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  1. Book ; Online: Stability analysis for circulant structured multi-agent molecular communication systems

    Kotsuka, Taishi / Hori, Yutaka

    2023  

    Abstract: 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 ... ...

    Abstract 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.
    Keywords Electrical Engineering and Systems Science - Systems and Control
    Publishing date 2023-01-23
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Stability analysis for large-scale multi-agent molecular communication systems

    Kotsuka, Taishi / Hori, Yutaka

    2023  

    Abstract: Molecular communication (MC) is recently featured as a novel communication tool to connect individual biological nanorobots in vivo. It is expected that a large number of nanorobots can form large multi-agent MC systems through MC to accomplish complex ... ...

    Abstract Molecular communication (MC) is recently featured as a novel communication tool to connect individual biological nanorobots in vivo. 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 the 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 to analyze the stability of 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.
    Keywords Electrical Engineering and Systems Science - Systems and Control ; Computer Science - Information Theory ; Quantitative Biology - Molecular Networks
    Subject code 006
    Publishing date 2023-11-11
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Frequency response of diffusion-based molecular communication channels in bounded environment

    Kotsuka, Taishi / Hori, Yutaka

    2022  

    Abstract: 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 ... ...

    Abstract 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.

    Comment: 6 pages, 5 figures
    Keywords Electrical Engineering and Systems Science - Systems and Control ; Computer Science - Information Theory ; Quantitative Biology - Molecular Networks
    Subject code 612
    Publishing date 2022-03-25
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Book ; Online: A Control-theoretic Model for Bidirectional Molecular Communication Systems

    Kotsuka, Taishi / Hori, Yutaka

    2022  

    Abstract: 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 ... ...

    Abstract 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.
    Keywords Electrical Engineering and Systems Science - Systems and Control ; Quantitative Biology - Quantitative Methods
    Subject code 000
    Publishing date 2022-10-26
    Publishing country us
    Document type Book ; Online
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  5. Article: L-2L ladder digital-to-analogue converter for dynamics generation of chemical concentrations.

    Chatani, Tomohito / Shiraishi, Suguru / Miyazako, Hiroki / Onoe, Hiroaki / Hori, Yutaka

    Royal Society open science

    2023  Volume 10, Issue 4, Page(s) 230085

    Abstract: Cellular response to dynamic chemical stimulation encodes rich information about the underlying reaction pathways and their kinetics. Microfluidic chemical stimulators play a key role in generating dynamic concentration waveforms by mixing several ... ...

    Abstract Cellular response to dynamic chemical stimulation encodes rich information about the underlying reaction pathways and their kinetics. Microfluidic chemical stimulators play a key role in generating dynamic concentration waveforms by mixing several aqueous solutions. In this article, we propose a multi-layer microfluidic chemical stimulator capable of modulating chemical concentrations by a simple binary logic based on the electronic-hydraulic analogy of electronic R-2R ladder circuits. The proposed device, which we call L-2L ladder digital-to-analogue converter (DAC), allows us to systematically modulate 2
    Language English
    Publishing date 2023-04-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2787755-3
    ISSN 2054-5703
    ISSN 2054-5703
    DOI 10.1098/rsos.230085
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A parametric logistic equation with light flux and medium concentration for cultivation planning of microalgae.

    Kambe, Kazuki / Hirokawa, Yasutaka / Koshi, Asuka / Hori, Yutaka

    Journal of the Royal Society, Interface

    2022  Volume 19, Issue 191, Page(s) 20220166

    Abstract: Microalgae are considered to be promising producers of bioactive chemicals, feeds and fuels from carbon dioxide by photosynthesis. Thus, the prediction of microalgal growth profiles is important for the planning of cost-effective and sustainable ... ...

