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
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 secondary structure of different Iβcellulose was analyzed by a molecular dynamics sim-ulation with MARTINI coarse-grained force field,where each chain of the cellulose includes 40 D-glucoses units.Calculation giv...The secondary structure of different Iβcellulose was analyzed by a molecular dynamics sim-ulation with MARTINI coarse-grained force field,where each chain of the cellulose includes 40 D-glucoses units.Calculation gives a satisfied description about the secondary structure of the cellulose.As the chain number increasing,the cellulose becomes the form of a helix,with the diameter of screw growing and spiral rising.Interestingly,the celluloses with chain number N of 4,6,24 and 36 do show right-hand twisting.On the contrast,the celluloses with N of 8,12,16 chains are left-hand twisting.These simulations indicate that the cellulose with chain number larger than 36 will break down to two parts.Besides,the result indicates that 36-chains cellulose model is the most stable among all models.Furthermore,the Lennard-Jones potential determines the secondary structure.In addition,an equation was set up to analyze the twisting structure.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
Ionic liquids(ILs)are a class of molten salts with a collection of exciting properties and have been employed for wide-ranging applications across chemistry,biology,and materials science.However,the high viscosity of ...Ionic liquids(ILs)are a class of molten salts with a collection of exciting properties and have been employed for wide-ranging applications across chemistry,biology,and materials science.However,the high viscosity of ionic liquids challenges atomistic molecular dynamics(MD)simulations in studying their structure–property relationships on large spatiotemporal scales.Coarse-grained(CG)models provide insight into the microscopic structure and intermolecular interactions underlying various properties by eliminating unnecessary atomic details.The general protocol for proposing a new CG model is reviewed,including determination of CG representation and force field(FF)parameterization.Recent advances in polarizable CG models were discussed with the emphasis on Drude oscillators and QM-based polarizable models.An overview was given on some recent applications of machine learning(ML)techniques on development of CG potentials,including the utilization of an ML surrogate model for FF parameterization and the development of ML potentials.Applications and challenges of IL CG models in treating complex systems,including pure solvents,mixtures,biological systems,and electrochemically confined environments,were presented.Finally,prospects for the development of transferable IL CG models are highlighted to extend the applicability to more mesoscopic systems.展开更多
A generic coarse-grained bead-and-spring model,mapped onto comb-shaped polycarboxylate-based(PCE)superplasticizers,is developed and studied by Langevin molecular dynamics simulations with implicit solvent and explicit...A generic coarse-grained bead-and-spring model,mapped onto comb-shaped polycarboxylate-based(PCE)superplasticizers,is developed and studied by Langevin molecular dynamics simulations with implicit solvent and explicit counterions.The agreement on the radius of gyration of the PCEs with experiments shows that our model can be useful in studying the equilibrium sizes of PCEs in solution.The effects of ionic strength,side-chain number,and side-chain length on the conformational behavior of PCEs in solution are explored.Single-chain equilibrium properties,including the radius of gyration,end-to-end distance and persistenee length of the polymer backbone,shape-asphericity parameter,and the mean span dimension,are determined.It is found that with the increase of ionic strength,the equilibrium sizes of the polymers decrease only slightly,and a linear dependenew of the persistence length of backbone on the Debye screening length is found,in good agreement with the theory developed by Dobrynin.Increasing side-chain numbers and/or side-chain lengths increases not only the equilibrium sizes(radius of gyration and mean span)of the polymer as a whole,but also the persistence length of the backbone due to excluded volume interactions.展开更多
We simulated rapid flow in transient plane Couette flows of granular particles using the smoothed particle hydrodynamics （SPH） solutions of a set of continuum equations, This simulation was performed to test the via...We simulated rapid flow in transient plane Couette flows of granular particles using the smoothed particle hydrodynamics （SPH） solutions of a set of continuum equations, This simulation was performed to test the viability of SPH in solving the equations for the solid phase of the two-fluid model associated with fluidization. We found that SPH requires the handling of fewer particles in simulating the collective behavior of rapid granular flow, thereby bolstering expectations of solving the equations for the solid phase in the two-fluid modeling of fluidization. Further work is needed to investigate the effect of terms describing pressure and viscous stress of solids on stability in simulations.展开更多
