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.Thi...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.展开更多
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...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.展开更多
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 sequencin...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.展开更多
To overcome the limitations of microscale experimental techniques and molecular dynamics(MD)simulations,a coarse-grained molecular dynamics(CGMD)method was used to simulate the wetting processes of clay aggregates.Bas...To overcome the limitations of microscale experimental techniques and molecular dynamics(MD)simulations,a coarse-grained molecular dynamics(CGMD)method was used to simulate the wetting processes of clay aggregates.Based on the evolution of swelling stress,final dry density,water distribution,and clay arrangements under different target water contents and dry densities,a relationship between the swelling behaviors and microstructures was established.The simulated results showed that when the clay-water well depth was 300 kcal/mol,the basal spacing from CGMD was consistent with the X-ray diffraction(XRD)data.The effect of initial dry density on swelling stress was more pronounced than that of water content.The anisotropic swelling characteristics of the aggregates are related to the proportion of horizontally oriented clay mineral layers.The swelling stress was found to depend on the distribution of tactoids at the microscopic level.At lower initial dry density,the distribution of tactoids was mainly controlled by water distribution.With increase in the bound water content,the basal spacing expanded,and the swelling stresses increased.Free water dominated at higher water contents,and the particles were easily rotated,leading to a decrease in the number of large tactoids.At higher dry densities,the distances between the clay mineral layers decreased,and the movement was limited.When bound water enters the interlayers,there is a significant increase in interparticle repulsive forces,resulting in a greater number of small-sized tactoids.Eventually,a well-defined logarithmic relationship was observed between the swelling stress and the total number of tactoids.These findings contribute to a better understanding of coupled macro-micro swelling behaviors of montmorillonite-based materials,filling a study gap in clay-water interactions on a micro scale.展开更多
Seepage in coarse-grained soil exhibits distinct non-Darcy characteristics,and the transition from linear to nonlinear seepage significantly affects the hydraulic characteristics and geotechnical applications.Due to t...Seepage in coarse-grained soil exhibits distinct non-Darcy characteristics,and the transition from linear to nonlinear seepage significantly affects the hydraulic characteristics and geotechnical applications.Due to the complexity of pore structure in heterogeneous coarse-grained soil,identifying the critical threshold for the transition from Darcy to non-Darcy seepage is challenging.This paper introduces equivalent particle size(dep)and relative roughness(λt)as indirect indicators reflecting the pore characteristics,quantifying the complex pore structure of heterogeneous coarse-grained soil.The formulae for the derivation of Reynolds number and resistance coefficient for heterogeneous coarse-grained soil are presented.By conducting permeability tests on coarse-grained soils with different pore structures,the effect of particle composition heterogeneity on seepage characteristics was analyzed.The flow regime of heterogeneous coarse-grained soil is divided into laminar,transitional,and turbulent stages based on the relationship between Reynolds number and resistance coefficient.The energy loss patterns in each stage are closely related to pore structure.By setting the permeability ratio k∗=0.95 as the critical threshold for the transition from Darcy to non-Darcy seepage,a method for calculating the critical Reynolds number(Recr)for heterogeneous coarse-grained soil is proposed.Furthermore,we applied this method to other published laboratory data,analyzing the differences in the critical threshold for seepage transition between homogeneous and heterogeneous coarse-grained soil.This study aims to propose a more accurate and general criterion for the transition from Darcy to non-Darcy seepage in heterogeneous coarse-grained soil.展开更多
The advent of coarse-grain superplasticity has provided a pathway for novel applications in material forming.This article investigated the underlying deformation mechanisms that enabled achieving superplastic elongati...The advent of coarse-grain superplasticity has provided a pathway for novel applications in material forming.This article investigated the underlying deformation mechanisms that enabled achieving superplastic elongation exceeding 230%in a coarse-grained Ni-Co-based superalloy.The deformed microstructure and fractographic characteristics of the alloy were examined utilizing optical microscopy(OM),scanning electron microscopy(SEM),and electron backscatter diffraction(EBSD).The results of the analysis revealed that below 1100℃,the process of dynamic recrystallization(DRX)occurred at a sluggish rate,resulting in low plasticity and the initiation of severe cracks.Complete DRX occurred when the deformation temperature exceeded 1100℃,leading to a more uniformly deformed microstructure,reduced crack initiation,and enhanced ductility demonstrated by elongation to failure surpassing 230%.The augmented occurrence of the DRX facilitated prolonged plastic-forming periods,which delayed fracture propagation and promoted the deformation flow within the alloy,thereby transitioning the fracture behavior from intergranular-brittle at 1050℃to ductile intergranular at 1140℃.At this temperature,the deformation was predominantly governed by the discontinuous-DRX(DDRX)mechanism and grain growth,facilitated by the formation of twin boundaries.展开更多
