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mathematical Simulation of Linear Ubiquitination in T Cell Receptor-Mediated NF-κB Activation Pathway

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Mathematical Simulation of Linear Ubiquitination in T Cell R...

International Symposium on Fusion of Mathematics and Biology, 2020

作者： Oikawa, Daisuke Hatanaka, Naoya Suzuki, Takashi Tokunaga, Fuminori Department of Pathobiochemistry Graduate School of Medicine Osaka City University Osaka Japan Division of Mathematical Science Department of Systems Innovation Graduate School of Engineering Science Osaka University Toyonaka Japan Center for Mathematical Modeling and Data Science Osaka University Toyonaka Japan

ISBN: (纸本)9789811648656

The linear ubiquitin chain assembly complex (LUBAC), composed of the HOIP, HOIL-1L, and SHARPIN subunits, activates the canonical nuclear factor-κB (NF-κB) pathway through the Met1 (M1)-linked linear ubiquitination activity. On the course of the T cell receptor (TCR)-mediated NF-κB activation pathway, LUBAC transiently associates with and linearly ubiquitinates the CARMA1-BCL10-MALT1 (CBM) complex. In contrast, the linear ubiquitination of NEMO, a substrate of the TNF-α-induced NF-κB activation pathway, was limited in the TCR pathway. A linear ubiquitin-specific deubiquitinase (DUB), OTULIN, plays a major role in downregulating LUBAC-mediated TCR signaling. mathematical modeling indicated that linear ubiquitination of the CBM complex accelerates the activation of IκB kinase (IKK), as compared with the activity induced by linear ubiquitination of NEMO alone. Moreover, simulations of the sequential linear ubiquitination of the CBM complex suggested that the allosteric regulation of linear (de)ubiquitination of CBM subunits is controlled by the ubiquitin-linkage lengths. Thus, unlike the TNF-α-induced NF-κB activation pathway, the TCR-mediated NF-κB activation in T cells has a characteristic mechanism to induce LUBAC-mediated NF-κB activation. © 2021, Springer Nature Singapore Pte Ltd.

关键词： Chemical activation

Trade Execution Games in a Markovian Environment

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Applied mathematical Finance 2025年第4期31卷

作者： Ohnishi, Masamitsu Shimoshimizu, Makoto Faculty of Informatics Yamato University Osaka Suita City Japan Center for Mathematical Modeling and Data Science Osaka University Osaka Toyonaka City Japan Department of Industrial and Systems Engineering Tokyo University of Science Noda City Chiba Japan

This paper examines trade execution games for two large traders in a generalized price impact model. We incorporate a stochastic and sequentially dependent factor, called Markovian environment, that exogenously affects the market price into financial market modeling. Our model accounts for how strategic and environmental uncertainties affect the large traders' execution strategies. We formulate an expected utility maximization problem for two large traders as a Markov game model. Applying the backward induction method of dynamic programming, we provide an explicit closed-form execution strategy at a Markov perfect equilibrium. Our theoretical results reveal that the execution strategy generally lies in a dynamic and non-randomized class;it becomes deterministic if the Markovian environment is also deterministic. In addition, our simulation-based numerical experiments suggest that the execution strategy captures various features observed in financial markets. © 2025 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

关键词： dynamic programming Markov perfect equilibrium Markovian environment Price impact trade execution game

Liouville’s formulae and Hadamard variation with respect to general domain perturbations

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arXiv 2022年

作者： Suzuki, Takashi Tsuchiya, Takuya Center of Mathematical Modeling and Data Science Osaka University Toyonaka560-8531 Japan Graduate School of Science and Engineering Ehime University Matsuyama790-8577 Japan

We study Hadamard variations with respect to general domain perturbations, particularly for the Neumann boundary condition. They are derived from new Liouville’s formulae concerning the transformation of volume and area integrals. Then, relations to several geometric quantities are discussed;differential forms and the second fundamental form on the *** Codes 35J25, 35R35 © 2022, CC BY-NC-ND.

关键词： Boundary conditions

Free Boundary Problem of Cell Deformation and Invasion

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Free Boundary Problem of Cell Deformation and Invasion

International Symposium on Fusion of Mathematics and Biology, 2020

作者： Loling Othman, Nuha Suzuki, Takashi Faculty of Computer Science and Information Technology Universiti Malaysia Sarawak Kota Samarahan Sarawak94300 Malaysia Center for Mathematical Modeling and Data Science Osaka University 1-3 Machikaneyama-cho Toyonaka Osaka560-8531 Japan

ISBN: (纸本)9789811648656

A novel approach of free boundary problem of invadopodia formation and invasion is proposed in this paper. The modeling of invadopodia formation and invasion of cell involving the interaction across plasma membrane is considered. The formation is formulated by Stefan problem approach which is known as free boundary problem where the boundary membrane is priori unknown. Changes in cell membrane will lead to protrusions of cell membrane. A normal growing cell in tissue on an organ will be altered into cancerous cells after some processes of mutation in genes. We proposed level set method to indicate the moving plasma membrane and to represent the behavior of the cell interface. An efficient and a straightforward enthalpy method (phase change problem) is then used to provide the description of the cell membrane diffusion. We successfully show the formation of invadopodia and migration of a single cell modeling. © 2021, Springer Nature Singapore Pte Ltd.

