Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules

A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. © 2013 Wiley Periodicals, Inc.     

Explicit–implicit mapping approach to nonlinear blind separation of sparse nonnegative dependent sources from a single mixture: pure component extraction from nonlinear mixture mass spectra

The nonlinear, nonnegative single‐mixture blind source separation problem consists of decomposing observed nonlinearly mixed multicomponent signal into nonnegative dependent component (source) signals. The problem is difficult and is a special case of the underdetermined blind source separation problem. However, it is practically relevant for the contemporary metabolic profiling of biological samples when only one sample is available for acquiring mass spectra; afterwards, the pure components are extracted. Herein, we present a method for the blind separation of nonnegative dependent sources from a single, nonlinear mixture. First, an explicit feature map is used to map a single mixture into a pseudo multi‐mixture. Second, an empirical kernel map is used for implicit mapping of a pseudo multi‐mixture into a high‐dimensional reproducible kernel Hilbert space. Under sparse probabilistic conditions that were previously imposed on sources, the single‐mixture nonlinear problem is converted into an equivalent linear, multiple‐mixture problem that consists of the original sources and their higher‐order monomials. These monomials are suppressed by robust principal component analysis and hard, soft, and trimmed thresholding. Sparseness‐constrained nonnegative matrix factorizations in reproducible kernel Hilbert space yield sets of separated components. Afterwards, separated components are annotated with the pure components from the library using the maximal correlation criterion. The proposed method is depicted with a numerical example that is related to the extraction of eight dependent components from one nonlinear mixture. The method is further demonstrated on three nonlinear chemical reactions of peptide synthesis in which 25, 19, and 28 dependent analytes are extracted from one nonlinear mixture mass spectra. The goal application of the proposed method is, in combination with other separation techniques, mass spectrometry‐based non‐targeted metabolic profiling, such as biomarker identification studies. Copyright © 2015 John Wiley & Sons, Ltd.     

非协调四结点平面等参位移元新列式方法

本文导出一种等参协调元位移函数的新的表示方法,在此基础上建立起了构造等参非协调元的新方法。作为实例,构造出两个可以给出单刚显式的四结点平面非协调新单元。     

计算圆板大振幅非线性振动频率的平均刚度法

本文用平均刚度法研究圆板大振幅非线性振动的频率问题，导出了相应的非线性广义特征值方程，构造了一种避免发散并能加速收敛的加权平均迭代法，计算结果与Ｋａｎｔｏｒｏｖｉｃｈ时间平均法的解十分吻合。     

A class of two-level explicit difference schemes for solving three dimensional heat conduction equation

ＩｎｔｒｏｄｕｃｔｉｏｎＴｈｉｓｐａｐｅｒｄｅａｌｓｗｉｔｈｔｈｅｉｎｉｔｉａｌ＿ｂｏｕｎｄａｒｙｖａｌｕｅｐｒｏｂｌｅｍｏｆｔｈｒｅｅ＿ｄｉｍｅｎｓｉｏｎａｌｈｅａｔｃｏｎｄｕｃｔｉｏｎｅｑｕａｔｉｏｎｉｎｔｈｅｒｅｇｉｏｎＤ :0≤ｘ,ｙ ,ｚ≤Ｌ ,0 ≤ｔ≤Ｔ ｕ ｔ= 2 ｕ ｘ2 2 ｕ ｙ2 2 ｕ ｚ2 ,ｕ｜ｘ=0 =ｆ1(ｙ,ｚ,ｔ) ,　ｕ｜ｘ=Ｌ =ｆ2 (ｙ ,ｚ,ｔ) ,ｕ｜ｙ=0 =ｇ1(ｚ,ｘ,ｔ) ,　ｕ｜ｙ=Ｌ =ｇ2 (ｚ,ｘ,ｔ) ,ｕ｜ｚ=0 =ｈ1(ｘ ,ｙ ,ｔ) ,　ｕ｜ｚ=Ｌ =ｈ2 (ｘ ,ｙ ,ｔ) ,ｕ｜ｔ=0 =φ(ｘ ,ｙ,ｚ) .(1 )(2 )…     

Finite difference method for 2-D and 3-D nonlinear free surface wave problems

A finite difference method is developed for the numerical modelling of the 2-D and 3-D unsteady potential flow generated by transient disturbances on the free surface, on which the nonlinear boundary conditions are fully satisfied. The unknown function is computed with an iteration scheme processing in a transformed time-invariant space. After the velocity is calculated, the location of the free surface is renewed and so is the value of velocity on it. The boundary-value problem of the governing equation is then solved at the next time step. The present method incorporates the FFT. Consequently, a tri-diagonal equation system is obtained which could be readily solved. The feasibility of this method has been demonstrated by 2-D and 3-D examples corresponding to different initial disturbances. This work is supported by the science foundation of Academia Sinica. The paper had been accepted by the XVIth International Congress of IUTAM, Lyngby, Denmark, August, 1984.     

一种大型结构特征值问题的并行解法

本文提出了一种求解大型结构固有频率与模态的并行解法。该方法在子空间迭代过程中,利用子结构刚度阵和质量阵并行进行凝聚,求得下一次的迭代基矢量,直到收敛。该算法在西安交通大学ELXS1-6400并行机上程序实现,计算结果表明能大幅度节省计算时间,同时也有效地节省了内存。     

非牛顿流体经波纹管流动的阻力特性

本文对Carreau流体经波纹管的蠕动流的阻力特性用差分方法作了数值求解。先施行坐标变换,提出一种保证周期性条件的混合迭代法,能较快得到问题的收敛解。流体的物质参数以及流动区域的几何参数对流动阻力特性的影响作了讨论,同时指出了直径均匀的毛管模型作为渗流模型的不足之处。     

Bäcklund transformations and abundant exact explicit solutions of the Sharma-Tasso-Olver equation

By using an extension of the homogeneous balance method and Maple, the Bäcklund transformations for the Sharma-Tasso-Olver equation are derived. The connections between the Sharma-Tasso-Olver equation and some linear partial differential equations are found. With the aid of the transformations given here and the computer program Maple 12, abundant exact explicit special solutions to the Sharma-Tasso-Olver equation are constructed. In addition to all known solutions re-deriving in a systematic way, several entirely new and more general exact explicit solitary wave solutions can also be obtained. These solutions include (a) the algebraic solitary wave solution of rational function, (b) single-soliton solutions, (c) double-soliton solutions, (d) N-soliton solutions, (e) singular traveling solutions, (f) the periodic wave solutions of trigonometric function type, and (g) many non-traveling solutions. By using the Airy’s function and the Bäcklund transformations obtained here, the exact explicit solution of the initial value problem for the STO equation is presented. The variety of the structure of the solutions for the Sharma-Tasso-Olver equation is illustrated.