A Parallel Algorithm for Nonequilibrium Molecular Dynamics Simulation of Shear Flow on Distributed Memory Machines

Abstract

An algorithm is described which allows Nonequilibrium Molecular Dynamics (NEMD) simulations of a fluid undergoing planar Couette flow (shear flow) to be carried out on a distributed memory parallel processor using a (spatial) domain decomposition technique. Unlike previous algorithms, this algorithm uses a co-moving, or Lagrangian, simulation box. Also, the shape of the simulation box changes throughout the course of the simulation. The algorithm, which can be used for two or three dimensional systems, has been tested on a Fujitsu AP1000 Parallel computer with 128 processors.     

体外循环血栓非侵入在线电阻抗成像方法

目的 在体外循环系统中,血栓的在线检测和可视化具有重要意义。本文提出了基于电阻抗成像（EIT）的体外循环血栓非侵入在线检测方法。方法 首先通过联合仿真研究了传感器尺寸对成像效果的影响。其次,根据仿真结果设计了直径为20 mm的16铜质电极EIT传感器,搭建了循环流动实验平台,并设计了静态和循环流动实验。使用尺寸为3～6 mm的猪血块代替血栓,将血块置于新鲜猪血样本中,采用Tikhonov正则化算法进行成像。将3 mm和5 mm的血块分别置于循环系统中,重建血块在传感器截面的大小和位置图像,并与高速相机拍摄结果进行对比。结果 仿真结果显示当目标物与传感器面积比（AR）不小于0.01时,传感器直径为20 mm和30 mm对应的图像相关系数（IC）均大于0.06,成像效果较好。静态成像结果显示,相对尺寸覆盖率误差（RCR）小于等于0.1。循环流动实验显示,血块经过传感器时,检测到归一化后的相对电导率变化值分别为80和200,结果显示该方法能够检测到循环系统中的血块。结论 该方法具有实时性和非侵入的优点,有望应用于体外血栓的检测。     

Multi-Representation Techniques for Multi-Scale Simulation: Reactive Microflows in a Catalytic Converter

Abstract

We describe the basic ideas behind a multi-representation (floating-point and integer) algorithm for the numerical simulation of reactive flows with heat transfer. In particular, we provide some details on the interface connecting the integerized to the floating-point components. An application to catalytic conversion is briefly discussed.     

Gibbs-Ensemble Molecular Dynamics: Liquid-Gas Equilibria for Lennard-Jones Spheres and n-Hexane

Abstract

We present a novel method to simulate phase equilibria in atomic and molecular systems. The method is a Molecular Dynamics version of the Gibbs-Ensemble Monte Carlo technique, which has been developed some years ago for the direct simulation of phase equilibria in fluid systems. The idea is to have two separate simulation boxes, which can exchange particles (or molecules) in a thermodynamically consistent fashion. Here we pres the derivation of the generalized equations of motion and discuss the relation of the resulting trajectory averages to the relevant ensemble. We test this Gibbs-Ensemble Molecular Dynamics algorithm by applying it to an atomic and a molecular system, i.e. to the liquid-gas coexistence in a Lennard-Jones fluid and in n-hexane. In both cases our results are in good accord with previous mean field and Gibbs-Ensemble Monte Carlo results as well as with the experimental data in the case of hexane. We also show that our Gibbs-Ensemble Molecular Dynamics algorithm like other Molecular Dynamics techniques can be used to study the dynamics of the system. Self-diffusion coefficients calculated with this method are in agreement with the result of conventional constant temperature Molecular Dynamics.     

