Monte-Carlo Calculations for Methane and Argon over a Wide Range of Density and Temperature,Including the Two-Phase Vapor-Liquid Region

Abstract

The Gibbs-ensemble simulation technique provides a powerful method to calculate vapor-liquid phase behavior [1]. To evaluate the configurational energy of a system of molecules, commonly used experessions describe the interaction between two molecules. Contributions from higher-body forces are usually implicitly taken into account by adjusting two-body potential parameters to give agreement with experimental data. Explicit expressions for higher-body potentials are not commonly used in simulations [8]. The work by Smit et al. [9] gives the appropriate expressions to evaluate the pressure as well as the chemical potential from a density-dependent two-body potential in an NVT ensemble.

In the present work, contributions to the potential from two-body interactions are separated from those due to higher-body interactions; to take higher-body forces into account, a mean-field term, proportional to (density)^0.9, is added to the two-body potential. NPT-simulations over a wide range of temperature and density, as well as Gibbs-ensemble simulations, are used to evaluate phase behavior of argon and of methane. The results indicate that a simple mean-field correction to the “true” two-body Kihara potential provides good agreement between experiment and simulation.     

360度评价法在住培学员岗位胜任能力评价中

目的 运用360度评价法对2015级住培学员岗位胜任力进行评价,对2015级住培学员岗位胜任力现状进行探讨分析。方法 采用问卷调查评价表分别从专业基地主任、学员指导教师、轮转带教教师、同学、自我评价5个角度,对202名住培学员岗位胜任力进行360度反馈评价,岗位胜任力评价内容包含基本能力、职业素养、医患沟通、医学知识等8个方面核心能力;应用EpiData3.02建立数据库,采用SPSS19.0软件进行统计分析,统计分析方法主要为描述性统计分析、单因素方差分析。结果 5类评价主体在基本能力和医学知识2项能力打分较高,在职业精神、沟通能力、职业道德、团队合作、学术研究等其他几项能力打分偏低;在基本能力、职业精神与素质、沟通能力、团队合作和学术研究几方面能力评分,差异均有统计学意义（P＜0.05）;本人各方面打分均偏高,轮转带教教师和同专业基地同学打分居中,专业基地主任、指导导师在各方面打分偏低 结论 360度评价法客观公正地评价住培学员岗位胜任能力,有助于提高住培学员岗位胜任能力,有利于加强团队意识,增强团队建设。     

Force and torque production in static multifinger prehension: biomechanics and control. II. Control

 The coordination of digits during combined force/torque production tasks was further studied using the data presented in the companion paper [Zatsiorsky et al. Biol Cybern this issue, Part I]. Optimization was performed using as criteria the cubic norms of (a) finger forces, (b) finger forces normalized with respect to the maximal forces measured in single-finger tasks, (c) finger forces normalized with respect to the maximal forces measured in a four-finger task, and (d) finger forces normalized with respect to the maximal moments that can be generated by the fingers. All four criteria failed to predict antagonist finger moments when these moments were not imposed by the task mechanics. Reconstruction of neural commands: The vector of neural commands c was reconstructed from the equation c=W ⁻¹ F, where W is the finger interconnection weight matrix and F is the vector of finger forces. The neural commands ranged from zero (no voluntary force production) to one (maximal voluntary contraction). For fingers producing moments counteracting the external torque (`agonist' fingers), the intensity of the neural commands was well correlated with the relative finger forces normalized to the maximal forces in a four-finger task. When fingers produced moments in the direction of the external torque (`antagonist' fingers), the relative finger forces were always larger than those expected from the intensity of the corresponding neural commands. The individual finger forces were decomposed into forces due to `direct' commands and forces induced by enslaving effects. Optimization of the neural commands resulted in the best correspondence between actual and predicted finger forces. The antagonist moments are, at least in part, due to enslaving effects: strong commands to agonist fingers also activated antagonist fingers. Received: 8 August 2001 / Accepted in revised form: 7 February 2002     

The Implementation of the Iterative Diagonalization Scheme and ab initio Molecular Dynamics Simulation with the LAPW Method

Abstract

A new ab initio molecular dynamics method based on the full-potential linearized-augmented-plane-wave (LAPW) basis set has been implemented. The LAPW basis set has been successfully employed for systems containing localized electrons such as first row atoms and transition metals. In our implementation of the LAPW-MD scheme, iterative residual minimization algorithm is used to solve the electronic states problem. The atoms are moved according to forces derived from the Hellman–Feynman theorem and incomplete basis set correction terms. The performance of the program is further enhanced by parallelization. We will discuss technical details of the program implementation and present results obtained from this code to the equilibrium structures and vibrational properties of simple diatomic molecules.     

