Efficient lookup table using a linear function of inverse distance squared

The major bottleneck in molecular dynamics (MD) simulations of biomolecules exist in the calculation of pairwise nonbonded interactions like Lennard‐Jones and long‐range electrostatic interactions. Particle‐mesh Ewald (PME) method is able to evaluate long‐range electrostatic interactions accurately and quickly during MD simulation. However, the evaluation of energy and gradient includes time‐consuming inverse square roots and complementary error functions. To avoid such time‐consuming operations while keeping accuracy, we propose a new lookup table for short‐range interaction in PME by defining energy and gradient as a linear function of inverse distance squared. In our lookup table approach, densities of table points are inversely proportional to squared pair distances, enabling accurate evaluation of energy and gradient at small pair distances. Regardless of the inverse operation here, the new lookup table scheme allows fast pairwise nonbonded calculations owing to efficient usage of cache memory. © 2013 Wiley Periodicals, Inc.     

超高压处理对荔枝果肉中两种酶和可溶性蛋白的影响

 为了研究超高压处理对荔枝果肉中过氧化物酶（POD）、果胶甲基酯酶（PME）及可溶性蛋白含量的影响,将荔枝（“淮枝”品种）果肉在100~400 MPa压力、10 ℃温度条件下处理30 min,采用分光光度法测定果肉中POD、PME的活性,用天然凝胶电泳法以及活性染色法测定POD、PME同工酶的变化,用SDS凝胶电泳法测定果肉中可溶性蛋白含量。结果表明：100~200 MPa超高压处理使荔枝果肉中POD活性上升且出现新的同工酶,300~400 MPa超高压处理则使其活性降低且新出现的同工酶消失;100 MPa压力处理使荔枝果肉中PME活性上升且出现新的同工酶,200~400 MPa超高压处理则使其活性降低且新出现的同工酶消失;100 MPa超高压处理使荔枝果肉中可溶性蛋白含量有所增加,而在200~400 MPa压力处理下其含量持续下降。     

超高压和酶抑制剂联合处理对荔枝果肉中过氧化物酶和果胶甲基酯酶的影响

 为了研究超高压与酶抑制剂联合处理对荔枝果肉中过氧化物酶（POD）和果胶甲基酯酶（PME）的影响，将荔枝（“淮枝”品种）果肉在两种酶抑制剂组合溶液（A：5 g/L柠檬酸+2.5 g/L L-抗坏血酸+5 g/L氯化钙；B：10 g/L柠檬酸+5 g/L L-抗坏血酸+10 g/L氯化钙）中分别浸泡10 min，并在100~400 MPa压力、10 ℃温度条件下处理30 min，采用分光光度法测定果肉中POD、PME的活性。结果表明：A、B两种组合处理能够明显钝化POD，但却显著激活了PME；超高压与A组合联合处理不能使POD、PME活性下降；超高压与B组合联合处理对POD、PME的影响与压力值有关系，100~300 MPa的超高压与B组合联合处理使POD活性下降，200~400 MPa的超高压与B组合联合处理则使PME活性升高。因此，超高压与酶抑制剂联合处理对荔枝果肉中POD的钝化存在一定的协同效应，且浓度越高，协同抑制效应越明显；而超高压与酶抑制剂联合处理对荔枝果肉中PME的钝化却表现出一定的拮抗性。     

The implementation of a fast and accurate QM/MM potential method in Amber

Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides sufficiently accurate gradients to run constant energy QM/MM MD simulations for many nanoseconds. The link atom approach used for treating the QM/MM boundary shows improved performance, and the user interface has been rewritten to bring the format into line with classical MD simulations. Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge density functional tight binding (SCC-DFTB) method. Performance has been improved to the point where using QM/MM, for a QM system of 71 atoms within an explicitly solvated protein using periodic boundaries and PME requires less than twice the cpu time of the corresponding classical simulation.     

Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5

Based on our critique of requirements for performing an efficient molecular dynamics simulation with the particle-mesh Ewald (PME) implementation in GROMACS 4.5, we present a computational tool to enable the discovery of parameters that produce a given accuracy in the PME approximation of the full electrostatics. Calculations on two parallel computers with different processor and communication structures showed that a given accuracy can be attained over a range of parameter space, and that the attributes of the hardware and simulation system control which parameter sets are optimal. This information can be used to find the fastest available PME parameter sets that achieve a given accuracy. We hope that this tool will stimulate future work to assess the impact of the quality of the PME approximation on simulation outcomes, particularly with regard to the trade-off between cost and scientific reliability in biomolecular applications.     

Spectral accuracy in fast Ewald-based methods for particle simulations

A spectrally accurate fast method for electrostatic calculations under periodic boundary conditions is presented. We follow the established framework of FFT-based Ewald summation, but obtain a method with an important decoupling of errors: it is shown, for the proposed method, that the error due to frequency domain truncation can be separated from the approximation error added by the fast method. This has the significance that the truncation of the underlying Ewald sum prescribes the size of the grid used in the FFT-based fast method, which clearly is the minimal grid. Both errors are of exponential-squared order, and the latter can be controlled independently of the grid size. We compare numerically to the established SPME method by Essmann et al. and see that the memory required can be reduced by orders of magnitude. We also benchmark efficiency (i.e. error as a function of computing time) against the SPME method, which indicates that our method is competitive. Analytical error estimates are proven and used to select parameters with a great degree of reliability and ease.     

Effects of ultrasonic treatment on color,carotenoid content,enzyme activity,rheological properties,and microstructure of pumpkin juice during storage

Freshly squeezed pumpkin juice (Cucurbita moschata D.) was sonicated at various power levels at a constant frequency of 25 kHz and a treatment time of 10 min. Samples were stored in the dark for 0, 4, 8, and 12 days at 4 °C and were subsequently analyzed. The combined effects of power level and storage period on color parameters, carotenoid content, particle size distribution, cloud value, rheological characteristics, and microstructure were investigated. The results showed ultrasonic-treated samples had little effect on carotenoid content, cloud value, particle size distribution, and polydispersity during storage compared to those of the untreated samples. The L^⁎, a^⁎, b^⁎, and C* values decreased significantly during 8–12 days of storage, resulting in a significant increase in ΔE, especially 400 W/10 min-treated samples. Meanwhile, the enzyme activity and rheological properties increased significantly on storage days 8–12. However, the microstructure of all samples did not change significantly during storage. Based on these results, during the storage period, the physical and chemical properties of 400 W/10 min-ultrasonic treated pumpkin juice were retained more than those in the untreated pumpkin juice. Therefore, ultrasonic treatment has broad application prospects in preserving bioactive substances and physicochemical properties and improving the storage life of fresh pumpkin juice.     

水稻耐铁毒基因型筛选及边缘细胞对铁毒的反应特性

以相对耐铁的水稻品种"中优9288"和敏感品种"汕优10号"作为实验材料,研究了铁毒对水稻离体边缘细胞的影响。结果表明,随铁浓度的升高(除400μmol/LFe2 外),处理时间的延长,边缘细胞存活率下降:400μmol/L浓度铁处理时,边缘细胞存活率增加;低浓度铁能促进PME活性增长,高浓度铁则抑制PME活性。     

Particle-Mesh Ewald(PME)算法的GPU加速

讨论在NVIDIACUDA开发环境下,用GPU加速分子动力学模拟中静电作用的长程受力计算部分.采用Particle-Mesh Ewald(PME)方法,将其分解为参数确定、点电荷网格离散、离散网格的傅立叶变换、静电热能求解与静电力求解5个部分,并分别分析各部分的GPU实现.此方法已成功用于7个不同大小的生物分子体系的模拟计算,达到了7倍左右的加速.该程序可耦合到现有分子动力学模拟软件中,或作为进一步开发的GPU分子动力学程序的一部分,显著加速传统分子动力学程序.