Numerical analysis of the failure process of soil-rock mixtures through computed tomography and PFC3D models

Soil-rock mixture （SRM） is a unique type of geomaterial characterized by a heterogeneous composition and a complicated structure. It is intractable for the continuum-based soil and rock mechanics theories to accurately characterize and predict the SRM＇s mechanical properties. This study reports a novel numerical method incorporating microfocus computed tomography and PFC3D codes to probe the deformation and failure processes of SRM. The three-dimensional （3D） PFC models that represent the SRM＇s complex structures were built. By simulating the entire failure process in PFC3D, the SRM＇s strength, elastic modulus and crack growth were obtained. The influence of rock ratios on the SRM＇s strength, deformation and failure processes, as well as its internal mesoscale mechanism, were analyzed. By comparing simulation results with experimental data, it was verified that the 3D PFC models were in good agreement with SRM＇s real structure and the SRM＇s compression process, deformation and failure patterns; its intrinsic mesomechanism can be effectively analyzed based on such 3D PFC models.

Modelling of Quasi 3-D Groundwater Flow and Studying of Equivalent Drainage Boundary in Beihai Peninsula,Guangxi

This paper describes a quasi 3-D finite element model of the groundwater flow in two -aquifer system which is constructed from a sequence of aquifer flow equations coupled by leakage terms representing flow through the aquitard . It is applied to evaluate the maximum rate of groundwater resources exploited from the coastal aquifer without seawater intrusion . The main task in this model is to determine the drainage boundary of the aquifer extending under the sea . The information of the boundary can be obtained from the fluctuations of the groundwater level caused by sea-tide fluctuations . A new idea, Equivalent Drainage Boundary (EDB), is proposed and the corresponding methods , determining the EDB, are developed with tidal fluctuations data observed in boreholes . The quasi 3-D model and the methods determining EDB have been applied to the aquifer system of Beihai peninsula , Guangxi Autonomous Region of China for calculating the available groundwater resources .

The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.

2D Coupled 3D:A New Numerical Model for Dual - Structured - Aquifer System

This paper points out that a successful numerical simulation is to construct a correct conceptional model which is very dose to the natural condition. A new model, two dimensional coupled three dimensional model (2D -3D ) is presented in the Present paper,which is the most suitable one for the dual - structured - aquifer system. An example of Wenyinghu area is shown.By using the 2D-3D model, a satisfied result of the simulated area is achieved.

3D atomic-scale growth characteristics of {10-12} twin in magnesium

In this work,we carried out three-dimensional(3D)atomic-scale study on the growth characteristics of{10-12}twin in magnesium(Mg).The study was performed by MD simulations on Mg single crystals with an initial twin nucleus structures.A detailed atomistic analysis reveals that a stabilized 3D{10-12}twin nucleus is bounded by basal/prismatic(BP)interfaces,prismatic/basal(PB)interfaces,and{10-11}interfaces.Later,a{10-12}twin boundary(TB)occurs at the junction of the BP and PB interface with the growth of the twin nucleus.In this process,two twinning mechanisms are involved:a pure-shuffle mechanism in which{10-11}interface migration along the[11-20]direction is mediated by atomic shuffle,and a glide-shuffle mechanism in which BP/PB and{10-12}TB movements are realized by the migration of disconnections along the relevant interfaces.In addition,we systematically investigate the stress state associated with the activation of twinning,aiming to discover the intrinsic relationship of the elastic stress field to twin growth on an atomic scale.The results suggest that the elastic stress in the matrix is an important driving force for twin growth,much similar to what stress does for a crack.In addition,it is rather remarkable that the{10-11}interface has a greater ability to migrate than other interfaces,and this is thought to be a main factor for the rapid growth of a{10-12}twin.