In Vivo MRI Assessment of Hepatic and Splenic Disease in a Murine Model of Schistosmiasis

BackgroundSchistosomiasis (or bilharzia), a major parasitic disease, affects more than 260 million people worldwide. In chronic cases of intestinal schistosomiasis caused by trematodes of the Schistosoma genus, hepatic fibrosis develops as a host immune response to the helminth eggs, followed by potentially lethal portal hypertension. In this study, we characterized hepatic and splenic features of a murine model of intestinal schistosomiasis using in vivo magnetic resonance imaging (MRI) and evaluated the transverse relaxation time T₂ as a non-invasive imaging biomarker for monitoring hepatic fibrogenesis.Conclusions/SignificanceOur multiparametric MRI approach confirms that this murine model replicates hepatic and splenic manifestations of human intestinal schistosomiasis. Quantitative T₂ mapping proved sensitive to assess liver fibrogenesis non-invasively and may therefore constitute an objective imaging biomarker for treatment monitoring in diseases involving hepatic fibrosis.     

基于深度学习的肝脏病理图像中肝脂肪变性分级研究

摘要 目的：设计基于深层神经网络模型用来分析肝脏全景病理切片图像（Whole slide images, WSI）的肝脂肪变性分级方法,以实现对非酒精性脂肪性肝病（Non-alcoholic fatty liver disease, NAFLD）病程的辅助诊断。方法：结合临床诊断,以非酒精性脂肪肝活动度积分（NAFLD activity score, NAS）为评价标准,将肝脂肪变性程度分为无、轻度、中度和重度等四级病程,本研究采用多示例学习的策略构建并训练深度神经网络模型,将训练获得的人工智能模型用来实现计算机自动化诊断肝脏病理切片中肝脂肪变性程度分级。结果：通过使用本研究中的人工智能方法可以在3分钟内对一张WSI进行完整的分析,得到该病患肝脏病理切片中肝脂肪变性分级,训练获得的人工智能模型的AUC为0.97,肝脂肪变性分级的平均准确率为78.18%,macro-F1 score、macro-Precision和macro-Recall分别为79.49、82.03和77.10,其结果展示获得的人工智能模型已满足可辅助临床诊断的水平。结论：本研究基于深度学习技术开发的人工智能方法初步实现快速自动化诊断肝脂肪变性分级,展现了其潜在的临床使用价值。     

基于动态聚焦的声聚焦光声内窥成像算法研究

目的 声聚焦光声内窥成像具有成像深度大的优点,是一种非常有前景的功能成像技术,该技术被广泛应用于直肠、食道等内窥成像中。声聚焦光声内窥成像通常采用基于单个聚焦超声传感器的侧向扫描方式,同时采用传统的B扫描方法进行重建,会大大降低图像质量。为了获得高质量的图像,本文提出了几种动态聚焦的声聚焦光声内窥成像算法。方法 本文使用几种动态聚焦算法进行了数值仿真,并搭建系统进行了仿体实验验证,从横向分辨率和信噪比等多方面比较了各算法在动态聚焦中的成像效果。结果 相比B扫描方法,动态聚焦后的图像在离焦区域的横向分辨率与信噪比方面都有提升,仿真模拟中最高可将离焦区域的成像目标分辨率提升约26倍,其信噪比经动态聚焦后最高可提高2.3倍左右,实验中的远距离点目标经动态聚焦重建后分辨率提升3～6倍。结论 整体而言,基于时空响应的算法和合成孔径聚焦重建算法是在实验条件下更为适用的算法。本工作对后续的声聚焦光声内窥成像的设计具有指导意义。     

Network pharmacology-based identification of significant pathway for protection of Yinhuang granule in a mice model of metabolic-associated fatty liver disease

