Namiko Mitarai

Namiko Mitarai

Associate Professor

ORCID: 0000-0003-0116-7606

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  1. Published

    Dynamics of the recovery from sRNA-mediated gene silencing

    Semsey, S., Bemjamin, J., Mitarai, Namiko, Krishna, S., Csiszovszki, Z., Sneppen, Kim & Masse, E., 2009, In: Cell Cycle. 8, 18, p. 2863-2864 1 p.

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

  2. Published

    Dynamic features of gene expression control by small regulatory RNAs

    Mitarai, Namiko, Bemjamin, J., Krishna, S., Semsey, S., Csiszovszki, Z., Masse, E. & Sneppen, Kim, 2009, In: Proceedings of the National Academy of Science of the United States of America. 106, 26, p. 10655-10659 4 p.

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

  3. 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

  4. 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

  5. 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

  6. Published

    Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy

    Cataudella, I., Sneppen, Kim, Gerdes, K. & Mitarai, Namiko, 1 Aug 2013, In: PLoS Computational Biology. 9, 8, e1003174.

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

  7. 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

  8. 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

  9. Published

    A growing microcolony can survive and support persistent propagation of virulent phages

    Eriksen, R. S., Svenningsen, Sine Lo, Sneppen, Kim & Mitarai, Namiko, 1 Jan 2018, In: Proceedings of the National Academy of Sciences USA (PNAS). 115, 2, p. 337-342

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

  10. Published

    Efficient degradation and expression prioritization with small RANs

    Mitarai, Namiko, Andersson, A. M. C., Krishna, S., Semsey, S. & Sneppen, Kim, 2007, In: Physical Biology. 4, 3, p. 164-171

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

  11. 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

  12. Published

    Ecosystems with Mutually Exclusive Interactions Self-Organize to a State of High Diversity

    Mathiesen, Joachim, Mitarai, Namiko, Sneppen, Kim & Trusina, Ala, 25 Oct 2011, In: Physical Review Letters. 107, 18, p. 188101

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

  13. 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

  14. 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

  15. 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

  16. Published

    Convective instability and structure formation in traffic flow

    Mitarai, Namiko & Nakanishi, H., 2 Nov 2000, In: Journal of the Physical Society of Japan. 69, 11, p. 3752-3761

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

  17. Published

    Entrainment of noise-induced and limit cycle oscillators under weak noise

    Mitarai, Namiko, Alon, U. & Jensen, Mogens Høgh, 1 Jun 2013, In: Chaos. 23, 2, 023125.

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

  18. Published

    Dynamic Modeling of Indole Glucosinolate Hydrolysis and Its Impact on Auxin Signaling

    Vik, D., Mitarai, Namiko, Wulff, N., Halkier, Barbara Ann & Burow, Meike, 2018, In: Frontiers in Plant Science. 9, 16 p., 550.

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

  19. Published

    Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli

    Pedersen, Steen, Terkelsen, Thilde Bagger, Eriksen, M., Hauge, M. K., Lund, C. C., Sneppen, Kim & Mitarai, Namiko, 2019, In: Journal of Molecular Biology. 431, 6, p. 1088-1097 10 p.

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

  20. 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

  21. 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

  22. 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

  23. Published

    Distinct Survival, Growth Lag, and rRNA Degradation Kinetics during Long-Term Starvation for Carbon or Phosphate

    Himeoka, Y., Gummesson, Bertil, Sørensen, Michael Askvad, Svenningsen, Sine Lo & Mitarai, Namiko, 20 Apr 2022, In: mSphere. 7, 3, 12 p., e01006-21.

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

  24. 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

  25. 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

  26. Published

    Circuit architecture explains functional similarity of bacterial heat shock responses

    Masayo, I., Mitarai, Namiko & Trusina, Ala, 1 Dec 2012, In: Physical Biology. 9, 6, p. 066003

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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. Published

    A scaling law of multilevel evolution: how the balance between within- and among-collective evolution is determined

    Takeuchi, N., Mitarai, Namiko & Kaneko, Kunihiko, 4 Feb 2022, In: Genetics. 220, 2, 9 p., 182.

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

  33. 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

  34. 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

  35. 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

  36. 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

  37. Published

    Collisional granular flow as a micropolar fluid

    Mitarai, Namiko, Hayakawa, H. & Nakanishi, H., 29 Apr 2002, In: Physical Review Letters. 88, 17, 174301.

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

  38. Published

    Broad distribution of stick-slip events in slowly sheared granular media: Table-top production of a Gutenberg-Richter-like distribution

    Bretz, M., Zaretzki, R., Field, S., Mitarai, Namiko & Nori, F., 2 Jun 2006, In: EPL. 74, 6, p. 1116-1122

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

  39. 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

  40. Published

    Deterministic extinction by mixing in cyclically competing species

    Feldager, C. W., Mitarai, Namiko & Ohta, H., 20 Mar 2017, In: Physical Review E. 95, 3, 032318.

    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. Erratum: Bagnold scaling, density plateau, and kinetic theory analysis of dense granular flow (Physical Review Letters (2005) 94 (128001))

    Mitarai, Namiko & Nakanishi, H., 13 Jul 2006, In: Physical Review Letters. 97, 1, 019902.

    Research output: Contribution to journal › Comment/debate › Research › peer-review

  43. 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

  44. 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

  45. Published

    Emergence of growth and dormancy from a kinetic model of the Escherichia coli central carbon metabolism

    Himeoka, Y. & Mitarai, Namiko, 30 Dec 2022, In: Physical Review Research. 4, 4, 23 p., 043223.

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

  46. 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

  47. 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

  48. 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

  49. Published

    Axelrod model: accepting or discussing

    Dybiec, B. M., Mitarai, Namiko & Sneppen, Kim, 1 Oct 2012, In: European Physical Journal B. Condensed Matter and Complex Systems. 85, 10, p. 357

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

  50. 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

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