In this work, the previously developed coarse-grained （CG） particle models for biomembranes and red blood cells （RBCs） are reviewed, and the advantages of the CG particle methods over the continuum and atomistic s...In this work, the previously developed coarse-grained （CG） particle models for biomembranes and red blood cells （RBCs） are reviewed, and the advantages of the CG particle methods over the continuum and atomistic simulations for modeling biological phenomena are discussed. CG particle models can largely increase the length scale and time scale of atomistic simulations by eliminating the fast degrees of freedom while preserving the mesoscopic structures and properties of the simulated system. Moreover, CG particle models can be used to capture the microstructural alternations in diseased RBCs and simulate the topological changes of biomembranes and RBCs, which are the major challenges to the typical continuum representations of membranes and RBCs. The power and versatility of CG particle methods are demonstrated：through simulating the dynamical processes mvolving significant topological .changes e.g. lipid self-assembly vesicle fusion and membrane budding.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
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
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
A simplified model is proposed for an easy understanding of the coarse-grained technique and for achieving a first approximation to the behavior of gases. A mole of a gas substance, within a cubic container, is repres...A simplified model is proposed for an easy understanding of the coarse-grained technique and for achieving a first approximation to the behavior of gases. A mole of a gas substance, within a cubic container, is represented by six particles symmetrically moving. The impacts of particles on container walls, the inter-particle collisions, as well as the volume of particles and the inter-particle attractive forces, obeying a Lennard-Jones curve, are taken into account. Thanks to the symmetry, the problem is reduced to the nonlinear dynamic analysis of a SDOF oscillator, which is numerically solved by a step-by-step time integration algorithm. Five applications of proposed model, on Carbon Dioxide, are presented: 1) Ideal gas in STP conditions. 2) Real gas in STP conditions. 3) Condensation for small molar volume. 4) Critical point. 5) Iso-kinetic energy curves and iso-therms in the critical point region. Results of the proposed model are compared with test data and results of the Van der Waals model for real gases.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
A heuristic algorithm is presented for a three-dimensional off-lattice AB model consisting of hydrophobic （A） and hydrophilic （B） residues in Fibonacci sequences. By incorporating extra energy contributions into t...A heuristic algorithm is presented for a three-dimensional off-lattice AB model consisting of hydrophobic （A） and hydrophilic （B） residues in Fibonacci sequences. By incorporating extra energy contributions into the original potential function, we convert the constrained optimization problem of AB model into an unconstrained optimization problem which can be solved by the gradient method. After the gradient minimization leads to the basins of the local energy minima, the heuristic off-trap strategy and subsequent neighborhood search mechanism axe then proposed to get out of local minima and search for the lower-energy configurations. Furthermore, in order to improve the efficiency of the proposed algorithm, we apply the improved version called the new PERM with importance sampling （nPERMis） of the chain-growth algorithm, pruned-enriched-Rosenbluth method （PERM）, to face-centered-cubic （FCC）-lattice to produce the initial configurations. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. In several cases, we found the ground state energies are lower than the best values reported in the present literature.展开更多
Model evaluation using benchmark datasets is an important method to measure the capability of large language models(LLMs)in specific domains,and it is mainly used to assess the knowledge and reasoning abilities of LLM...Model evaluation using benchmark datasets is an important method to measure the capability of large language models(LLMs)in specific domains,and it is mainly used to assess the knowledge and reasoning abilities of LLMs.Therefore,in order to better assess the capability of LLMs in the agricultural domain,Agri-Eval was proposed as a benchmark for assessing the knowledge and reasoning ability of LLMs in agriculture.The assessment dataset used in Agri-Eval covered seven major disciplines in the agricultural domain:crop science,horticulture,plant protection,animal husbandry,forest science,aquaculture science,and grass science,and contained a total of 2283 questions.Among domestic general-purpose LLMs,DeepSeek R1 performed best with an accuracy rate of 75.49%.In the realm of international general-purpose LLMs,Gemini 2.0 pro exp 0205 standed out as the top performer,achieving an accuracy rate of 74.28%.As an LLMs in agriculture vertical,Shennong V2.0 outperformed all the LLMs in China,and the answer accuracy rate of agricultural knowledge exceeded that of all the existing general-purpose LLMs.The launch of Agri-Eval helped the LLM developers to comprehensively evaluate the model's capability in the field of agriculture through a variety of tasks and tests to promote the development of the LLMs in the field of agriculture.展开更多
