Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field

To promote accuracy of the atom‐bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc‐Zn, Y‐Cd, and Lu‐Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO‐3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy. © 2014 Wiley Periodicals, Inc.     

Covariate model-based fault tree analysis for risk assessment in chemical process industries: A case study of a chlorine manufacturing facility

Fault tree analysis (FTA) is a promising quantitative technique for risk analysis in chemical process industries (CPIs). In FTA, a certain sequence of basic events (causes) leads to one specific Top event (critical event of interest). However, the conventional fault tree analysis has the limitations of staticity and uncertainty. The staticity in conventional FTA arises due to its inability to accommodate time-dependent characteristics of the process system. Whereas uncertainty primarily lies in the failure probability data of basic events. This paper proposes an innovative methodology that uses a time-dependent covariate model to update the failure probability values of major contributing basic events in FTA. A novel subclass of the family of phase-type distributions is used to model the covariates corresponding to the basic events. The newly developed methodology is applied for a case study in a chlorine manufacturing facility to estimate the chlorine release probability. The blockage in the pipeline was identified as the significant reason for chlorine release from expert opinion and sensitivity analysis. The results of the proposed model of FTA are compared with that of conventional FTA.     

基于机器学习的直接电离质谱爆炸物检测方法

直接电离质谱系统在现场快速检测中的应用日益广泛,主要用于爆炸物、毒品、食品添加剂等的检测。然而,直接电离质谱系统中质谱信号波动大且同一浓度样品峰强呈现对数正态分布,严重影响了检出限附近低浓度样品的检测准确性。该研究将乙酰水杨酸(115个样品)作为爆炸物模拟物,利用介质阻挡放电离子源与质谱系统,研究了基于机器学习的直接电离质谱数据预处理和分类算法,以提高低浓度样品的检测准确率。对两种浓度为1 ng/mL的常见爆炸物样本(三硝基甲苯和硝酸铵分别为110、90个)及空白对照样本(366个)开展了应用实验。结果表明,与传统提取离子流方法和高斯混合模型方法相比,采用随机森林算法可将F_score从0.74、0.89提升至0.96,显著提高了检测准确率,且单个样本数据分析时间远少于0.1 s,满足实时检测需求。     

Automatic analysis of microscopic photo-pictures of undeveloped and developed nuclear emulsions

Methods of automatic computer analyses of images have large impotence in numerous physical problems with different kinds of radiations, which use such solid-state detectors as nuclear photographic emulsions, plastics and others. We described a method of expanding boundaries of dark areas for such computer analyses of micro-pictures. We demonstrated effectiveness of this method by the example of the search of microcrystals size distributions in two undeveloped nuclear emulsions and similar distribution of background grains in the developed emulsion.     

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

We report a methodology to calculate the free energy of a shape transformation in a lipid membrane directly from a molecular dynamics simulation. The bilayer need not be homogeneous or symmetric and can be atomically detailed or coarse grained. The method is based on a collective variable that quantifies the similarity between the membrane and a set of predefined density distributions. Enhanced sampling of this “Multi-Map” variable re-shapes the bilayer and permits the derivation of the corresponding potential of mean force. Calculated energies thus reflect the dynamic interplay of atoms and molecules, rather than postulated effects. Evaluation of deformations of different shape, amplitude, and range demonstrates that the macroscopic bending modulus assumed by the Helfrich–Canham model is increasingly unsuitable below the 100-Å scale. In this range of major biological significance, direct free-energy calculations reveal a much greater plasticity. We also quantify the stiffening effect of cholesterol on bilayers of different composition and compare with experiments. Lastly, we illustrate how this approach facilitates analysis of other solvent reorganization processes, such as hydrophobic hydration. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.     

A probabilistic analysis of a discrete-time evolution in recombination

We study the discrete-time evolution of a recombination transformation in population genetics. The transformation acts on a product probability space, and its evolution can be described by a Markov chain on a set of partitions that converges to the finest partition. We describe the geometric decay rate to this limit and the quasi-stationary behavior of the Markov chain when conditioned on the event that the chain does not hit the limit.     

Taylor Expansions of Distributions

Classical Taylor expansions of holomorphic functions in the complex plane are extended to distributions in Rⁿand in domains     

On Time Dynamics of Coagulation-Fragmentation Processes

We establish a characterization of coagulation-fragmentation processes, such that the induced birth and death processes depicting the total number of groups at time t≥0 are time homogeneous. Based on this, we provide a characterization of mean-field Gibbs coagulation-fragmentation models, which extends the one derived by Hendriks et al. As a by-product of our results, the class of solvable models is widened and a question posed by N. Berestycki and Pitman is answered, under restriction to mean-field models.     

On a Property of Subexponential Distributions

Let F be a distribution function (d.f.) on [0, ) with finite first moment m >0. We define the integrated tail distribution function F ₁ of F by F ₁(t)=m^-1 ₀ ^t (1- F(u))du, t0. In this paper, we obtain sufficient conditions under which implications FSF ₁S and F ₁S FS hold, where S is the class of subexponential distributions.