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Mean-Field Games are games with a continuum of players that incorporate the time-dimension through a control-theoretic approach. Recently, simpler approaches relying on the Best Reply Strategy have been proposed. They assume that the agents navigate their strategies towards their goal by taking the direction of steepest descent of their cost function (i.e. the opposite of the utility function). In this paper, we explore the link between Mean-Field Games and the Best Reply Strategy approach. This is done by introducing a Model Predictive Control framework, which consists of setting the Mean-Field Game over a short time interval which recedes as time moves on. We show that the Model Predictive Control offers a compromise between a possibly unrealistic Mean-Field Game approach and the sub-optimal Best Reply Strategy.

Current methods cannot tell us what the nature of the protein universe is concretely. They are based on different models of amino acid substitution and multiple sequence alignment which is an NP-hard problem and requires manual intervention. Protein structural analysis also gives a direction for mapping the protein universe. Unfortunately, now only a minuscule fraction of proteins' 3-dimensional structures are known. Furthermore, the phylogenetic tree representations are not unique for any existing tree construction methods. Here we develop a novel method to realize the nature of protein universe. We show the protein universe can be realized as a protein space in 60-dimensional Euclidean space using a distance based on a normalized distribution of amino acids. Every protein is in one-to-one correspondence with a point in protein space, where proteins with similar properties stay close together. Thus the distance between two points in protein space represents the biological distance of the corresponding two proteins. We also propose a natural graphical representation for inferring phylogenies. The representation is natural and unique based on the biological distances of proteins in protein space. This will solve the fundamental question of how proteins are distributed in the protein universe.

We consider the solution of large-scale Lyapunov and Stein equations. For Stein equations, the well-known Smith method will be adapted, with A_k = A^{2^k} not explicitly computed but in the recursive form A_k = A^{2^k}, and the fast growing but diminishing components in the approximate solutions truncated. Lyapunov equations will be first treated with the Cayley transform before the Smith method is applied. For algebraic equations with numerically low-ranked solutions of dimension <i>n</i>, the resulting algorithms are of an efficient <i>O</i>(<i>n</i>) computational complexity and memory requirement per iteration and converge essentially quadratically. An application in the estimation of a lower bound of the condition number for continuous-time algebraic Riccati equations is presented, as well as some numerical results.