In this paper,we establish and study a single-species logistic model with impulsive age-selective harvesting.First,we prove the ultimate boundedness of the solutions of the system.Then,we obtain conditions for the asy...In this paper,we establish and study a single-species logistic model with impulsive age-selective harvesting.First,we prove the ultimate boundedness of the solutions of the system.Then,we obtain conditions for the asymptotic stability of the trivial solution and the positive periodic solution.Finally,numerical simulations are presented to validate our results.Our results show that age-selective harvesting is more conducive to sustainable population survival than non-age-selective harvesting.展开更多
In recent years,there has been an increasing need for climate information across diverse sectors of society.This demand has arisen from the necessity to adapt to and mitigate the impacts of climate variability and cha...In recent years,there has been an increasing need for climate information across diverse sectors of society.This demand has arisen from the necessity to adapt to and mitigate the impacts of climate variability and change.Likewise,this period has seen a significant increase in our understanding of the physical processes and mechanisms that drive precipitation and its variability across different regions of Africa.By leveraging a large volume of climate model outputs,numerous studies have investigated the model representation of African precipitation as well as underlying physical processes.These studies have assessed whether the physical processes are well depicted and whether the models are fit for informing mitigation and adaptation strategies.This paper provides a review of the progress in precipitation simulation overAfrica in state-of-the-science climate models and discusses the major issues and challenges that remain.展开更多
Utilizing finite element analysis,the ballistic protection provided by a combination of perforated D-shaped and base armor plates,collectively referred to as radiator armor,is evaluated.ANSYS Explicit Dynamics is empl...Utilizing finite element analysis,the ballistic protection provided by a combination of perforated D-shaped and base armor plates,collectively referred to as radiator armor,is evaluated.ANSYS Explicit Dynamics is employed to simulate the ballistic impact of 7.62 mm armor-piercing projectiles on Aluminum AA5083-H116 and Steel Secure 500 armors,focusing on the evaluation of material deformation and penetration resistance at varying impact points.While the D-shaped armor plate is penetrated by the armor-piercing projectiles,the combination of the perforated D-shaped and base armor plates successfully halts penetration.A numerical model based on the finite element method is developed using software such as SolidWorks and ANSYS to analyze the interaction between radiator armor and bullet.The perforated design of radiator armor is to maintain airflow for radiator function,with hole sizes smaller than the bullet core diameter to protect radiator assemblies.Predictions are made regarding the brittle fracture resulting from the projectile core′s bending due to asymmetric impact,and the resulting fragments failed to penetrate the perforated base armor plate.Craters are formed on the surface of the perforated D-shaped armor plate due to the impact of projectile fragments.The numerical model accurately predicts hole growth and projectile penetration upon impact with the armor,demonstrating effective protection of the radiator assemblies by the radiator armor.展开更多
The National Geophysical Data Center(NGDC)of the United States has collected aeromagnetic data for input into a series of geomagnetic models to improve model resolution;however,in the Tibetan Plateau region,ground-bas...The National Geophysical Data Center(NGDC)of the United States has collected aeromagnetic data for input into a series of geomagnetic models to improve model resolution;however,in the Tibetan Plateau region,ground-based observations remain insufficient to clearly reflect the characteristics of the region’s lithospheric magnetism.In this study,we evaluate the lithospheric magnetism of the Tibetan Plateau by using a 3D surface spline model based on observations from>200 newly constructed repeat stations(portable stations)to determine the spatial distribution of plateau geomagnetism,as well as its correlation with the tectonic features of the region.We analyze the relationships between M≥5 earthquakes and lithospheric magnetic field variations on the Tibetan Plateau and identify regions susceptible to strong earthquakes.We compare the geomagnetic results with those from an enhanced magnetic model(EMM2015)developed by the NGDC and provide insights into improving lithospheric magnetic field calculations in the Tibetan Plateau region.Further research reveals that these magnetic anomalies exhibit distinct differences from the magnetic-seismic correlation mechanisms observed in other tectonic settings;here,they are governed primarily by the combined effects of compressional magnetism,thermal magnetism,and deep thermal stress.This study provides new evidence of geomagnetic anomalies on the Tibetan Plateau,interprets them physically,and demonstrates their potential for identifying seismic hazard zones on the Plateau.展开更多
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.
