磷酸化调控泛素单体与Rad23A/Ubiquilin-1中泛素结合域互作的检测

泛素（ubiquitin，Ub）是一种广泛存在、高度保守的信号蛋白质，它能够特异性识别成千上万种靶蛋白，以非共价方式行使不同的功能，其中包含蛋白质降解．Ubiquilin-1（Ubql-1）和Rad23A作为两种蛋白降解的转运因子，都包含有与泛素结合的结构域，被称为泛素结合域（ubiquitin-associated domain，UBA）．2014年，泛素S65位磷酸化修饰的特异性激酶PINK1被发现，磷酸化使泛素在溶液中呈现舒展态与收缩态两种互相转换的构象．本文通过核磁共振（nuclear magnetic resonance，NMR）技术对UBA和磷酸化泛素之间的相互作用进行检测，观测磷酸化对UBA和泛素结合的影响．实验结果表明Rad23A-UBA2与Ubql-1 UBA都特异性的与磷酸化泛素的舒展态相互作用，但是磷酸化未改变泛素与UBA之间的亲和力．值得注意的是与Ubql-1 UBA相互作用时，磷酸化促进了泛素收缩态向舒展态的转换．     

基于有限体积虚拟区域方法的两相流动直接模拟

为提高计算效率，提出有限体积法离散下的虚拟区域颗粒两相流动直接模拟方法.在控制方程中加入相应的虚拟区域源项，保证了颗粒内部的刚体运动特性.该源项中含有颗粒信息部分及流体信息部分.在每次迭代后，对源项中的流体信息部分进行更新，从而更好地保证颗粒内速度的刚体分布.计算静止颗粒圆柱绕流及单个颗粒的沉降过程，验证了算法的准确性.     

Homogenization of Periodically Heterogeneous Thin Beams

Consider an elastic thin three-dimensional body made of a periodic distribution of elastic inclusions. When both the thickness of the beam and the size of the heterogeneities tend simultaneously to zero the authors obtain three different one-dimensional models of beam depending upon the limit of the ratio of these two small parameters.     

The improvement of numerical modeling in the solution of incompressible viscous flow problems using finite element method based on spherical Hankel shape functions

In this paper, the finite element method with new spherical Hankel shape functions is developed for simulating 2‐dimensional incompressible viscous fluid problems. In order to approximate the hydrodynamic variables, the finite element method based on new shape functions is reformulated. The governing equations are the Navier‐Stokes equations solved by the finite element method with the classic Lagrange and spherical Hankel shape functions. The new shape functions are derived using the first and second kinds of Bessel functions. In addition, these functions have properties such as piecewise continuity. For the enrichment of Hankel radial basis functions, polynomial terms are added to the functional expansion that only employs spherical Hankel radial basis functions in the approximation. In addition, the participation of spherical Bessel function fields has enhanced the robustness and efficiency of the interpolation. To demonstrate the efficiency and accuracy of these shape functions, 4 benchmark tests in fluid mechanics are considered. Then, the present model results are compared with the classic finite element results and available analytical and numerical solutions. The results show that the proposed method, even with less number of elements, is more accurate than the classic finite element method.     

Order-Stability in Complex Biological,Social, and AI-Systems from Quantum Information Theory

This paper is our attempt, on the basis of physical theory, to bring more clarification on the question “What is life?” formulated in the well-known book of Schrödinger in 1944. According to Schrödinger, the main distinguishing feature of a biosystem’s functioning is the ability to preserve its order structure or, in mathematical terms, to prevent increasing of entropy. However, Schrödinger’s analysis shows that the classical theory is not able to adequately describe the order-stability in a biosystem. Schrödinger also appealed to the ambiguous notion of negative entropy. We apply quantum theory. As is well-known, behaviour of the quantum von Neumann entropy crucially differs from behaviour of classical entropy. We consider a complex biosystem S composed of many subsystems, say proteins, cells, or neural networks in the brain, that is, S=(Si). We study the following problem: whether the compound system S can maintain “global order” in the situation of an increase of local disorder and if S can preserve the low entropy while other Si increase their entropies (may be essentially). We show that the entropy of a system as a whole can be constant, while the entropies of its parts rising. For classical systems, this is impossible, because the entropy of S cannot be less than the entropy of its subsystem Si. And if a subsystems’s entropy increases, then a system’s entropy should also increase, by at least the same amount. However, within the quantum information theory, the answer is positive. The significant role is played by the entanglement of a subsystems’ states. In the absence of entanglement, the increasing of local disorder implies an increasing disorder in the compound system S (as in the classical regime). In this note, we proceed within a quantum-like approach to mathematical modeling of information processing by biosystems—respecting the quantum laws need not be based on genuine quantum physical processes in biosystems. Recently, such modeling found numerous applications in molecular biology, genetics, evolution theory, cognition, psychology and decision making. The quantum-like model of order stability can be applied not only in biology, but also in social science and artificial intelligence.     

Bifurcation analysis of visual angle model with anticipated time and stabilizing driving behavior

In the light of the visual angle model (VAM), an improved car-following model considering driver's visual angle, anticipated time and stabilizing driving behavior is proposed so as to investigate how the driver's behavior factors affect the stability of the traffic flow. Based on the model, linear stability analysis is performed together with bifurcation analysis, whose corresponding stability condition is highly fit to the results of the linear analysis. Furthermore, the time-dependent Ginzburg-Landau (TDGL) equation and the modified Korteweg-de Vries (mKdV) equation are derived by nonlinear analysis, and we obtain the relationship of the two equations through the comparison. Finally, parameter calibration and numerical simulation are conducted to verify the validity of the theoretical analysis, whose results are highly consistent with the theoretical analysis.     

Improved third‐order weighted essentially nonoscillatory scheme

A new third‐order WENO scheme is proposed to achieve the desired order of convergence at the critical points for scalar hyperbolic equations. A new reference smoothness indicator is introduced, which satisfies the sufficient condition on the weights for the third‐order convergence. Following the truncation error analysis, we have shown that the proposed scheme achieves the desired order accurate for smooth solutions with arbitrary number of vanishing derivatives if the parameter ε satisfies certain conditions. We have made a comparative study of the proposed scheme with the existing schemes such as WENO‐JS, WENO‐Z, and WENO‐N3 through different numerical examples. The result shows that the proposed scheme (WENO‐MN3) achieves better performance than these schemes.     

Domain decomposition methods in a geometrical multiscale domain using finite volume schemes

The heat equation is solved by using a finite volume discretization in a domain that consists of a two-dimensional central node and several one-dimensional outgoing branches. Several interface connection options to match the submodels set on the node and on the branches, with or without continuity, are looked at. For each of them, a monolithic scheme is defined, and existence and uniqueness of the solution is proved. New schemes are deduced, which are obtained through domain decomposition methods in the form of interface systems, with one or two unknowns per interface. A comparative systematic study is carried out from an algebraic and numerical point of view according to the interface conditions: Dirichlet, Neumann, or Robin. An efficient diagonal preconditioning is proposed.