关键词： Cell membranes

A prediction-correction based iterative convolution-thresholding method for topology optimization of heat transfer problems

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arXiv 2024年

作者： Chen, Huangxin Dong, Piaopiao Wang, Dong Wang, Xiao-Ping School of Mathematical Sciences Fujian Provincial Key Laboratory on Mathematical Modeling and High Performance Scientific Computing Xiamen University Fujian361005 China School of Science and Engineering The Chinese University of Hong Kong Guangdong Shenzhen518172 China Shenzhen International Center for Industrial and Applied Mathematics Shenzhen Research Institute of Big Data Guangdong518172 China

In this paper, we propose an iterative convolution-thresholding method (ICTM) based on prediction-correction for solving the topology optimization problem in steady-state heat transfer equations. The problem is formulated as a constrained minimization problem of the complementary energy, incorporating a perimeter/surface-area regularization term, while satisfying a steady-state heat transfer equation. The decision variables of the optimization problem represent the domains of different materials and are represented by indicator functions. The perimeter/surface-area term of the domain is approximated using Gaussian kernel convolution with indicator functions. In each iteration, the indicator function is updated using a prediction-correction approach. The prediction step is based on the variation of the objective functional by imposing the constraints, while the correction step ensures the monotonically decreasing behavior of the objective functional. Numerical results demonstrate the efficiency and robustness of our proposed method, particularly when compared to classical approaches based on the ICTM. Copyright © 2024, The Authors. All rights reserved.

关键词： Convolution

Trade execution games in a Markovian environment

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arXiv 2024年

作者： Ohnishi, Masamitsu Shimoshimizu, Makoto Faculty of Informatics Yamato University Osaka Suita City564-0082 Japan Center for Mathematical Modeling and Data Science Osaka University Toyonaka City Osaka560-8531 Japan Department of Industrial and Systems Engineering Tokyo University of Science 2641 Yamazaki Noda City Chiba278-8510 Japan

This paper examines a trade execution game for two large traders in a generalized price impact model. We incorporate a stochastic and sequentially dependent factor that exogenously affects the market price into financial markets. Our model accounts for how strategic and environmental uncertainties affect the large traders' execution strategies. We formulate an expected utility maximization problem for two large traders as a Markov game model. Applying the backward induction method of dynamic programming, we provide an explicit closed-form execution strategy at a Markov perfect equilibrium. Our theoretical results reveal that the execution strategy generally lies in a dynamic and non-randomized class;it becomes deterministic if the Markovian environment is also deterministic. In addition, our simulation-based numerical experiments suggest that the execution strategy captures various features observed in financial markets. Copyright © 2024, The Authors. All rights reserved.

关键词： Dynamic programming

A Prediction-Correction Based Iterative Convolution-Thresholding Method for Topology Optimization of Heat Transfer Problems

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SSRN

SSRN 2024年

关键词： Convolution

Agglomeration triggered by the effect of the number of regions: A model in NEG with a quadratic subutility

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arXiv 2021年

作者： Ohtake, Kensuke Center for Mathematical Modeling and Data Science Osaka University Osaka Toyonaka560-8531 Japan

We extend the mathematical model proposed by Ottaviano-Tabuchi-Thisse (2002) to a multi-regional case and investigate the stability of the homogeneous stationary solution of the model in a one-dimensional periodic space. When the number of regions is two and three, the homogeneous stationary solution is stable under sufficiently high transport cost. On the other hand, when the number of regions is a multiple of four, the homogeneous stationary solution is unstable under any values of the transport cost. Copyright © 2021, The Authors. All rights reserved.

关键词： Differential equations

Usage Coordination Utilizing Flexible Contracts in Free-floating Car Sharing

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Usage Coordination Utilizing Flexible Contracts in Free-floa...

IEEE International Conference on Agents (ICA)

作者： Yuto Iwata Shigeo Matsubara Kyoto University Kyoto Japan Center for Mathematical Modeling and Data Science Osaka University Toyonaka Japan

ISBN: (纸本)9781665407175

We propose a novel distributed user-car matching method based on a contract between users to mitigate the imbalance problem between vehicle distribution and demand in free-floating car sharing. The previous contract-based regulation method assumes that contracts are binding. However, car-sharing systems users are in dynamic environments, and such binding fails to accommodate future events. Therefore, to overcome this drawback, we introduce a leveled-commitment contract into contract-based coordination among drop-off and pick-up users. In our method, an auction is conducted for drop-off users’ intended drop-off locations, and users are allowed to decommit from contracts by paying penalties. The amount of penalty is determined by considering the trade-off between the sunk cost due to movement and social surplus. We thoroughly evaluated the proposed method with a baseline method on a free-floating car-sharing simulator. The results show that it achieved a higher social surplus than the existing method when demand frequently occurred.

关键词： Costs Conferences Regulation Automobiles Vehicle dynamics Contracts