BackgroundMetabolic-associated fatty liver disease (MAFLD) is a spectrum of liver disorders. Nonalcoholic steatohepatitis (NASH) is defined as a more serious process of MAFLD with liver inflammation.PurposeThis study aims to observe the alleviation of Yinhuang granule (YHG), a Chinese patent medicine, on methionine and choline-deficient diet (MCD)-induced MAFLD in mice.MethodsNetwork pharmacology was used to analyze the improving effect of YHG on MAFLD and possible targets. MAFLD was induced in mice by MCD diet feeding for 6 weeks. In the last 2 weeks, the mice were orally given with YHG (400, 800 mg/kg) every day. Biochemical parameters of serum and liver, as well as hepatic gene expression were detected.ResultsNetwork pharmacology showed that YHG could improve MAFLD, inflammation, liver fibrosis, and oxidative stress. In animal experiments, YHG reduced hepatocellular damage and hepatic lipids accumulation which induced by MCD. In terms of liver inflammation, YHG attenuated MCD-induced liver inflammation in mice. YHG also inhibited the activation of hepatic stellate cells (HSCs) and alleviated liver fibrosis in MCD-fed mice. Through nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway, YHG alleviated liver oxidative stress injury in mice which induced by MCD.ConclusionYHG ameliorated MCD-induced MAFLD in mice by reducing hepatic lipids accumulation, alleviating liver oxidative, inflammatory injury and attenuating hepatic fibrosis.     

Hemodynamic simulation of intracranial aneurysm growth with virtual silk stent implantation

Abstract

Longitudinal hemodynamic assessment of intracranial aneurysms (IAs) with endovascular treatment is essential for clinical decision making. We proposed a hemodynamic simulation method to explore the hemodynamic characteristics of a certain growth process of IA with virtual Silk stent implantation. Eight growth point models of IA were created by applying a bidirectional linear growing algorithm on patient 3D rotational angiography images. Simulated experiments showed that the WSS and velocity were significantly decreased with virtual Silk stent implantation at all growth points considered. The simulations revealed the flow pattern and WSS characteristics of IA growth.     

Monte Carlo simulation for Neptun 10 PC medical linear accelerator and calculations of output factor for electron beam

AimExact knowledge of dosimetric parameters is an essential pre-requisite of an effective treatment in radiotherapy. In order to fulfill this consideration, different techniques have been used, one of which is Monte Carlo simulation.Materials and methodsThis study used the MCNP-4C^b to simulate electron beams from Neptun 10 PC medical linear accelerator. Output factors for 6, 8 and 10 MeV electrons applied to eleven different conventional fields were both measured and calculated.ResultsThe measurements were carried out by a Wellhofler-Scanditronix dose scanning system. Our findings revealed that output factors acquired by MCNP-4C simulation and the corresponding values obtained by direct measurements are in a very good agreement.ConclusionIn general, very good consistency of simulated and measured results is a good proof that the goal of this work has been accomplished.     

Inhibition of transient receptor potential melastain 7 channel increases HSCs apoptosis induced by TRAIL

AimsTransient receptor potential melastain 7 (TRPM7) channels are known to have a fundamental role in many cellular processes and pathology of various diseases. The objective of this study was to investigate the potential relationship between TRPM7 and the apoptosis of hepatic stellate cells (HSCs) induced by TNF-related apoptosis inducing-ligand (TRAIL).Main methodsIn this study, using a combination of Western blotting, RT-PCR and flow cytometric analysis, we investigated the influence and potential function of TRPM7 channels on the apoptosis induced by TRAIL in HSCs which is the key cell of formation of extracellular matrix (ECM) and is also the core link of occurrence of hepatic fibrosis (HF).Key findingsWe observed significant expression of TRPM7 mRNA and protein in HSCs. Suppression of TRPM7 channels by 2-aminoethoxydiphenyl borate (2-APB) or Gd³⁺ not only markedly eliminated TRPM7 expression, but also increased the apoptosis of HSCs induced by TRAIL, a major apoptosis stimulator of HSCs.SignificanceOur findings strongly suggest that TRPM7 channels are involved in the apoptosis of HSCs induced by TRAIL, probably by regulating the sensitivity of HSCs to TRAIL.     

