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
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
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
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.O...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.展开更多
The spinodal decomposition method emerges as a promising methodology,showcasing its potential in exploring the design space for metamaterial structures.However,spinodal structures design is still largely limited to re...The spinodal decomposition method emerges as a promising methodology,showcasing its potential in exploring the design space for metamaterial structures.However,spinodal structures design is still largely limited to regular structures,due to their relatively easy parameterization and controllability.Efficiently predicting the mechanical properties of 3D spinodal membrane structure remains a challenge,given that the features of the membrane necessitate adaptive mesh through the modelling process.This paper proposes an integrated approach for morphological design with customized mechanical properties,incorporating the spinodal decomposition method and adaptive coarse-grained modeling,which can produce various morphologies such as lamellar,columnar,and cubic structures.Pseudo-periodic parameterβand orientational parameterΘ(θ_(1),θ_(2),θ_(3))are identified to achieve the optimal goal of anisotropic mechanical properties.Parametric analysis is conducted to reveal the correlation between the customized spinodal structure and mechanical performance.Our work provides an integrated approach for morphological variation and tuning mechanical properties,paving the way for the design and development of customized functional materials similar to 3D spinodal membrane structures.展开更多
The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many pro...The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many protein com-plexes are available in the protein data bank,their assembly/disassembly orders of subunits are largely unknown.In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex,computational methods can be used to predict the assembly/disassembly order.Since sampling is a nontrivial issue in simulating the assembly/disassembly process,coarse-grained simulations are more efficient than atomic simulations are.In this work,we developed computational protocols for predicting the assembly/disassembly orders of protein complexes via coarse-grained simulations.The protocols were illustrated via two protein complexes,and the predicted assembly/disassembly orders were consistent with the available experimental data.展开更多
Understanding the liquid-liquid phase separation(LLPS)of immunoglobulin G(IgG)is crucial,as it profoundly influences IgG’s biological activity and stability.In this study,we employed coarse-grained molecular dynamics...Understanding the liquid-liquid phase separation(LLPS)of immunoglobulin G(IgG)is crucial,as it profoundly influences IgG’s biological activity and stability.In this study,we employed coarse-grained molecular dynamics simulations to systematically investigate the phase separation behavior of IgG.We first constructed two types of IgG models:all-pair IgG model and partial-pair IgG model,and compared the coexistence curve from our simulations with experimental data.Our results showed that the partial-pair IgG model aligns better with the experimental critical temperature and critical density.Using this model,we then calculated the temperature-dependent variations of IgG’s radius of gyration,surface tension,viscosity,etc.More importantly,we demonstrated that variations in the interaction strengths among IgG molecules significantly influence their phase separation behavior.Specifically,a higher standard deviation of interaction strength at different temperatures is found to lead to more stable phase-separated states.Furthermore,we observed that the introduction of repulsive polymers and strongly attractive polymers consistently enhances IgG phase separation,while weakly attractive polymers exhibit a dual regulatory effect on the phase separation.Overall,this study provides valuable insights into the mechanisms governing IgG phase behavior,with potential implications for optimizing biopharmaceutical products.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
The fracture mechanisms of coarse-grained heat-affected zone(CGHAZ)for Mg and Mg–Ca deoxidized high-strength low-alloy(HSLA)steels after high heat input welding(HHIW)were investigated based on the microstructures,cra...The fracture mechanisms of coarse-grained heat-affected zone(CGHAZ)for Mg and Mg–Ca deoxidized high-strength low-alloy(HSLA)steels after high heat input welding(HHIW)were investigated based on the microstructures,crack behaviors and mechanical properties.Compared to Mg–Ca steel,the proportion of intergranular acicular ferrites(IAFs)and polygonal ferrites(PFs)in Mg steel increases from 59.97%to 90.16%.The high-angle grain boundaries(HAGBs)and geometrically necessary dislocations density increase from 55.5%and 4.30×10^(14) m^(-2)to 70.4%and 5.48×10^(14) m^(–2),respectively,while effective grain size decreases from 9.46 to 8.12μm.The area fraction of radial zone in Mg steel decreases from 80.8%to 37.7%and cleavage plane is smaller with more curved and finer tearing ridges.The inclusions distributed at the center of cleavage planes and along river lines can serve as crack initiation sites.The zigzag pattern of primary crack propagation path has width of 476μm and the length of secondary cracks remains below 10μm.These cracks are deflected or arrested by IAFs,PFs and HAGBs,and tend to propagate along{110}plane family.These factors contribute to superior overall mechanical properties of Mg steel,especially increasing low-temperature impact toughness from 23 to 175 J.展开更多