    Abstract Microalgae are considered to be promising producers of bioactive chemicals, feeds and fuels from carbon dioxide by photosynthesis. Thus, the prediction of microalgal growth profiles is important for the planning of cost-effective and sustainable cultivation-harvest cycles. This paper proposes a mathematical model capable of predicting the effect of light flux into culture and medium concentration on the growth profiles of microalgae by incorporating these growth-limiting factors into a logistic equation. The specific form of the equation is derived based on the experimentally measured growth profiles of
    MeSH term(s) Biomass ; Carbon Dioxide ; Microalgae ; Photosynthesis
    Chemical Substances Carbon Dioxide (142M471B3J)
    Language English
    Publishing date 2022-06-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2156283-0
    ISSN 1742-5662 ; 1742-5689
    ISSN (online) 1742-5662
    ISSN 1742-5689
    DOI 10.1098/rsif.2022.0166
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online: Interval Analysis of Worst-case Stationary Moments for Stochastic Chemical Reactions with Uncertain Parameters

    Sakurai, Yuta / Hori, Yutaka

    2021  

    Abstract: The dynamics of cellular chemical reactions are variable due to stochastic noise from intrinsic and extrinsic sources. The intrinsic noise is the intracellular fluctuations of molecular copy numbers caused by the probabilistic encounter of molecules and ... ...

    Abstract The dynamics of cellular chemical reactions are variable due to stochastic noise from intrinsic and extrinsic sources. The intrinsic noise is the intracellular fluctuations of molecular copy numbers caused by the probabilistic encounter of molecules and is modeled by the chemical master equation. The extrinsic noise, on the other hand, represents the intercellular variation of the kinetic parameters due to the variation of global factors affecting gene expression. The objective of this paper is to propose a theoretical framework to analyze the combined effect of the intrinsic and the extrinsic noise modeled by the chemical master equation with uncertain parameters. More specifically, we formulate a semidefinite program to compute the intervals of the stationary solution of uncertain moment equations whose parameters are given only partially in the form of the statistics of their distributions. The semidefinite program is derived without approximating the governing equation in contrast with many existing approaches. Thus, we can obtain guaranteed intervals of the worst possible values of the moments for all parameter distributions satisfying the given statistics, which are prohibitively hard to estimate from sample-path simulations since sampling from all possible uncertain distributions is difficult. We demonstrate the proposed optimization approach using two examples of stochastic chemical reactions and show that the solution of the optimization problem gives informative upper and lower bounds of the statistics of the stationary copy number distributions.
    Keywords Electrical Engineering and Systems Science - Systems and Control ; Quantitative Biology - Quantitative Methods
    Subject code 510
    Publishing date 2021-02-08
    Publishing country us
    Document type Book ; Online
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  8. Article ; Online: Optimization-based synthesis of stochastic biocircuits with statistical specifications.

    Sakurai, Yuta / Hori, Yutaka

    Journal of the Royal Society, Interface

    2018  Volume 15, Issue 138

    Abstract: Model-guided design has become a standard approach to engineering biomolecular circuits in synthetic biology. However, the stochastic nature of biomolecular reactions is often overlooked in the design process. As a result, cell-cell heterogeneity causes ... ...

    Abstract Model-guided design has become a standard approach to engineering biomolecular circuits in synthetic biology. However, the stochastic nature of biomolecular reactions is often overlooked in the design process. As a result, cell-cell heterogeneity causes unexpected deviation of biocircuit behaviours from model predictions and requires additional iterations of design-build-test cycles. To enhance the design process of stochastic biocircuits, this paper presents a computational framework to systematically specify the level of intrinsic noise using well-defined metrics of statistics and design highly heterogeneous biocircuits based on the specifications. Specifically, we use descriptive statistics of population distributions as an intuitive specification language of stochastic biocircuits and develop an optimization-based computational tool that explores parameter configurations satisfying design requirements. Sensitivity analysis methods are also performed to ensure the robustness of a biocircuit design against extrinsic perturbations. These design tools are formulated with convex optimization programs to enable rigorous and efficient quantification of the statistics. We demonstrate these features by designing a stochastic negative feedback biocircuit that satisfies multiple statistical constraints and perform an in-depth study of noise propagation and regulation in negative feedback pathways.
    MeSH term(s) Animals ; Humans ; Models, Biological ; Signal Transduction ; Stochastic Processes ; Synthetic Biology
    Language English
    Publishing date 2018-01-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2156283-0
    ISSN 1742-5662 ; 1742-5689
    ISSN (online) 1742-5662
    ISSN 1742-5689
    DOI 10.1098/rsif.2017.0709
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Analysing diffusion and flow-driven instability using semidefinite programming.

