A Hybrid Immersed Boundary/Coarse-Graining Method for Modeling Inextensible Semi-Flexible Filaments in Thermally Fluctuating Fluids Dedicated to Professor Karl Stark Pister for his 95th birthday

A new and computationally efficient version of the immersed boundary method,which is combined with the coarse-graining method,is introduced for modeling inextensible filaments immersed in low-Reynolds number flows.This is used to represent actin biopolymers,which are constituent elements of the cytoskeleton,a complex network-like structure that plays a fundamental role in shape morphology.An extension of the traditional immersed boundary method to include a stochastic stress tensor is also proposed in order to model the thermal fluctuations in the fluid at smaller scales.By way of validation,the response of a single,massless,inextensible semiflexible filament immersed in a thermally fluctuating fluid is obtained using the suggested numerical scheme and the resulting time-averaged contraction of the filament is compared to the theoretical value obtained from the worm-like chain model.

Coarse-Graining Method Based on Hierarchical Clustering on Complex Networks

With the rapid development of big data, the scale of realistic networks is increasing continually. In order to reduce the network scale, some coarse-graining methods are proposed to transform large-scale networks into mesoscale networks. In this paper, a new coarse-graining method based on hierarchical clustering (HCCG) on complex networks is proposed. The network nodes are grouped by using the hierarchical clustering method, then updating the weights of edges between clusters extract the coarse-grained networks. A large number of simulation experiments on several typical complex networks show that the HCCG method can effectively reduce the network scale, meanwhile maintaining the synchronizability of the original network well. Furthermore, this method is more suitable for these networks with obvious clustering structure, and we can choose freely the size of the coarse-grained networks in the proposed method.

Comparative Study on Microstructure and Mechanical Properties of Coarse-grained WC-based Cemented Carbides Sintered with Ultrafine WC or (W+C) as Additives

The effects of ultrafine WC(WC_(UF),0.5μm) or W(1μm) and C(0.3μm)(W+C)_(UF) additives on the densification,microstructure and mechanical properties of coarse-grained cemented carbides were compared systematically.Overall,the cemented carbides with WC_(UF)/(W+C)_(UF) additives are almost fully densification to be higher than 99%,and the average grain size is kept above 2.8μm.The WC_(UF) additive assists grains to(truncated)trigonal prism shape by two dimensional(2D) growth,whereas the(W+C)_(UF) additive assists grains to rounded shape by three dimensional(3D) growth,lowers WC contiguity and increases face-centered-cubic Co.The hardness and bending strength of(75WC_(C)-15WC_(UF))-10Co are 86.6 HRA and 2 272 MPa,respectively,both higher than those of(75WC_(C)-15(W+C)_(UF))-10Co,which could be ascribed to the enhanced densification and unblemished grains.However,the fracture toughness of the(75WC_(C)-15(W+C)_(UF))-10Co is 23.5 MPa·m^(1/2),higher than that of the(75WC_(C)-15WC_(UF))-10Co due to the uniform WC-Co structure and flexible binder phase.

RECOGNICER:A coarse-graining approach for identifying broad domains from ChIP-seq data

Background:Histone modifications are major factors that define chromatin states and have functions in regulating gene expression in eukaryotic cells.Chromatin immunoprecipitation coupled with high-throughput sequencing(ChIP-seq)technique has been widely used for profiling the genome-wide distribution of chromatin-associating protein factors.Some histone modifications,such as H3K27me3 and H3K9me3,usually mark broad domains in the genome ranging from kilobases(kb)to megabases(Mb)long,resulting in diffuse patterns in the ChIP-seq data that are challenging for signal separation.While most existing ChIP-seq peak-calling algorithms are based on local statistical models without account of multi-scale features,a principled method to identify scale-free board domains has been lacking.Methods:Here we present RECOGNICER(Recursive coarse-graining identification for ChIP-seq enriched regions),a computational method for identifying ChIP-seq enriched domains on a large range of scales.The algorithm is based on a coarse-graining approach,which uses recursive block transformations to determine spatial clustering of local enriched elements across multiple length scales.Results:We apply RECOGNICER to call H3K27me3 domains from ChIP-seq data,and validate the results based on H3K27me3's association with repressive gene expression.We show that RECOGNICER outperforms existing ChIP-seq broad domain calling tools in identifying more whole domains than separated pieces.Conclusion:RECOGNICER can be a useful bioinformatics tool for next-generation sequencing data analysis in epigenomics research.

