A combination of the tree-code and IPS method to simulate large scale systems by molecular dynamics

An IPS/Tree method which is a combination of the isotropic periodic sum (IPS) method and tree-based method was developed for large-scale molecular dynamics simulations, such as biological and polymer systems, that need hundreds of thousands of molecules. The tree-based method uses a hierarchical tree structure to reduce the calculation cost of long-range interactions. IPS/Tree is an efficient method like IPS/DFFT, which is a combination of the IPS method and FFT in calculating large-scale systems that require massively parallel computers. The IPS method has two different versions: IPSn and IPSp. The basic idea is the same expect for the fact that the IPSn method is applied to calculations for point charges, while the IPSp method is used to calculate polar molecules. The concept of the IPS/Tree method is available for both IPSn and IPSp as IPSn/Tree and IPSp/Tree. Even though the accuracy of the Coulomb forces with tree-based method is well known, the accuracy for the combination of the IPS and tree-based methods is unclear. Therefore, in order to evaluate the accuracy of the IPS/Tree method, we performed molecular dynamics simulations for 32,000 bulk water molecules, which contains around 10(5) point charges. IPSn/Tree and IPSp/Tree were both applied to study the interaction calculations of Coulombic forces. The accuracy of the Coulombic forces and other physical properties of bulk water systems were evaluated. The IPSp/Tree method not only has reasonably small error in estimating Coulombic forces but the error was almost the same as the theoretical error of the ordinary tree-based method. These facts show that the algorithm of the tree-based method can be successfully applied to the IPSp method. On the other hand, the IPSn/Tree has a relatively large error, which seems to have been derived from the interaction treatment of the original IPSn method. The self-diffusion and radial distribution functions of water were calculated each by both the IPSn/Tree and IPSp/Tree methods, where both methods showed reasonable agreement with the Ewald method. In conclusion, the IPSp/Tree method is a potentially fast and sufficiently accurate technique for predicting transport coefficients and liquid structures of water in a homogeneous system.     

Development of effective Stokesian dynamics method for ferromagnetic colloidal dispersions (cluster-based Stokesian dynamics method)

We have developed a new Stokesian dynamics (SD) method for nondilute colloidal dispersions, which enables us to reduce drastically the computation time. To verify the validity of the present method, which is called the "cluster-based SD method," three-dimensional simulations of a ferromagnetic colloidal dispersion have been carried out for a simple shear flow. The correlation function and viscosity have been evaluated to compare the results obtained by the present method with those obtained by the ordinary SD method and by the method of ignoring hydrodynamic interactions between particles. The results obtained here are summarized as follows. The transient properties from an initial state obtained by the present method agree well with those obtained by the ordinary method, even if a radius r(clstr), which defines the cluster formation, is taken as a small value such as r(clstr)=1.2d (d is the particle diameter). Also, the equilibrium properties such as the pair correlation function and viscosity obtained by the present cluster-based method are in satisfactory agreement with those obtained by the ordinary SD method. Furthermore, the cluster-based method drastically reduces the computation time to about one-fourteenth to one-seventieth that of the ordinary method. It is clear from these results that the cluster-based SD method is significantly superior to the ordinary SD method for ferromagnetic colloidal dispersions for which a large model system such as N=1000 or 10,000 is indispensable in simulations.     

按独立组元计算复杂化学平衡的方法

本文通过分析独立组元的本质,提出了一个按独立组元来计算复杂化学平衡的方法。这个方法中的未知数和方程数比现有的自由能最小化法、质量作用方程组的方法和反应进度的方法中的未知数和方程数显著减少,因而计算过程大为简化。例如,对于计算一个由3个元素10个组元组成的复杂化学平衡体系来说,若采用其它方法须用电子计算机,而采用独立组元法仅须使用袖珍可编程序计算器即可完成。本文叙述了独立组元法的基本原理和具体方法,并根据理论分析和计算实践,将独立组元法与其它方法的优劣作了对比。     