Membrane fusion is essential for many cellular physiological functions,which is modulated by highly precise molecular mechanism involving multiple energy barriers.Nanoparticles(NPs),which exhibit immense potential in ...Membrane fusion is essential for many cellular physiological functions,which is modulated by highly precise molecular mechanism involving multiple energy barriers.Nanoparticles(NPs),which exhibit immense potential in the field of biomedical applications,can act as fusogen proteins to initiate and regulate membrane fusion.However,the underlying mechanisms of NP-induced membrane fusion and the molecular details involved remain largely elusive.Here,using coarse-grained molecular dynamics simulations,we systematically investigate the NP-induced membrane fusion behaviors and the influences of NP properties(size,hydrophobicity and hydrophilicity).Our results show that the vesicle-bilayer fusion induced by a hydrophobic NP is an intricately state-wise process,involving the approach and local deformation of the vesicle and bilayer bridging by the NP,the flip-flop of lipids from proximal leaflets and the formation of a fusion stalk,as well as further lipid interactions between distal leaflets and complete fusion.Moreover,we find that NP properties have distinct effects on membrane fusion and thus the optimal NP conditions for facilitating membrane fusion are obtained.Our work provides a mechanistic understanding of NP-induced membrane fusion and offers useful insights for efficient and controlled regulation of membrane fusion.展开更多
Two experimental X80 steels with different Cr contents(0.13,0.40 wt.%)were designed to study the influence of Cr content on the microstructure transformation and properties in the coarse-grained heat-affected zone by ...Two experimental X80 steels with different Cr contents(0.13,0.40 wt.%)were designed to study the influence of Cr content on the microstructure transformation and properties in the coarse-grained heat-affected zone by using a Formastor-F II thermal dilatometer and to simulate the microstructure of the subcritically reheated coarse-grained heat-affected zone(SCGHAZ)by means of the Gleeble-3500 thermal simulator,along with the scanning electron microscope,transmission electron microscope,and electron backscattering diffraction test methods to characterize the microstructures at 650℃.The findings indicate that a higher Cr content can promote the formation of bainitic ferrite(BF),while the microhardness and impact toughness of SCGHAZ are improved.Granular bainite and BF dominated the microstructures formed by the two experimental steels at 650℃,respectively.For experimental steels mainly composed of BF,they have a high proportion of high-angle grain boundaries(HAGB),and the misorientation angle of HAGB is mostly greater than 55°.Moreover,the distribution of martensite-austenite(M-A)constituents in SCGHAZ altered from dense to sparse,and the form altered from elongated to island-like when the Cr concentration was changed from 0.13 to 0.40 wt.%.Consequently,by suitably increasing the concentration of Cr,it is possible to raise the density of HAGB and improve the shape of M-A constituents,allowing SCGHAZ to have a higher toughness.展开更多
In nature,cavitation bubbles typically appear in clusters,engaging in interactions that create a variety of dynamicmotion patterns.To better understand the behavior ofmultiple bubble collapses and the mechanisms of in...In nature,cavitation bubbles typically appear in clusters,engaging in interactions that create a variety of dynamicmotion patterns.To better understand the behavior ofmultiple bubble collapses and the mechanisms of interbubble interaction,this study employs molecular dynamics simulation combined with a coarse-grained force field.By focusing on collapsemorphology,local density,and pressure,it elucidates how the number and arrangement of bubbles influence the collapse process.The mechanisms behind inter-bubble interactions are also considered.The findings indicate that the collapse speed of unbounded bubbles located in lateral regions is greater than that of the bubbles in the center.Moreover,it is shown that asymmetrical bubble distributions lead to a shorter collapse time overall.展开更多
A metallurgical model for austenite coarsening in the coarse-grained heat-affected zone(CGHAZ)containing titanium nitride(TiN)precipitation was studied.Unlike traditional methods estimating pinning capability based on...A metallurgical model for austenite coarsening in the coarse-grained heat-affected zone(CGHAZ)containing titanium nitride(TiN)precipitation was studied.Unlike traditional methods estimating pinning capability based on the precipitation size after welding,a proposed dissolution and coarsening model was applied to study the changes in TiN precipitation size and the associated pinning forces.The transmission electron microscope was used to analyze the size distribution of TiN particles before and after the welding thermal cycle.The size distribution showed a log-normal distribution before the thermal cycle.The prediction of post-thermal cycle size distributions with the proposed model was in agreement with the experimental results.Considering the short holding time at high temperature during welding,the thermodynamic stability conditions required for limiting grain size model cannot be achieved.A simple kinetic model for the prediction of austenite grain size in CGHAZ was established.Finally,the predicted austenite grain sizes agree better with experimental results than the conventional approach.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Funded by the Technology Innovation Leading Program of Shaanxi(No.2022QFY08-02)。
文摘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.
