Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

Summary Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.     

Mixed finite volume methods on nonstaggered quadrilateral grids for elliptic problems

We construct and analyze a mixed finite volume method on quadrilateral grids for elliptic problems written as a system of two first order PDEs in the state variable (e.g., pressure) and its flux (e.g., Darcy velocity). An important point is that no staggered grids or covolumes are used to stabilize the system. Only a single primary grid system is adopted, and the degrees of freedom are imposed on the interfaces. The approximate flux is sought in the lowest-order Raviart-Thomas space and the pressure field in the rotated- nonconforming space. Furthermore, we demonstrate that the present finite volume method can be interpreted as a rotated- nonconforming finite element method for the pressure with a simple local recovery of flux. Numerical results are presented for a variety of problems which confirm the usefulness and effectiveness of the method.

     

投影器的标定方法

随着近景摄影测量的发展,投影器的使用越来越频繁和广泛。为了更好地使用和充分地利用投影器,需要求解投影器的内方位元素,即对投影器进行标定。提出了一种方便有效的投影器标定的方法。只需要一架投影器、一部数码相机、一个平面格网和一台计算机,设备的连接和使用相对方便灵活。基于近景摄影测量的理论,结合二维直接线性变换(2D-DLT)和共线方程,运用图像处理的方法,利用光束法平差对投影器进行标定。实验及其结果证明了该标定方法的正确性和有效性。     

非结构网格上温度扩散方程的能流计算方法

讨论非结构网格上温度扩散方程的能流计算方法.应用有限点方法(Finite Point Method,简称FPM)导出基于有限点两点公式和三点公式的能流计算公式,该公式适用于任意多边形及非匹配网格等非结构网格;给出网格角点温度新的计算公式.数值试验表明:基于两点公式的离散解和基于三点公式的离散解均具有平方阶的收敛速度;基于三点公式的离散解的精度总优于基于两点公式的离散解.     

Numerical simulation of 2D lid‐driven cavity flow with CLEARER algorithm on extremely highly skewed grids at high Reynolds numbers

It is crucial to deal with the grid non‐orthogonality effectively in solving the flow in complex geometries, especially at high Reynolds numbers. In this study, the newly proposed Coupled and Linked Equations Algorithm Revised‐ER (CLEARER) algorithm is adopted to solve this problem successfully. In CLEARER algorithm the second relaxation factor is introduced in constructing the contravariant interface velocities, by setting it to a low value. CLEARER algorithm can overcome the severe grid non‐orthogonality and non‐linearity of equations effectively. After the numerical results with CLEARER are validated with the benchmark solutions, this algorithm is used to solve the lid‐driven flow in inclined cavity with inclination angles varying from 10 to 170^°, and Reynolds numbers varying from 5000 to 15 000. The streamlines and the centerline velocity distributions are provided in detail for all cases, which may offer some guidance for the study in this area. Copyright © 2010 John Wiley & Sons, Ltd.     

Resolution of computational aeroacoustics problems on unstructured grids with a higher-order finite volume scheme

Computational fluid dynamics (CFD) has become increasingly used in the industry for the simulation of flows. Nevertheless, the complex configurations of real engineering problems make the application of very accurate methods that only work on structured grids difficult. From this point of view, the development of higher-order methods for unstructured grids is desirable. The finite volume method can be used with unstructured grids, but unfortunately it is difficult to achieve an order of accuracy higher than two, and the common approach is a simple extension of the one-dimensional case. The increase of the order of accuracy in finite volume methods on general unstructured grids has been limited due to the difficulty in the evaluation of field derivatives. This problem is overcome with the application of the Moving Least Squares (MLS) technique on a finite volume framework. In this work we present the application of this method (FV-MLS) to the solution of aeroacoustic problems.     

Conceptual linearization of Euler governing equations to solve high speed compressible flow using a pressure‐based method

The main objective of the current work is to introduce a new conceptual linearization strategy to improve the performance of a primitive shock‐capturing pressure‐based finite‐volume method. To avoid a spurious oscillatory solution in the chosen collocated grids, both the primitive and extended methods utilize two convecting and convected momentum expressions at each cell face. The expressions are obtained via a physical‐based discretization of two inclusive statements, which are constructed via a novel incorporation of the continuity and momentum governing equations. These two expressions in turn provide a strong coupling among the Euler conservative statements. Contrary to the primitive work, the linearization in the current work respects the definitions and essence of physics behind deriving the Euler governing equations. The accuracy and efficiency of the new formulation are then investigated by solving the shock tube as a problem with moving normal and expansion waves and the converging‐diverging nozzle as a problem with strong stationary normal shock. The results show that there is good improvement in performance of the primitive pressure‐based shock‐capturing method while its superior accuracy is not deteriorated at all. © 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2008     

A vortex axis and vortex core border grid adaptation algorithm

In the design process of hydrodynamical and aerodynamical technical applications, the numerical simulation of massively separated vortical flow is crucial for predicting, for example, lift or drag. To obtain reliable numerical results, it is mandatory to accurately predict the physical behavior of vortices. Thus, the dominant vortical flow structures have to be resolved in detail, which requires a local grid refinement and certain adaptation techniques. In this paper, a vortex flow structure adaptation algorithm is presented, which is particularly designed for local grid refinement at vortex axes positions and associated vortex core border locations. To this end, a fast and efficient vortex axis detection scheme is introduced and the algorithm for the vortex core border determination is explained. As the interaction between vortices makes the assignment of grid points to a certain vortex axis difficult, a helicity‐based vortex distinction approach in combination with a geometrical rotational sensor is developed. After describing the combined different techniques in detail, the vortex feature adaptation algorithm is applied to analytical and more realistic examples, which show that the described grid adaptation algorithm is able to enhance the grid cell resolution locally such that all significant vortical flow phenomena are resolved. Copyright © 2008 John Wiley & Sons, Ltd.     

CartGen: Robust,efficient and easy to implement uniform/octree/embedded boundary Cartesian grid generator

An efficient and easy to implement method to generate Cartesian grids is presented. The presented method generates various kinds of Cartesian grids such as uniform, octree and embedded boundary grids. It supports the variation of grid size along each spatial direction as well as anisotropic and non‐graded refinements. The efficiency and ease of implementation are the main benefits of the presented method in contrast to the alternative methods. Regarding octree grid generation, applying a simple and efficient data compression method permits to store all grid levels without considerable memory overhead. The presented method generates octree grids up to a 13‐level refinement (8192³ grids on the finest level) from a complicated geometry in a few minutes on the traditional desktop computers. The FORTRAN 90 implementation of the presented method is freely available under the terms of the GNU general public license. Copyright © 2007 John Wiley & Sons, Ltd.