文摘The secondary structure of different Iβcellulose was analyzed by a molecular dynamics sim-ulation with MARTINI coarse-grained force field,where each chain of the cellulose includes 40 D-glucoses units.Calculation gives a satisfied description about the secondary structure of the cellulose.As the chain number increasing,the cellulose becomes the form of a helix,with the diameter of screw growing and spiral rising.Interestingly,the celluloses with chain number N of 4,6,24 and 36 do show right-hand twisting.On the contrast,the celluloses with N of 8,12,16 chains are left-hand twisting.These simulations indicate that the cellulose with chain number larger than 36 will break down to two parts.Besides,the result indicates that 36-chains cellulose model is the most stable among all models.Furthermore,the Lennard-Jones potential determines the secondary structure.In addition,an equation was set up to analyze the twisting structure.
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supported by the National Natural Science Foundation of China(Grant No.22033004,22373049)the Natural Science Foundation of Jiangsu Province(BK20232012).
文摘Ionic liquids(ILs)are a class of molten salts with a collection of exciting properties and have been employed for wide-ranging applications across chemistry,biology,and materials science.However,the high viscosity of ionic liquids challenges atomistic molecular dynamics(MD)simulations in studying their structure–property relationships on large spatiotemporal scales.Coarse-grained(CG)models provide insight into the microscopic structure and intermolecular interactions underlying various properties by eliminating unnecessary atomic details.The general protocol for proposing a new CG model is reviewed,including determination of CG representation and force field(FF)parameterization.Recent advances in polarizable CG models were discussed with the emphasis on Drude oscillators and QM-based polarizable models.An overview was given on some recent applications of machine learning(ML)techniques on development of CG potentials,including the utilization of an ML surrogate model for FF parameterization and the development of ML potentials.Applications and challenges of IL CG models in treating complex systems,including pure solvents,mixtures,biological systems,and electrochemically confined environments,were presented.Finally,prospects for the development of transferable IL CG models are highlighted to extend the applicability to more mesoscopic systems.
文摘A generic coarse-grained bead-and-spring model,mapped onto comb-shaped polycarboxylate-based(PCE)superplasticizers,is developed and studied by Langevin molecular dynamics simulations with implicit solvent and explicit counterions.The agreement on the radius of gyration of the PCEs with experiments shows that our model can be useful in studying the equilibrium sizes of PCEs in solution.The effects of ionic strength,side-chain number,and side-chain length on the conformational behavior of PCEs in solution are explored.Single-chain equilibrium properties,including the radius of gyration,end-to-end distance and persistenee length of the polymer backbone,shape-asphericity parameter,and the mean span dimension,are determined.It is found that with the increase of ionic strength,the equilibrium sizes of the polymers decrease only slightly,and a linear dependenew of the persistence length of backbone on the Debye screening length is found,in good agreement with the theory developed by Dobrynin.Increasing side-chain numbers and/or side-chain lengths increases not only the equilibrium sizes(radius of gyration and mean span)of the polymer as a whole,but also the persistence length of the backbone due to excluded volume interactions.
基金financially supported by the Ministry of Science and Technology of the People's Republic of China under Grant No.2012CB215003the National Natural Science Foundation of China under Grant Nos.21176240 and 21406081the Strategic Priority Research Program of the Chinese Academy of Sciences under Grant No.XDA07080100
文摘We simulated rapid flow in transient plane Couette flows of granular particles using the smoothed particle hydrodynamics （SPH） solutions of a set of continuum equations, This simulation was performed to test the viability of SPH in solving the equations for the solid phase of the two-fluid model associated with fluidization. We found that SPH requires the handling of fewer particles in simulating the collective behavior of rapid granular flow, thereby bolstering expectations of solving the equations for the solid phase in the two-fluid modeling of fluidization. Further work is needed to investigate the effect of terms describing pressure and viscous stress of solids on stability in simulations.
