首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献,搜索用时 0 毫秒
1.
    
This article is dedicated to the computation of a parametric representation of solvent excluded surfaces and isosurfaces by smooth four-sided patches. Such surface representations allow for the isoparametric discretization of the boundary integral equations which arise from solvation continuum models. Thus, higher-order ansatz functions can be applied in the boundary element method that is commonly used to solve the underlying equations, yielding a more accurate approximation of the sought apparent surface charge. Numerical results are reported to illustrate the approach.  相似文献   

2.
3.
    
Computational fluid dynamics (CFD) has already proven to be an important tool to study fluids flow characteristics. Due to the rapid growth of powerful computers, CFD has become more applicable nowadays. In the field of nanofluids, this tool has also been applied by different approaches to understand and explain the effective phenomena. This article reviews and summarizes the numerical investigations implemented on nanofluids including conventional and novel methods. The studies conducted using methods such as Lattice Boltzmann, Eulerian–Lagrangian, thermal dispersion, Eulerian–Eulerian, and so forth are assessed.  相似文献   

4.
    
Zeta potential is a surface characteristic formed on the solid surface and liquid interface. It is an interesting way to describe the surface properties of materials; thus, a series of four homemade polar embedded stationary phases that contain phosphate groups incorporated into hydrophobic ligands were investigated according to surface zeta potential. Measurements were carried out using Zetasizer Nano ZS for the stationary phases suspensions prepared in various solvent and solvent binary mixtures. The negative zeta potential values were obtained for most cases due to negatively charged residual silanols and phosphate groups. However, in some solvents: tetrahydrofuran, isopropanol, and toluene zeta potential are positive. Additionally, it was observed that the zeta potential seems to be independent of the type of silica gel used for the stationary phase synthesis.  相似文献   

5.
Non-exponential electron transfer kinetics in complex systems are often analyzed in terms of a quenched, static disorder model. In this work we present an alternative analysis in terms of a simple dynamic disorder model where the solvent is characterized by highly non-exponential dynamics. We consider both low and high barrier reactions. For the former, the main result is a simple analytical expression for the survival probability of the reactant. In this case, electron transfer, in the long time, is controlled by the solvent polarization relaxation—in agreement with the analyses of Rips and Jortner and of Nadler and Marcus. The short time dynamics is also non-exponential, but for different reasons. The high barrier reactions, on the other hand, show an interesting dynamic dependence on the electronic coupling element,V el.  相似文献   

6.
    
Gauss's law or Poisson's equation is conventionally used to calculate solvation free energy. However, the near‐solute dielectric polarization from Gauss's law or Poisson's equation differs from that obtained from molecular dynamics (MD) simulations. To mimic the near‐solute dielectric polarization from MD simulations, the first‐shell water was treated as two layers of surface charges, the densities of which are proportional to the electric field at the solvent molecule that is modeled as a hard sphere. The intermediate water was treated as a bulk solvent. An equation describing the solvation free energy of ions using this solvent scheme was derived using the TIP3P water model. © 2013 Wiley Periodicals, Inc.  相似文献   

7.
    
A realistic representation of water molecules is important in molecular dynamics simulation of proteins. However, the standard method of solvating biomolecules, that is, immersing them in a box of water with periodic boundary conditions, is computationally expensive. The primary hydration shell (PHS) method, developed more than a decade ago and implemented in CHARMM, uses only a thin shell of water around the system of interest, and so greatly reduces the computational cost of simulations. Applying the PHS method, especially to larger proteins, revealed that further optimization and a partial reworking was required and here we present several improvements to its performance. The model is applied to systems with different sizes, and both water and protein behaviors are compared with those observed in standard simulations with periodic boundary conditions and, in some cases, with experimental data. The advantages of the modified PHS method over its original implementation are clearly apparent when it is applied to simulating the 82 kDa protein Malate Synthase G. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009  相似文献   

8.
    
The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library.  相似文献   

9.
    
Green extraction of the active lignans from Schisandra chinensis has received considerable attention due to their promising applications in the biomedical field. In this study, microwave-assisted deep eutectic solvent method was used to simultaneously extract five lignans: Schizandrol A, Schizandrol B, Schisantherin A, Schisandrin A and Schizandrin B. The extraction parameters were optimized according to the calculated comprehensive score obtained from the analytic hierarchy process combined with the entropy weight method. The optimal extraction conditions were that the molar ratio of choline chloride and glycolic acid is 4:1, water content is 30% (V/V), solid–liquid ratio is 1:20 (Wg:VmL), extraction time is 20 min, and extraction temperature is 70°C, under which the extraction rate of the five lignans were 10.89, 8.616, 4.019, 4.893, and 5.318 mg/g. These results confirmed that our extraction method is efficient and feasible for green extraction of lignans from S. chinensis.  相似文献   

10.
    