Computer Simulation of Two-Dimensional Continuum Flows by the Direct Simulation Monte Carlo Method

Abstract

Computer simulations using particles are an attractive method to extract microscopic information of flow phenomena [1]. The molecular dynamics (MD) method, in which Newton's equations of motions are integrated, gives the temporal development of the system. In the MD simulation of fluid flows, the computational region is limited to atomistic scales [2]. On the other hand, the direct simulation Monte Carlo (DSMC) method, in which collisions of particles are made on a probabilistic basis, has a potential of treating a realistic system with a macroscopic scale length retaining the atomistic details. The DSMC method provides an efficient way to integrate the Boltzmann equation from the rarefied gas to the near-continuum region. Bird clarified the validity of the DSMC method in the near-continuum flow region [3]. However, the DSMC method has not been applied to the continuum region and compared with the continuum hydrodynamics.     

Evaluating a sensitive issue: reliability of a clinical evaluation for allodynia severity

Abstract

Purpose/Aim: Allodynia is a common feature of neuropathic pain with few validated clinical evaluation options. We identified a need to estimate the measurement properties of the standardised evaluation procedure for static mechanical allodynia severity popularised by the somatosensory rehabilitation of pain method, known as the rainbow pain scale. This study (www.clinicaltrials.gov. NCT02070367) undertook preliminary investigation of the inter-rater and test-retest reliability of the rainbow pain scale.

Methods: Persons with pain in one upper extremity after Complex Regional Pain Syndrome, a peripheral nerve injury or a recent hand fracture were recruited for assessment of static mechanical allodynia threshold using calibrated monofilaments by two raters at baseline, and repeated assessment one week later.

Results: Single measures estimates suggested inter-rater reliability was substantial for the rainbow pain scale [intra-class correlation coefficient?=?0.78 (n?=?31), p?<?0.001]. Test-retest reliability was also excellent at with an intraclass correlation coefficient of 0.87 [n?=?28, p?<?0.001]. However, confidence intervals suggest the true values could be more moderate, with lower bounds of the 95% confidence interval at 0.60 and 0.74, respectively.

Conclusions: This pilot study has generated preliminary support for the inter-rater and test-retest reliability of the rainbow pain scale. Future studies should seek to increase confidence in estimates of reliability, and estimate validity and responsiveness to change in persons with somatosensory disorders.     

基于TOPSIS综合评价法的医疗保险规制措施评价

?????? 目的 评价我国医疗保险规制效果,筛选优先干预措施,为建立有效的医院规制体系提供依据。方法 运用文献研究法明确现行医疗保险规制策略,通过问卷调查法调查策略实施情况,运用加权TOPSIS综合评价法对医疗保险规制的主要策略进行多维度综合评价。 结果 医疗保险支付方式是下一步规制改革的首要内容,接下来依次为医疗保险定点机构管理及医疗保险筹资和费用补偿。结论 在促进后付制（按项目付费）向预付制转变的同时,积极探索多种支付方式的结合运用。     

基于德尔菲法的外科手术风险因素评价指标构建

目的 构建外科手术风险因素评价指标体系,为有效监管外科手术质量与安全提供参考依据。方法 运用文献分析法、德尔菲法、层次分析法进行外科手术风险因素评价体系的构建和指标权重的确定。结果 建立了一个由手术固有风险、医疗机构风险、医务人员风险、患者风险4 个一级指标和手术本身风险、医务人员专业技术水平、患者个体差异、医务人员责任心、医学科学的局限性、医院诊疗流程、医务人员团队协作,医院诊疗服务水平、工作负荷等等20 个二级指标组成的手术风险因素评价指标体系。结论 建立一套完善的外科手术风险因素评价指标体系,对于保障手术患者安全、有效进行外科手术质量与安全监管具有重要意义。     

Nonadditive Monte Carlo Simulation of Liquid Hydrogen Chloride Difference Algorithm and Parallel Implementation

Abstract

This paper continues our Monte Carlo simulation study of liquid hydrogen chloride [1]. The importance of non-additive interactions is carefully analyzed. Computed atom pair correlation functions are compared to neutron scattering experiments [2]. A difference algorithm (“Δ—algorithm”) is developed, which makes non-additive Monte Carlo simulations practicable. We also report an implementation of this algorithm on a transputer network, taking advantage of the inherent parallelism of the Δ — algorithm.     