    Hori, Yutaka / Miyazako, Hiroki

    Journal of the Royal Society, Interface

    2017  Volume 16, Issue 150, Page(s) 20180586

    Abstract: Diffusion and flow-driven instability, or transport-driven instability, is one of the central mechanisms to generate inhomogeneous gradient of concentrations in spatially distributed chemical systems. However, verifying the transport-driven instability ... ...

    Abstract Diffusion and flow-driven instability, or transport-driven instability, is one of the central mechanisms to generate inhomogeneous gradient of concentrations in spatially distributed chemical systems. However, verifying the transport-driven instability of reaction-diffusion-advection systems requires checking the Jacobian eigenvalues of infinitely many Fourier modes, which is computationally intractable. To overcome this limitation, this paper proposes mathematical optimization algorithms that determine the stability/instability of reaction-diffusion-advection systems by finite steps of algebraic calculations. Specifically, the stability/instability analysis of Fourier modes is formulated as a sum-of-squares optimization program, which is a class of convex optimization whose solvers are widely available as software packages. The optimization program is further extended for facile computation of the destabilizing spatial modes. This extension allows for predicting and designing the shape of the concentration gradient without simulating the governing equations. The streamlined analysis process of self-organized pattern formation is demonstrated with a simple illustrative reaction model with diffusion and advection.
    MeSH term(s) Algorithms ; Computer Simulation ; Models, Theoretical ; Programming Languages
    Language English
    Publishing date 2017-05-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2156283-0
    ISSN 1742-5662 ; 1742-5689
    ISSN (online) 1742-5662
    ISSN 1742-5689
    DOI 10.1098/rsif.2018.0586
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  10. Article ; Online: Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space.

    Nishikawa, Saki / Sato, Gaku / Takada, Sakura / Kohyama, Shunshi / Honda, Gen / Yanagisawa, Miho / Hori, Yutaka / Doi, Nobuhide / Yoshinaga, Natsuhiko / Fujiwara, Kei

    Advanced science (Weinheim, Baden-Wurttemberg, Germany)

    2023  Volume 11, Issue 6, Page(s) e2308030

    Abstract: Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various ... ...

    Abstract Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various macromolecules in cell-size space remains still elusive. Here, using a constructive approach, it is demonstrated that the co-existence of various macromolecules themselves has the ability to tune protein localization for spatiotemporal regulation and a biochemical reaction system in a cell-size space. Both experimental and theoretical analyses reveal that enhancement of interfacial effects by a large surface-area-to-volume ratio facilitates membrane localization of molecules in the cell-size space, and the interfacial effects are alleviated by competitive binding to lipid membranes among multiple proteins even if their membrane affinities are weak. These results indicate that competition for membrane binding among various macromolecules in the cell-size space plays a role in regulating the spatiotemporal molecular organization and biochemical reaction networks. These findings shed light on the importance of surrounding molecules for biochemical reactions using purified elements in small spaces.
    MeSH term(s) Proteins/chemistry ; Protein Transport
    Chemical Substances Proteins
    Language English
    Publishing date 2023-12-06
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2808093-2
    ISSN 2198-3844 ; 2198-3844
    ISSN (online) 2198-3844
    ISSN 2198-3844
    DOI 10.1002/advs.202308030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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