arXiv subjects

Sohei Tasaki

Publications and source records attributed to Sohei Tasaki.

5 recordsLinked to original sources

arXiv2026

Model-based optimization of bacterial motility strategies for maximizing population yield

Bacterial motility is a fundamental trait for territorial expansion and resource acquisition. While existing models of nutrient-dependent motility often do not explicitly account for the metabolic costs associated with motility, these costs become critical in nutrient-limited or closed systems. In this study, we developed a mathematical framework using partial differential equations (PDEs) that explicitly incorporates the energetic trade-offs of motility. By formulating an optimization problem focused on maximizing population yield---defined by the total cell count---we evaluated various motility strategies across different environmental contexts. Our results demonstrate that the optimal motility response is highly sensitive to resource distribution. Specifically, we show that in unpredictable environments, a non-monotonic motility response emerges as the optimal strategy, providing a robust theoretical explanation for dose-response curves observed in experimental microbiology. This framework serves as a powerful, interpretable tool for predicting bacterial behavior in resource-constrained ecosystems and offers new insights into how such adaptive strategies are shaped by environmental pressures.

q-bio.PE↗

arXiv2026

Turing patterns on non-fluctuating surfaces under mechanical stresses

This paper presents a numerical study of Turing patterns (TPs) governed by reaction diffusion equations for the activator $u$ and the inhibitor $v$ on two- and three-dimensional lattices without vertex fluctuations. In this framework, $u$ and $v$ are fixed at discrete spatial locations, as pigment cells on zebrafish skin or shell patterns. Mechanical effects are incorporated through the Finsler geometry modeling formulation, which introduces an internal degree of freedom, $\vec{\tau}$, representing the direction of mechanical stress. A tensile-stress formula based on the Gaussian bond potential is shown to be well defined on non-fluctuating lattices, enabling the entropy associated with stress relaxation to be evaluated in a manner analogous to that on fluctuating surfaces. The results indicate that biological TPs respond to external mechanical forces in much the same way as TPs on fluctuating membranes. Simulation codes are provided in the Supplementary Material.

nlin.PS↗

arXiv2023

Numerical study of anisotropic diffusion in Turing patterns based on Finsler geometry modeling

We numerically study the anisotropic Turing patterns (TPs) of an activator-inhibitor system, focusing on anisotropic diffusion by using the Finsler geometry (FG) modeling technique. In the FG modeling prescription, the diffusion coefficients are dynamically generated to be direction dependent owing to an internal degree of freedom (IDOF) and its interaction with the activator and inhibitor under the presence of thermal fluctuations. In this sense, FG modeling contrasts sharply with the standard numerical technique, where direction-dependent diffusion coefficients are assumed in the reaction-diffusion (RD) equations of Turing. To find the solution of the RD equations, we use a hybrid numerical technique as a combination of the metropolis Monte Carlo method for IDOF updates and discrete RD equations for steady-state configurations of activator-inhibitor variables. We find that the newly introduced IDOF and its interaction are one possible origin of spontaneously emergent anisotropic patterns on living organisms such as zebra and fishes. Moreover, the IDOF makes TPs controllable by external conditions if the IDOF is identified with lipids on cells or cell mobility.

nlin.PS↗

arXiv2020

Necessary and sufficient condition for hysteresis in the mathematical model of the cell type regulation of \textit{Bacillus subtilis}

The key to a robust life system is to ensure that each cell population is maintained in an appropriate state. In this work, a mathematical model was used to investigate the control of the switching between the migrating and non-migrating states of the Bacillus subtilis cell population. In this case, the motile cells and matrix producers were the predominant cell types in the migrating cell population and non-migrating state, respectively, and could be suitably controlled according to the environmental conditions and cell density information. A minimal smooth model consisting of four ordinary differential equations was used as the mathematical model to control the B. subtilis cell types. Furthermore, the necessary and sufficient conditions for the hysteresis, which pertains to the change in the pheromone concentration, were clarified. In general, the hysteretic control of the cell state enables stable switching between the migrating and growth states of the B. subtilis cell population, thereby facilitating the biofilm life cycle. The results of corresponding culture experiments were examined, and the obtained corollaries were used to develop a model to input environmental conditions, especially, the external pH. On this basis, the environmental conditions were incorporated in a simulation model for the cell type control. In combination with a mathematical model of the cell population dynamics, a prediction model for colony growth involving multiple cell states, including concentric circular colonies of B. subtilis, could be established.

q-bio.CB↗

arXiv2018

Non-invasive force measurement reveals the number of active kinesins on a synaptic vesicle precursor in axonal transport regulated by ARL-8

Kinesin superfamily protein UNC-104, a member of the kinesin-3 family, transports synaptic vesicle precursors (SVPs). In this study, the number of active UNC-104 molecules hauling a single SVP in axons in the worm Caenorhabditis elegans was counted by applying a newly developed non-invasive force measurement technique. The distribution of the force acting on a SVP transported by UNC-104 was spread out over several clusters, implying the presence of several force-producing units (FPUs). We then compared the number of FPUs in the wild-type worms with that in arl-8 gene-deletion mutant worms. ARL-8 is a SVP-bound arf-like small guanosine triphosphatase, and is known to promote unlocking of the autoinhibition of the motor, which is critical for avoiding unnecessary consumption of adenosine triphosphate when the motor does not bind to a SVP. There were fewer FPUs in the arl-8 mutant worms. This finding indicates that a lack of ARL-8 decreased the number of active UNC-104 motors, which then led to a decrease in the number of motors responsible for SVP transport.

physics.bio-ph↗