Sedimentary Processes and Depositional Characteristics of Coarse-grained Subaqueous Fans along Steep Slopes in a Lacustrine Rift Basin:A Case Study from the Dongying Depression,Bohai Bay Basin,China

Coarse-grained subaqueous fans are vital oil and gas exploration targets in the Bohai Bay basin,China.The insufficient understanding of their sedimentary processes,depositional patterns,and controlling factors restricts efficient exploration and development.Coarse-grained subaqueous fans in the Yong′an area,Dongying Depression,are investigated in this study.These fans include nearshore subaqueous fans,and sublacustrine fans,and their sedimentary processes,depositional patterns and distribution characteristics are mainly controlled by tectonic activity and paleogeomorphology.Nearshore subaqueous fans developed near the boundary fault during the early–middle deposition stage due to strong tectonic activity and large topographic subsidence.Early sublacustrine fans developed at the front of the nearshore subaqueous fans in the area where the topography changed from gentle to steep along the source direction.While the topography was gentle,sublacustrine fans did not develop.During the late weak tectonic activity stage,late sublacustrine fans developed with multiple stages superimposed.Frequent fault activity and related earthquakes steepened the basin margin,and the boundary fault slopes were 25.9°–34°.During the early–middle deposition stage,hyperpycnal flows triggered by outburst floods developed.During the late deposition stage,with weak tectonic activity,seasonal floods triggered hyperpycnal flows,and hybrid event beds developed distally.

Role of Crystal Seed in Aluminum Hydroxide Crystallization from Ammonia System with Added NH_(4)Al(SO_(4))_(2)·12H_(2)O

A method to promote aluminum hydroxide crystal growth through pickling Al(OH)_(3)as seed in the ammonia system was proposed to overcome these defects.The experimental results show that,under the conditions of pickling time of 15 min,the acid concentration of 10%,the addition of 70 g/L pickling-Al(OH)_(3)seed,and the coarse granular Al(OH)_(3)products(d0.5=85.667)can be obtained.The characterization results show that the phase of the product is gibbsite,consistent with the seed.Moreover,the steps and ledges can be formed on pickling Al(OH)_(3)seed surface under the ammonia system,effectively promoting crystal growth.During crystal growth,the roughness of the crystal surface was first increased and then decreased,and the lamellar structure was deposited on the crystal seed surface.The final particles are approximately round,the surface is compact and dense.The growth of the product is surface reaction controlled.In addition,the content of the AlO_(6)unit is increased and contributed to Al(OH)_(3)crystal growth.

Influence of Topological Properties of Complex Networks on the Effect of Spectral Coarse-Grained Network

Recently, some coarse-graining methods based on network synchronization have been proposed to reduce the network size while preserving the synchronizability of the original network. In this paper, we investigate the effects of the coarse graining process on synchronizability over complex networks under different average path lengths and different degrees of distribution. A large amount of experiments demonstrate a close correlation between the average path length, the heterogeneity of the degree distribution and the ability of spectral coarse-grained scheme in preserving the network synchronizability. We find that synchronizability can be well preserved in spectral coarse-grained networks when the considered networks have a longer average path length or a larger degree of variance.

coarse-grained CFD-DEM方法在不同流态流化床中的模拟验证

传统CFD-DEM方法的计算量随着系统内颗粒数目的增加而显著增加,coarse-grained CFD-DEM(粗颗粒)方法将若干个真实颗粒打包成虚拟颗粒从而显著减小系统计算量。在coarse-grained CFD-DEM方法进行应用之前,对其进行广泛的验证是有必要的。采用coarse-grained CFD-DEM方法模拟得到不同流态流化床的气固流动特征(固含率、压降、颗粒速度等),与传统CFD-DEM和实验测量吻合较好。另外,系统的计算效率随着粗颗粒放大系数的增加显著提升。研究表明,粗颗粒方法能够以较小的计算精度损失而使计算速度大幅提升,能够适用于大尺度稠密气固流动系统的模拟。

EFFECT OF Zr ADDITION TO Ti-KILLED STEEL ON INCLUSION FORMATION AND MICROSTRUCTURAL EVOLUTION IN WELDING INDUCED COARSE-GRAINED HEAT AFFECTED ZONE