Dissipative particle dynamics simulation of the soft micro actuator using polymer chain displacement in electro-osmotic flow

ABSTRACT

In this research, the numerical simulation of a soft polymer micro actuator performance has been investigated using the dissipative particle dynamics method in electro-osmotic flow. Effective factors including electro-osmotic flow and polymer chain parameters have been studied. First of all, considering a wide range of electro-osmotic parameters, the validation of analytical results is carried out in a simple micro channel. The electric field and zeta potential changes are linearly related to the flow rate, and the kh parameter behaves nonlinearly to around the kh?=?10. In the following, a convergent–divergent channel is used for the soft micro actuator simulation in which a polymer chain as a heart of actuation is embedded in the middle. As the main control parameter, the direction of the electric field is changed every 4?s, and it leads to a reciprocating motion. The numerical results indicate that the displacement of the soft polymer chain will be increased by enhancing the electric field, the number of beads, decreasing the harmonic bond coefficient and also exposing more length of a polymer chain in front of fluid flow. The results of this study may be useful for some future applications such as artificial fibres and muscles.     

基于微波热声层析成像定量重建生物组织电导率的改进方法

目的 生物电磁学参数中的电导率与组织的功能性信息直接相关,精准重建生物组织电导率在医学成像技术和医学诊断领域中有着重要意义。本文改进定量微波热声层析成像（microwave-induced thermoacoustic tomography,MTAT）算法,使组织电导率的重建精度提高。方法 本文在利用有限元离散法求解热声波动方程和亥姆霍兹方程的基础之上,提出了一种基于正则化牛顿迭代法（regularized Newton iteration method,RNIM）定量重建组织电导率的改进方法。结果 通过数值模拟实验和含不同浓度NaCl溶液的仿体实验,验证了算法改进的有效性。组织仿体实验结果表明,目标在不同位置、不同大小、不同对比度情况下,相比于定量微波热声层析成像采用拟合（fitting）的方法,采用正则化牛顿法定量重建的仿体电导率相对误差明显降低,重建目标精度提高。在仿体实验中采用RNIM方法重建相同浓度的单目标在不同位置的电导率变化幅度更小,以及重建多目标电导率的相对比值与实际更接近,实验结果验证了改进方法的稳定性。结论 研究结果表明优化算法能更加准确地定量重建组织仿体的电导率,...     

Murine model of hepatic breast cancer

Background and aimsBreast cancer is the most common cancer in women and the second leading cause of cancer-related deaths in this population. Breast cancer related deaths have declined due to screening and adjuvant therapies, yet a driving clinical need exists to better understand the cause of the deadliest aspect of breast cancer, metastatic disease. Breast cancer metastasizes to several distant organs, the liver being the third most common site. To date, very few murine models of hepatic breast cancer exist.MethodsIn this study, a novel murine model of liver breast cancer using the MDA-MB-231 cell line is introduced as an experimental (preclinical) model.ResultsHistological typing revealed consistent hepatic breast cancer tumor foci. Common features of the murine model were vascular invasion, lung metastasis and peritoneal seeding.ConclusionsThe novel murine model of hepatic breast cancer established in this study provides a tool to be used to investigate mechanisms of hepatic metastasis and to test potential therapeutic interventions.     

趋流行为下斑马鱼幼鱼的全脑成像

目的 趋流,意即在水中调整身体方向并逆流而上的能力,是一种在大多数鱼类与两栖类动物中存在的保守行为。虽然关于趋流的研究已有一段很长的历史,并且近年来斑马鱼幼鱼趋流行为的理论机制也被提出,但是分布式的神经环路是如何整合多感知信息、做出决策、并实现行为控制仍然是个未知数。对自由运动的斑马鱼进行全脑神经活动成像为理解这一困难的问题提供了特殊的机会。方法 本文开发了一种微流控装置精确控制环境水流并激发斑马鱼的趋流行为。将该微流控芯片与扩增视野光场显微镜以及追踪系统整合,从而记录自由行为下斑马鱼全脑的神经活动。结果 在整合的微流控装置中稳定观察到了斑马鱼在水流中保持自身位置不变、逆流而上等刻板的趋流行为现象。与此同时,实现了对斑马鱼幼鱼趋流行为过程中的全脑钙活动记录。本文初步发现了几个脑区的神经活动与趋流行为相关。结论 本研究第一次展示了在斑马鱼幼鱼趋流行为的同时记录全脑神经活动的技术。接下来对神经活动和行为数据的分析与建模将有助于更好地理解一种重要自然行为背后的感觉运动转换机制。     

How important is differentiation in the therapeutic effect of mesenchymal stromal cells in liver disease?

