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
The oscillation behavior of a two-dimension lattice-gas Brusselator model was investigated. We have adopted a coarse-grained kinetic Monte Carlo （CG-KMC） procedure, where m×m microscopic lattice sites are group...The oscillation behavior of a two-dimension lattice-gas Brusselator model was investigated. We have adopted a coarse-grained kinetic Monte Carlo （CG-KMC） procedure, where m×m microscopic lattice sites are grouped together to form a CG cell, upon which CG processes take place with well-defined CG rates. Such a CG approach almost fails if the CG rates are obtained by a simple local mean field （s-LMF） approximation, due to the ignorance of correlation among adjcent cells resulting fl＇om the trimolecular reaction in this nonlinear system. By proper incorporating such boundary effects, thus introduce the so-cMled b-LMF CG approach. Extensive numerical simulations demonstrate that the b-LMF method can reproduce the oscillation behavior of the system quite well, given that the diffusion constant is not too small. In addition, the deviation from the KMC results reaches a nearly zero minimum level at an intermediate cell size, which lies in between the effective diffusion length and the minimal size required to sustain a well-defined temporal oscillation.展开更多
Spectrin, the principal protein of the cytoskeleton of erythrocyte, plays a crucial role in the stability and flexibility of the plasma membrane of erythrocyte. In this work, we investigate the interactions between sp...Spectrin, the principal protein of the cytoskeleton of erythrocyte, plays a crucial role in the stability and flexibility of the plasma membrane of erythrocyte. In this work, we investigate the interactions between spectrins and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. We focus on the preference of spectrins with different lipids, the effects of the anionic lipids and the residue mutation on the interactions between spectrins and the lipid bilayers. The results indicate that spectrins prefer to contact with phosphatidylethanolamine(PE) lipids rather than with phosphatidylcholine(PC) lipids, and tend to contact with the liquid-disordered(Ld) domains enriched in unsaturated PE.Additionally, the anionic lipids, which show specific interaction with the positively charged or polar amino acids on the surface of the spectrins, can enhance the attraction between the spectrins and lipid domains. The mutation leads to the decrease of the structural stability of spectrins and increases the curvature of the lipid bilayer. This work provides some theoretical insights into understanding the erythrocyte structure and the mechanism of some blood diseases.展开更多
Self-assembly of block copolymers(BCPs)is highly intricate and is adsorbing extensive experimental and simulation efforts to reveal it for maximizing structural order and device performances.The coarse-grained(CG)mole...Self-assembly of block copolymers(BCPs)is highly intricate and is adsorbing extensive experimental and simulation efforts to reveal it for maximizing structural order and device performances.The coarse-grained(CG)molecular dynamics(MD)simulation offers a microscopic angle to view the self-assembly of BCPs.Although some molecular details are sacrificed during CG processes,this method exhibits remarkable computational efficiency.In this study,a comprehensive CG model for polystyrene-block-poly(2-vinylpyridine),PS-b-P2VP,one of the most extensively studied BCPs for its high Flory-Huggins interaction parameter,is constructed,with parameters optimized using target values derived from all-atom MD simulations.The CG model precisely coincides with various classical self-assembling morphologies observed in experimental studies,matching the theoretical phase diagrams.Moreover,the conformational asymmetry of the experimental phase diagram is also clearly revealed by our simulation results,and the phase boundaries obtained from simulations are highly consistent with experimental results.The CG model is expected to extend to simulate the self-assembly behaviors of other BCPs in addition to PS-b-P2VP,thus increasing understanding of the microphase separation of BCPs from the molecular level.展开更多
The rapid advancement of machine learning based tight-binding Hamiltonian(MLTB)methods has opened new avenues for efficient and accurate electronic structure simulations,particularly in large-scale systems and long-ti...The rapid advancement of machine learning based tight-binding Hamiltonian(MLTB)methods has opened new avenues for efficient and accurate electronic structure simulations,particularly in large-scale systems and long-time scenarios.This review begins with a concise overview of traditional tight-binding(TB)models,including both(semi-)empirical and first-principles approaches,establishing the foundation for understanding MLTB developments.We then present a systematic classification of existing MLTB methodologies,grouped into two major categories:direct prediction of TB Hamiltonian elements and inference of empirical parameters.A comparative analysis with other ML-based electronic structure models is also provided,highlighting the advancement of MLTB approaches.Finally,we explore the emerging MLTB application ecosystem,highlighting how the integration of MLTB models with a diverse suite of post-processing tools from linear-scaling solvers to quantum transport frameworks and molecular dynamics interfaces is essential for tackling complex scientific problems across different domains.The continued advancement of this integrated paradigm promises to accelerate materials discovery and open new frontiers in the predictive simulation of complex quantum phenomena.展开更多