基金Project supported by the National Institutes of Health of U.S.A.(No.U01HL114476)the National Science Foundation of U.S.A.(Nos.CMMI-1235025 and PHY-1205910)
文摘In this work, the previously developed coarse-grained （CG） particle models for biomembranes and red blood cells （RBCs） are reviewed, and the advantages of the CG particle methods over the continuum and atomistic simulations for modeling biological phenomena are discussed. CG particle models can largely increase the length scale and time scale of atomistic simulations by eliminating the fast degrees of freedom while preserving the mesoscopic structures and properties of the simulated system. Moreover, CG particle models can be used to capture the microstructural alternations in diseased RBCs and simulate the topological changes of biomembranes and RBCs, which are the major challenges to the typical continuum representations of membranes and RBCs. The power and versatility of CG particle methods are demonstrated：through simulating the dynamical processes mvolving significant topological .changes e.g. lipid self-assembly vesicle fusion and membrane budding.
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.
文摘A simplified model is proposed for an easy understanding of the coarse-grained technique and for achieving a first approximation to the behavior of gases. A mole of a gas substance, within a cubic container, is represented by six particles symmetrically moving. The impacts of particles on container walls, the inter-particle collisions, as well as the volume of particles and the inter-particle attractive forces, obeying a Lennard-Jones curve, are taken into account. Thanks to the symmetry, the problem is reduced to the nonlinear dynamic analysis of a SDOF oscillator, which is numerically solved by a step-by-step time integration algorithm. Five applications of proposed model, on Carbon Dioxide, are presented: 1) Ideal gas in STP conditions. 2) Real gas in STP conditions. 3) Condensation for small molar volume. 4) Critical point. 5) Iso-kinetic energy curves and iso-therms in the critical point region. Results of the proposed model are compared with test data and results of the Van der Waals model for real gases.
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Project supported by the Foundation of Nanjing University of Information Science and Technologythe Excellent Youth Foundation of Education Office of Hunan Province,China (Grant No 07B009)
文摘A heuristic algorithm is presented for a three-dimensional off-lattice AB model consisting of hydrophobic （A） and hydrophilic （B） residues in Fibonacci sequences. By incorporating extra energy contributions into the original potential function, we convert the constrained optimization problem of AB model into an unconstrained optimization problem which can be solved by the gradient method. After the gradient minimization leads to the basins of the local energy minima, the heuristic off-trap strategy and subsequent neighborhood search mechanism axe then proposed to get out of local minima and search for the lower-energy configurations. Furthermore, in order to improve the efficiency of the proposed algorithm, we apply the improved version called the new PERM with importance sampling （nPERMis） of the chain-growth algorithm, pruned-enriched-Rosenbluth method （PERM）, to face-centered-cubic （FCC）-lattice to produce the initial configurations. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. In several cases, we found the ground state energies are lower than the best values reported in the present literature.
文摘Model evaluation using benchmark datasets is an important method to measure the capability of large language models(LLMs)in specific domains,and it is mainly used to assess the knowledge and reasoning abilities of LLMs.Therefore,in order to better assess the capability of LLMs in the agricultural domain,Agri-Eval was proposed as a benchmark for assessing the knowledge and reasoning ability of LLMs in agriculture.The assessment dataset used in Agri-Eval covered seven major disciplines in the agricultural domain:crop science,horticulture,plant protection,animal husbandry,forest science,aquaculture science,and grass science,and contained a total of 2283 questions.Among domestic general-purpose LLMs,DeepSeek R1 performed best with an accuracy rate of 75.49%.In the realm of international general-purpose LLMs,Gemini 2.0 pro exp 0205 standed out as the top performer,achieving an accuracy rate of 74.28%.As an LLMs in agriculture vertical,Shennong V2.0 outperformed all the LLMs in China,and the answer accuracy rate of agricultural knowledge exceeded that of all the existing general-purpose LLMs.The launch of Agri-Eval helped the LLM developers to comprehensively evaluate the model's capability in the field of agriculture through a variety of tasks and tests to promote the development of the LLMs in the field of agriculture.