Effects of Zirconium on the chemical component and size distribution of Ti-bearing inclusions, favored the grain refinement of the welding reduced, coarse-grained heat affected zone （CGHAZ） with enhanced impact toughness in Ti-killed steels, which were examined based on experimental observations and thermodynamic calculations. It indicated that the chemical constituents of inclusions gradually varied from the TiO oxide to the Ti-O＋Zr-O compound oxide and a single phase of the ZrO2 oxide, as the Zr content increased from zero to 0.0100%. A trace of Zr （0.0030%-0.0080%, depending on the oxygen content in liquid steel） provided a large amount of nucleating core for Ti oxide because of the larger specific density of ZrO2 oxide, and produced a small size distribution of the inclusions favorable for acicular ferrite transformation with a high nucleation rate in the CGHAZ, and a high volume fraction of acicular ferrite was obtained in the CGHAZ, with enhanced impact toughness. Otherwise, a high content of Zr （-0.0100%） produced a single phase Zr02, which was impotent to nucleate acicular ferrite, and a microstructure composed of ferrite side plate and grain boundary ferrite developed in the CGHAZ. The experimental results were confirmed by thermodynamic calculations.

Coarse-grained Simulations of Chemical Oscillation in Lattice Brusselator System

The oscillation behavior of a two-dimension lattice-gas Brusselator model was investigated. We have adopted a coarse-grained kinetic Monte Carlo （CG-KMC） procedure, where m×m microscopic lattice sites are grouped together to form a CG cell, upon which CG processes take place with well-defined CG rates. Such a CG approach almost fails if the CG rates are obtained by a simple local mean field （s-LMF） approximation, due to the ignorance of correlation among adjcent cells resulting fl＇om the trimolecular reaction in this nonlinear system. By proper incorporating such boundary effects, thus introduce the so-cMled b-LMF CG approach. Extensive numerical simulations demonstrate that the b-LMF method can reproduce the oscillation behavior of the system quite well, given that the diffusion constant is not too small. In addition, the deviation from the KMC results reaches a nearly zero minimum level at an intermediate cell size, which lies in between the effective diffusion length and the minimal size required to sustain a well-defined temporal oscillation.

Mechanical and electrical properties of coarse-grained soilaffected by cyclic freeze-thaw in high cold regions

To evaluate the geotechnical properties of coarse-grained soil affected by cyclic freeze-thaw,the electrical resistivity and mechanical tests are conducted.The soil specimens are prepared under different water contents,dry densities and exposed to 0?20 freeze-thaw cycles.As a result,the stress?strain behavior of the specimen(w=14.0%andρd=1.90 g/cm^3)changes from strain-hardening into strain-softening due to the freeze-thaw effect.The electrical resistivity of test specimen increases with the freeze-thaw cycles change,but the mechanical parameters(the unconfined compressive strength qu and the deformation modulus E)and brittleness index decrease considerably at the same conditions.All of them tend to be stable after 7?9 cycles.Moreover,both the dry density and the water content have reciprocal effects on the freeze-thaw actions.The failure and pore characteristics of specimens affected by freeze-thaw cycles are discussed by using the image analysis method.Then,an exponential function equation is developed to assess the electrical resistivity of specimens affected by the cyclic freeze-thaw.Linear relations between the mechanical parameters and the electrical resistivity of specimens are established to evaluate the geotechnical properties of the soil exposed to freeze-thaw actions through the corresponding electrical resistivity.

New Evidence for Hydrothermal Sedimentary Genesis of the Ni-Mo Deposits in Black Rock Series of the Basal Cambrian, Guizhou Province: Discovery of Coarse-Grained Limestones and its Geochemical Characteristics

The molybdenum-nickel deposits in Shuidong District of Nayong County （Guizhou Province, Southwest China） are found mainly in black shale series of Lower Cambrian Niutitang Formation, which is another Mo-Ni-rich region besides Zunyi District （Guizhou province）. Our systematic study on the Mo-Ni deposits in Tangjiaba of Nayong reveals that layered coarse-grained limestones, spherical beaded limestones concretions are hosted at the lower seam of the Mo-Ni deposits. Its strong negative carbon isotope anomaly （the carbon isotope value of the coarse-grained limestones varies from -2.148‰ to 8.223‰） is similar to that in the modern submarine black smoker chimney. The carbon in the coarse-grained limestones from black rock series of Nayong County might be deep source inorganic carbon. The seams, coarse-grained limestones, ore-bearing coarse-grained limestones and the roof and floor of the deposits are characterized by co-variation on the trace element spider diagram, showing good homology. The extraordinary enrichment of Ag, As and Sb resembles hydrothermal sedimentation. Pro-Earth＇s core elements Se is strongly enriched in Ni-Mo ore-bearing coarse-grained limestones. The ore-bearing rock series has an extremely low Th/U value （0.012-0.19）; in the logU-logTh Cartesian Coordinates, the samples of the roof and floor of the deposits and ore-bearing coarse-grained limestones are found in the East Pacific tise; and the samples of coarse-grained limestones are found between the paleo-hydrothermal dedimentary area and the East Pacific tise. The chondrite-normalized rare earth element patterns of the Ni-Mo deposits show LREE enrichment, Ce negative anomaly, and Eu negative anomaly （which is supposed to be influenced by the deep magmatic processes in an extensional environment） resembles the rare earth element distribution patterns of the fluid and its sediments in modern submarine hydrothermal system. It proves that coarse-grained limestones is characterized by typical hydrothermal limestones, being closely related with the genesis of Mo-Ni deposits in Nayong County, which provides new evidence for hydrothermal sedimentary genesis of Mo-Ni deposit and negative carbon anomaly in the basal Cambrian on a global scale.

