On the Effect of the Various Assumptions and Approximations used in Molecular Simulations on the Properties of Bio-Molecular Systems: Overview and Perspective on Issues

Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed.     

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.     

基于拟相对内部集值优化问题弱有效元的最优性条件

本文研究了基于拟相对内部的非凸集值优化问题弱有效元的最优性条件.首先,讨论了弱有效元与线性子空间之间的关系,利用涉及拟相对内部的凸集分离定理,获得了弱有效元的最优性条件.其次,给出了基于拟相对内部弱有效元的Lagrange乘子定理.     

Stabilized Nonconforming Mixed Finite Element Method for Linear Elasticity on Rectangular or Cubic Meshes

Based on the primal mixed variational formulation, a stabilized nonconforming mixed finite element method is proposed for the linear elasticity on rectangular and cubic meshes. Two kinds of penalty terms are introduced in the stabilized mixed formulation, which are the jump penalty term for the displacement and the divergence penalty term for the stress. We use the classical nonconforming rectangular and cubic elements for the displacement and the discontinuous piecewise polynomial space for the stress, where the discrete space for stress are carefully chosen to guarantee the well-posedness of discrete formulation. The stabilized mixed method is locking-free. The optimal convergence order is derived in the $L^2$-norm for stress and in the broken $H^1$-norm and $L^2$-norm for displacement. A numerical test is carried out to verify the optimal convergence of the stabilized method.     

UPLC-Q/TOF-MS coupled with multivariate analysis for comparative analysis of metabolomic in Dendrobium nobile from different growth altitudes

Dendrobium nobile alkaloids (DNLA) and glycosides are the main active components extracted from Dendrobium nobile Lindl. (D. nobile) used for thousands of years in China. The pharmacological effects of the above chemical components are significantly different. D. nobile is mainly grown at an altitude ranging from 230 to 800 m in Chishui City, Northwest Guizhou Province. However, it is unclear whether the metabolite in D. nobile is influenced by the planting altitude. Hence, to reveal the different metabolite in D. nobile cultivated at the altitude of 336 m, 528 m, and 692 m, ultra-high performance liquid chromatography with Q/TOF-MS couple with multivariate analysis were developed. Using the orthogonal partial least squares-discriminant analysis, 19 different metabolites were discovered and then tentatively assigned their structures as alkaloids and glycosides by comparing mass spectrometry data with in-house database and literature. Moreover, the result of semiquantitative analysis showed the content of dendrobine that was belonged to alkaloids significantly increased at the altitude of 692 m, whereas the content of glycosides demonstrated an accumulation trend at the altitude of 528 m. The results could provide valuable information for the optimal clinical drug therapeutics and provide a reference for quality control.     

New traveling wave solutions of Drinefel’d–Sokolov–Wilson Equation using Tanh and Extended Tanh methods

Traveling wave solutions are obtained by using a relatively new technique which is called Tanh and extended Tanh method for Drinefel’d–Sokolov–Wilson Equations. Solution procedure and obtained results re-confirm the efficiency of the proposed scheme.     

An approach for solving a fuzzy multiobjective programming problem

In this paper we present a new approach, based on the Nearest Interval Approximation Operator, for dealing with a multiobjective programming problem with fuzzy-valued objective functions.     

Solvability of the boundary value problem for stationary magnetohydrodynamic equations under mixed boundary conditions for the magnetic field

The global solvability of the boundary value problem for stationary magnetohydrodynamic equations under the Dirichlet boundary condition for the velocity and mixed boundary conditions for the magnetic field is proved.     

Modeling method and preliminary model of Asteroid Toutatis from Chang’E-2 optical images

Shape modeling is fundamental to the analysis of dynamic environment and motion around asteroid. Chang＇E- 2 successfully made a flyby of Asteroid 4179 Toutatis and obtained plenty of high-resolution images during the mis- sion. In this paper, the modeling method and preliminary model of Asteroid Toutatis are discussed. First, the optical images obtained by Chang＇E-2 are analyzed. Terrain and silhouette features in images are described. Then, the modeling method based on previous radar model and preliminary information from optical images is proposed. A preliminary polyhedron model of Asteroid Toutatis is established. Finally, the spherical harmonic coefficients of Asteroid Toutatis based on the polyhedron model are obtained. Some parameters of model are analyzed and compared. Although the model proposed in this paper is only a preliminary model, this work offers a valuable reference for future high-resolution models.