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891.
本文研究一类二维非线性的广义sine-Gordon(简称SG)方程的有限差分格式.首先构造三层时间的紧致交替方向隐式差分格式,并用能量分析法证明格式具有二阶时间精度和四阶空间精度.然后应用改进的Richardson外推算法将时间精度提高到四阶.最后,数值算例证实改进后的算法在空间和时间上均达到四阶精度. 相似文献
892.
Gutman and Wagner proposed the concept of matching energy (ME) and pointed out that the chemical applications of ME go back to the 1970s. Let G be a simple graph of order n and be the roots of its matching polynomial. The ME of G is defined to be the sum of the absolute values of . In this article, we characterize the graphs with minimal ME among all unicyclic and bicyclic graphs with a given diameter d. © 2014 Wiley Periodicals, Inc. Complexity 21: 224–238, 2015 相似文献
893.
Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules 下载免费PDF全文
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. 相似文献
894.
Yuanpeng Liang Bin Xiang Chao Liu Xiangdong Zhou Dan Wang Shan Song Genghua Bai Qi An Quehong Huang Shujun Chen Xuefeng Wei 《Tetrahedron》2014
Novel fluorine-containing ultraviolet absorbers (FBPs) with low surface energy were successfully synthesized based on 2,4-dihydroxy benzophenone (BP-1), and their structures were characterized by 1H NMR, 13C NMR, FTIR, and HRMS. UV absorption of FBPs was studied in 10−4 M dichloromethane (CH2Cl2), which demonstrated the superior UV absorption capability of FBPs (ca. ?=1.7×104 to 2.2×104 at λmax) over the matrix (?=1.7×104 at λmax). Quantum chemistry calculation was performed to investigate the stable structure and UV electronic absorption bands of FBPs. The surface chemistry information of high-chlorinated polyethylene (HCPE) coating films embedded with ultraviolet absorbers (UVAs) was given by X-ray photoelectron spectroscopy (XPS) and contact angle measurement. The results show that the surface enrichment capability of FBPs is remarkably better than traditional UVAs (including BP-1, BP-3, BP-12) because of the low surface energy properties of FBPs. 相似文献
895.
We present a new implementation of a recent open‐ended response theory formulation for time‐ and perturbation‐dependent basis sets (Thorvaldsen et al., J. Chem. Phys. 2008, 129, 214108) at the Hartree–Fock and density functional levels of theory. A novel feature of the new implementation is the use of recursive programming techniques, making it possible to write highly compact code for the analytic calculation of any response property at any valid choice of rule for the order of perturbation at which to include perturbed density matrices. The formalism is expressed in terms of the density matrix in the atomic orbital basis, allowing the recursive scheme presented here to be used in linear‐scaling formulations of response theory as well as with two‐ and four‐component relativistic wave functions. To demonstrate the new code, we present calculations of the third geometrical derivatives of the frequency‐dependent second hyperpolarizability for HSOH at the Hartree–Fock level of theory, a seventh‐order energy derivative involving basis sets that are both time and perturbation dependent. © 2014 Wiley Periodicals, Inc. 相似文献
896.
On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase 下载免费PDF全文
Takeshi Baba Ryuhei Harada Masayoshi Nakano Yasuteru Shigeta 《Journal of computational chemistry》2014,35(16):1240-1247
We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc. 相似文献
897.
The READY program: Building a global potential energy surface and reactive dynamic simulations for the hydrogen combustion 下载免费PDF全文
READY (REActive DYnamics) is a program for studying reactive dynamic systems using a global potential energy surface (PES) built from previously existing PESs corresponding to each of the most important elementary reactions present in the system. We present an application to the combustion dynamics of a mixture of hydrogen and oxygen using accurate PESs for all the systems involving up to four oxygen and hydrogen atoms. Results at the temperature of 4000 K and pressure of 2 atm are presented and compared with model based on rate constants. Drawbacks and advantages of this approach are discussed and future directions of research are pointed out. © 2014 Wiley Periodicals, Inc. 相似文献
898.
Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies 下载免费PDF全文
Förster resonance energy transfer (FRET) measurements are widely used to investigate (bio)molecular interactions or/and association. FRET efficiencies, the primary data obtained from this method, give, in combination with the common assumption of isotropic chromophore orientation, detailed insight into the lengthscale of molecular phenomena. This study illustrates the application of a FRET efficiency restraint during classical atomistic molecular dynamics simulations of a mutant mastoparan X peptide in either water or 7 M aqueous urea. The restraint forces acting on the donor and acceptor chromophores ensure that the sampled peptide configurational ensemble satisfies the experimental primary data by modifying interchromophore separation and chromophore transition dipole moment orientations. By means of a conformational cluster analysis, it is seen that indeed different configurational ensembles may be sampled without and with application of the restraint. In particular, while the FRET efficiency and interchromophore distances monitored in an unrestrained simulation may differ from the experimentally‐determined values, they can be brought in agreement with experimental data through usage of the FRET efficiency restraining potential. Furthermore, the present results suggest that the assumption of isotropic chromophore orientation is not always justified. The FRET efficiency restraint allows the generation of configurational ensembles that may not be accessible with unrestrained simulations, and thereby supports a meaningful interpretation of experimental FRET results in terms of the underlying molecular degrees of freedom. Thus, it offers an additional tool to connect the realms of computer and wet‐lab experimentation. © 2014 Wiley Periodicals, Inc. 相似文献
899.
Hybrid density functional theory has been applied for investigations of the electronic and atomic structure of bulk phases, nanolayers, and nanotubes based on titanium and zirconium disulfides. Calculations have been performed on the basis of the localized atomic functions by means of the CRYSTAL‐2009 computer code. The full optimization of all atomic positions in the regarded systems has been made to study the atomic relaxation and to determine the most favorable structures. The different layered and isotropic bulk phases have been considered as the possible precursors of the nanotubes. Calculations on single‐walled TiS2 and ZrS2 nanotubes confirmed that the nanotubes obtained by rolling up the hexagonal crystalline layers with octahedral 1T morphology are the most stable. The strain energy of TiS2 and ZrS2 nanotubes is small, does not depend on the tube chirality, and approximately obeys to D–2 law (D is nanotube diameter) of the classical elasticity theory. It is greater than the strain energy of the similar TiO2 and ZrO2 nanotubes; however, the formation energy of the disulfide nanotubes is considerably less than the formation energy of the dioxide nanotubes. The distance and interaction energy between the single‐wall components of the double‐wall nanotubes is proved to be close to the distance and interaction energy between layers in the layered crystals. Analysis of the relaxed nanotube shape using radial coordinate of the metal atoms demonstrates a small but noticeable deviation from completely cylindrical cross‐section of the external walls in the armchair‐like double‐wall nanotubes. © 2013 Wiley Periodicals, Inc. 相似文献
900.