An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simulations. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1830-1842, 2001  相似文献   

11.
2-chloropyrimidine, 2-chloro- and 2-bromo-4,6-dimethylpyrimidines, 2-chloro- and 2-bromo-4,6-diphenylpyrimidines have been dimerized to the corresponding 2,2′-bipyrimidines in good yields by Tiecco's method using NiCl2, triphenylphosphine and zinc in DMF.  相似文献   

12.
    
Although quantities derived from solvent accessible surface areas (SASA) are useful in many applications in protein design and structural biology, the computational cost of accurate SASA calculation makes SASA-based scores difficult to integrate into commonly used protein design methodologies. We demonstrate a method for maintaining accurate SASA during a Monte Carlo search of sequence and rotamer space for a fixed protein backbone. We extend the fast Le Grand and Merz algorithm (Le Grand and Merz, J Comput Chem, 14, 349), which discretizes the solvent accessible surface for each atom by placing dots on a sphere and combines Boolean masks to determine which dots are exposed. By replacing semigroup operations with group operations (from Boolean logic to counting dot coverage) we support SASA updates. Our algorithm takes time proportional to the number of atoms affected by rotamer substitution, rather than the number of atoms in the protein. For design simulations with a one hundred residue protein our approach is approximately 145 times faster than performing a Le Grand and Merz SASA calculation from scratch following each rotamer substitution. To demonstrate practical effectiveness, we optimize a SASA-based measure of protein packing in the complete redesign of a large set of proteins and protein-protein interfaces.  相似文献   

13.
正负离子混合表面活性剂由于其特异的自组织行为及良好的稳定性,已成为研究生物膜和用于生物活性物质分离分析的理想模型[1-2],近年来,该体系在界面化学性质中得到了广泛的研究,但是由于正负电性中和,其水溶液很不稳定,一旦超过临界胶束浓度(CMC),极易发生沉淀,从而失去表面活性,使其应用受到限制.  相似文献   

14.
Response surface methodology (RSM) was used for the determination of optimum extraction parameters to reach maximum lipid extraction yield with yeast. Total lipids were extracted from oleaginous yeast (Rhodotorula glutinis) using pressurized liquid extraction (PLE). The effects of extraction parameters on lipid extraction yield were studied by employing a second-order central composite design. The optimal condition was obtained as three cycles of 15 min at 100°C with a ratio of 144 g of hydromatrix per 100 g of dry cell weight. Different analysis methods were used to compare the optimized PLE method with two conventional methods (Soxhlet and modification of Bligh and Dyer methods) under efficiency, selectivity and reproducibility criteria thanks to gravimetric analysis, GC with flame ionization detector, High Performance Liquid Chromatography linked to Evaporative Light Scattering Detector (HPLC-ELSD) and thin-layer chromatographic analysis. For each sample, the lipid extraction yield with optimized PLE was higher than those obtained with referenced methods (Soxhlet and Bligh and Dyer methods with, respectively, a recovery of 78% and 85% compared to PLE method). Moreover, the use of PLE led to major advantages such as an analysis time reduction by a factor of 10 and solvent quantity reduction by 70%, compared with traditional extraction methods.  相似文献   

15.
成膜溶剂与氟化嵌段共聚物膜的表面富集行为   总被引:1,自引:0,他引:1  
利用接触角、XPS、SFG、AFM等技术研究了环己酮、甲苯和三氟甲苯为成膜溶剂所得聚甲基丙烯酸甲酯-b-聚(甲基丙烯酸-2-全氟辛基乙酯)(PMMA—b—PFMA)嵌段共聚物膜的表面结构与性能.发现浇铸成膜时成膜溶剂对聚合物氟化组分向表面富集程度的影响相对较小,而旋涂成膜时溶剂的影响很大.不管以何种形式成膜,三氟甲苯溶剂最有利于氟化组分向表面富集,甲苯次之,环己酮最差.这一现象与溶剂的挥发速度无关.聚合物在溶液中的聚集结构、气/液界面结构是造成成膜方式对聚合物表面结构与性能产生巨大影响的主要原因.当聚合物在溶液中形成以PFMA为核、PMMA为冠的胶束结构时,在溶液固化过程中氟化组分向表面富集需要较长的时间,这时由于成膜方法直接影响溶液的固化速度,造成其对氟化组分向表面富集的程度影响很大.当聚合物在溶液中以单分子或松散聚集体存在,在溶液固化过程中氟化组分向表面富集的速度很快,这时成膜方法对氟化组分向表面富集的程度影响很小.以上结果无论对理论研究还是应用研究都具有重要意义.  相似文献   

16.
This work describes a new and low-scaling implementation of the polarizable continuum model (PCM) for computing the self-consistent solvent reaction field. The PCM approach is both general and accurate. It is applicable in the framework of both quantum and classical calculations, and also to hybrid quantum/classical methods. In order to further extend the range of applicability of PCM we addressed the problem of its computational cost. The generation of the finite-elements molecular cavity has been reviewed and reimplemented, achieving linear scaling for systems containing up to 500 atoms. Linear scaling behavior has been achieved also for the iterative solution of the PCM equations, by exploiting the fast multipole method (FMM) for computing electrostatic interactions. Numerical results for large (both linear and globular) chemical systems are discussed.  相似文献   

17.
    
