arXiv subjects

Taishi Kotsuka

Publications and source records attributed to Taishi Kotsuka.

7 recordsLinked to original sources

arXiv2025

Model Reduction of Multicellular Communication Systems via Singular Perturbation: Sender Receiver Systems

We investigate multicellular sender receiver systems embedded in hydrogel beads, where diffusible signals mediate interactions among heterogeneous cells. Such systems are modeled by PDE ODE couplings that combine three dimensional diffusion with nonlinear intracellular dynamics, making analysis and simulation challenging. We show that the diffusion dynamics converges exponentially to a quasi steady spatial profile and use singular perturbation theory to reduce the model to a finite dimensional multiagent network. A closed form communication matrix derived from the spherical Green's function captures the effective sender receiver coupling. Numerical results show the reduced model closely matches the full dynamics while enabling scalable simulation of large cell populations.

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arXiv2025

Controlling Peak Sharpness in Multimodal Biomolecular Systems via the Chemical Fokker-Planck Equation

Intracellular biomolecular systems exhibit intrinsic stochasticity due to low molecular copy numbers, leading to multimodal probability distributions that play a crucial role in probabilistic differentiation and cellular decision-making. Controlling the dispersion of multimodal probability distributions in biomolecular systems is critical for regulating stochastic behavior, robustness, and adaptability. However, modifying system parameters to adjust dispersion often affects peak positions, potentially altering a desired phenotype or even fundamental behavior in a genetic pathway. In this paper, we establish a theoretical framework that enables independent control of dispersion while preserving peak positions and modality using the Chemical Fokker-Planck Equation (CFPE) and sharpness, a measure of probability concentration around individual peaks. By analyzing the steady-state solution of the CFPE, we derive explicit conditions under which peak sharpness can be tuned monotonically without changing peak positions or modality. We validate our approach through Monte Carlo simulations on a bimodal chemical system, demonstrating effective dispersion control while maintaining structural stability. This framework provides a systematic approach for designing biomolecular systems with tunable stochastic properties, contributing to advancements in synthetic biology and probabilistic cellular regulation.

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arXiv2024

Analysis of Signal Distortion in Molecular Communication Channels Using Frequency Response

Molecular communication (MC) is a concept in communication engineering, where diffusive molecules are used to transmit information between nano or micro-scale chemical reaction systems. Engineering MC to control the reaction systems in cells is expected for many applications such as targeted drug delivery and biocomputing. Toward control of the reaction systems as desired via MC, it is important to transmit signals without distortion by MC since the reaction systems are often triggered depending on the concentration of signaling molecules arriving at the cells. In this paper, we propose a method to analyze signal distortion caused by diffusion-based MC channels using frequency response of channels. The proposed method provides indices that quantitatively evaluate the magnitude of distortion and shows parameter conditions of MC channels that suppress signal distortion. Using the proposed method, we demonstrate the design procedure of specific MC channels that satisfy given specifications. Finally, the roles of MC channels in nature are discussed from the perspective of signal distortion.

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arXiv2024

Stability analysis for large-scale multi-agent molecular communication systems

Molecular communication (MC) is recently featured as a novel communication tool to connect individual biological nanorobots. It is expected that a large number of nanorobots can form large multi-agent MC systems through MC to accomplish complex and large-scale tasks that cannot be achieved by a single nanorobot. However, most previous models for MC systems assume a unidirectional diffusion communication channel and cannot capture the feedback between each nanorobot, which is important for multi-agent MC systems. In this paper, we introduce a system theoretic model for large-scale multi-agent MC systems using transfer functions, and then propose a method to analyze the stability for multi-agent MC systems. The proposed method decomposes the multi-agent MC system into multiple single-input and single-output (SISO) systems, which facilitates the application of simple analysis technique for SISO systems to the large-scale multi-agent MC system. Finally, we demonstrate the proposed method by analyzing the stability of a specific large-scale multi-agent MC system and clarify a parameter region to synchronize the states of nanorobots, which is important to make cooperative behaviors at a population level.

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arXiv2023

A Control-theoretic Model for Bidirectional Molecular Communication Systems

Molecular communication (MC) enables cooperation of spatially dispersed molecular robots through the feedback control mediated by diffusing signal molecules. However, conventional analysis frameworks for the MC channels mostly consider the dynamics of unidirectional communication, lacking the effect of feedback interactions. In this paper, we propose a general control-theoretic modeling framework for bidirectional MC systems capable of capturing the dynamics of feedback control via MC in a systematic manner. The proposed framework considers not only the dynamics of molecular diffusion but also the boundary dynamics at the molecular robots that captures the lag due to the molecular transmission/reception process affecting the performance of the entire feedback system. Thus, methods in control theory can be applied to systematically analyze various dynamical properties of the feedback system. We perform a frequency response analysis based on the proposed framework to show a general design guideline for MC channels to transfer signal with desired control bandwidth. Finally, these results are demonstrated by showing the step-by-step design procedure of a specific MC channel satisfying a given specification.

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arXiv2023

Stability analysis for circulant structured multi-agent molecular communication systems

In this paper, we introduce the system theoretic model for the multi-agent MC systems represented by multi-input and multi-output (MIMO) systems using the transfer functions, and then propose a method to analyze the stability for the special case of the circulant structured multi-agent MC systems. The proposed method decomposes the MIMO MC system into multiple single-input and single-output (SISO) systems, which facilitates to analyze of the stability of the large-scale multi-agent MC system. Finally, we demonstrate the proposed method to analyze the stability of a specific MC system.

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arXiv2022

Frequency response of diffusion-based molecular communication channels in bounded environment

Recently, molecular communication (MC) has been studied as a micro-scale communication between cells or molecular robots. In previous works, the MC channels in unbounded environment was analyzed. However, many of the experimentally implemented MC channels are surrounded by walls, thus the boundary condition should be explicitly considered to analyze the dynamics of MC channels. In this paper, we propose a framework to analyze the frequency response of one-dimensional MC channels based on a diffusion equation with a boundary. In particular, we decompose the MC channel into the diffusion system and the boundary system, and show the relation between the cut-off frequency of the MC channel and the communication distance based on the transfer function. We then analyze the frequency response of a specific MC channel and reveal that the boundary can restrict the communication bandwidth of the MC channel.

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