, 14, p. 8180-8189 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    Switching between oscillations and homeostasis in competing negative and positive feedback motifs

    Li, W., Krishna, S., Pigolotti, S., Mitarai, Namiko & Jensen, Mogens Høgh, 21 Aug 2012, In: Journal of Theoretical Biology. 307, p. 205-210

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    Sustainable diversity of phage-bacteria systems

    Mitarai, Namiko, Marantos, Anastasios & Sneppen, Kim, 1 Jun 2023, In: Current Opinion in Systems Biology. 35, 6 p., 100468.

    Research output: Contribution to journal › Review › Research › peer-review

  16. Published

    Sustainability of spatially distributed bacteria-phage systems

    Eriksen, R. S., Mitarai, Namiko & Sneppen, Kim, 2020, In: Scientific Reports. 10, 1, p. 1-12 3154.

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    Stochastic microbial dispersal drives local extinction and global diversity

    Garrido Zornoza, Miguel, Mitarai, Namiko & Härter, Jan Olaf Mirko, 23 May 2024, In: Royal Society Open Science. 11, 5, 20 p., 231301.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. Published

    Stability analysis of optimal velocity model for traffic and granular flow under open boundary condition

    Mitarai, Namiko & Nakanishi, H., 1 Aug 1999, In: Journal of the Physical Society of Japan. 68, 8, p. 2475-2478

    Research output: Contribution to journal › Journal article › Research › peer-review

  19. Published

    Stability analysis of collisional granular flow on a slope

    Mitarai, Namiko & Nakanishi, H., 30 Sep 2003, In: International Journal of Modern Physics B. 17, 22-24 II, p. 4290-4294 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    Speciation, diversification, and coexistence of sessile species that compete for space

    Mitarai, Namiko, Heinsalu, E. & Sneppen, Kim, 12 May 2014, In: PloS One. 9, 5, p. e96665

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Spatiotemporal structure of traffic flow in a system with an open boundary

    Mitarai, Namiko & Nakanishi, H., 21 Aug 2000, In: Physical Review Letters. 85, 8, p. 1766-1769

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Simple model for wet granular materials with liquid cluster

    Mitarai, Namiko & Nakanishi, H., 1 Dec 2009, In: EPL. 88, 6, p. 64001

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    Simple Interaction Model for Particlly Wet Granular Materials

    Mitarai, Namiko & Nakanishi, H., 1 Feb 2010, In: A I P Conference Proceedings Series. 1227, p. 214-220

    Research output: Contribution to journal › Conference article › Research › peer-review

  24. Published

    Shear Thickening Oscillation in a Dilatant Fluid

    Nakanishi, H. & Mitarai, Namiko, 25 Feb 2011, In: Journal of the Physical Society of Japan. 80, 3, p. 033801

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

    Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization

    Mitarai, Namiko, Sneppen, Kim & Pedersen, Steen, 2008, In: Journal of Molecular Biology. 382, 1, p. 236-245 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  26. Published

    Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Encoded mRNases

    Tian, C., Roghanian, Mohammad, Jørgensen, M. G., Sneppen, Kim, Sørensen, Michael Askvad, Gerdes, K. & Mitarai, Namiko, Jul 2016, In: Journal of Bacteriology. 198, 14, p. 1918-1926

    Research output: Contribution to journal › Journal article › Research › peer-review

  27. Published

    Protein Localization with Flexible DNA or RNA

    Bernhardsson, P. J. S., Mitarai, Namiko & Sneppen, Kim, 10 Feb 2012, In: PLoS.ONE.. 7, 2, p. e29218

    Research output: Contribution to journal › Journal article › Research › peer-review

  28. Published

    Protection of bacteriophage-sensitive Escherichia coli by lysogens

    Brown, Stanley, Mitarai, Namiko & Sneppen, Kim, 2 Apr 2022, In: Proceedings of the National Academy of Sciences USA (PNAS). 119, 4, e2106005119.

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    Population Dynamics of Phage and Bacteria in Spatially Structured Habitats Using Phage lambda and Escherichia coli

    Mitarai, Namiko, Brown, Stanley & Sneppen, Kim, 11 Apr 2016, In: Journal of Bacteriology. 198, 12, p. 1783-1793

    Research output: Contribution to journal › Journal article › Research › peer-review

  30. Published

    Phage and bacteria support mutual diversity in a narrowing staircase of coexistence

    Härter, Jan Olaf Mirko, Mitarai, Namiko & Sneppen, Kim, 3 Nov 2014, In: I S M E Journal. 28, 11, p. 2317-2326

    Research output: Contribution to journal › Journal article › Research › peer-review

  31. Published

    On Phage Adsorption to Bacterial Chains

    Eriksen, R. S., Mitarai, Namiko & Sneppen, Kim, 3 Nov 2020, In: Biophysical Journal. 119, 9, p. 1896-1904 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  32. Published

    Occlusion of the ribosome binding site connects the translational initiation frequency, mRNA stability and premature transcription termination

    Eriksen, M., Sneppen, Kim, Pedersen, Steen & Mitarai, Namiko, 14 Mar 2017, In: Frontiers in Microbiology. 8, 7 p., 362.