The aging of biomolecular condensates has been implicated in the pathogenesis of various neurodegenerative diseases,characterized by a transition from a physiologically liquid-like state to a pathologically ordered st...The aging of biomolecular condensates has been implicated in the pathogenesis of various neurodegenerative diseases,characterized by a transition from a physiologically liquid-like state to a pathologically ordered structure.However,the mechanisms governing the formation of these pathological aggregates remain poorly understood.To address this,the present study utilizes coarse-grained molecular dynamics simulations based on Langevin dynamics to explore the structural,dynamical,and material property changes of protein condensates during the aging process.Here,we further develop a nonequilibrium simulation algorithm that not only captures the characteristics of time-dependent amount of aging beads but also reflects the structural information of chain-like connections between aging beads.Our findings reveal that aging induces compaction of the condensates,accompanied by a decrease in diffusion rates and an increase in viscosity.Further analysis suggests that the heterogeneous diffusivity within the condensates may drive the aging process to initiate preferentially at the condensate surface.Our simulation results align with the experimental phenomena and provide a clear physical picture of the aging dynamics.展开更多
This work focuses on the influence of Al content on the precipitation of nanoprecipitates,growth of prior austenite grains(PAGs),and impact toughness in simulated coarse-grained heat-affected zones (CGHAZs) of two exp...This work focuses on the influence of Al content on the precipitation of nanoprecipitates,growth of prior austenite grains(PAGs),and impact toughness in simulated coarse-grained heat-affected zones (CGHAZs) of two experimental shipbuilding steels after being subjected to high-heat input welding at 400 kJ·cm^(-1).The base metals (BMs) of both steels contained three types of precipitates Type Ⅰ:cubic (Ti,Nb)(C,N),Type Ⅱ:precipitate with cubic (Ti,Nb)(C,N) core and Nb-rich cap,and Type Ⅲ:ellipsoidal Nb-rich precipitate.In the BM of 60Al and 160Al steels,the number densities of the precipitates were 11.37×10^(5) and 13.88×10^(5) mm^(-2),respectively The 60Al and 160Al steel contained 38.12% and 6.39% Type Ⅲ precipitates,respectively.The difference in the content of Type Ⅲ precipitates in the 60Al steel reduced the pinning effect at the elevated temperature of the CGHAZ,which facilitated the growth of PAGs The average PAG sizes in the CGHAZ of the 60Al and 160Al steels were 189.73 and 174.7μm,respectively.In the 60Al steel,the low lattice mismatch among Cu_(2)S,TiN,and γ-Al_(2)O_(3)facilitated the precipitation of Cu_(2)S and TiN onto γ-Al_(2)O_(3)during welding,which decreased the number density of independently precipitated (Ti,Nb)(C,N) particles but increased that of γ-Al_(2)O_(3)–Ti N–Cu_(2)S particles.Thus abnormally large PAGs formed in the CGHAZ of the 60Al steel,and they reached a maximum size of 1 mm.These PAGs greatly reduced the microstructural homogeneity and consequently decreased the impact toughness from 134 (0.016wt%Al) to 54 J (0.006wt%Al)at-40℃.展开更多
This study investigated the hydraulic and mechanical behaviors of unsaturated coarse-grained railway embankment fill materials(CREFMs)using a novel unsaturated large-scale triaxial apparatus equipped with the axis tra...This study investigated the hydraulic and mechanical behaviors of unsaturated coarse-grained railway embankment fill materials(CREFMs)using a novel unsaturated large-scale triaxial apparatus equipped with the axis translation technique(ATT).Comprehensive soil-water retention and constant-suction triaxial compression tests were conducted to evaluate the effects of initial void ratio,matric suction,and confining pressure on the properties of CREFMs.Key findings reveal a primary suction range of 0 e100 kPa characterized by hysteresis,which intensifies with decreasing density.Notably,the air entry value and residual suction are influenced by void ratio,with higher void ratios leading to decreased air entry values and residual suctions,underscoring the critical role of void ratio in hydraulic behavior.Additionally,the critical state line(CSL)in the bi-logarithmic space of void ratio and mean effective stress shifts towards higher void ratios with increasing matric suction,significantly affecting dilatancy and critical states.Furthermore,the study demonstrated that the mobilized friction angle and modulus properties depend on confining pressure and matric suction.A novel modified dilatancy equation was proposed,which enhances the predictability of CREFMs'responses under variable loading,particularly at high stress ratios defined by the deviatoric stress over the mean effective stress.This research advances the understanding of CREFMs'performance,especially under fluctuating environmental conditions that alter suction levels.展开更多