一种提高化妆品中甲醛含量检测的稳定性和灵敏度的双波长光谱方法

提出了一种基于双波长光谱法(以500 nm吸光度为基准并结合414 nm处的吸光度)快速测定化妆品中甲醛含量的方法。结果表明:采用单波长的计算方法(不考虑基线漂移)产生的误差时,平行试验结果之间的相对标准偏差(RSD)可达11.5%,而该方法的RSD最大仅为0.46%。同时该方法能够有效地校正扣除萃取液颜色和基线漂移的影响,且定量下限为7.4 mg/kg。该方法具有分析时间短、操作便捷、灵敏度高、结果准确的优点,适用于化妆品中甲醛的检测。     

Internal‐to‐Cartesian back transformation of molecular geometry steps using high‐order geometric derivatives

In geometry optimizations and molecular dynamics calculations, it is often necessary to transform a geometry step that has been determined in internal coordinates to Cartesian coordinates. A new method for performing such transformations, the high‐order path‐expansion (HOPE) method, is here presented. The new method treats the nonlinear relation between internal and Cartesian coordinates by means of automatic differentiation. The method is reliable, applicable to any system of internal coordinates, and computationally more efficient than the traditional method of iterative back transformations. As a bonus, the HOPE method determines not just the Cartesian step vector but also a continuous step path expressed in the form of a polynomial, which is useful for determining reaction coordinates, for integrating trajectories, and for visualization. © 2013 Wiley Periodicals, Inc.     

An improved sealed quartz‐tube method for the determination of hydrogen isotopes in water

Hydrogen stable isotope analysis has been a valuable tool in the fields of geochemistry and ecological research as well as many other research fields. The methods are mainly divided into the dual‐inlet method (off‐line method) and continuous flow method. The dual‐inlet method is complicated and inefficient, but it is still important because of its high precision and wide application range. Although the continuous flow method improves the experimental efficiency, the memory effect is noticeable and the accuracy is reduced. An improved sealed quartz‐tube method is proposed in this paper. The sample is sealed in a capillary tube and placed in a quartz tube containing chromium powder. It is then packaged, evacuated, reacted at a high temperature, and analyzed for hydrogen isotope ratio. Excellent data accuracy, good reproducibility (<1‰), and no memory effect occurred in the method. The process is relatively simple, and the experimental efficiency is greatly improved, which provides an effective method for the analysis of hydrogen isotopes in complex liquid samples.     

New background correction method for liquid chromatography with diode array detection, infrared spectroscopic detection and Raman spectroscopic detection

A new method to eliminate the background spectrum (EBS) during analyte elution in column liquid chromatography (LC) coupled to spectroscopic techniques is proposed. This method takes into account the shape and also intensity differences of the background eluent spectrum. This allows the EBS method to make a better estimation of the background eluent spectrum during analyte elution. This is an advantage for quantification as well as for identification of analytes. The EBS method uses a two-step procedure. First, the baseline spectra are modeled using a limited number of principal components (PCs). Subsequently, an asymmetric least squares (asLS) regression method is applied using these principal components to correct the measured spectra during elution for the background contribution. The asymmetric least squares regression needs one parameter, the asymmetry factor p. This asymmetry factor determines relative weight of positive and negative residuals. Simulations are performed to test the EBS method in well-defined situations. The effect of spectral noise on the performance and the sensitivity of the EBS method for the value of the asymmetry factorp is tested. Two applications of the EBS method are discussed. In the first application, the goal is to extract the analyte spectrum from an LC-Raman analysis. In this case, the EBS method facilitates easy identification of unknown analytes using spectral libraries. In a second application, the EBS method is used for baseline correction in LC-diode array detection (DAD) analysis of polymeric standards during a gradient elution separation. It is shown that the EBS method yields a good baseline correction, without the need to perform a blank chromatographic run.     

Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods

We present a robust and efficient numerical method for solution of the nonlinear Poisson-Boltzmann equation arising in molecular biophysics. The equation is discretized with the box method, and solution of the discrete equations is accomplished with a global inexact-Newton method, combined with linear multilevel techniques we have described in an article appearing previously in this journal. A detailed analysis of the resulting method is presented, with comparisons to other methods that have been proposed in the literature, including the classical nonlinear multigrid method, the nonlinear conjugate gradient method, and nonlinear relaxation methods such as successive overrelaxation. Both theoretical and numerical evidence suggests that this method will converge in the case of molecules for which many of the existing methods will not. In addition, for problems which the other methods are able to solve, numerical experiments show that the new method is substantially more efficient, and the superiority of this method grows with the problem size. The method is easy to implement once a linear multilevel solver is available and can also easily be used in conjunction with linear methods other than multigrid. © 1995 by John Wiley & Sons, Inc.     

