Embedded Files
Elucidating the Bell-Shaped Dependence of Protein Translation Activity on EF-Tu Concentration in a Reconstituted Cell-Free System Using a Mechanistic Model
Shunnosuke Ban, Yusuke Himeoka, Ako Kagawa, Yoshihiro Shimizu, Tomoaki Matsuura, and Chikara Furusawa
ACS Synthetic Biology, 10.1021/acssynbio.6c00333 (2026)
Population dynamics of generalist and specialist strategies under feast-famine cycles
Rintaro Niimi, Chikara Furusawa, and Yusuke Himeoka
PLoS Computational Biology 22(4): e1014265, (2026)
Analysis of metabolic stability under environmental perturbations using a kinetic model
Atsuki Hishida, Yusuke Himeoka, and Chikara Furusawa
Biophysics and Physicobiology, 23, 1 e230001, (2026)
Local stabilizability implies global controllability in catalytic reaction systems
Yusuke Himeoka, Shuhei A. Horiguchi, Naoto Shiraishi, Fangzhou Xiao, Tetsuya J. Kobayashi
arXiv:2505.06834, (2025)
Theoretical basis for cell deaths
Yusuke Himeoka, Shuhei A. Horiguchi, and Tetsuya J. Kobayashi
Phys. Rev. Res. 6, 043217, (2024)
Press release (JP, EN)
Commantary (JP)
Perturbation-response analysis of in silico metabolic dynamics revealed
hard-coded responsiveness in the cofactor and network sparsity
Yusuke Himeoka and Chikara Furusawa
eLife 13:RP98800, (2025)
Press release (JP, EN)
Evolution of hierarchy and irreversibility in theoretical cell differentiation model
Yoshiyuki T. Nakamura, Yusuke Himeoka, Nen Saito, and Chikara Furusawa
PNAS Nexus, 3, 1, 454, (2023)
Roles of network topology in the relaxation dynamics of simple chemical reaction network models
Yusuke Himeoka, Julius B. Kirkegaard,
Namiko Mitarai, and Sandeep Krishna
Scientific Reports, 14, 22187, (2024)
Emergence of growth and dormancy
from a kinetic model of the Escherichia coli central carbon metabolism
Yusuke Himeoka, and Namiko Mitarai
Physical Review Research 4, 043223 (2022)
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
mSphere, e01006-21., (2022)
When to wake up? The optimal waking-up strategies
for starvation-induced persistence
Yusuke Himeoka, and Namiko Mitarai
PLoS Computational Biology, 17(2):e1008655, (2021)
Dynamics of bacterial populations under the feast-famine cycles
Yusuke Himeoka, and Namiko Mitarai
Physical Review Research, 2, (2020), 013372
Modeling slow-processing of toxin messenger RNAs in type-I Toxin-Antitoxin systems:
post-segregational killing and noise filtering
Yusuke Himeoka, and Namiko Mitarai
Physical Biology, 16, (2019), 026001
Epigenetic Ratchet: Spontaneous Adaptation via Stochastic Gene Expression
Yusuke Himeoka, and Kunihiko Kaneko
Scientific Reports, 10, 459, (2020)
Theory for Transitions Between Exponential and Stationary Phases:
Universal Laws for Lag Time
Yusuke Himeoka, and Kunihiko Kaneko
Enzyme oscillation can enhance the thermodynamic efficiency of cellular metabolism: consequence of anti-phase coupling between reaction flux and affinity
Yusuke Himeoka, and Kunihiko Kaneko
Entropy production of a steady-growth cell with catalytic reactions
Yusuke Himeoka, and Kunihiko Kaneko
Phys. Rev. E 90, 042714 (2014)
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