Tetsuya J. Kobayashi

The University of Tokyo

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Gene Toggle Switches Only with Positive Feedback Loops

Proceedings Genome Informatics Workshop/Genome informatics (2001)

Tetsuya J. Kobayashi Luonan Chen Kazuyuki Aihara

1 Department of Mathematical Engineering and Information Physics, Faculty of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan 2 Department of Electrical Engineering and Electronics Faculty of Engineering, Osaka Sangyo University, 3-1-1 Nakagaito, Daito, 574-8530 Osaka, Japan 3 Department of Complexity Science and Engineering, Faculty of Frontier Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, 113-8656 Tokyo, Japan CREST, Japan Science and Technology Corporation (JST), 4-1-8 Hon-cho, Kawaguchi, Saitama 332, Japan

Frontier

Science and engineering

10.11234/gi1990.12.294

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Citations (2)

61 STRUCTURAL RELATIONSHIPS OF SESQUITERPENS OBTAINED FROM ALPINIA JAPONICA (THUNB.) MIQ.

天然有機化合物討論会講演要旨集 (1985)

Hideji Itokawa Hiroshi Morita Kenji Osawa Tetsuya J. Kobayashi H. Kubota

Alpinia

Source

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Regional characteristics in the requirement certification rate of Long-term Care Insurance : An analysis of the tendency of requirement certification rate in the 47 prefectures of Japan

Tetsuya J. Kobayashi

Source

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Citations (1)

Individual Sensing can Gain more Fitness than its Information

arXiv (Cornell University) (2017)

Tetsuya J. Kobayashi Yuki Sughiyama

Mutual information and its causal variant, directed information, have been widely used to quantitatively characterize the performance of biological sensing and information transduction. However, once coupled with selection in response to decision-making, the sensing signal could have more or less evolutionary value than its mutual or directed information. In this work, we show that an individually sensed signal always has a better fitness value, on average, than its mutual or directed information. The fitness gain, which satisfies fluctuation relations (FRs), is attributed to the selection of organisms in a population that obtain a better sensing signal by chance. A new quantity, similar to the coarse-grained entropy production in information thermodynamics, is introduced to quantify the total fitness gain from individual sensing, which also satisfies FRs. Using this quantity, the optimizing fitness gain from individual sensing is shown to be related to fidelity allocations for individual environmental histories. Our results are supplemented by numerical verifications of FRs, and a discussion on how this problem is linked to information encoding and decoding.

Information gain

Information Theory

Value of information

SIGNAL (programming language)

10.48550/arxiv.1712.09462

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Mean-Field Control Approach to Decentralized Stochastic Control with Finite-Dimensional Memories

arXiv (Cornell University) (2022)

Takehiro Tottori Tetsuya J. Kobayashi

Decentralized stochastic control (DSC) considers the optimal control problem of a multi-agent system. However, DSC cannot be solved except in the special cases because the estimation among the agents is generally intractable. In this work, we propose memory-limited DSC (ML-DSC), in which each agent compresses the observation history into the finite-dimensional memory. Because this compression simplifies the estimation among the agents, ML-DSC can be solved in more general cases based on the mean-field control theory. We demonstrate ML-DSC in the general LQG problem. Because estimation and control are not clearly separated in the general LQG problem, the Riccati equation is modified to the decentralized Riccati equation, which improves estimation as well as control. Our numerical experiment shows that the decentralized Riccati equation is superior to the conventional Riccati equation.

Algebraic Riccati equation

10.48550/arxiv.2209.05067

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Data center energy conservation utilizing a heat pipe based ice storage system

Gerald Cabusao Masataka Mochizuki Koichi Mashiko Tetsuya J. Kobayashi Randeep Singh

