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Generalized Born solvation models offer a popular method of including electrostatic aspects of solvation free energies within an analytical model that depends only upon atomic coordinates, charges, and dielectric radii. Here, we describe how second derivatives with respect to Cartesian coordinates can be computed in an efficient manner that can be distributed over multiple processors. This approach makes possible a variety of new methods of analysis for these implicit solvation models. We illustrate three of these methods here: the use of Newton-Raphson optimization to obtain precise minima in solution; normal mode analysis to compute solvation effects on the mechanical properties of DNA; and the calculation of configurational entropies in the MM/GBSA model. An implementation of these ideas, using the Amber generalized Born model, is available in the nucleic acid builder (NAB) code, and we present examples for proteins with up to 45,000 atoms. The code has been implemented for parallel computers using both the OpenMP and MPI environments, and good parallel scaling is seen with as many as 144 OpenMP processing threads or MPI processing tasks. 相似文献
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This paper presents in detail a robust, efficient and accurate methodology for the computation of equilibrium composition in gaseous mixtures. The methodology is founded on the concept of the chemical basis, which is defined and formalized using a powerful matricial approach. The method is specially designed to be general, thus providing basic thermodynamic data in several areas, such as combustion, plasma chemistry and, more generally speaking, computational fluid dynamics. The performance of the method is given in terms of CPU usage and the computed results are compared with those in the published literature. The method is shown to yield results of very high quality in terms of accuracy and smoothness. 相似文献
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Josep Maria Anglada Emili Besalú Josep Maria Bofill 《Theoretical chemistry accounts》1999,103(2):163-166
We present a matrix diagonalization method where the diagonalization is carried out through a normal Lagrange–Newton–Raphson method solved in a subspace. The subspace is generated using the correction vector that predicts the standard Lagrange–Newton–Raphson formula in the full space. Some numerical examples and the performance of the algorithm are given. Received: 16 February 1999 / Accepted: 10 May 1999 / Published online: 9 September 1999 相似文献
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分析了“化学平衡常数”的教材内容和相关教学设计,针对实际教学中存在的2个问题:简化的数据探究难以让学生体会到科学研究的复杂性;纯粹的知识性教学难以体现科学知识的价值和意义。提出在教学中融合化学史和数据探究,能帮助学生全面深入地理解概念,促进学生进一步认识科学本质和学科价值。 相似文献
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Protic ionic liquid (PIL) triethylammonium acetate was prepared by mixing equimolar amounts of acetic acid and triethylamine, and then studied using the combination of the Attenuated Total Reflection Fourier Transform Infrared spectroscopy, in-situ infrared spectroscopy, pH, and conductivity titration measurements. It was found that the equimolar synthesized triethylammonium acetate was separated into two layers, which suggesting that there were both chemical and phase equilibrium in this solution. Molecular species could be directly observed in the IR spectra over the range of 1200-1800 cm-1 and also checked by 1H NMR. Based on analysis, the upper layer was rich in amine with little acid and PIL, and the down layer was rich in PIL with residual acetic acid and amine. And single PIL-rich layer could be separated into two layers again when the mole ratio of newly added triethyamine to the theoretical produced triethylammonium acetate reached 0.12. 相似文献
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Wenjuan Cheng Lu‐Tao Weng Yongjie Li Arthur Lau Chak Chan Chi‐Ming Chan 《Surface and interface analysis : SIA》2014,46(7):480-488
Size‐segregated particles were collected with a ten‐stage micro‐orifice uniform deposit impactor from a busy walkway in a downtown area of Hong Kong. The surface chemical compositions of aerosol samples from each stage were analyzed using time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) operated in the static mode. The ToF‐SIMS spectra of particles from stage 2 (5.6–10 µm), stage 6 (0.56–1 µm), and stage 10 (0.056–0.1 µm) were compared, and the positive ion spectra from stage 2 to stage 10 were analyzed with principal component analysis (PCA). Both spectral analysis and PCA results show that the coarse‐mode particles were associated with inorganic ions, while the fine particles were associated with organic ions. PCA results further show that the particle surface compositions were size dependent. Particles from the same mode exhibited more similar surface features. Particles from stage 2 (5.6–10 µm), stage 6 (0.56–1 µm), and stage 10 (0.056–0.1 µm) were further selected as representatives of the three modes, and the chemical compositions of these modes of particles were examined using ToF‐SIMS imaging and depth profiling. The results reveal a non‐uniform chemical distribution from the outer to the inner layer of the particles. The coarse‐mode particles were shown to contain inorganic salts beneath the organics surface. The accumulation‐mode particles contained sulfate, nitrate, ammonium salts, and silicate in the regions below a thick surface layer of organic species. The nucleation‐mode particles consisted mainly of soot particles with a surface coated with sulfate, hydrocarbons, and, possibly, fullerenic carbon. The study demonstrated the capability of ToF‐SIMS depth profiling and imaging in characterizing both the surface and the region beneath the surface of aerosol particles. It also revealed the complex heterogeneity of chemical composition in size and depth distributions of atmospheric particles. Copyright © 2014 John Wiley & Sons, Ltd. 相似文献