This paper presents a new methodology for coarse-grained atomistic simulation of inelastic material behavior including phase transformations in ceramics and dislocation mediated plasticity in metals. The methodology c...This paper presents a new methodology for coarse-grained atomistic simulation of inelastic material behavior including phase transformations in ceramics and dislocation mediated plasticity in metals. The methodology combines an atomistic formulation of balance equations and a modified finite element method. With significantly fewer degrees of freedom than those of a fully atomistic model and without additional constitutive rules but the interatomic force field, the new coarse-grained （CG） method is shown to be feasible in predicting the nonlinear constitutive re- sponses of materials and also reproducing atomic-scale phenomena such as phase transformations （diamond --, 13-Sn） in silicon and dislocation nucleation and migration, formation of dislocation loops and stacking faults ribbons in single crystal nickel. Direct comparisons between CG and the corresponding full molecular dynamics （MD） simulations show that the present methodology is efficient and promising in modeling and simulation of inelastic material behavior without losing the essential atomistic features. The potential applications and the limitations of the CG method are also discussed.展开更多
The present work proposes a novel methodology for constructing coarse-grained （CG） models, which aims at minimizing the difference between CG model and the corresponding original system. The difference is defined as...The present work proposes a novel methodology for constructing coarse-grained （CG） models, which aims at minimizing the difference between CG model and the corresponding original system. The difference is defined as a functional of their equilibrium conformationaJ probability densities, then is estimated from equilibrium averages of many independent physical quantities denoted as basis functions. An orthonormalization strategy is adopted to get the independent basis functions from su^ciently preselected interesting physical quantities of the system. Thus the current method is named as probability density matching coarse-graining （PMCG） scheme, which effectively takes into account the overall cha,~acteristics of the original systems to construct CG model, and it is a rtatural improvement of the usual CG scheme wherein some physical quantities are intuitively chosen without considering their correlations. We verify the general PMCG framework in constructing a one-site CG water model from TIP3P model. Both structure of liquids and pressure of the TIP3P water system are found to be well reproduced at the same time in the constructed CG model.展开更多
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 e...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.展开更多
Effects of Mg on the chemical component and size distribution of Ti-bearing inclusions favored grain refinement of the welding induced coarse-grained heat affected zone （CGHAZ）, with enhanced impact toughness in Ti-...Effects of Mg on the chemical component and size distribution of Ti-bearing inclusions favored grain refinement of the welding induced coarse-grained heat affected zone （CGHAZ）, with enhanced impact toughness in Ti-killed steels, which were examined based on experimental observations and thermodynamic calculations. The results indicated that the chemical constituents of the inclusions gradually varied from the Ti-O＋Ti-Mg-O compound oxide to the Ti-Mg-O＋MgO compound oxide and the single-phase MgO, as the Mg content increased from 0.002 3M to 0.006%. A trace addition of Mg （approximately 0. 002%） led to the refinement of Ti-bearing inclusions by creating the Ti-Mg-O compound oxide and provided favorable size distribution of the inclusions 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 Mg （approximately 0. 006%） produced a single-phase MgO, which was impotent to nucleate an acicular ferrite, and a microstructure comprised of a ferrite side plate and a grain boundary ferrite developed in the CGHAZ. The experimental results were confirmed by thermodynamic calculations.展开更多
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 toug...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.展开更多
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 content...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.展开更多
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 group...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.展开更多
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 regi...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.展开更多
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 ...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.展开更多
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-grain...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.展开更多
文摘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.