Data centers constantly expand and upgrade their capacity due to the ever-increasing demand for remote file storage. It is estimated that around 50% of the total data center power consumption is for cooling. With this trend, a reduction in the cooling power consumption would result in a substantial reduction in overall power consumption, as well as C02 emission. With the focus going towards renewable and natural sources of energy, a heat pipe based ice storage system is being proposed. This system is being considered as one good solution to reduce the power consumption, as well as CO2 emission of data centers. This Ice storage system is aimed at utilizing the low temperature of cold areas to form ice and cold water. The freezing index, which is the combined duration and magnitude of below freezing temperatures at a given freezing season, would be the criteria for choosing the data center location. The data center will be constructed in cold regions wherein the freezing index is 400°C-days and above. The thermosiphon, which acts as a thermal diode, can effectively cool down the water until ice is formed. This ice storage system can be integrated with the existing cooling system and can be utilized as an alternate cooling system or a back-up cooling system. The existing cooling system may be utilized during the warmer periods of the year. The actual ice storage system container, which is made of concrete, is to be constructed under ground, and integrated in parallel with the existing cooling system.

Data center

Upgrade

10.1109/cpmtsympj.2010.5680287

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Citations (13)

On the Capacity of Write-Constrained Memories

IEEE Transactions on Information Theory (2017)

Tetsuya J. Kobayashi Hiroyoshi Morita Akiko Manada

Rivest and Shamir introduced a write-once memory (WOM), a model of storage devices whose storage elements have restrictions on state transitions, and they presented some coding methods to reuse a WOM. An interesting question about a WOM is how efficiently we can reuse it with the best coding method, and as an answer to the question, Fu and Han Vinck determined the capacity of Fiat and Shamir's generalized WOMs. In this paper, we extend their results, introducing write-constrained memories (WCMs) that consider state transition costs, and determining the capacity of WCMs under a certain type of cost constraints.

10.1109/tit.2017.2739781

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Citations (3)

Chemical Thermodynamics for Growing Systems

arXiv (Cornell University) (2022)

Yuki Sughiyama Atsushi Kamimura Dimitri Loutchko Tetsuya J. Kobayashi

We consider growing open chemical reaction systems (CRSs), in which autocatalytic chemical reactions are encapsulated in a finite volume and its size can change in conjunction with the reactions. The thermodynamics of growing CRSs is indispensable for understanding biological cells and designing protocells by clarifying the physical conditions and costs for their growing states. In this work, we establish a thermodynamic theory of growing CRSs by extending the Hessian geometric structure of non-growing CRSs. The theory provides the environmental conditions to determine the fate of the growing CRSs; growth, shrinking or equilibration. We also identify thermodynamic constraints; one to restrict the possible states of the growing CRSs and the other to further limit the region where a nonequilibrium steady growing state can exist. Moreover, we evaluate the entropy production rate in the steady growing state. The growing nonequilibrium state has its origin in the extensivity of thermodynamics, which is different from the conventional nonequilibrium states with constant volume. These results are derived from general thermodynamic considerations without assuming any specific thermodynamic potentials or reaction kinetics; i.e., they are obtained based solely on the second law of thermodynamics.

Entropy production

Protocell

Equilibrium thermodynamics

10.48550/arxiv.2201.09417

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The Geometry of Thermodynamic Uncertainty Relations in Chemical Reaction Networks

arXiv (Cornell University) (2023)

Dimitri Loutchko Yuki Sughiyama Tetsuya J. Kobayashi

Recently, Hessian geometry - an extension of information geometry - has emerged as a framework to naturally connect the geometries appearing in the theory of chemical reaction networks (CRN) to their inherent thermodynamical and kinetic properties. This framework is used in this letter to derive multivariate thermodynamic uncertainty relations (TUR) for CRN. The matrices featured in the TUR are shown to be representations of Riemmanian metric tensors, whereby one tensor characterizes the pseudo entropy production rate and the other the current fluctuations. It is shown that the latter tensor is a restriction of the former one to a linear subspace in the flux tangent space. Therefore, in addition to clarifying the geometric origin of TUR in CRN, the Hessian geometric setup yields a characterization of the error term in the TUR as the norm of a linear subspace component of the flux vector and thus characterizes the fluxes where TUR become equalities.

Hessian matrix

10.48550/arxiv.2308.04806

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Citations (1)

Modeling Genetic Switches with Positive Feedback Loops

Journal of Theoretical Biology (2003)

Tetsuya J. Kobayashi Luonan Chen Kazuyuki Aihara

Oscillation (cell signaling)

10.1006/jtbi.2003.3190

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Citations (113)