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.

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.

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.

Simplified Coarse-Grained Dynamic Model for Real Gases

A simplified model is proposed for an easy understanding of the coarse-grained technique and for achieving a first approximation to the behavior of gases. A mole of a gas substance, within a cubic container, is represented by six particles symmetrically moving. The impacts of particles on container walls, the inter-particle collisions, as well as the volume of particles and the inter-particle attractive forces, obeying a Lennard-Jones curve, are taken into account. Thanks to the symmetry, the problem is reduced to the nonlinear dynamic analysis of a SDOF oscillator, which is numerically solved by a step-by-step time integration algorithm. Five applications of proposed model, on Carbon Dioxide, are presented: 1) Ideal gas in STP conditions. 2) Real gas in STP conditions. 3) Condensation for small molar volume. 4) Critical point. 5) Iso-kinetic energy curves and iso-therms in the critical point region. Results of the proposed model are compared with test data and results of the Van der Waals model for real gases.

Soft coarse-grained particle model for particle-fluid systems

By modeling a group of neighboring real particles as a single coarse-grained particle(CGP),discrete particle method(DPM)is now capable of simulating industrial-scale particle-fluid systems.However,a systematic approach to determine the CGP properties and develop their interaction models is still lacking,which casts uncertainty on the predictivity of the method.In this study,collisions between predefined particle groups are analyzed to construct kernel functions for modeling the CGPs and then the model parameters are determined by equating the statistical properties of the CGPs and the real particles in the physical process studied.This approach is implemented for homogeneous cooling of granular gas,then demonstrated effective in simulating experimental fluidized beds.

Differences of polygonal faults related to upper Miocene channels:a case study from the Beijiao sag of Qiongdongnan basin,South China Sea

Deep-water coarse-grained channels are embedded within a polygonal fault tier,and the polygonal faults(PFs)present non-polygonal geometries rather than classic polygonal geometry in plan view.However,PFs present differences when they encounter deep-water(coarse-grained vs.fine-grained)channels with different lithology,which has not been further studied to date.Three-dimensional(3D)seismic data and a drilling well from Beijiao sag of Qiongdongnanbasin,South China Sea were utilized to document the plan view and cross-sectional properties of the PFs and their differences and genetic mechanism were investigated.Results show that,first,PFs can be divided morphologically into channel-segmenting PFs and channel-bounding PFs in plan view.The former virtually cuts or segments the axes of channels in highand low-amplitudes,and the latter nearly parallels the boundaries of the channels.Both are approximately perpendicular to each other.Secondly,channel-bounding PFs that related to low-amplitude channels are much longer than those of high-amplitude ones;channel-segmenting PFs related to low-amplitude channels are slightly longer than the counterparts related to high-amplitude channels.Lastly,the magnitudes(e.g.,heights)of the PFs are proportional to the scales(e.g.,widths and heights)of low-amplitude channels,whereas the magnitudes of the PFs are inversely proportional to the scales of high amplitude channels.Coarse-grained(high amplitude)channels act as a mechanical barrier to the propagation of PFs,whereas fine-grained(low-amplitude)channels are beneficial to the propagation and nucleation of PFs.Additionally,the genetic mechanism of PFs is discussed and reckoned as combined geneses of gravitational spreading and overpressure hydrofracture.The differences of the PFs can be used to reasonably differentiate coarse-grained channels from fine-grained channels.This study provides new insights into understanding the different geometries of the PFs related to coarse-grained and fine-grained channels and their genetic mechanism.

3D coarse-grained DPM simulation of the MIP reaction-regeneration loop

The reactor-regenerator loop is the core facility of the maximizing iso-paraffin(MIP)process.Although the discrete particle method(DPM)simulation can provide detailed information at the particle scale,it has been unable to simulate such a complex loop system due to limitations of coarse-grained(CG)models,computing software,and hardware.In this study,a newly proposed soft-shell CG-DPM model with a CG ratio of up to 800 is used to simulate a 3.5 Mt/a industrial-scale MIP reactor-regenerator loop.The solid fraction distribution obtained is found to agree well with in-situ measurements.Hydrodynamic properties including the distribution of solid fraction,gas and solid velocity,standard derivation of solid fraction with time,temporal distribution of the flow field,and particle residence time distribution are measured in the simulation,which are meaningful to better design and operate such systems in the future.

Multi-level coarse-grained discrete element method modeling of cylinder particle flow in a rotating drum

The coarse-grained discrete element method(DEM)is probably a feasible option for simulating an actual drum-type biomass boiler,which contains over 10 million cylinder particles.A multi-level study was conducted based on particle and coarse-grained level data to evaluate the adequacy of the coarse-grained approach in terms of geometrical characteristics,kinematic features,and dynamic properties.Two scaling laws for contact parameters were used and compared during the simulations.The results show that the coarse-grained approach can accurately predict the positions of the free surface and active-passive interface,the mixing index,and the orientation properties.Deviations in the velocity fields may occur due to the worse flowability of coarse-grained particles near the free surface.The efficiency is significantly improved by the coarse-grained model compared with the corresponding original case(the same DEM code without a coarse-grained model was used for the original simulations).

Evaluation of coarse-grained CFD-DEM models with the validation of PEPT measurements

Computational Fluid Dynamics coupled with Discrete Element Method (CFD-DEM) is a commonly used numerical method to model gas-solid flow in fluidised beds and other multiphase systems. A significant limitation of CFD-DEM is the feasibility of the realistic simulation of large numbers of particles. Coarse-graining (CG) approaches, through which groups of multiple individual particles are represented by single, larger particles, can substantially reduce the total number of particles while maintaining similar system dynamics. As these three CG models have not previously been compared, there remains some debate, however, about the best practice in the application of CG in CFD-DEM simulations. In this paper, we evaluate the performance of three typical CG methods based on simulations of a bubbling fluidised bed. This is achieved through the use of a numerical validation framework, which makes full use of the high-resolution 3D positron emission particle tracking (PEPT) measurements to rigorously validate the outputs of CFD-DEM simulations conducted using various different coarse-graining models, and various different degrees of coarse-graining. The particle flow behaviours in terms of the particle occupancy field, velocity field, circulation time, and bubble size and velocity, are comprehensively analysed. It is shown that the CG simulation starts to fail when the size ratio between the bed chamber and the particles decreases to approximately 20. It is also observed, somewhat surprisingly, that the specific CG approach applied to interparticle contact parameters does not have a substantial effect on the simulation results for the bubbling bed simulations across a wide range of CG factors.