计算机辅助蛋白质分子理性设计:从肌红蛋白到一氧化氮还原酶

计算机辅助蛋白质分子理性设计在解决化学及生物学重要问题中被证实十分有效。在NOR本身三维结构未知的情况下通过计算机分子模拟,使用肌红蛋白(Mb)作为蛋白质分子模型,设计了结构功能型一氧化氮还原酶(NOR),所设计的NOR蛋白质模型——Fe_BMb一年后被天然NOR的晶体结构所证实。本文综述了设计Fe_BMb, I107E Fe_BMb以及Fe_BMb(-His)的研究过程及其设计合理性,评述了通过使用计算机分子模拟,获得Mb处于双组氨酸配位的非天然状态的原子层次结构信息,而这些信息很难通过实验方法来获得。计算机辅助蛋白质分子理性设计的广泛应用将会为生物体系提供更深刻的内涵。     

Synthesis of narrow bandwidth flat-top ns pulse with multi-ultra-short pulses

Making use of the spectral narrowing of ultra-short pulses subject to amplification in the gain bandwidth media, a multi-ultra-short pulse coherent synthesizer (MUSPCS) developed from the traditional regenerative amplifier is proposed, and its operational principle is described. In the small signal gain regime, the theoretical analysis and numerical simulation on the MUSPCS have been made. The simulation results show that the narrow bandwidth flat-top long pulse can be composed if the parameters were controlled carefully.     

GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows

We have developed a GPU-based molecular dynamics simulation for the study of flows of fluids with anisotropic molecules such as liquid crystals. An application of the simulation to the study of macroscopic flow (backflow) generation by molecular reorientation in a nematic liquid crystal under the application of an electric field is presented. The computations of intermolecular force and torque are parallelized on the GPU using the cell-list method, and an efficient algorithm to update the cell lists was proposed. Some important issues in the implementation of computations that involve a large number of arithmetic operations and data on the GPU that has limited high-speed memory resources are addressed extensively. Despite the relatively low GPU occupancy in the calculation of intermolecular force and torque, the computation on a recent GPU is about 50 times faster than that on a single core of a recent CPU, thus simulations involving a large number of molecules using a personal computer are possible. The GPU-based simulation should allow an extensive investigation of the molecular-level mechanisms underlying various macroscopic flow phenomena in fluids with anisotropic molecules.     

全息图的计算机模拟及重现

根据光学全息原理,分析了在计算机模拟中把物光、参考光和再现光离散化的方法,并对基元全息和无透镜傅里叶全息进行模拟,实验结果逼真,这有助于学生更好地理解全息摄影的相关理论,为光学全息的理论和实验教学提供了可视化的验证。     

单缝夫琅禾费衍射实验的计算机辅助教学

传统的衍射实验往往过多强调光波波动性的一面,而忽略其粒子性的一面,从而使学生对衍射现象的物理过程缺乏全面的认识。在进行光学实验的同时,借助于计算机辅助教学,可弥补这一缺点。应用蒙特卡罗方法对单缝夫琅禾费衍射现象进行了模拟,对模拟结果进行了分析和讨论。与传统方法相比,这种方法更为形象和直观,可以帮助学生理解光子等微观粒子的波粒二象性及随机性与确定性的统一。     

Revealing sol-gel type main effects by exploring a molecular cluster behavior in model in-plane amphiphilic aggregations

In-plane (bio)matter aggregations of amphiphilic nature are modeled extensively by Monte Carlo simulation in their natural entropic contexts. The modeling starts by designing the aggregations at a molecular level, pointing to its well-known configuration vs conformation character. Then, the conformational behavior is distributed over the aggregations obtained, with the aim of revealing their main sol-gel type (viscoelastic) effects. The passage between the resulting sol and gel phases is not controlled by a scan in the temperature domain, on the contrary, the control parameter is selected to be the hydrophobic-interaction strength while the temperature remains unchanged. The distribution of ordered fringed micelles, and the overall crystalline inclusions of the gel phase, suggested a first-order phase change, reasonably conceivable in terms of Avrami-Kolmogorov formalism for such hydrophobic-force driven and percolation-in-nature systems. A phase transition diagram has been presented as a novel proposition to discern between sol vs gel phases. As specific results, also of high experimental value, a damped-oscillating cluster-involving effect on the resulting hydrophobic-polar matrices has been detected and analysed. Other additional intermolecular-sharing entropy-influenced effects on clustering, as seen in terms of chain-to-chain connectivities, have been addressed as being of sufficient relevance to the gelation mechanism described. The microcrystalline inclusions downgrade to some extent the overall picture of entropy-affected gelation, being all together suitable for experimental check-out.     

A boundary condition for arbitrary shaped inlets in lattice–Boltzmann simulations

We introduce a mass‐flux‐based inlet boundary condition for the lattice‐Boltzmann method. The proposed boundary condition requires minimal amount of boundary data, it produces a steady‐state velocity field which is accurate close to the inlet even for arbitrary inlet geometries, and yet it is simple to implement. We demonstrate its capability for both simple and complex inlet geometries by numerical experiments. For simple inlet geometries, we show that the boundary condition provides very accurate inlet velocities when Re?1. Even with moderate Reynolds number, the inlet velocities are accurate for practical purposes. Furthermore, the potential of our boundary condition to produce inlet velocities which convincingly adapt to complex inlet geometries is highlighted with two specific examples. Copyright © 2009 John Wiley & Sons, Ltd.     

Three‐dimensional simulation of planar contraction viscoelastic flow by penalty finite element method

The planar contraction flow is a benchmark problem for the numerical investigation of viscoelastic flow. The mathematical model of three‐dimensional viscoelastic fluids flow is established and the numerical simulation of its planar contraction flow is conducted by using the penalty finite element method with a differential Phan‐Thien–Tanner constitutive model. The discrete elastic viscous split stress formulation in cooperating with the inconsistent streamline upwind scheme is employed to improve the computation stability. The distributions of velocity and stress obtained by simulation are compared with that of Quinzani's experimental results detected by laser–doppler velocimetry and flow‐induced birefringence technologies. It shows that the numerical results agree well with the experimental results. The numerical methods proposed in the study can be well used to predict complex flow patterns of viscoelastic fluids. Copyright © 2009 John Wiley & Sons, Ltd.     

A comparison between a collocation and weak implementation of the rigid‐body motion constraint on a particle surface

In this work, we implemented and compared two different methods to impose the rigid‐body motion constraint on a solid particle moving inside a fluid. We consider a fictitious domain method to easily manage the particle motion. As the solid as well as the fluid inertia are neglected, the particle can be discretized through its boundary only. The rigid‐body motion is imposed via Lagrange multipliers on the boundary. In the first method, such constraints are imposed in discrete points on the boundary (collocation), whereas in the second the constraint is imposed in a weak way on elements dividing the particle surface. Two test problems, that is, a spherical and an ellipsoidal particle in a sheared Newtonian fluid, are chosen to compare the methods. In both cases, the analysis is carried out in 2D as well as in 3D. The results show that for the collocation method an optimal number of collocation points exist leading to the smallest error. However, small variations in the optimal value can generate large deviations. In the weak implementation, the error is only mildly affected by the number of elements used to discretize the particle boundary and by the Lagrange multiplier's interpolation space. A further analysis is carried out to study the effect of an approximated integration of weak constraints. A comparison between the two methods showed that the same accuracy can be achieved by using less constraints if the weak discretization is used. Finally, the rigid‐body motion imposed via weak constraints leads to better conditioned linear systems. Copyright © 2009 John Wiley & Sons, Ltd.