基金supported by the National Natural Science Foundation of China(Grant No.11872278)the Science and Technology Commission of Shanghai Municipality(Grant No.21ZR1467200)the Fundamental Research Funds for the Central Universities.
文摘The spinodal decomposition method emerges as a promising methodology,showcasing its potential in exploring the design space for metamaterial structures.However,spinodal structures design is still largely limited to regular structures,due to their relatively easy parameterization and controllability.Efficiently predicting the mechanical properties of 3D spinodal membrane structure remains a challenge,given that the features of the membrane necessitate adaptive mesh through the modelling process.This paper proposes an integrated approach for morphological design with customized mechanical properties,incorporating the spinodal decomposition method and adaptive coarse-grained modeling,which can produce various morphologies such as lamellar,columnar,and cubic structures.Pseudo-periodic parameterβand orientational parameterΘ(θ_(1),θ_(2),θ_(3))are identified to achieve the optimal goal of anisotropic mechanical properties.Parametric analysis is conducted to reveal the correlation between the customized spinodal structure and mechanical performance.Our work provides an integrated approach for morphological variation and tuning mechanical properties,paving the way for the design and development of customized functional materials similar to 3D spinodal membrane structures.
基金This work was supported by the National Key Research and Development Program of China(2021YFA1301504)the Chinese Academy of Sciences Strategic Priority Research Program(XDB37040202)the National Natural Science Foundation of China(91953101).
文摘The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many protein com-plexes are available in the protein data bank,their assembly/disassembly orders of subunits are largely unknown.In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex,computational methods can be used to predict the assembly/disassembly order.Since sampling is a nontrivial issue in simulating the assembly/disassembly process,coarse-grained simulations are more efficient than atomic simulations are.In this work,we developed computational protocols for predicting the assembly/disassembly orders of protein complexes via coarse-grained simulations.The protocols were illustrated via two protein complexes,and the predicted assembly/disassembly orders were consistent with the available experimental data.
基金supported by the National Natural Science Foundation of China(Grant Nos.12222506,12347102,and 12174184).
文摘Understanding the liquid-liquid phase separation(LLPS)of immunoglobulin G(IgG)is crucial,as it profoundly influences IgG’s biological activity and stability.In this study,we employed coarse-grained molecular dynamics simulations to systematically investigate the phase separation behavior of IgG.We first constructed two types of IgG models:all-pair IgG model and partial-pair IgG model,and compared the coexistence curve from our simulations with experimental data.Our results showed that the partial-pair IgG model aligns better with the experimental critical temperature and critical density.Using this model,we then calculated the temperature-dependent variations of IgG’s radius of gyration,surface tension,viscosity,etc.More importantly,we demonstrated that variations in the interaction strengths among IgG molecules significantly influence their phase separation behavior.Specifically,a higher standard deviation of interaction strength at different temperatures is found to lead to more stable phase-separated states.Furthermore,we observed that the introduction of repulsive polymers and strongly attractive polymers consistently enhances IgG phase separation,while weakly attractive polymers exhibit a dual regulatory effect on the phase separation.Overall,this study provides valuable insights into the mechanisms governing IgG phase behavior,with potential implications for optimizing biopharmaceutical products.
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.
基金financial support by the National Natural Science Foundation of China(No.52474361)the Independent Research Project of State Key Laboratory of Advanced Special Steel,Shanghai Key Laboratory of Advanced Ferrometallurgy,Shanghai University(No.SKLASS 2023-Z01)the Science and Technology Commission of Shanghai Municipality(No.19DZ2270200).
文摘The fracture mechanisms of coarse-grained heat-affected zone(CGHAZ)for Mg and Mg–Ca deoxidized high-strength low-alloy(HSLA)steels after high heat input welding(HHIW)were investigated based on the microstructures,crack behaviors and mechanical properties.Compared to Mg–Ca steel,the proportion of intergranular acicular ferrites(IAFs)and polygonal ferrites(PFs)in Mg steel increases from 59.97%to 90.16%.The high-angle grain boundaries(HAGBs)and geometrically necessary dislocations density increase from 55.5%and 4.30×10^(14) m^(-2)to 70.4%and 5.48×10^(14) m^(–2),respectively,while effective grain size decreases from 9.46 to 8.12μm.The area fraction of radial zone in Mg steel decreases from 80.8%to 37.7%and cleavage plane is smaller with more curved and finer tearing ridges.The inclusions distributed at the center of cleavage planes and along river lines can serve as crack initiation sites.The zigzag pattern of primary crack propagation path has width of 476μm and the length of secondary cracks remains below 10μm.These cracks are deflected or arrested by IAFs,PFs and HAGBs,and tend to propagate along{110}plane family.These factors contribute to superior overall mechanical properties of Mg steel,especially increasing low-temperature impact toughness from 23 to 175 J.
