-
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
-
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
-
When to wake up? The optimal waking-up strategies for starvation-induced persistence
Yusuke Himeoka and Namiko Mitarai
arXiv:1912.12682
bioRxiv:2019.12.29.890285v1
-
Scaling laws of multilevel selection: a striking difference between continuous-trait and binary-trait models
Nobuto Takeuchi, Namiko Mitarai, Kunihiko Kaneko
arxiv:2005.04421
-
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
-
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)
-
Dynamics of bacterial populations under the feast-famine cycles
Yusuke Himeoka and Namiko Mitarai
Phys. Rev. Res. 2, 013372 (2000)
aRxiv:1910.05673
-
Sustainability of spatially distributed bacteria-phage systems
Rasmus Skytte Eriksen, Namiko Mitarai, Kim Snpeppen
Sci. Rep. 10, 3154 (2000)
BioRxiv 495671
-
How pirate phage interferes with helper phage: Comparison of the two distinct strategies
Namiko Mitarai
J. Theor. Biol. 486, 110096 (2020).
BioRxiv 576587
-
Finite response time in stripe formation by bacteria with density-suppressed motility
Xingyu Zhang and Namiko Mitarai
aRxiv:1905.02933
-
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).
-
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).
-
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.
-
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
-
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).
-
Theory of invasion extinction dynamics in minimal food webs
Jan O. Haerter, Namiko Mitarai, and Kim Sneppen
Phys. Rev. E vol. 97, 022404 (2018).
PDF
-
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).
PDF
Preprint:
bioRxiv 149062; doi: https://doi.org/10.1101/149062
-
Toxins, Targets, and Triggers: An Overvis of Toxin-Antitoxin Biology
Alexander Harms, Ditlev Egeskov Brodersen, Namiko Mitarai,
Kenn Gerdes
(Review)
Molecular Cell (2018), https://doi.org/10.1016/j.molcel.2018.01.003
-
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: https://doi.org/10.1101/097907
-
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
-
Deterministic extinction by mixing in cyclically competing species
Cilie W. Feldager, Namiko Mitarai, and Hiroki Ohta.
Phys. Rev. E, vol. 95, 032318 (2017)
PDF
Preprint:
arXiv:1609.08297
-
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)
.
-
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)
PDF
Preprint:
arXiv:1611.00171
-
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)
PDF
-
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).
PDF
Chosen for
SPOTLIGHT
-
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)
PDF
preprint: arXiv:1512.00769
-
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
-
Bifurcation of Transition Paths Induced by Coupled Bistable Systems
Chengzhe Tian and Namiko Mitarai
J. Chem. Phys. vol 144, 215102 (2016)
PDF
preprint: arXiv:1603.04477
-
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
-
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).
PDF
-
Fixation in cyclically competing species on a directed graph with quenched disorder
Hiroki Ohta and Namiko Mitarai.
In revision.
Preprint:
arXiv:1402.6624
-
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
-
Speciation, Diversification, and Coexistence of Sessile Species that Compete for Space
Namiko Mitarai, Els Heinsalu, and Kim Sneppen.
Plos One, vol 9, e96665 (2014).
PDF
-
Modeling rises and falls in money addicted social hierarchies
Bartlomiej Dybiec, Namiko Mitarai, and Kim Sneppen
Physica Scripta, 89, 085002 (2014).
-
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
-
Experimental observation of shear thickening oscillation
Shin-ichiro Nagahiro, Hiizu Nakanishi, Namiko Mitarai
EPL (Europhysics Leters), 104, 28002 (2013).
Preprint:
arXiv:1211.2886
-
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
-
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
-
Entrainment of noise-induced and limit cycle oscillators under weak noise
Namiko Mitarai, Uri Alon, Mogens H. Jensen
Chaos 23, 023125 (2013).
PDF
Preprint:
arXiv:1301.2440
-
Circuit architecture explains
functional similarity of bacterial heat shock responses
Masayo Inoue, Namiko Mitarai, and Ala Trusina.
Phys. Biol. 9, 066003 (2012)
PDF
arXiv:1209.2504
-
Multistability with a Metastable Mixed State
Kim Sneppen and Namiko Mitarai
Phys. Rev. Lett. 109, 100602 (2012)
PDF
-
Emergence of diversity in a model ecosystem
Namiko Mitarai, Joachim Mathiesen, Kim Sneppen
Phys. Rev. E 86, 011929 (2012)
PDF
arXiv:1204.3398
-
Axelrod model: accepting or discussing
Bartlomiej Dybiec, Namiko Mitarai, Kim Sneppen
Eur. Phys. J. B, 85, 357 (2012)
-
Information spreading and development of cultural centers
Bartlomiej Dybiec, Namiko Mitarai, Kim Sneppen
Phys. Rev. E 85, 056116 (2012).
PDF
arXiv:1201.3052
-
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).
