20,591 research outputs found

    An Introduction to Rule-based Modeling of Immune Receptor Signaling

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    Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory response) depending on the type and number of receptor molecules on the cell surface and the specific intracellular signaling pathways activated by those receptors. Explicitly modeling and simulating kinetic interactions between molecules allows us to pose questions about the dynamics of a signaling network under various conditions. However, the application of chemical kinetics to biochemical signaling systems has been limited by the complexity of the systems under consideration. Rule-based modeling (BioNetGen, Kappa, Simmune, PySB) is an approach to address this complexity. In this chapter, by application to the Fcε\varepsilonRI receptor system, we will explore the origins of complexity in macromolecular interactions, show how rule-based modeling can be used to address complexity, and demonstrate how to build a model in the BioNetGen framework. Open source BioNetGen software and documentation are available at http://bionetgen.org.Comment: 5 figure

    Approximate Equilibrium and Incentivizing Social Coordination

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    We study techniques to incentivize self-interested agents to form socially desirable solutions in scenarios where they benefit from mutual coordination. Towards this end, we consider coordination games where agents have different intrinsic preferences but they stand to gain if others choose the same strategy as them. For non-trivial versions of our game, stable solutions like Nash Equilibrium may not exist, or may be socially inefficient even when they do exist. This motivates us to focus on designing efficient algorithms to compute (almost) stable solutions like Approximate Equilibrium that can be realized if agents are provided some additional incentives. Our results apply in many settings like adoption of new products, project selection, and group formation, where a central authority can direct agents towards a strategy but agents may defect if they have better alternatives. We show that for any given instance, we can either compute a high quality approximate equilibrium or a near-optimal solution that can be stabilized by providing small payments to some players. We then generalize our model to encompass situations where player relationships may exhibit complementarities and present an algorithm to compute an Approximate Equilibrium whose stability factor is linear in the degree of complementarity. Our results imply that a little influence is necessary in order to ensure that selfish players coordinate and form socially efficient solutions.Comment: A preliminary version of this work will appear in AAAI-14: Twenty-Eighth Conference on Artificial Intelligenc
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