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Imaging surfaces and interfaces with structural and chemical specificity has been essential for understanding a variety of phenomena occurring in adsorbed layers during surface chemical reactions. A recent achievement of chemical imaging with spectroscopic analysis is the experimental proof of theoretically predicted spontaneous formation of regular patterns of metal adatoms during surface chemical reactions. An attractive feature of this finding is that the reaction rate and adlayer coverage can be employed to precisely control the morphology of the structures. The mechanisms of these self-organisation phenomena, driven by the interplay between energetic principles and kinetics, opens a conceptually novel route to creating a wide range of surface-supported functional structures at the micro- and nanometre length scales. 相似文献
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Muhammad Asif Javed;Abuzar Ghaffari;Sami Ullah Khan;Ehab Elattar; 《Macromolecular theory and simulations》2024,33(4):2400017
The coating process is widely used in various industries to enhance the production quality and efficiency. This study gives a comprehensive analysis of non-isothermal blade coating of non-Newtonian nanofluid incorporating magnetic, thermophoresis, and Brownian effects. The mathematical equations derived from mass, momentum, and energy conservation laws are initially streamlined by means of lubrication approximation theory (LAT). Subsequently, these dimensionless equations are solved in dimensionless form numerically using fourth order Runge–Kutta and Newton–Raphson methods. This study includes the effects of the slip parameter, magnetohydrodynamic (MHD) and other material parameters on the coating thickness (h1${{h}_1}$), blade load, velocity, temperature, concentration, and pressure profiles through graphs and tables. The velocity of molten polymer increases near the substrate while it decreases near the blade surface as the slip parameter increases. The temperature distribution increases as the Brinkman number rises, with the maximum temperature occurring in the nip region of the flow. The coating thickness and load-carrying force for both plane and exponential coater increase with higher values of the magnetohydrodynamic (MHD) parameter. 相似文献
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《Physics and Chemistry of Liquids》2012,50(2):91-113
Abstract When molecules of chemical compounds are represented by graphs, thermodynamic properties may be connected with numbers of certain classes of walks on graphs. The basic proposition of summing up contributions resulting from interactions of walks is related to fluid distribution functions. The principle of corresponding volumes and structural schemes are discussed. Exemplary calculations for normal alkanes and their binary mixtures give in many cases values within limits of the experimental accuracy 相似文献
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Dr. Fang‐Kun Deng Dr. Liang Zhang Dr. Ya‐Ting Wang Prof. Dr. Olaf Schneewind Prof. Dr. Stephen B. H. Kent 《Angewandte Chemie (International ed. in English)》2014,53(18):4662-4666
The enzyme sortase A is a ligase which catalyzes transpeptidation reactions. 1 , 2 Surface proteins, including virulence factors, that have a C terminal recognition sequence are attached to Gly5 on the peptidoglycan of bacterial cell walls by sortase A. 1 The enzyme is an important anti‐virulence and anti‐infective drug target for resistant strains of Gram‐positive bacteria. 2 In addition, because sortase A enables the splicing of polypeptide chains, the transpeptidation reaction catalyzed by sortase A is a potentially valuable tool for protein science. 3 Here we describe the total chemical synthesis of enzymatically active sortase A. The target 148 residue polypeptide chain of sortase AΔN59 was synthesized by the convergent chemical ligation of four unprotected synthetic peptide segments. The folded protein molecule was isolated by size‐exclusion chromatography and had full enzymatic activity in a transpeptidation assay. Total synthesis of sortase A will enable more sophisticated engineering of this important enzyme molecule. 相似文献
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在化学平衡教学后,通过测试和评价学生在“化学平衡”核心主题内容中的认识发展情况,确定下一阶段教学的关键点和发展点,选取电离平衡影响因素为教学载体,设计和实施促进学生认识发展的教学,通过学生测查数据说明基于学生认识发展情况进行教学改进是提高教学效率的有效手段。 相似文献
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Ying Peng Lulu Zhao Dongju Lin Yuyang Liu Mengyu Zhang ShaoJiang Song 《Biomedical chromatography : BMC》2016,30(4):508-519
In this work, high‐performance liquid chromatography (HPLC) coupled with a hybrid quadrupole time of‐flight mass spectrometry (Q‐TOF‐MS/MS) was used to study chemical compositions of different processed products of Rhizoma Anemarrhenae (RA). A Grace AlltimaTM C18 column (250 × 4.6 mm, 5 µm) was used for separation. Mobile phase consisted of 0.1% formic acid and acetonitrile, using gradient elution. ESI‐MS data was acquired in both positive and negative mode. The experiment was established on the basis of a series of reference substances (two xanthone and seven saponins) to qualitatively identify the chemical compounds of different processed products of RA by MS analysis. There was no difference in the type of chemical constituents between different processed products of RA. A total of 25 compounds were identified, including four xanthones, 21 steroidal saponins and eight pairs of isomers. Copyright © 2015 John Wiley & Sons, Ltd. 相似文献
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根据认知心理学关于概念结构的理论,对高中生“化学平衡”概念的自由分类进行多维标度和聚类分析,得出高中生的“化学平衡”概念由2个维度组成,学生的分类属于关联聚类,揭示了影响学生概念结构的因素,并对概念教学提出了建议。 相似文献
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利用自制木制固定器、注射器等设计实验装置,借助压强传感器展示压强对\"2NO2?N2O4\"平衡体系的影响,实验操作简单,直观地展现了平衡移动过程,对于学生学习化学平衡尤其是理解勒夏特列原理有很大的帮助。 相似文献