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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.

Surface flow phenomena, such as rain water flowing down a tree trunk and progressive water front in a shower room, are common in real life. However, compared with the 3D spatial fluid flow, these surface flow problems have been much less studied in the graphics community. To tackle this research gap, we present an efficient, robust and high-fidelity simulation approach based on the shallow-water equations. Specifically, the standard shallow-water flow model is extended to general triangle meshes with a feature-based bottom friction model, and a series of coherent mathematical formulations are derived to represent the full range of physical effects that are important for real-world surface flow phenomena. In addition, by achieving compatibility with existing 3D fluid simulators and by supporting physically realistic interactions with multiple fluids and solid surfaces, the new model is flexible and readily extensible for coupled phenomena. A wide range of simulation examples are presented to demonstrate the performance of the new approach.

The endoscopic classification via the stable trace formula comparison provides certain character relations between irreducible cuspidal automorphic representations of classical groups and their global Arthur parameters, which are certain automorphic representations of general linear groups. It is a question of J. Arthur and W. Schmid that asks how to construct concrete modules for irreducible cuspidal automorphic representations of classical groups in term of their global Arthur parameters? In this paper, we formulate a general construction of concrete modules, using Bessel periods, for cuspidal automorphic representations of classical groups with generic global Arthur parameters. Then we establish the theory for orthogonal and unitary groups, based on certain well expected conjectures. Among the consequences of the theory in this paper is that the global Gan-Gross-Prasad conjecture for those classical groups is proved in full generality in one direction and with a global assumption in the other direction.

The Onsager's reciprocal relation plays a fundamental role in the nonequilibrium thermodynamics. However, unfortunately, its classical version is valid only within a narrow region near equilibrium due to the linear regression hypothesis, which largely restricts its usage. In this paper, based on the conservation-dissipation formalism, a generalized version of Onsager's relations for the master equations and Fokker-Planck equations was derived. Nonlinear constitutive relations with nonsymmetric and positively stable operators, which become symmetric under the detailed balance condition, constitute key features of this new generalization. Similar conclusions also hold for many other classical models in physics and chemistry, which in turn make the current study as a benchmark for the application of generalized Onsager's relations in nonequilibrium thermodynamics.