Generating conformational transition paths with low potential-energy barriers for proteins

The knowledge of conformational transition paths in proteins can be useful for understanding protein mechanisms. Recently, we have introduced the As-Rigid-As-Possible (ARAP) interpolation method, for generating interpolation paths between two protein conformations. The method was shown to preserve well the rigidity of the initial conformation along the path. However, because the method is totally geometry-based, the generated paths may be inconsistent because the atom interactions are ignored. Therefore, in this article, we would like to introduce a new method to generate conformational transition paths with low potential-energy barriers for proteins. The method is composed of three processing stages. First, ARAP interpolation is used for generating an initial path. Then, the path conformations are enhanced by a clash remover. Finally, Nudged Elastic Band, a path-optimization method, is used to produce a low-energy path. Large energy reductions are found in the paths obtained from the method than in those obtained from the ARAP interpolation method alone. The results also show that ARAP interpolation is a good candidate for generating an initial path because it leads to lower potential-energy paths than two other common methods for path interpolation.     

Thermodynamic integration from classical to quantum mechanics

We present a new method for calculating quantum mechanical corrections to classical free energies, based on thermodynamic integration from classical to quantum mechanics. In contrast to previous methods, our method is numerically stable even in the presence of strong quantum delocalization. We first illustrate the method and its relationship to a well-established method with an analysis of a one-dimensional harmonic oscillator. We then show that our method can be used to calculate the quantum mechanical contributions to the free energies of ice and water for a flexible water model, a problem for which the established method is unstable.     

Efficient binomial leap method for simulating chemical kinetics

The binomial tau-leaping method of simulating the stochastic time evolution in a reaction system uses a binomial random number to approximate the number of reaction events. Theory implies that this method can avoid negative molecular numbers in stochastic simulations when a larger time step tau is used. Presented here is a modified binomial leap method for improving the accuracy and application range of the binomial leap method. The maximum existing population is first defined in this approach in order to determine a better bound of the number reactions. To derive a general leap procedure in chemically reacting systems, in this method a new sampling procedure based on the species is also designed for the maximum bound of consumed molecules of a reactant species in reaction channel. Numerical results indicate that the modified binomial leap method can be applied to a wider application range of chemically reacting systems with much better accuracy than the existing binomial leap method.     

Size distribution analysis of polymer latex systems by use of extrema in the angular scattering intensity

The angular position of the extrema of the vertically polarized scattering intensity has previously been utilized for a method of particle size analysis for systems of monodisperse, spherical, isotropic particles which conform to the Rayleigh-Gans-Debye theory. The consequences of a finite polydispersity, which is always present in real systems, was not assessed and the application of the method has resulted in erroneous characterization of some latex systems. This work is concerned with (1) reporting the effects of finite polydispersity on the method of analysis, (2) pointing out previous misuse of the method, and (3) introducing a method of analysis which is based on the position of the extrema but which also considers polydispersity and the exact Mie calculation. This method enables one to characterize a scattering system in terms of a modal diameter and a distribution-width parameter by utilizing prepared diagrams for a particular relative refractive index.     

Computer-assisted optimization of selectivity (mobile phase,pH, and ion concentration) in high-perfomance liquid chromatography

A computer-assisted method is presented for optimization of mobile phase composition in reverse-phase and normal-phase HPLC. The method is based on window diagrams, but only three preliminary tests are required. The method is successfully applied to two examples and there is good agreement between predicted and experimental results. Optimal values for ion concentration and pH in ion chromatography from a published optimization method are compared to values calculated using the computer-assisted method presented in this paper. The same results are obtained, but the method presented here is simpler and faster than previously published one.     

