Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano‐objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano‐objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. © 2013 Wiley Periodicals, Inc.     

An Approximate Expression for the Degree of Counterion Binding of Dressed Micelles

A simple formula for calculating the degree of counterion binding of dressed micelles is presented. This approximate expression for the spherical micelle is derived from the extending Langmuir's method in the case of high surface potentials. It works quite well for the estimation of the degree of counterion binding of micelles. The simple form is very convenient for practical use.     

一种在色噪声环境下的信号检测方法

为了抑制蛟龙号载人潜水器水声通信受母船色噪声干扰的影响,本文提出了一种统计匹配滤波器在色噪声环境下使用的新方法,它通过将接收信号映射到一个生成子空间中进行信号检测,可提高输出水声通信信号的信噪比。受客观条件限制,向阳红09船——蛟龙号载人潜水器的试验母船噪声环境比较恶劣,对水声通信产生了较强的干扰。如何在向阳红09船的这种强、色噪声环境下,提升水声同步信号的检测能力,对提高水声通信的可靠性是非常有帮助的。实际采集试验数据分析结果验证了该检测算法比传统匹配滤波器有更强的信号检测能力。     

光静态散射测试系统的研究与实现

随着科学技术的发展,对粒子的大小、浓度及其他特性的探测已经发展成为一个专门的研究领域和现代测量学中的一个重要分支,而光散射法已经成为一种常用的粒子测量方法。为了满足应用需求,文中提出了一种基于C8051F500单片机的光静态散射测试系统方案,详细介绍了该测试系统的设计理论原理、硬件电路的设计依据、固件程序的设计思想和测试系统的具体实现。选取一定浓度的样品溶液,运用该系统进行光散射的角度依赖性测试,实际测量值与理论依据基本相符;在不同激光功率下,对同一角度的散射光强进行测试,将测量得到的数据分析,线性度良好,满足设计要求。     

红外成像系统NETD参数测试算法及应用研究

噪声等效温差(NETD)是表征红外成像系统灵敏度的关键参数,也是评估红外成像系统性能的重要参数之一,应用广泛。通过对红外成像系统3D噪声、信号传递函数(SiTF)、NETD等参数测试方法、算法和流程研究,给出一种基于视频文件的3D噪声离线对比测试方法和一种SiTF线性区自动判断计算斜率算法,在此基础上针对某型技术保障装备国产化光电检测平台开发了配套应用软件功能模块。实现了通过计算单位均方根噪声所对应的SiTF斜率值,分析得出系统NETD参数值的功能。以某型热像仪为被测对象,开展了测试结果重复性和一致性试验,并与美国Optikos公司I-SITE红外整机测试系统进行了对比测试。实验结果表明开发的NETD参数测试功能模块测试精度和重复性满足设计要求,具有较高实用价值,已进行了工程应用。     

Interpolating solutions of the Poisson equation in the disk based on Radon projections

We consider an algebraic method for reconstruction of a function satisfying the Poisson equation with a polynomial right-hand side in the unit disk. The given data, besides the right-hand side, is assumed to be in the form of a finite number of values of Radon projections of the unknown function. We first homogenize the problem by finding a polynomial which satisfies the given Poisson equation. This leads to an interpolation problem for a harmonic function, which we solve in the space of harmonic polynomials using a previously established method. For the special case where the Radon projections are taken along chords that form a regular convex polygon, we extend the error estimates from the harmonic case to this Poisson problem. Finally we give some numerical examples.     

Existence of global weak solutions for Navier‐Stokes‐Poisson equations with quantum effect and convergence to incompressible Navier‐Stokes equations

In this paper, we consider a three dimensional quantum Navier‐Stokes‐Poisson equations. Existence of global weak solutions is obtained, and convergence toward the classical solution of the incompressible Navier‐Stokes equation is rigorously proven for well prepared initial data. Furthermore, the associated convergence rates are also obtained. Copyright © 2014 John Wiley & Sons, Ltd.     

CORSICA: correction of structured noise in fMRI by automatic identification of ICA components

When applied to functional magnetic resonance imaging (fMRI) data, spatial independent component analysis (sICA), a data-driven technique that addresses the blind source separation problem, seems able to extract components specifically related to physiological noise and brain movements. These components should be removed from the data to achieve structured noise reduction and improve any subsequent detection and analysis of signal fluctuations related to neural activity. We propose a new automatic method called CORSICA (CORrection of Structured noise using spatial Independent Component Analysis) to identify the components related to physiological noise, using prior information on the spatial localization of the main physiological fluctuations in fMRI data. As opposed to existing spectral priors, which may be subject to aliasing effects for long-TR data sets (typically acquired with TR >1 s), such spatial priors can be applied to fMRI data, regardless of the TR of the acquisitions. By comparing the proposed automatic selection to a manual selection performed visually by a human operator, we first show that CORSICA is able to identify the noise-related components for long-TR data with a high sensitivity and a specificity of 1. On short-TR data sets, we validate that the proposed method of noise reduction allows a substantial improvement of the signal-to-noise ratio evaluated at the cardiac and respiratory frequencies, even in the gray matter, while preserving the main fluctuations related to neural activity.     

Mathematical model of electromigration allowing the deviation from electroneutrality

The structure of the double layer on the boundary between solid and liquid phases is described by various models, of which the Stern–Gouy–Chapman model is still commonly accepted. Generally, the solid phase is charged, which also causes the distribution of the electric charge in the adjacent diffuse layer in the liquid phase. We propose a new mathematical model of electromigration considering the high deviation from electroneutrality in the diffuse layer of the double layer when the liquid phase is composed of solution of weak multivalent electrolytes of any valence and of any complexity. The mathematical model joins together the Poisson equation, the continuity equation for electric charge, the mass continuity equations, and the modified G-function. The model is able to calculate the volume charge density, electric potential, and concentration profiles of all ionic forms of all electrolytes in the diffuse part of the double layer, which consequently enables to calculate conductivity, pH, and deviation from electroneutrality. The model can easily be implemented into the numerical simulation software such as Comsol. Its outcome is demonstrated by the numerical simulation of the double layer composed of a charged silica surface and an adjacent liquid solution composed of weak multivalent electrolytes. The validity of the model is not limited only to the diffuse part of the double layer but is valid for electromigration of electrolytes in general.