基于注意力机制的RNA碱基关联图预测方法

目的 长链非编码RNA在遗传、代谢和基因表达调控等方面发挥着重要作用。然而，传统的实验方法解析RNA的三级结构耗时长、费用高且操作要求高。此外，通过计算方法来预测RNA的三级结构在近十年来无突破性进展。因此，需要提出新的预测算法来准确的预测RNA的三级结构。所以，本文发展可以用于提高RNA三级结构预测准确性的碱基关联图预测方法。方法 为了利用RNA理化特征信息，本文应用多层全卷积神经网络和循环神经网络的深度学习算法来预测RNA碱基间的接触概率，并通过注意力机制处理RNA序列中碱基间相互依赖的特征。结果 通过多层神经网络与注意力机制结合，本文方法能够有效得到RNA特征值中局部和全局的信息，提高了模型的鲁棒性和泛化能力。检验计算表明，所提出模型对序列长度L的4种标准（L/10、L/5、L/2、L）碱基关联图的预测准确率分别达到0.84、0.82、0.82和0.75。结论 基于注意力机制的深度学习预测算法能够提高RNA碱基关联图预测的准确率，从而帮助RNA三级结构的预测。     

Modelling Diffusion in Zeolites by Molecular Dynamics Simulations

Abstract

The diffusion of molecules sorbed in zeolites is of growing interest for understanding the mechanisms of chemical processes with regard to selectivity and reactivity [1].

MD simulations give insight into physical systems on the molecular level allowing to study and visualize the motion of molecules even beyond the possibilities of experiments [2,3]. Single system parameters can easily be varied to study their influence, also those parameters that are fixed in reality (e.g., the size of particles). We present a cross section of our recent work to illustrate the capabilities of MD: The self diffusion coefficients (D) of a mixture of methane and xenon in silicalite show remarkable deviations from those of the pure species. This is shown and confirmed by PFG NMR experiments [4].

Simulating ethane in zeolite A the mechanism of diffusion has been studied. The effects of rotation on the diffusion lead to cases where D decreases with growing temperature [5].

The independence of self diffusion on lattice vibrations is proven even for zeolites with windows of guest particle size comparing simulations with rigid and vibrating zeolite lattice [6].     

失效模式与效应分析法在护理安全管理中的应用

目的 通过失效模式与效应分析法评估医院血液科护理风险的薄弱环节,探究护理风险的发生原因,并提出有针对性的改进措施。 方法 采用FMEA法对血液科护理风险进行识别。结果 分析得出血液科护理风险由高至低依次为输血风险、用药风险、职业暴露、针刺伤、坠床跌倒、患者投诉、压疮和医疗器械风险。结论 失效模式与效应分析法可以用于血液科护理风险的识别,在识别结果基础上制定改进措施,可以有效地避免护理风险,保证患者安全。

     

Kinetic and molecular orbital studies on the rate of oxidation of monosubstituted phenols and anilines by lactoperoxidase compound II in comparison with the case of horseradish peroxidase

The second-order rate constant (k4) for the oxidation of monosubstituted phenols and anilines by lactoperoxidase compound II was examined by Chance's method [B. Chance, Arch. Biochem. Biophys. 71 (1957), 130–136]. When the electronic states of these substrates were calculated by an ab initio molecular orbital method, it was found that the log k4 value correlates well with the highest occupied molecular orbital (HOMO) energy level but not with the net charge or frontier electron density. These results are essentially similar to those reported previously in the case of horseradish peroxidase [J. Sakurada, R. Sekiguchi, K. Sato, and T. Hosoya, Biochemistry 29 (1990), 4093–4098], showing some dissimilar features which are considered to reflect the structural difference between the two enzymes.Abbreviations HOMO highest occupied molecular orbital - HRP horseradish peroxidase - LPO lactoperoxidase (EC 1.11.1.7) - LUMO lowest unoccupied molecular orbital     

Attending a social event and consuming alcohol is associated with changes in serum microRNA: a before and after study in healthy adults

Abstract

Purpose: Circulating microRNAs represent a reservoir for biomarker discovery. Our objective was to profile the change in human circulating microRNA associated with recreational use of alcohol at a social event.