文摘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.
基金the U.S.National Institutes of Health(NIH)R35GM133712 to C.Z.R01 AI121080 and R01AI139874 to W.P.
文摘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.
基金supported by the National Natural Science Foundation of China(Grant No.42172308)the Youth Innovation Promotion Association CAS(Grant No.2022331)the Key Research and Development Program of Hubei Province(Grant No.2022BAA036).
文摘To overcome the limitations of microscale experimental techniques and molecular dynamics(MD)simulations,a coarse-grained molecular dynamics(CGMD)method was used to simulate the wetting processes of clay aggregates.Based on the evolution of swelling stress,final dry density,water distribution,and clay arrangements under different target water contents and dry densities,a relationship between the swelling behaviors and microstructures was established.The simulated results showed that when the clay-water well depth was 300 kcal/mol,the basal spacing from CGMD was consistent with the X-ray diffraction(XRD)data.The effect of initial dry density on swelling stress was more pronounced than that of water content.The anisotropic swelling characteristics of the aggregates are related to the proportion of horizontally oriented clay mineral layers.The swelling stress was found to depend on the distribution of tactoids at the microscopic level.At lower initial dry density,the distribution of tactoids was mainly controlled by water distribution.With increase in the bound water content,the basal spacing expanded,and the swelling stresses increased.Free water dominated at higher water contents,and the particles were easily rotated,leading to a decrease in the number of large tactoids.At higher dry densities,the distances between the clay mineral layers decreased,and the movement was limited.When bound water enters the interlayers,there is a significant increase in interparticle repulsive forces,resulting in a greater number of small-sized tactoids.Eventually,a well-defined logarithmic relationship was observed between the swelling stress and the total number of tactoids.These findings contribute to a better understanding of coupled macro-micro swelling behaviors of montmorillonite-based materials,filling a study gap in clay-water interactions on a micro scale.
基金supported by the National Nature Science Foundation of China (Grant No.42072303)the State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project (Grant No.SKLGP2021Z004).
文摘Seepage in coarse-grained soil exhibits distinct non-Darcy characteristics,and the transition from linear to nonlinear seepage significantly affects the hydraulic characteristics and geotechnical applications.Due to the complexity of pore structure in heterogeneous coarse-grained soil,identifying the critical threshold for the transition from Darcy to non-Darcy seepage is challenging.This paper introduces equivalent particle size(dep)and relative roughness(λt)as indirect indicators reflecting the pore characteristics,quantifying the complex pore structure of heterogeneous coarse-grained soil.The formulae for the derivation of Reynolds number and resistance coefficient for heterogeneous coarse-grained soil are presented.By conducting permeability tests on coarse-grained soils with different pore structures,the effect of particle composition heterogeneity on seepage characteristics was analyzed.The flow regime of heterogeneous coarse-grained soil is divided into laminar,transitional,and turbulent stages based on the relationship between Reynolds number and resistance coefficient.The energy loss patterns in each stage are closely related to pore structure.By setting the permeability ratio k∗=0.95 as the critical threshold for the transition from Darcy to non-Darcy seepage,a method for calculating the critical Reynolds number(Recr)for heterogeneous coarse-grained soil is proposed.Furthermore,we applied this method to other published laboratory data,analyzing the differences in the critical threshold for seepage transition between homogeneous and heterogeneous coarse-grained soil.This study aims to propose a more accurate and general criterion for the transition from Darcy to non-Darcy seepage in heterogeneous coarse-grained soil.