Kinematic error modeling and error compensation of desktop 3D printer

Desktop 3D printers have revolutionized how designers and makers prototype and manufacture certain products.Highly popular fuse deposition modeling(FDM)desktop printers have enabled a shift to low-cost consumer goods markets,through reduced capital equipment investment and consumable material costs.However,with this drive to reduce costs,the computer numerical control(CNC)systems implemented in FDM printers are often compromised by poor accuracy and contouring errors.This condition is most critical as users begin to use 3D-printed components in load-bearing applications or to perform mechanical functions.Improved methods of low-cost 3D printer calibration are needed before their open-design potential can be realized in applications,including 3D-printed orthotics and prosthetics.This paper applies methodologies associated with high-precision CNC machining systems,namely,kinematic error modeling and compensation coupled with standardized test methods from ISO230-4,such as the ballbar for kinematic and dynamic error measurements,to examine the influence and feasibility for use on low-cost CNC/3D printing platforms.Recently,the U.S.Food and Drug Administration's"Technical considerations for additive manufactured medical devices"highlighted the need to develop standards specific to additive manufacturing in regulated manufacturing environments.This paper shows the benefits of the methods described within ISO230-4 for error assessment,alongside applying kinematic error modeling and compensation to the popular kinematic configuration of an Ultimaker 3D printer.A Renishaw ballbar QC10 is used to quantify the Ultimaker's errors and thereby populate the error model.This method quantifies machine errors and populates these in a mathematical model of the CNC system.Then,a post-processor can be used to compensate the printing code.Subsequently,the ballbar is used to demonstrate the dramatic impact of the error compensation model on the accuracy and contouring of the Ultimaker printer with 58%reduction in overall circularity error and 90%reduction in squareness error.

NUMERICAL SIMULATION OF 3-D TURBULENT FLOWS OVER DREDGED TRENCHES

A 3- D free surface flow in open channels based on the Reynolds equations with the k-ε turbulence closure model is presented in this paper. Insted of the 'rigid lid' approximation, the solution of the free surface equation is implemented in the velocity-pressure iterative procedure on the basis of the conventional SIMPLE method. This model was used to compute the flow in rectangular channels with trenches dredged across the bottom. The velocity, eddy viscosity coefficient, turbulent shear stress, turbulent kinetic energy and elevation of the free surface can be obtained. The computed results are in good agreement with previous experimental data.

Evaluation of Quantum Chemical Methods and Basis Sets Applied in the Molecular Modeling of Artemisinin

In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artemisinin in the region of the endoperoxide ring compared to crystallographic data. We also classify these methods using statistical analysis. The results of PCA were based on three main components, explaining 98.0539% of the total variance, for the geometrical parameters C3O13, O1O2C3, O13C12C12a, and O2C3O13C12. The DFT method (B3LYP) corresponded well with the experimental data in the hierarchical cluster analysis (HCA). The experimental and theoretical angles were analyzed by simple linear regression, and statistical parameters (correlation coefficients, significance, and predictability) were evaluated to determine the accuracy of the calculations. The statistical analysis exhibited a good correlation and high predictive power for the DFT (B3LYP) method in the 6-31G** basis set.

Tumor necrosis factor-alpha(TNF-α) in spotted halibut Verasper variegatus at the embryonic and metamorphic stages

As an aquatic fish,the spotted halibut Verasper variegatus is highly susceptible to bacterial and virus infections.Tumor necrosis factor-alpha(TNF-α)as a cytokine could control the inflammatory responses.The functions of TNF-αin many species have been widely studied,particularly in mammals.However,little is known about the TNF-αfunctions in V.variegatus.We first cloned and sequenced the TNF-αgene in V.variegatus(VvTNF-α).The two conserved cysteine residues,transmembrane sequence,Thr-Leu motif,and TNF family signature,as well as the TA-rich motifs of its proteins related to inflammatory responses had high similarity to those of the other teleost and mammalian TNF-α.The phylogenetic analysis showed that VvTNF-αwas consistent with TNF-αgenes of other vertebrates.The VvTNF-αtranscripts were extensively distributed in the peripheral blood leukocytes(PBLs),spleen,and gill,indicating that the VvTNF-αhad a role in immune function.Furthermore,treatment with pathogen-associated molecular patterns(PAMPs)could induce a rapid and significant increase of VvTNF-αin the PBLs,which reveals that VvTNF-αdoes participate in the host immune responses against bacterial and viral pathogens.We found that VvTNF-αhad an interesting expression pattern during metamorphosis,showing that the flatfish TNF-αmay have some novel functions during specific developmental stages.In addition,the 3 D structure prediction of VvTNF-αprovided an indication of how it is likely to interact with other proteins.Therefore,VvTNF-αhas multiple functions,and provides valuable information to explore novel functions of TNF-α.