Strength and deformation behaviour of coarse-grained soil by true triaxial tests

In order to investigate the influence of intermediate principal stress on the stress-strain and strength behaviour of a coarse-grained soil, a series of true triaxial tests were performed. The tests were conducted in a recently developed true triaxial apparatus with constant minor principal stress σ3 and constant value of intermediate principal stress ratio b=（σ2-σ3）/（σ1-σ3） （al is the vertical stress, and % is the horizontal stress）. It is found that the intermediate principal strain, ε2, increases from negative to positive value with the increase of parameter b from zero to unity under a constant minor principal stress. The minor principal strain, ε3, is always negative. This implies that the specimen exhibits an evident anisotropy. The relationship between b and friction angle obtained from the tests is different from that predicted by LADE-DUNCAN and MATSUOKA-NAKAI criteria. Based on the test results, an empirical equation of g（b） that is the shape function of the failure surface on re-plane was presented. The proposed equation is verified to be reasonable by comparing the predicted results using the equation with true triaxial test results of soils, such as coarse-grained soils in this study, sands and gravels in other studies.

Gradation equation of coarse-grained soil and its applicability

Gradation equation is one way to describe the gradation of coarse-grained soil conveniently,exactly and quantitatively.With the gradation equation,the influence of gradation on the mechanical behaviors of coarse-grained soil can be expressed quantitatively.A new gradation equation with a parameter is proposed.The basic properties and applicability of the new equation are studied.The results show that the proposed equation has the applicability to express coarse-grained soil gradation(CSG),and the range of the parameter β is found to be 0<β<1.The value ofbdetermines the gradation curve shape.If β>0.5,the gradation curve is sigmoidal,otherwise the gradation curve is hyperbolic.For well graded gradations,the parameter has the value of 0.13<β<1.Several CSGs used in domestic and foreign earth-rockfill dams are probed,and the value of the parameterbfalls in the range of 0.18 to 0.97.The investigation of the range of β is of value to guide the design for CSG of earth-rockfill dam.

Deformation characteristics of coarse-grained soil with various gradations

By using large scale triaxial shearing apparatus,consolidated-drained shear tests were conducted on coarse-grained soil with different gradations.In order to describe their deformation rules,three main characteristics of tangent Poisson ratio curves were summarized and the reason was revealed by dividing the movement of soil particles into two kinds: the movement of fine particles and the movement of coarse particles.Then,a volumetric strain expression and a tangent Poisson ratio expression were put forward,and two defects of widely used Duncan-Chang model were fixed.Results calculated from them agree well with test results.There are three parameters,namely L,G and F,in this new model.Parameter L reflects the dilatancy of a specimen and L=4 can be used as a criterion to estimate whether a certain kind of soil has dilatancy quality or not.Parameters G and F relate to the initial slope of tangent Poisson ratio curves,and G=F=0 indicates a special situation which happens in dense granular material of the same diameter.Influences of various gradations on volume deformation are mainly reflected in parameter L which is smaller when there are more gravels in specimens.

