关键词： Electrical energy   Energy   Electron density   QM/MM   Molecules  

摘要： The implementation and performance of the atom-centered density matrix propagation (ADMP) [J. Chem. Phys. 2001, 114, 9758] and the curvy-steps (CURV) methods [J. Chem. Phys. 2004, 121, 1152] are described. These methods solve the electronic Schrodinger equation approximately by propagating the electronic degrees of freedom using the extended Lagrangian molecular dynamics (ELMD) simulation approach. The ADMP and CURV methods are implemented and parallelized to accelerate semiempirical quantum mechanical (QM) methods (such as the MNDO, AM1, PM3, MNDO/d, and AM1/d methods). Test calculations show that both the ADMP and the CURV methods are 2 similar to 4 times faster than the Born-Oppenheimer molecular dynamics (BOMD) method and conserve the total energy well. The accuracy of the ADMP and CURV simulations is comparable to the BOMD simulations. The parallel implementation accelerates the MD simulation by up to 28 fold for the ADMP method and 25 fold for the CURV method, respectively, relative to the speed of the single core BOMD. In addition, a multiple time scale (MTS) approach is introduced to further speed up the semiempirical QM and QM/MM ELMD simulations. Since a larger integration time step is used for the propagation of the nuclear coordinates than that for the electronic degrees of freedom, the MTS approach allows the ELMD simulation to be carried out with a time step that is larger than the time step accessible by the original ADMP and CURV methods. It renders MD simulation to be carried out about 20 times faster than the BOMD simulation, and yields results that are comparable to the single time scale simulation results. The use of the methods introduced in the present work provides an efficient way to extend the length of the QM and QM/MM molecular dynamics simulations beyond the length accessible by BOMD simulation.

关键词： Clearance joint   Contact   Wear   Simulation  

摘要： In this work, the dynamics and wear phenomenon of clearance joint in planar mechanical system is presented using a computational methodology. The contact model in clearance joint is established using a hybrid nonlinear contact force model and the friction effect is considered by using a modified Coulomb friction model. The wear prediction of revolute clearance joint in mechanical systems is presented based on the Archard wear model. Finally, the integration of dynamics analysis and wear analysis is presented. An academic four-bar multibody mechanical system with revolute clearance joint is used as numerical example application to perform the investigation. (C) 2013 Elsevier Ltd. All rights reserved.

关键词： Peptides and proteins   Binding energy   Inhibitors   Chemical calculations   Molecular interactions  

摘要： A molecular modeling study on dihydrofolate reductase (DHFR) inhibitors was carried out. By combining molecular dynamics simulations with semiempirical (PM6), ab initio, and density functional theory (DFT) calculations, a simple and generally applicable procedure to evaluate the binding energies of DHFR inhibitors interacting with the human enzyme is reported here, providing a clear picture of the binding interactions of these ligands from both structural and energetic viewpoints. A reduced model for the binding pocket was used. This approach allows us to perform more accurate quantum mechanical calculations as well as to obtain a detailed electronic analysis using the quantum theory of atoms in molecules (QTAIM) technique. Thus, molecular aspects of the binding interactions between inhibitors and the DHFR are discussed in detail. A significant correlation between binding energies obtained from DFT calculations and experimental IC50 values was obtained, predicting with an acceptable qualitative accuracy the potential inhibitor effect of nonsynthesized compounds. Such correlation was experimentally corroborated synthesizing and testing two new inhibitors reported in this paper.

关键词： Bulk-fill resin based composites   Irradiance   Hardness   Modulus of elasticity   Polymerisation kinetic  

摘要： Objectives: To assess the effect of irradiation time and distance of the light tip on the micro-mechanical properties and polymerisation kinetics of two bulk-fill resin-based composites at simulated clinically relevant filling depth. Methods: Micro-mechanical properties (Vickers hardness (HV), depth of cure (DOC) and indentation modulus (E)) and polymerisation kinetics (real-time increase of degree of cure (DC)) of two bulk-fill resin-based composites (Tetric EvoCeram (R) Bulk Fill, Ivoclar Vivadent and x-tra base, Voco) were assessed at varying depth (0.1-6 mm in 100 mu m steps for E and HV and 0.1, 2, 4 and 6 mm for DC), irradiation time (10, 20 or 40 s, Elipar Freelight2) and distances from the light tip (0 and 7 mm). Curing unit's irradiance was monitored in 1 mm steps at distances up to 10 mm away from the light tip on a laboratory-grade spectrometer. Results: Multivariate analysis (alpha = 0.05), Student's t-test and Pearson correlation analysis were considered. The influence of material on the measured mechanical properties was significant (eta(2) = 0.080 for E and 0.256 for HV), while the parameters irradiation time, distance from the light tip and depth emphasise a stronger influence on Tetric EvoCeram (R) Bulk Fill. The polymerisation kinetics could be described by an exponential sum function, distinguishing between the gel and the glass phase. The above mentioned parameters strongly influenced the start of polymerisation (gel phase), and were of less importance for the glass phase. Conclusions: Both materials enable at least 4 mm thick increments to be cured in one step under clinically relevant curing conditions. Clinical significance: The susceptibility to variation in irradiance was material dependent, thus properties measured under clinically simulated curing conditions might vary to a different extent from those measured under ideal curing conditions. (c) 2013 Elsevier Ltd. All rights reserved.