基金Supported by the National Natural Science Foundation of China(12261018)Universities Key Laboratory of Mathematical Modeling and Data Mining in Guizhou Province(2023013)。
文摘In this paper,we establish and study a single-species logistic model with impulsive age-selective harvesting.First,we prove the ultimate boundedness of the solutions of the system.Then,we obtain conditions for the asymptotic stability of the trivial solution and the positive periodic solution.Finally,numerical simulations are presented to validate our results.Our results show that age-selective harvesting is more conducive to sustainable population survival than non-age-selective harvesting.
基金the World Climate Research Programme(WCRP),Climate Variability and Predictability(CLIVAR),and Global Energy and Water Exchanges(GEWEX)for facilitating the coordination of African monsoon researchsupport from the Center for Earth System Modeling,Analysis,and Data at the Pennsylvania State Universitythe support of the Office of Science of the U.S.Department of Energy Biological and Environmental Research as part of the Regional&Global Model Analysis(RGMA)program area。
文摘In recent years,there has been an increasing need for climate information across diverse sectors of society.This demand has arisen from the necessity to adapt to and mitigate the impacts of climate variability and change.Likewise,this period has seen a significant increase in our understanding of the physical processes and mechanisms that drive precipitation and its variability across different regions of Africa.By leveraging a large volume of climate model outputs,numerous studies have investigated the model representation of African precipitation as well as underlying physical processes.These studies have assessed whether the physical processes are well depicted and whether the models are fit for informing mitigation and adaptation strategies.This paper provides a review of the progress in precipitation simulation overAfrica in state-of-the-science climate models and discusses the major issues and challenges that remain.
文摘Utilizing finite element analysis,the ballistic protection provided by a combination of perforated D-shaped and base armor plates,collectively referred to as radiator armor,is evaluated.ANSYS Explicit Dynamics is employed to simulate the ballistic impact of 7.62 mm armor-piercing projectiles on Aluminum AA5083-H116 and Steel Secure 500 armors,focusing on the evaluation of material deformation and penetration resistance at varying impact points.While the D-shaped armor plate is penetrated by the armor-piercing projectiles,the combination of the perforated D-shaped and base armor plates successfully halts penetration.A numerical model based on the finite element method is developed using software such as SolidWorks and ANSYS to analyze the interaction between radiator armor and bullet.The perforated design of radiator armor is to maintain airflow for radiator function,with hole sizes smaller than the bullet core diameter to protect radiator assemblies.Predictions are made regarding the brittle fracture resulting from the projectile core′s bending due to asymmetric impact,and the resulting fragments failed to penetrate the perforated base armor plate.Craters are formed on the surface of the perforated D-shaped armor plate due to the impact of projectile fragments.The numerical model accurately predicts hole growth and projectile penetration upon impact with the armor,demonstrating effective protection of the radiator assemblies by the radiator armor.
基金supported by the CAS Pioneer Hundred Talents Program and Second Tibetan Plateau Scientific Expedition Research Program(2019QZKK0708)as well as the Basic Research Program of Qinghai Province:Lithospheric Geomagnetic Field of the Qinghai‒Tibet Plateau and the Relationship with Strong Earthquakes(2021-ZJ-969Q).
文摘The National Geophysical Data Center(NGDC)of the United States has collected aeromagnetic data for input into a series of geomagnetic models to improve model resolution;however,in the Tibetan Plateau region,ground-based observations remain insufficient to clearly reflect the characteristics of the region’s lithospheric magnetism.In this study,we evaluate the lithospheric magnetism of the Tibetan Plateau by using a 3D surface spline model based on observations from>200 newly constructed repeat stations(portable stations)to determine the spatial distribution of plateau geomagnetism,as well as its correlation with the tectonic features of the region.We analyze the relationships between M≥5 earthquakes and lithospheric magnetic field variations on the Tibetan Plateau and identify regions susceptible to strong earthquakes.We compare the geomagnetic results with those from an enhanced magnetic model(EMM2015)developed by the NGDC and provide insights into improving lithospheric magnetic field calculations in the Tibetan Plateau region.Further research reveals that these magnetic anomalies exhibit distinct differences from the magnetic-seismic correlation mechanisms observed in other tectonic settings;here,they are governed primarily by the combined effects of compressional magnetism,thermal magnetism,and deep thermal stress.This study provides new evidence of geomagnetic anomalies on the Tibetan Plateau,interprets them physically,and demonstrates their potential for identifying seismic hazard zones on the Plateau.