基金financially supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDC0140000)the National Science and Technology Major Project(No.J2019-VI-0006-0120)+3 种基金the Science and Technology Major Project of Liaoning Province(No.2024JH1/11700037)the Youth Innovation Promotion Association,CAS(No.2023202)the Natural Science Foundation Project of Liaoning Province(No.2023-MS-024)the National Science and Technology Major Project(No.2024ZD0600600).
文摘The advent of coarse-grain superplasticity has provided a pathway for novel applications in material forming.This article investigated the underlying deformation mechanisms that enabled achieving superplastic elongation exceeding 230%in a coarse-grained Ni-Co-based superalloy.The deformed microstructure and fractographic characteristics of the alloy were examined utilizing optical microscopy(OM),scanning electron microscopy(SEM),and electron backscatter diffraction(EBSD).The results of the analysis revealed that below 1100℃,the process of dynamic recrystallization(DRX)occurred at a sluggish rate,resulting in low plasticity and the initiation of severe cracks.Complete DRX occurred when the deformation temperature exceeded 1100℃,leading to a more uniformly deformed microstructure,reduced crack initiation,and enhanced ductility demonstrated by elongation to failure surpassing 230%.The augmented occurrence of the DRX facilitated prolonged plastic-forming periods,which delayed fracture propagation and promoted the deformation flow within the alloy,thereby transitioning the fracture behavior from intergranular-brittle at 1050℃to ductile intergranular at 1140℃.At this temperature,the deformation was predominantly governed by the discontinuous-DRX(DDRX)mechanism and grain growth,facilitated by the formation of twin boundaries.
基金supported by the National Key Research and Development Program of China(Grant No.2022YFA1405000)the National Natural Science Foundation of China(Grant Nos.12274212,12347102,and 12174184)Innovation Program for Quantum Science and Technology(Grant No.2024ZD0300101).
文摘The aging of biomolecular condensates has been implicated in the pathogenesis of various neurodegenerative diseases,characterized by a transition from a physiologically liquid-like state to a pathologically ordered structure.However,the mechanisms governing the formation of these pathological aggregates remain poorly understood.To address this,the present study utilizes coarse-grained molecular dynamics simulations based on Langevin dynamics to explore the structural,dynamical,and material property changes of protein condensates during the aging process.Here,we further develop a nonequilibrium simulation algorithm that not only captures the characteristics of time-dependent amount of aging beads but also reflects the structural information of chain-like connections between aging beads.Our findings reveal that aging induces compaction of the condensates,accompanied by a decrease in diffusion rates and an increase in viscosity.Further analysis suggests that the heterogeneous diffusivity within the condensates may drive the aging process to initiate preferentially at the condensate surface.Our simulation results align with the experimental phenomena and provide a clear physical picture of the aging dynamics.