Material and methods: Blood was collected from healthy volunteers (N?=?16) before and after recreational consumption of alcohol (ethanol). Biochemistry, hematology and ethanol measurements were performed. The change in the serum small RNA fraction was quantified by RNA sequencing.

Results: Blood ethanol was undetectable at study entry in all subjects [<10?mg/dL]. After consuming alcohol the median concentration was 89?mg/dL [IQR: 71–138. Min–max 20–175]. There were no changes in biochemistry and hematology parameters. Serum RNA sequencing identified 1371 small RNA species (1305 microRNAs). There were significant increases [adjusted p-value <0.05, fold increase 2 or more] in 265 microRNAs, around a fifth of the total [median fold increase 2.3 [IQR: 2.1–2.5; Max: 3.7]]. miR-185-5p decreased following alcohol exposure [adjusted p-value <0.05, fold decrease 2 or more].

Conclusions: The microRNA composition of human serum is dynamic and environmental factors may have a significant impact. Within its context of use the fold change ‘signal’ of a microRNA must be large enough to negate the risk of false results due to background ‘noise’.     

Mathematical modeling of capillary formation and development in tumor angiogenesis: penetration into the stroma

The purpose of this paper is to present a mathematical model for the tumor vascularization theory of tumor growth proposed by Judah Folkman in the early 1970s and subsequently established experimentally by him and his coworkers [Ausprunk, D. H. and J. Folkman (1977) Migration and proliferation of endothelial cells in performed and newly formed blood vessels during tumor angiogenesis, Microvasc Res., 14, 53–65; Brem, S., B. A. Preis, ScD. Langer, B. A. Brem and J. Folkman (1997) Inhibition of neovascularization by an extract derived from vitreous Am. J. Opthalmol., 84, 323–328; Folkman, J. (1976) The vascularization of tumors, Sci. Am., 234, 58–64; Gimbrone, M. A. Jr, R. S. Cotran, S. B. Leapman and J. Folkman (1974) Tumor growth and neovascularization: an experimental model using the rabbit cornea, J. Nat. Cancer Inst., 52, 413–419]. In the simplest version of this model, an avascular tumor secretes a tumor growth factor (TGF) which is transported across an extracellular matrix (ECM) to a neighboring vasculature where it stimulates endothelial cells to produce a protease that acts as a catalyst to degrade the fibronectin of the capillary wall and the ECM. The endothelial cells then move up the TGF gradient back to the tumor, proliferating and forming a new capillary network. In the model presented here, we include two mechanisms for the action of angiostatin. In the first mechanism, substantiated experimentally, the angiostatin acts as a protease inhibitor. A second mechanism for the production of protease inhibitor from angiostatin by endothelial cells is proposed to be of Michaelis-Menten type. Mathematically, this mechanism includes the former as a subcase. Our model is different from other attempts to model the process of tumor angiogenesis in that it focuses (1) on the biochemistry of the process at the level of the cell; (2) the movement of the cells is based on the theory of reinforced random walks; (3) standard transport equations for the diffusion of molecular species in porous media. One consequence of our numerical simulations is that we obtain very good computational agreement with the time of the onset of vascularization and the rate of capillary tip growth observed in rabbit cornea experiments [Ausprunk, D. H. and J. Folkman (1977) Migration and proliferation of endothelial cells in performed and newly formed blood vessels during tumor angiogenesis, Microvasc Res., 14, 73–65; Brem, S., B. A. Preis, ScD. Langer, B. A. Brem and J. Folkman (1997) Inhibition of neovascularization by an extract derived from vitreous Am. J. Opthalmol., 84, 323–328; Folkman, J. (1976) The vascularization of tumors, Sci. Am., 234, 58–64; Gimbrone, M. A. Jr, R. S. Cotran, S. B. Leapman and J. Folkman (1974) Tumor growth and neovascularization: An experimental model using the rabbit cornea, J. Nat. Cancer Inst., 52, 413–419]. Furthermore, our numerical experiments agree with the observation that the tip of a growing capillary accelerates as it approaches the tumor [Folkman, J. (1976) The vascularization of tumors, Sci. Am., 234, 58–64]. An erratum to this article is available at .     

