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.

This paper is a follow-up of the work [Chen, J.-S.: J. Optimiz. Theory Appl., Submitted for publication (2004)] where an NCP-function and a descent method were proposed for the nonlinear complementarity problem. An unconstrained reformulation was formulated due to a merit function based on the proposed NCP-function. We continue to explore properties of the merit function in this paper. In particular, we show that the gradient of the merit function is globally Lipschitz continuous which is important from computational aspect. Moreover, we show that the merit function is <i>SC</i> ¹ function which means it is continuously differentiable and its gradient is semismooth. On the other hand, we provide an alternative proof, which uses the new properties of the merit function, for the convergence result of the descent method considered in [Chen, J.-S.: J. Optimiz. Theory Appl., Submitted for publication (2004)].

We establish the full global non-linear stability of the Kerr–de Sitter family of black holes, as solutions of the initial value problem for the Einstein vacuum equations with positive cosmological constant, for small angular momenta, and without any symmetry assumptions on the initial data. We achieve this by extending the linear and non-linear analysis on black hole spacetimes described in a sequence of earlier papers by the authors: we develop a general framework which enables us to deal systematically with the diffeomorphism invariance of Einstein’s equations. In particular, the iteration scheme used to solve Einstein’s equations automatically finds the parameters of the Kerr–de Sitter black hole that the solution is asymptotic to, the exponentially decaying tail of the solution, and the gauge in which we are able to find the solution; the gauge here is a wave map/DeTurck type gauge, modified by source terms which are treated as unknowns, lying in a suitable finite-dimensional space.

Due to the highly degeneracy and singularities of the entropy equation, the physical entropy for viscous and heat conductive polytropic gases behave singularly in the presence of vacuum and it is thus a challenge to study its dynamics. It is shown in this paper that the uniform boundedness of the entropy and the inhomogeneous Sobolev regularities of the velocity and temperature can be propagated for viscous and heat conductive gases in $\mathbb R^3$, provided that the initial vacuum occurs only at far fields with suitably slow decay of the initial density. Precisely, it is proved that for any strong solution to the Cauchy problem of the heat conductive compressible Navier--Stokes equations, the corresponding entropy keeps uniformly bounded and the $L^2$ regularities of the velocity and temperature can be propagated, up to the existing time of the solution, as long as the initial density vanishes only at far fields with a rate no more than $O(\frac{1}{|x|^2})$. The main tools are some singularly weighted energy estimates and an elaborate De Giorgi type iteration technique. The De Giorgi type iterations are carried out to different equations in establishing the lower and upper bounds of the entropy.

We study the averaging of fronts moving with positive oscillatory normal velocity, which is periodic in space and stationary ergodic in time. The problem can be formulated as the homogenization of coercive level set Hamilton-Jacobi equations with spatio-temporal oscillations. To overcome the difficulties due to the oscillations in time and the linear growth of the Hamiltonian, we first study the long time averaged behavior of the associated reachable sets using geometric arguments. The results are new for higher than one dimensions even in the space-time periodic setting.