基金supported by the National Natural Science Foundation of China (Nos.22303060,12274307,32230063,12347102 and 22203059)Natural Science Foundation of Jiangsu Province (Nos.BK20230470 and BK20210100)+2 种基金the Natural Science Foundation of Guangdong Province of China (No.2023A1515011610)the Program of Jiangsu Provincial Key Lab of Thin Films (No.KJS2131)the open research fund of State Key Laboratory of Surface Physics of Fudan University (No.KF2023_03)
文摘Membrane fusion is essential for many cellular physiological functions,which is modulated by highly precise molecular mechanism involving multiple energy barriers.Nanoparticles(NPs),which exhibit immense potential in the field of biomedical applications,can act as fusogen proteins to initiate and regulate membrane fusion.However,the underlying mechanisms of NP-induced membrane fusion and the molecular details involved remain largely elusive.Here,using coarse-grained molecular dynamics simulations,we systematically investigate the NP-induced membrane fusion behaviors and the influences of NP properties(size,hydrophobicity and hydrophilicity).Our results show that the vesicle-bilayer fusion induced by a hydrophobic NP is an intricately state-wise process,involving the approach and local deformation of the vesicle and bilayer bridging by the NP,the flip-flop of lipids from proximal leaflets and the formation of a fusion stalk,as well as further lipid interactions between distal leaflets and complete fusion.Moreover,we find that NP properties have distinct effects on membrane fusion and thus the optimal NP conditions for facilitating membrane fusion are obtained.Our work provides a mechanistic understanding of NP-induced membrane fusion and offers useful insights for efficient and controlled regulation of membrane fusion.
基金support from the PipeChina Engineering Technology Innovation Co.,Ltd.(CLZB202301).
文摘Two experimental X80 steels with different Cr contents(0.13,0.40 wt.%)were designed to study the influence of Cr content on the microstructure transformation and properties in the coarse-grained heat-affected zone by using a Formastor-F II thermal dilatometer and to simulate the microstructure of the subcritically reheated coarse-grained heat-affected zone(SCGHAZ)by means of the Gleeble-3500 thermal simulator,along with the scanning electron microscope,transmission electron microscope,and electron backscattering diffraction test methods to characterize the microstructures at 650℃.The findings indicate that a higher Cr content can promote the formation of bainitic ferrite(BF),while the microhardness and impact toughness of SCGHAZ are improved.Granular bainite and BF dominated the microstructures formed by the two experimental steels at 650℃,respectively.For experimental steels mainly composed of BF,they have a high proportion of high-angle grain boundaries(HAGB),and the misorientation angle of HAGB is mostly greater than 55°.Moreover,the distribution of martensite-austenite(M-A)constituents in SCGHAZ altered from dense to sparse,and the form altered from elongated to island-like when the Cr concentration was changed from 0.13 to 0.40 wt.%.Consequently,by suitably increasing the concentration of Cr,it is possible to raise the density of HAGB and improve the shape of M-A constituents,allowing SCGHAZ to have a higher toughness.
基金funded by the Natural Science Foundation of China[U20A20292]Shandong Province Science andTechnology SMES InnovationAbility Improvement Project[2023TSGC0005]China Postdoctoral Science Foundation[2024M752697].
文摘In nature,cavitation bubbles typically appear in clusters,engaging in interactions that create a variety of dynamicmotion patterns.To better understand the behavior ofmultiple bubble collapses and the mechanisms of interbubble interaction,this study employs molecular dynamics simulation combined with a coarse-grained force field.By focusing on collapsemorphology,local density,and pressure,it elucidates how the number and arrangement of bubbles influence the collapse process.The mechanisms behind inter-bubble interactions are also considered.The findings indicate that the collapse speed of unbounded bubbles located in lateral regions is greater than that of the bubbles in the center.Moreover,it is shown that asymmetrical bubble distributions lead to a shorter collapse time overall.
基金supported by the National Natural Science Foundation of China(U21A20116).
文摘A metallurgical model for austenite coarsening in the coarse-grained heat-affected zone(CGHAZ)containing titanium nitride(TiN)precipitation was studied.Unlike traditional methods estimating pinning capability based on the precipitation size after welding,a proposed dissolution and coarsening model was applied to study the changes in TiN precipitation size and the associated pinning forces.The transmission electron microscope was used to analyze the size distribution of TiN particles before and after the welding thermal cycle.The size distribution showed a log-normal distribution before the thermal cycle.The prediction of post-thermal cycle size distributions with the proposed model was in agreement with the experimental results.Considering the short holding time at high temperature during welding,the thermodynamic stability conditions required for limiting grain size model cannot be achieved.A simple kinetic model for the prediction of austenite grain size in CGHAZ was established.Finally,the predicted austenite grain sizes agree better with experimental results than the conventional approach.