Novel Functions of Interleukin-1 Beta in Spotted Halibut(Verasper variegatus) at Its Embryonic and Metamorphic Stages

Interleukin-lbeta （IL-1β） is a cytokine involved in the control of inflammatory responses. The functions of IL-1β have been extensively studied in many vertebrates. However, few studies focused on the functions of IL-1β in the spotted halibut （Verasper variegatus）, an endangered aquatic fish that easily suffers from bacterial and viral infections. We first cloned and sequenced the IL-1β gene from V. variegatus （VvIL-1β）. Its conservative interleukin-1 propeptide and interleukin-1/18 domains corresponding regions, characteristics of the IL-1 protein family and TA-rich motifs relating to inflammatory responses were similar to those of the IL-1β genes from other teleost and mammals. The phylogenetic analysis showed that VvIL-1β was homologous to the IL-1β gene of other vertebrates. Treatment with pathogen-associated molecular patterns （PAMPs） induced a significant and rapid up-regulation of VvIL-1β expression in the peripheral blood leukocytes （PBLs）, revealing that VvIL-1β is actively involved in the host ilmnune responses against bacterial and viral pathogens. The expression level of VvIL-1β was relatively high in the PBLs, gill, and intestine, indicating the immunological function of VvIL-1β . VvIL-1β also had interesting expression patterns at specific developmental stages, implying that the IL-1β of flatfishes may have some novel functions during embryonic development and metamorphosis. The 3D structure prediction also provided information about how VvIL-113 interacts with its receptor protein. These results suggested that VvIL-1β may have multiple functions in V. variegatus and provided us valuable information for understanding the novel functions of IL- 1β.

A full-length 3D structure for MAPK/ERK kinase 2 (MEK2)

As a pivotal signal pathway,the Ras/Raf/MEK/ERK cascade can be activated by multiple extracellular stimuli and can transmit signals to diverse substrates.It remains to be elucidated how so many different signals can be variously transferred by only two MEK molecules(MEK1 and MEK2) .Because of technological limitations the complete structures of the MEKs are still unavailable.Here,we report the full-length structure of MEK2 obtained by homology modeling and molecular dynamics simulations.The simulations show that the N-terminal part of MEK2 is highly flexible and this flexibility may enable MEK2 to interact with ERKs and other ligands in diverse manners that correspond to various upstream signals and downstream consequences.

Similarity-Based 3-D Atmospheric Nucleation Data Visualization and Analysis

Atmospheric nucleation is a process of phase transformation, which serves a significant role in many atmospheric and technological processes. To simulate atmospheric nucleation activities, certain molecular models with three-dimensional （3-D） structures are generated. Analyzing these 3-D molecular models can help promote understanding of nucleation processes. Unfortunately, the ability to understand atmospheric nucleation processes is greatly restricted due to lack of efficient visual data exploration tools. In this paper, we present a data visualization solution to visualize and classify 3-D molecular crystals. We developed a novel algorithm for calculating similarity between the 3-D molecular crystals, and further improved the overall system performance with GPU （graphics processing unit） acceleration.

光线跟踪算法在高质量三维分子模型设计中的应用

本文分析了显示分子三维结构的光线跟踪算法,介绍了POV-Ray开放源代码软件的用法及其脚本语言。在此基础上,我们应用光线跟踪算法渲染三维分子模型,并进一步给出了增强模型逼真性的方法和途径。

GABA_A/BZ受体激动剂4-喹啉酮衍生物的DISCOtech及CoMFA研究

γ-氨基丁酸是重要的抑制性神经传递物质,4-喹啉酮衍生物作用于GABA_A受体具有广泛的生物活性。本文采用DIS- COtech法构建大鼠GABA_A/BZ受体4-喹啉酮衍生物激动剂的药效团模型,同时根据分子骨架叠合规则构建CoMFA模型,模型的交叉验证系数为0.681,非交叉验证系数为0.967,药效团模型和CoMFA模型具有一致性。根据模型分析配体-受体间的相互作用,设计一系列化合物并预报了其活性,为设计高活性的化合物提供参考。

Green-Kubo公式在不同维数模拟系统中的比较分析

在平衡态分子动力学模拟的基础上,利用Green-Kubo公式分别计算周期性边界条件下二维及三维系统的液态氩流体的输运系数,归纳出三维模型压强结果与计算空间尺度之间的变化规律;在对零剪切粘度模拟结果的比较分析的基础上,探究出不同维数模型系统对剪切粘度模拟结果的影响,总结出了二维模型替代三维模型进行剪切粘度的计算方案;通过对两种模型的模拟计算,得出某一单一模型不可简单替代三维模型进行输运系数计算的结论。