The molecular behaviors of proteins under crowding conditions are crucial for understanding the protein actions in intracellular environments. Under a crowded environment, the distance between protein molecules is almost the same size as the molecular level, thus, both the excluded volume effect and short ranged soft chemical interaction on protein surface could induce the complicated influence on the protein behavior cooperatively. Recently, various kinds of analytical approaches from macroscopic to microscopic aspects have been made to evaluate the crowding effect. The method, however, has not been established to evaluate the surface specific interactions on protein surface. In this study, the analytical method to evaluate the crowding effect has been suggested by using a charge-transfer fluorescence probe, ANS. By employing the unique property of ANS attaching to charged residues on the surface of lysozyme, the crowding effect was focused, while the case was compared as a reference, in which ANS is confined in hydrophobic pockets of BSA. Consequently, the surface specific changes of fluorescence spectra were readily observed under the crowded environment, whereas the fluorescence spectra of ANS in protein inside did not change. This result suggests the fluorescence spectra of ANS binding to protein surface have the capability to estimate the crowding effect of proteins.  相似文献   

18.
通过五元环酸酐(NCA)开环聚合的方法成功合成了聚(γ-苄基-L-谷氨酸酯)(PBLG)聚肽均聚物和聚(γ-苄基-L-谷氨酸酯)-b-聚乙二醇(PBLG-b-PEG)聚肽嵌段共聚物,并通过酸解脱苄基及与肉桂醇的酯化反应对PBLG-b-PEG嵌段共聚物改性,制备了聚(γ-苄基-L-谷氨酸酯-co-肉桂基-L-谷氨酸酯)-b-聚乙二醇(P(BLG/CLG)-b-PEG)改性嵌段共聚物,其聚肽侧链上修饰了可光交联的肉桂酰氧基,其C=C双键在紫外光照射下能发生环加成反应交联聚肽链段。采用四氢呋喃-N,N-二甲基甲酰胺(THF-DMF)有机共溶剂溶解、选择性溶剂(水)沉淀的自组装方法制备了PBLG纳米棒;然后向纳米棒水溶液中加入THF溶剂诱导纳米棒弯曲,制备了纳米弯棒。通过THF的加入量可以调控纳米棒的弯曲程度。利用类似的方法,通过PBLG与PBLG-b-PEG或P(BLG/CLG)-b-PEG共组装制备了螺旋纳米棒(其中PBLG均聚物形成棒状内核、PBLG-b-PEG或P(BLG/CLG)-b-PEG形成表面纳米螺纹),然后向螺旋纳米棒水溶液中加入THF溶剂,但是仅得到了光滑纳米弯棒(表面螺纹消失)。对PBLG/P(BLG/CLG)-b-PEG螺旋纳米棒进行紫外照射,交联CLG链段来固定螺纹外壳,然后加入THF溶剂,制备了螺旋纳米弯棒,P(BLG/CLG)-b-PEG链段交联能够保持纳米棒表面的螺纹结构,同时对纳米棒的弯曲过程影响不显著。稳定测试表明,PBLG纳米弯棒和交联的PBLG/P(BLG/CLG)-b-PEG螺旋纳米弯棒在水溶液中保持形貌稳定。采用圆二色谱表征PBLG侧基苯环的有序排列状态,结果表明,加入THF溶剂后PBLG侧链苯环的收缩,是诱导纳米棒弯曲的驱动力。  相似文献   

19.
    
A new method for approximate analytical calculations of solvent accessible surface area (SASA) for arbitrary molecules and their gradients with respect to their atomic coordinates was developed. This method is based on the recursive procedure of pairwise joining of neighboring atoms. Unlike other available methods of approximate SASA calculations, the method has no empirical parameters, and therefore can be used with comparable accuracy in calculations of SASA in folded and unfolded conformations of macromolecules of any chemical nature. As shown by tests with globular proteins in folded conformations, average errors in absolute atomic surface area is around 1 A2, while for unfolded protein conformations it varies from 1.65 to 1.87 A2. Computational times of the method are comparable with those by GETAREA, one of the fastest exact analytical methods available today.  相似文献   

20.
设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号