PDF
arXiv:1204.3760
-
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
-
Granular flow: Dry and wet
Namiko Mitarai and Hiizu Nakanishi
Eur. Phys. J. Special Topics 204, 5-17 (2012)
-
Fluid dynamics of dilatant fluid
Hiizu Nakanishi, Shin-ichiro Nagahiro, and Namiko Mitarai.
Phys. Rev. E 85, 011401 (2012)
PDF
arXiv:1112.4593
-
Protein localization with flexible DNA or RNA
Sebastian Bernhardsson, Namiko Mitarai, and Kim Sneppen.
Plos One, Vol. 7, e29218 (2012)
PDF
and
Supporting Material
-
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)
PDF
arXiv:1108.2011
-
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)
PDF
arXiv:1101.3998
-
Shear Thickening Oscillation in a Dilatant Fluid
Hiizu Nakanishi and Namiko Mitarai
J. Phys. Soc. Jpn., Vol.80, No.3, p.033801 (2011)
PDF
arXiv:1010.5063
-
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)
-
Theory for stability and regulation of epigenetic landscapes
Mille A. Micheelsen, Namiko Mitarai, Kim Sneppen, and Ian. B. Dodd
Phys. Biol. 7, 026010 (2010)
PDF
arXiv:1002.1600v1
-
Simple Model for Wet Granular Materials with Liquid Clusters
Namiko Mitarai and Hiizu Nakanishi
Europhys. Lett. 88, 64001 (2009)
arXiv:0908.1477v2
-
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)
arXiv:0909.2125v1
-
Loewner driving functions for off-critical percolation clusters
Yoichiro Kondo, Namiko Mitarai, and Hiizu Nakanishi
Phys. Rev. E 80, 050102R (2009)
arXiv:0908.1275v1
-
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)
-
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
-
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)
arXiv:0807.5031v3
-
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)
PDF
arXiv:0809.4310v1
-
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).
arXiv:0810.2145v1
-
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)
arXiv:0711.4504v1
-
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).
cond-mat/0611397
-
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)
q-bio.MN/0611069
-
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)
cond-mat/0606256
-
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
- Wet granular materials
Namiko MITARAI and Franco NORI
Adv. Phys. Vol. 55, No. 01-02, pp.1-45 (2006)
cond-mat/0601660
- Bagnold scaling, density plateau, and kinetic theory analysis of
dense granular flow
Namiko MITARAI and Hiizu NAKANISHI
Phys. Rev. Lett. Vol. 94, 128001 (2005)
cond-mat/0407651
- 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
- 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
- Collisional Granular Flow as a Micropolar Fluid
Namiko MITARAI, Hisao HAYAKAWA, and Hiizu NAKANISHI
Phys. Rev. Lett. 88, 174301 (2002)
cond-mat/0108192
-
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
- 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
- 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
-
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
-
流れる粉体の動力学--バグノルド則をめぐって-- (解説)
御手洗菜美子、中西秀
日本物理学会誌、vol. 62, pp. 676- 684 (2007年9月号)
Conference Proceedings (with review)
- 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).
- 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)
-
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
-
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
- Essay "Physics: see how the world works" (in Japanese)
Namiko Mitarai
in booklet published to steer girls towards scientific careers,
Kyushu University, Japan (2007).
-
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.
-
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.
-
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.
- Instability of Granular Flow on Rough Inclined Plane
Namiko MITARAI and Hiizu NAKANISHI
Proceedings of Powders and Grains 2001, p.455 (2001).
- Particle diffusion in the cooling process of granular gas
Hiizu NAKANISHI and Namiko MITARAI
Proceedings of Powders and Grains 2001, p.581 (2001).
- 極性流体としての粉体斜面流
御手洗菜美子、早川尚男、中西秀
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.
- 斜面上の粉体流とその安定性
御手洗菜美子、早川尚男、中西秀
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)
Thesis
- 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
Organizations
- Aug. 2-Aug.8 2015,
one of the organizers of
Summer School & Workshop "Models of Life",
at Krogerup Hoejskole, Humlebaek, Denmark.
- Aug. 12-Aug.17 2012,
one of the organizers of
Summer School "DNA dynamics and life strategies",
at Krogerup Hoejskole, Humlebaek, Denmark.
- Aug. 25-Aug.27 2011,
one of the organizers of
Minischool / workshop "Signals and Space: Spatio-temporal patterns
in simple bio-systems", at Niels Bohr Institute, Denmark.
- May 13, 2011, "the Oeresund Bio Battle", NBI, Copenhagen, Denmark.
- Jul. 21-Aug.21 2009,
Organizing committee member of
YKIS 2009 ``Frontiers
in Nonequilibrium Physics''
-
Nov. 2008-Oct. 2009,
日本物理学会領域11役員
-
Nov. 2002,
Organized a workshop on Complex Systems with A. Awazu
at Oita, Japan.