    Research output: Contribution to journal › Journal article › Research › peer-review

  33. Published

    Nonideal behavior of intramolecular structure factor of dilute polymers in a theta solvent

    Shimomura, K., Nakanishi, H. & Mitarai, Namiko, 2009, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). 80, 5, Part 1, p. 051804

    Research output: Contribution to journal › Journal article › Research › peer-review

  34. Published

    Multistability with a Metastable Mixed State

    Sneppen, Kim & Mitarai, Namiko, 5 Sep 2012, In: Physical Review Letters. 109, 10, p. 100602 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  35. Published

    Motility mediates satellite formation in confined biofilms

    Cordero, Mireia, Mitarai, Namiko & Jauffred, Liselotte, 17 Aug 2023, In: ISME Journal. 17, p. 1819-1827 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  36. Published

    Modeling the spatial dynamics of culture spreading in the presence of cultural strongholds

    Lizana, G. L., Mitarai, Namiko & Sneppen, Kim, 28 Jun 2011, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). 83, 6, p. 066116 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  37. Published

    Modeling slow-processing of toxin messenger RNAs in type-I toxin-antitoxin systems: post-segregational killing and noise filtering

    Himeoka, Y. & Mitarai, Namiko, Mar 2019, In: Physical Biology. 16, 2, 026001.

    Research output: Contribution to journal › Journal article › Research › peer-review

  38. Published

    Modeling rises and falls in money addicted social hierarchies

    Dybiec, B., Mitarai, Namiko & Sneppen, Kim, 2014, In: Physica Scripta. 89, 8, 085002.

    Research output: Contribution to journal › Journal article › Research › peer-review

  39. Published

    Loewner driving functions for off-critical percolation clusters

    Kondo, Y., Mitarai, Namiko & Nakanishi, H., 2009, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). 80, 5, Part 1, p. 050102

    Research output: Contribution to journal › Journal article › Research › peer-review

  40. Published

    Linear stability analysis of rapid granular flow down a slope and density wave formation

    Mitarai, Namiko & Nakanishi, H., 25 May 2004, In: Journal of Fluid Mechanics. 507, p. 309-334

    Research output: Contribution to journal › Journal article › Research › peer-review

  41. Lattice model of sweeping interface for drying process in water-granule mixture

    Nakanishi, H., Yamamoto, R., Hayase, Y. & Mitarai, Namiko, 1 Feb 2007, In: Journal of the Physical Society of Japan. 76, 2, 024003.

    Research output: Contribution to journal › Journal article › Research › peer-review

  42. Published

    Instability of dilute granular flows on rough slope

    Mitarai, Namiko & Nakanishi, H., 1 Oct 2001, In: Journal of the Physical Society of Japan. 70, 10, p. 2809-2812

    Research output: Contribution to journal › Journal article › Research › peer-review

  43. Published

    Information spreading and development of cultural centers

    Dybiec, B. M., Mitarai, Namiko & Sneppen, Kim, 18 May 2012, In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. 85, 5, p. 056116 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  44. Published

    How pirate phage interferes with helper phage: Comparison of the two distinct strategies

    Mitarai, Namiko, 7 Feb 2020, In: Journal of Theoretical Biology. 486, 9 p., 110096.

    Research output: Contribution to journal › Journal article › Research › peer-review

  45. Published

    Hard-sphere limit of soft-sphere model for granular materials: Stiffness dependence of steady granular flow

    Mitarai, Namiko & Nakanishi, H., 19 Feb 2003, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). 67, 2, 021301.

    Research output: Contribution to journal › Journal article › Research › peer-review

  46. Published

    Granular flow: dry and wet

    Mitarai, Namiko & Nakanishi, H., 2012, In: European Physical Journal. Special Topics. 204, 1, p. 5-17 13 p.

    Research output: Contribution to journal › Review › Research › peer-review

  47. Published

    Gene Expression Changes with Minor Effects on the Population Average Have Major Effects on the Occurrence of Cells with Extreme Protein Concentrations

    Svenningsen, Mikkel Skjoldan, Semsey, S. & Mitarai, Namiko, 2019, In: mSphere. 4, 1, p. 1-6 e00575-18.

    Research output: Contribution to journal › Journal article › Research › peer-review

  48. Published

    From kill the winner to eliminate the winner in open phage-bacteria systems

    Marantos, Anastasios, Mitarai, Namiko & Sneppen, Kim, 8 Aug 2022, In: PLOS Computational Biology. 18, 8, 15 p., e1010400.

    Research output: Contribution to journal › Journal article › Research › peer-review

  49. Published

    Food Web Assembly Rules for Generalized Lotka-Volterra Equations

    Härter, Jan Olaf Mirko, Mitarai, Namiko & Sneppen, Kim, Feb 2016, In: PLoS Computational Biology. 12, 2, e1004727.

    Research output: Contribution to journal › Journal article › Research › peer-review

  50. Published

    Fluid dynamics of dilatant fluid

    Nakanishi, H., Nagahiro, S. & Mitarai, Namiko, 12 Jan 2012, In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). 85, 1, p. 011401 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

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