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    A Boolean network control algorithm guided by forward dynamic programming

    , Article PLoS ONE ; Volume 14, Issue 5 , 2019 ; 19326203 (ISSN) Moradi, M ; Goliaei, S ; Foroughmand Araabi, M. H ; Sharif University of Technology
    Public Library of Science  2019
    Abstract
    Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized as a mathematical model for gene regulatory networks. This paper provides an algorithm to solve the control problem in Boolean networks. The proposed algorithm is implemented and applied on two biological systems: T-cell receptor network and Drosophila melanogaster network. Results show that the proposed algorithm works faster in solving the control problem over these networks, while having similar accuracy, in comparison to previous exact methods. Source... 

    Theoretical modeling of actin-retrograde-flow passing clusters of confined T cell receptors

    , Article Mathematical Biosciences ; Volume 283 , 2017 , Pages 1-6 ; 00255564 (ISSN) Ghasemi V., A ; Firoozabadi, B ; Saidi, M. S ; Sharif University of Technology
    Elsevier Inc  2017
    Abstract
    Through the activation process of T cells, actin filaments move from the cell periphery toward the cell center. The moving filaments engage with T cell receptors and thus contribute to transportation of the signaling molecules. To study the connection between the moving actin filaments and T cell receptors, an experiment available in the literature has measured filaments flow velocity passing over a region of confined clusters of receptors. It shows that flow velocity decreases in the proximity of the receptors, and then regains its normal value after traversing the region, suggesting a dissipative friction-like connection. In this work, we develop a minimal theoretical model to re-examine...