基金support from the National Natural Science Foundation of China (No. U1960202)the Opening Foundation from Shanghai Engineering Research Center of Hot Manufacturing, China (No. 18DZ2253400)。
文摘This work focuses on the influence of Al content on the precipitation of nanoprecipitates,growth of prior austenite grains(PAGs),and impact toughness in simulated coarse-grained heat-affected zones (CGHAZs) of two experimental shipbuilding steels after being subjected to high-heat input welding at 400 kJ·cm^(-1).The base metals (BMs) of both steels contained three types of precipitates Type Ⅰ:cubic (Ti,Nb)(C,N),Type Ⅱ:precipitate with cubic (Ti,Nb)(C,N) core and Nb-rich cap,and Type Ⅲ:ellipsoidal Nb-rich precipitate.In the BM of 60Al and 160Al steels,the number densities of the precipitates were 11.37×10^(5) and 13.88×10^(5) mm^(-2),respectively The 60Al and 160Al steel contained 38.12% and 6.39% Type Ⅲ precipitates,respectively.The difference in the content of Type Ⅲ precipitates in the 60Al steel reduced the pinning effect at the elevated temperature of the CGHAZ,which facilitated the growth of PAGs The average PAG sizes in the CGHAZ of the 60Al and 160Al steels were 189.73 and 174.7μm,respectively.In the 60Al steel,the low lattice mismatch among Cu_(2)S,TiN,and γ-Al_(2)O_(3)facilitated the precipitation of Cu_(2)S and TiN onto γ-Al_(2)O_(3)during welding,which decreased the number density of independently precipitated (Ti,Nb)(C,N) particles but increased that of γ-Al_(2)O_(3)–Ti N–Cu_(2)S particles.Thus abnormally large PAGs formed in the CGHAZ of the 60Al steel,and they reached a maximum size of 1 mm.These PAGs greatly reduced the microstructural homogeneity and consequently decreased the impact toughness from 134 (0.016wt%Al) to 54 J (0.006wt%Al)at-40℃.
基金jointly supported by the Science Fund for Distinguished Young Scholars of Hunan Province,China(Grant No.2024JJ2073)the National Natural Science Foundation of China(Grant No.52178443)the Fundamental Research Funds for the Central Universities of Central South University,China(Grant No.2022ZZTS0620)。
文摘This study investigated the hydraulic and mechanical behaviors of unsaturated coarse-grained railway embankment fill materials(CREFMs)using a novel unsaturated large-scale triaxial apparatus equipped with the axis translation technique(ATT).Comprehensive soil-water retention and constant-suction triaxial compression tests were conducted to evaluate the effects of initial void ratio,matric suction,and confining pressure on the properties of CREFMs.Key findings reveal a primary suction range of 0 e100 kPa characterized by hysteresis,which intensifies with decreasing density.Notably,the air entry value and residual suction are influenced by void ratio,with higher void ratios leading to decreased air entry values and residual suctions,underscoring the critical role of void ratio in hydraulic behavior.Additionally,the critical state line(CSL)in the bi-logarithmic space of void ratio and mean effective stress shifts towards higher void ratios with increasing matric suction,significantly affecting dilatancy and critical states.Furthermore,the study demonstrated that the mobilized friction angle and modulus properties depend on confining pressure and matric suction.A novel modified dilatancy equation was proposed,which enhances the predictability of CREFMs'responses under variable loading,particularly at high stress ratios defined by the deviatoric stress over the mean effective stress.This research advances the understanding of CREFMs'performance,especially under fluctuating environmental conditions that alter suction levels.
基金supported by the National Science Foundation under award numbers CMMI-0855795 and 1129976DARPA under award number N66001-10-1-4018+1 种基金Department of Energy under award number DOE/DE-SC0006539supported in part by the National Science Foundation through Teragrid resources provided by TACC
文摘This paper presents a new methodology for coarse-grained atomistic simulation of inelastic material behavior including phase transformations in ceramics and dislocation mediated plasticity in metals. The methodology combines an atomistic formulation of balance equations and a modified finite element method. With significantly fewer degrees of freedom than those of a fully atomistic model and without additional constitutive rules but the interatomic force field, the new coarse-grained （CG） method is shown to be feasible in predicting the nonlinear constitutive re- sponses of materials and also reproducing atomic-scale phenomena such as phase transformations （diamond --, 13-Sn） in silicon and dislocation nucleation and migration, formation of dislocation loops and stacking faults ribbons in single crystal nickel. Direct comparisons between CG and the corresponding full molecular dynamics （MD） simulations show that the present methodology is efficient and promising in modeling and simulation of inelastic material behavior without losing the essential atomistic features. The potential applications and the limitations of the CG method are also discussed.