Background aimsThe protocols for differentiation of hepatocyte-like cells (HLCs) from mesenchymal stromal cells (MSCs) have been well established. Previous data have shown that MSCs and their derived HLCs were able to engraft injured liver and alleviate injuries induced by carbon tetrachloride. The goal of the current study was to determine the differences of MSCs and their derived HLCs in terms of therapeutic functions in liver diseases.MethodsAfter hepatic differentiation of umbilical cord–derived MSCs in vitro, we detected both MSC and HLC expressions of adhesion molecules and chemokine receptor CXCR4 by flow cytometry; immunosuppressive potential and hepatocyte growth factor expression were determined by means of enzyme-linked immunosorbent assay. We compared the therapeutic effect for fulminant hepatic failure in a mouse model.ResultsMSC-derived-HLCs expressed lower levels of hepatocyte growth factor, accompanied by impaired immunosuppression in comparison with MSCs. Furthermore, undifferentiated MSCs showed rescuing potentials superior to those in HLCs for the treatment of fulminant hepatic failure.ConclusionsAfter differentiation, HLCs lost several major properties in comparison with undifferentiated MSCs, which are beneficial for their application in liver diseases. Undifferentiated MSCs may be more appropriate than are HLCs for the treatment of liver diseases.     

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.     

Combined Diffusive and Viscous Transport of Methane in a Carbon Slit Pore

Abstract

The transport of mass through porous materials can occur by essentially two different mechanisms: (1) diffusion and (2) viscous flow. The former occurs when there is a gradient in chemical potential of the pore fluid, while the latter occurs in the presence of a pressure gradient. In general, fluid transport occurs by both of these mechanisms and their respective contributions to the total intra-pore flux are approximately additive. Experimentally, there is no unambiguous way of determining the individual contributions to the total flux of these two modes of transport. Fortunately, molecular simulations does provide a solution.

We present a novel simulation method in which the separate contributions to the total flux are determined. The method involves the use of two non-equilibrium molecular dynamics techniques: dual control volume grand canonical molecular dynamics (DCV GCMD) and an algorithm for simulating planar Poiseuille flow. We apply this technique to study the combined (viscous and diffusive) transport of methane through single slit-shaped graphite pores of width 2.5, 5.0 and 10.0 methane diameters. We find that the viscous contribution to the total intrapore flux through each of these pores is 10%, 15% and 34%, respectively.     

EGS_cbct: Simulation of a fan beam CT and RMI phantom for measured HU verification

IntroductionA mathematical 3D model of an existing computed tomography (CT) scanner was created and used in the EGSnrc-based BEAMnrc and egs_cbct Monte Carlo codes. Simulated transmission dose profiles of a RMI-465 phantom were analysed to verify Hounsfield numbers against measured data obtained from the CT scanner.Methods and materialsThe modelled CT unit is based on the design of a Toshiba Aquilion 16 LB CT scanner. As a first step, BEAMnrc simulated the X-ray tube, filters, and secondary collimation to obtain phase space data of the X-ray beam. A bowtie filter was included to create a more uniform beam intensity and to remove the beam hardening effects. In a second step the Interactive Data Language (IDL) code was used to build an EGSPHANT file that contained the RMI phantom which was used in egs_cbct simulations. After simulation a series of profiles were sampled from the detector model and the Feldkamp-Davis-Kress (FDK) algorithm was used to reconstruct transversal images. The results were tested against measured data obtained from CT scans.ResultsThe egs_cbct code can be used for the simulation of a fan beam CT unit. The calculated bowtie filter ensured a uniform flux on the detectors. Good correlation between measured and simulated CT numbers was obtained.ConclusionsIn principle, Monte Carlo codes such as egs_cbct can model a fan beam CT unit. After reconstruction, the images contained Hounsfield values comparable to measured data.