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.

No abstract uploaded!

How to properly specify boundary conditions for pressure is a longstanding problem for the incompressible Navier–Stokes equations with no-slip boundary conditions. An analytical resolution of this issue stems from a recently developed formula for the pressure in terms of the commutator of the Laplacian and Leray projection operators. Here we make use of this formula to (a) improve the accuracy of computing pressure in two kinds of existing time-discrete projection methods implicit in viscosity only, and (b) devise new higher-order accurate time-discrete projection methods that extend a slip-correction idea behind the well-known finite-difference scheme of Kim and Moin. We test these schemes for stability and accuracy using various combinations of C0 finite elements. For all three kinds of time discretization, one can obtain third-order accuracy for both pressure and velocity without a time-step stability restriction of diffusive type. Furthermore, two kinds of projection methods are found stable using piecewise-linear elements for both velocity and pressure.

No abstract uploaded!

Principal component analysis (PCA) is fundamental to statistical machine learning. It extracts latent principal factors that contribute to the most variation of the data. When data are stored across multiple machines, however, communication cost can prohibit the computation of PCA in a central location and distributed algorithms for PCA are thus needed. This paper proposes and studies a distributed PCA algorithm: each node machine computes the top K eigenvectors and transmits them to the central server; the central server then aggregates the information from all the node machines and conducts a PCA based on the aggregated information. We investigate the bias and variance for the resulting distributed estimator of the top K eigenvectors. In particular, we show that for distributions with symmetric innovation, the empirical top eigenspaces are unbiased, and hence the distributed PCA is unbiased. We derive the