关键词： polymer blends   thermogravimetry   kinetics   mechanical properties   polypropylene   high-density polyethylene  

摘要： In this study, the mechanical properties and non-isothermal degradation kinetics of polypropylene (PP), high-density polyethylene (HDPE) with dilauroyl peroxide and their blends in different mixture ratios were investigated. The effects of adding dilauroyl peroxide (0-0.20 wt%) on the mechanical and thermal properties of PP + HDPE blends have been studied. On the other hand, the kinetics of the thermal degradation and thermal oxidative degradation of PP + HDPE (80/ 20 wt%) blends were studied in different atmospheres, to analyze their thermal stability. The kinetic and thermodynamic parameters such as the activation energy, Ea, the pre-exponential factor, A, the reaction order, n, the entropy change, the enthalpy change, and the free energies of activated complex related to PP, HDPE, and blend systems were calculated by means of the several methods on the basis of the single heating rate. A computer program was developed for automatically processing the data to estimate the reaction parameters by using different models. Most appropriate method was determined for each decomposition step according to the least-squares linear regression. Copyright (c) 2013 John Wiley & Sons, Ltd.

关键词： disturbance specialist   annual plant   seed bank   stochastic integral projection model   density dependence   Monte Carlo simulation  

摘要： Seed banks are critically important for disturbance specialist plants because seeds of these species germinate only in disturbed soil. Disturbance and seed depth affect the survival and germination probability of seeds in the seed bank, which in turn affect population dynamics. We develop a density-dependent stochastic integral projection model to evaluate the effect of stochastic soil disturbances on plant population dynamics with an emphasis on mimicking how disturbances vertically redistribute seeds within the seed bank. We perform a simulation analysis of the effect of the frequency and mean depth of disturbances on the population's quasi-extinction probability, as well as the long-term mean and variance of the total density of seeds in the seed bank. We show that increasing the frequency of disturbances increases the long-term viability of the population, but the relationship between the mean depth of disturbance and the long-term viability of the population are not necessarily monotonic for all parameter combinations. Specifically, an increase in the probability of disturbance increases the long-term viability of the total seed bank population. However, if the probability of disturbance is too low, a shallower mean depth of disturbance can increase long-term viability, a relationship that switches as the probability of disturbance increases. However, a shallow disturbance depth is beneficial only in scenarios with low survival in the seed bank.

关键词： Concentration   Electroseparation   Electrostatics   Dielectric liquids  

摘要： This paper deals with the problem of dielectric liquids purification. The separation process of mechanical impurities from dielectric liquids in an electric field is analyzed and an experimentally validated mathematical model is proposed for the electroseparation process. The main objective is to find a relationship to describe the kinetics of particles electroseparation, solving the problem of establishing a relationship of dependency between initial concentration and final concentration with time, and determining the electroseparation time depending on particles and liquid dielectric properties. (C) 2013 Elsevier B.V. All rights reserved.

关键词： LIGANDS   COPPER ions   WATER   QUANTUM mechanics   NUCLEAR charge   MOLECULAR dynamics   MOLECULAR structure  

摘要： Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment. (C) 2013 AIP Publishing LLC.

关键词： amyloid   fibril fragmentation   steered molecular dynamics (SMD)   structural defects  

摘要： We examine how the different steric packing arrangements found in amyloid fibril polymorphs can modulate their mechanical properties using steered molecular dynamics simulations. Our calculations demonstrate that for fibrils containing structural defects, their ability to resist force in a particular direction can be dominated by both the number and molecular details of the defects that are present. The simulations thereby suggest a hierarchy of factors that govern the mechanical resilience of fibrils, and illustrate the general principles that must be considered when quantifying the mechanical properties of amyloid fibres containing defects.

关键词： 轮式工程机械   串联式   混合动力  

摘要： 本文在比较了现有的轮式工程机械混合动力技术优缺点的基础上,对轮式工程机械的串联式混合动力系统进行了研究,介绍了系统的组成和工作方式,分析了串联式系统的优点,提出了串联式液压混合动力系统不但适用于轮式工程机械而且适用于频繁起停的中小型城市公交车、军用轮式汽车等车辆的行走装置。