基金Supported by National Natural Science Foundation of China under Grant No.11175250
文摘The present work proposes a novel methodology for constructing coarse-grained （CG） models, which aims at minimizing the difference between CG model and the corresponding original system. The difference is defined as a functional of their equilibrium conformationaJ probability densities, then is estimated from equilibrium averages of many independent physical quantities denoted as basis functions. An orthonormalization strategy is adopted to get the independent basis functions from su^ciently preselected interesting physical quantities of the system. Thus the current method is named as probability density matching coarse-graining （PMCG） scheme, which effectively takes into account the overall cha,~acteristics of the original systems to construct CG model, and it is a rtatural improvement of the usual CG scheme wherein some physical quantities are intuitively chosen without considering their correlations. We verify the general PMCG framework in constructing a one-site CG water model from TIP3P model. Both structure of liquids and pressure of the TIP3P water system are found to be well reproduced at the same time in the constructed CG model.
文摘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.
文摘Effects of Mg on the chemical component and size distribution of Ti-bearing inclusions favored grain refinement of the welding induced coarse-grained heat affected zone （CGHAZ）, with enhanced impact toughness in Ti-killed steels, which were examined based on experimental observations and thermodynamic calculations. The results indicated that the chemical constituents of the inclusions gradually varied from the Ti-O＋Ti-Mg-O compound oxide to the Ti-Mg-O＋MgO compound oxide and the single-phase MgO, as the Mg content increased from 0.002 3M to 0.006%. A trace addition of Mg （approximately 0. 002%） led to the refinement of Ti-bearing inclusions by creating the Ti-Mg-O compound oxide and provided favorable size distribution of the inclusions 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 Mg （approximately 0. 006%） produced a single-phase MgO, which was impotent to nucleate an acicular ferrite, and a microstructure comprised of a ferrite side plate and a grain boundary ferrite developed in the CGHAZ. The experimental results were confirmed by thermodynamic calculations.
文摘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.
基金Project(2016ZGHJ/XZHTL-YQSC-26)supported by the Key Scientific Research Project of China Gold GroupProject(SQ2019QZKK2806)supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program,China+1 种基金Project(300102268716)supported by the Fundamental Research Funds for the Central Universities,ChinaProject(LHKA-G201701)supported by the Science and Technology Project of Yalong River Hydropower Development Company,China。
文摘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.
文摘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.
基金sponsored by the Doctoral Fund of Ministry of Education of China (Grant no.20105201110002)Research Fund of Guizhou Province and Doctoral Programme Fund of Guizhou University
文摘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.
基金Project(50639050) supported by the National Natural Science Foundation of China and Er-Tan Hydraulicpower Limited CompanyProject(50579014) supported by the National Natural Science Foundation of China+3 种基金Project(09KJD560003) supported by the Natural Science Foundation of Jiangsu Higher Education Institutions of ChinaProject(BK2007582) supported by Jiangsu Provincial Natural Science Foundation of ChinaProject(20070294002) supported by the Specialized Research Fund for the Doctoral Program of Higher Education of ChinaProject(GH200904) supported by Key Laboratory of Ministry of Education for Geomechanics and Embankment Engineering,Hohai University,China
文摘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.
基金Project(2018YFC1508505)supported by the National Key Research and Development Program of ChinaProject(U1865104)supported by Yalong River Joint Fund of Natural Science Foundation of China-Yalong River Basin Hydropower Development Co.,Ltd.,China+1 种基金Project(51479052)supported by National Natural Science of ChinaProject(2019T120443)supported by China Postdoctoral Science Foundation。
文摘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.