Coarse-Grained Free-Energy Simulations of Conformational State Transitions in an Adenosine 5′-Triphosphate-binding Cassette Exporter

ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics simulations of the potential of mean force along the conformational transition pathway [J. Phys. Chem. B 119, 1295(2015)]. However, the occluded conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this work, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1-d2, which are the COM distances between the two sides of the internal(d1)and the external gate(d2). The potential of mean force is thus obtained to identify the transition pathway, along which several outward-facing, inward-facing, and occluded state structures are predicted in good agreement with structural experiments. Our coarse-grained molecular dynamics free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the inward-facing to outward-facing transition and vice versa during the inward-facing to outward-facing transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the previous result, in which both the internal and external gates are open reported in an X-ray experiment [Proc. Natl. Acad. Sci. USA 104,19005(2007)]. Our study sheds light on the molecular mechanism of the state transitions in an ATP-binding cassette exporter.

Influence of fines content on the anti-frost properties of coarse-grained soil

This paper aims to determine the optimal fines content of coarse-grained soil required to simultaneously achieve weaker frost susceptibility and better bearing capacity. We studied the frost susceptibility and strength properties of coarse-grained soil by means of frost heaving tests and static triaxial tests, and the results are as follows： （1） the freezing temperature of coarse-grained soil decreased gradually and then leveled off with incremental increases in the percent content of fines; （2） the fines content proved to be an important factor influencing the frost heave susceptibility and strength properties of coarse-grained soil. With incremental increases in the percent content of fines, the frost heave ratio increased gradually and the cohesion function of fines effectively enhanced the shear strength of coarse-grained soil before freeze-thaw, but the frost susceptibility of fines weakened the shear strength of coarse-grained soil after freeze-thaw; （3） with increasing numbers of freeze-thaw cycles, the shear strength of coarse-grained soil decreased and then stabilized after the ninth freeze-thaw cycle, and therefore the mechanical indexes of the ninth freeze-thaw cycle are recommended for the engi- neering design values; and （4） considering frost susceptibility and strength properties as a whole, the optimal fines content of 5% is recommended for railway sub,fade coarse-~rained soil fillings in frozen re^ions.

Modeling biomembranes and red blood cells by coarse-grained particle methods

In this work, the previously developed coarse-grained （CG） particle models for biomembranes and red blood cells （RBCs） are reviewed, and the advantages of the CG particle methods over the continuum and atomistic simulations for modeling biological phenomena are discussed. CG particle models can largely increase the length scale and time scale of atomistic simulations by eliminating the fast degrees of freedom while preserving the mesoscopic structures and properties of the simulated system. Moreover, CG particle models can be used to capture the microstructural alternations in diseased RBCs and simulate the topological changes of biomembranes and RBCs, which are the major challenges to the typical continuum representations of membranes and RBCs. The power and versatility of CG particle methods are demonstrated：through simulating the dynamical processes mvolving significant topological .changes e.g. lipid self-assembly vesicle fusion and membrane budding.

Multi-Peptide Adsorption on Uncharged Solid Surfaces:A Coarse-Grained Simulation Study

On-aim control of protein adsorption onto a solid surface remains challenging due to the complex interactions involved in this process.Through computational simulation,it is possible to gain molecular-level mechanistic insight into the movement of proteins at the water-solid interface,which allows better prediction of protein behaviors in adsorption and fouling systems.In this work,a mesoscale coarse-grained simulation method was used to investigate the aggregation and adsorption processes of multiple 12-alanine(12-Ala)hydrophobic peptides onto a gold surface.It was observed that around half(46.6%)of the 12-Ala peptide chains could form aggregates.30.0% of the individual peptides were rapidly adsorbed onto the solid surface;after a crawling process on the surface,some of these(51.0%)merged into each other or merged with floating peptides to form adsorbed aggregates.The change in the solid–liquid interface due to peptide deposition has a potential influence on the further adsorption of single peptide chains and aggregates in the bulk water.Overall,the findings from this work help to reveal the mechanism of multi-peptide adsorption,and consequentially build a basis for the understanding of multi-protein adsorption onto a solid surface.

Direct shear tests of coarse-grained fillings from high-speed railway subgrade in cold regions

In order to study the shear behavior of coarse-grained fillings taken from the subgrade bottom layer of a cold region high-speed railway,large scale direct shear tests were conducted with different normal pressures,water contents and temperatures.The results indicate that the relationship between shear displacement and shear stress changed from strain-softening at lower normal pressures to strain-hardening at higher normal pressures,in both unfrozen and frozen states.This phenomenon was mainly due to the shear dilatation deformation effect.The shear displacement-shear stress curves show similar stages.Besides,the shear stress rapidly increased and there was not an increment in the shear displacement during the initial stage of the shear process in the frozen state.In both the unfrozen or frozen states at the same water contents,the shear strength increased with increasing normal pressure.