以管理成效为导向的医院职能部门绩效考核方法研究

目的 探索适应公立医院绩效评价背景的职能部门绩效考核方法。方法 在文献复习、专题小组讨论和专家访谈的基础上,调研不同类别公立医院进行分析,梳理公立医院职能部门绩效考核的概况、职能部门职责发展变化以及职能部门待解决的问题。结果 发现职能部门任务复杂化,面临系列问题亟待解决,现有的职能部门绩效考核方法有待发展。提出以管理成效为导向的职能部门绩效考核方法;从重点工作、日常行政工作、管理能力进行考核,旨在激励约束职能部门改进管理成效。结论 建立健全以管理成效为导向的职能部门绩效考核方法是促进公立医院执行公立医院绩效评价政策的有益探索。     

基于模糊综合评判法的医院费用规制效果综合评价

??????? 目的 评价我国医疗费用规制策略效果,筛选优先干预策略。方法 运用模糊综合评判法对医院费用的重要规制手段：医疗服务定价方式、药品流通体制、医疗保险支付方式的重要性、可操作性、失效程度、干预迫切性四个维度进行综合评价。 结果 导致我国医疗费用控制效果不佳的首要原因在于药品流通体制的管制失效;现行医保支付方式对医疗费用的规制作用不强,这是导致快速上涨的医疗费用难以得到有效遏制控制的第二位原因。 结论 改善我国医疗费用规制效果的优先策略是进一步强化药品流通体制规制改革的推进力度;其次,亟待深化医保制度支付方式的费用控制机制探索,发挥医保制度作为第三方对医疗费用的重要规制作用。     

An eigenvalue-eigenvector approach to predicting protein folding types

The accuracy of predicting protein folding types can be significantly enhanced by a recently developed algorithm in which the coupling effect among different amino acid components is taken into account [Chou and Zhang (1994)J. Biol. Chem. 269, 22014-22020]. However, in practical calculations using this powerful algorithm, one may sometimes face illconditioned matrices. To overcome such a difficulty, an effective eigenvalue-eigenvector approach is proposed. Furthermore, the new approach has been used to predict a recently constructed set of 76 proteins not included in the training set, and the accuracy of prediction is also much higher than those of other methods.     

Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition

A number of methods to predicting the folding type of a protein based on its amino acid composition have been developed during the past few years. In order to perform an objective and fair comparison of different prediction methods, a Monte Carlo simulation method was proposed to calculate the asymptotic limit of the prediction accuracy [Zhang and Chou (1992),Biophys. J. 63, 1523–1529, referred to as simulation method I]. However, simulation method I was based on an oversimplified assumption, i.e., there are no correlations between the compositions of different amino acids. By taking into account such correlations, a new method, referred to as simulation method II, has been proposed to recalculate the objective accuracy of prediction for the least Euclidean distance method [Nakashimaet al. (1986),J. Biochem. 99, 152–162] and the least Minkowski distance method [Chou (1989),Prediction in Protein Structure and the Principles of Protein Conformation, Plenum Press, New York, pp. 549–586], respectively. The results show that the prediction accuracy of the former is still better than that of the latter, as found by simulation method I; however, after incorporating the correlative effect, the objective prediction accuracies become lower for both methods. The reason for this phenomenon is discussed in detail. The simulation method and the idea developed in this paper can be applied to examine any other statistical prediction method, including the computersimulated neural network method.     

Structure of Supercritical Fluid Krypton at Small Scattering Angle Using Parallel Molecular Dynamics Simulation

Abstract

We present a parallel algorithm for molecular dynamics involving short-range two- and three-body potentials and the pair-correlation function, g(r). The method is based on a spatial decomposition of the simulation box that takes advantage of a linked-cell list, and allows a load balanced partition of the computations of both the forces and g(r) over the processors. The tests of the program is conducted by evaluating the efficiency for both the thermalization phase and the production phase of the simulation. This method is successfully applied to the calculation of the direct correlation function of fluid krypton at small scattering angle along the T = 297 K supercritical isotherm.