Screening of acetylcholinesterase inhibitors in natural extracts by CE with electrophoretically mediated microanalysis technique

An electrophoretically mediated microanalysis (EMMA) method for screening acetylcholinesterase (AChE) inhibitors in natural extracts is described. In this method, solutions of AChE and the mixture of the substrate and the natural extract were successively injected into the capillary, and mixed electrophoretically by applying a voltage for a short time. Afterwards the voltage was reapplied to separate the product from the unreacted substrate and the natural extract. The measured peak area of the product at UV 230 nm represents the enzyme activity. Since the extract is mixed with the substrate, there is no need to separate the components before testing the inhibition. The inhibitory activity of the natural extract as a whole can be easily found if the peak area of the product is reduced. This makes the present method suitable for screening inhibitors in complex mixtures, such as natural extracts. Compared to the commonly used spectrometric method for screening of AChE inhibitors, the major advantage of the present method is the elimination of Ellman reagent, which is essential for the spectrometric method. This not only simplifies the experimental procedure but also minimizes false-positive results. Moreover, it is an obvious advantage of combining the separation power with the on-column enzyme assay for further investigating which compound(s) is/are responsible for the inhibition. The method was validated using a commercially available AChE inhibitor tacrine and a small chemical library containing four AChE inhibitors and 32 natural extracts. Inhibitors in natural extracts were identified with the present method.     

反应类等键反应方法及类反应热动力学参数计算

本文提出了反应类等键反应方法,将通常用于热力学性质计算的等键反应方法推广用于类反应中反应势垒和反应焓变的计算. 对碳氢燃料低温燃烧反应机理中的一类重要反应类：?烷基自由基过氧化氢裂解生成烯烃和HO2自由基的反应势垒和反应焓变进行了计算. 通过对该类16个反应中的5个代表反应分别在不同计算水平HF、DFT、MP2、CCSD(T)的比较计算发现,采用等键反应方法可在较低从头算级别计算得到类反应较高精度的反应势垒,提高了计算的效率和精度. 本文采用反应类等键反应方法在B3LYP/6-311G(d,p)计算水平对该类16个反应进行了反应势垒和反应焓变的计算,并建立了反应势垒和反应能的线性自由能关系：delta V=71.02+0.41?delta E.     

A Numerical technique for solving carrier-mediated transport problems

A numerical technique and a computer program based on the method of orthogonal collocation on finite elements for solving steady state carrier-mediated transport problems is presented. The method is especially suitable in solving boundary layer type of problems as arise in carrier-mediated transport. The method uses an efficient LU decomposition of a blockdiagonal matrix. A residual criterion is used for the placement of elements which can be easily implemented using an interactive feature in the computer program. Numerical results for three different systems; a system with simple kinetics and equal diffusivities for carrier and its complex, a system with simple kinetics and unequal diffusivities and a system with complex kinetics and equal diffusivities, indicate that the method is very versatile and has very good convergence properties. The method can be used very easily for all these systems by making minor modifications to the computer program.     

Improvement in the generation of adsorption isotherm data in the elution by characteristic points method--the ECP-slope approach

The elution by characteristic points (ECP) method is a very rapid and precise method for determination of the phase system equilibrium of phase systems in broad solute concentration ranges. Thus, the method is especially suitable for rapid characterization of high efficient separation systems. One important source of error, the effects by the post-loop dispersion, was eliminated in a recent investigation. In this study, the systematic error caused by the selection of the integration starting point at concentration equal to 0 is eliminated. This is done by developing and validating a new procedure for isotherm data generation; the ECP-slope method. The method generates raw slope data of the adsorption isotherm instead of raw adsorption data by integrations as the classical ECP does. Both numerical and experimental data were used for the comparison of the classical ECP approach with the slope-ECP method.     

The use of polyanions of hydrazines in the synthesis of heterocycles

A novel method for the synthesis of cyclic hydrazine derivatives is reported. The new method for the generation of nitrogen-containing heterocycles is based on a polyanion strategy. The described method provides a convenient access to cyclic hydrazine derivatives, which are extensively used in drug industry and agriculture. The advantages and limitations of the new method are also demonstrated.     

Applications of artificial intelligence for chemical inference—X : Intsum. A data interpretation and summary program applied to the collected mass spectra of estrogenic steroids

A method for systematic interpretation and summary of evidence found for all possible mass spectral fragmentations of a molecule or set of related molecules is described. The method is embodied in a computer program (INTSUM) which interprets, in terms of fragmentation processes, mass spectral data collected on known compounds. Utilizing high resolution mass spectra from 47 estrogenic steroids, the method is verified and new findings are discussed. Finally, the method is used to explore the fragmentations of equilenins and several acetate and benzoate ester derivatives.