Vitrimers belong to a class of polymeric materials capable of bond exchange reactions,showing great promise for environmental protection and sustainable development.However,studies on the coupling mechanism between th...Vitrimers belong to a class of polymeric materials capable of bond exchange reactions,showing great promise for environmental protection and sustainable development.However,studies on the coupling mechanism between the bond exchange kinetics and segmental dynamics near the glass transition temperature(T_(g))remain scarce.Herein,we employed molecular dynamics simulations to investigate the dynamic heterogeneity of the segment motion and bond exchange in vitrimers.The simulation results revealed that the bond exchange energy barrier exerts a much stronger influence on the bond exchange kinetics than on the segmental dynamics.At lower temperatures,slower segmental relaxation further constraind the bond exchange rate.Additionally,increasing the bond exchange energy barrier markedly enhanced the dynamic heterogeneity of segment motion.A close correlation was observed between heterogeneity and bond exchange.This study elucidated the coupling mechanism between bond exchange and segmental dynamics at the molecular scale,thereby providing a theoretical basis for designing vitrimer materials with tunable dynamic properties.展开更多
This study develops a surrogate super-resolution(SR)framework that accelerates finite element method(FEM)-based computational fluid dynamics(CFD)using deep learning.High-resolution(HR)FEM-based CFDremains computationa...This study develops a surrogate super-resolution(SR)framework that accelerates finite element method(FEM)-based computational fluid dynamics(CFD)using deep learning.High-resolution(HR)FEM-based CFDremains computationally prohibitive for time-sensitive applications,including patient-specific aneurysm hemodynamics where rapid turnaround is valuable.The proposed pipeline learns to reconstruct HR velocity-magnitude fields fromlow-resolution(LR)FEM solutions generated under the same governing equations and boundary conditions.It consistsof three modules:(i)offline pre-training of a residual network on representative vascular geometries;(ii)lightweightfine-tuning to adapt the pretrained model to geometric variability,including patient-specific aneurysm morphologies;and(iii)an unstructured-to-structured sampling strategy with region-of-interest upsampling that concentrates resolution in flow-critical zones(e.g.,the aneurysm sac)rather than the full domain.This targeted reconstruction substantiallyreduces inference and post-processing cost while preserving key HR flow features.Experiments on cerebral aneurysmmodels show that HR velocity-magnitude fields can be recovered with accuracy comparable to direct HR simulationsat less than 1%of the direct HR simulation cost per analysis(LR simulation and SR inference),while adaptation to newgeometries requires only lightweight fine-tuning with limited target-specific HR data.While clinical endpoints andadditional variables(e.g.,pressure or wall-based metrics)are left for future work,the results indicate that the proposedsurrogate SR approach can streamline FEM-based CFD workflows toward near real-time hemodynamic analysis acrossmorphologically similar vascular models.展开更多
Urban Heat Island(UHI)effects are exacerbated by the expansion of impervious surfaces and loss of vegetation in urban centers,leading to elevated air and surface temperatures and reduced thermal comfort.Urban trees,th...Urban Heat Island(UHI)effects are exacerbated by the expansion of impervious surfaces and loss of vegetation in urban centers,leading to elevated air and surface temperatures and reduced thermal comfort.Urban trees,through shading and evapotranspiration,are among the most effective Nature-based Solutions(NbS)for passive cooling.This study assesses the cooling potential of selected tree species by analyzing their morphological and physiological traits using a combination of ENVI-met microclimate simulations and multiple regression modeling.A total of 15 urban tree species were selected from the literature and analyzed based on their dependency of their cooling efficacy.Later validated in urban setting by Envi-met simulations.Key traits,such as Leaf Area Index(LAI),canopy density,transpiration rate,tree height,rooting depth,and water availability,were analyzed.Multiple linear regression analysis was conducted to quantify the contribution of each trait to ambient temperature reduction.Results revealed that LAI(R^(2)=0.76,p<0.001)and transpiration rate(R^(2)=0.71,p<0.001)were the most significant predictors of daytime cooling,while canopy openness and tree height were more strongly correlated with nighttime heat dissipation.High-performing species,such as Ficus benghalensis,Azadirachta indica,and Samanea saman,demonstrated a maximum temperature reduction of 2.5-4.2℃,especially in compact,low-rise,and mid-rise zones.The study provides a quantitative trait-based framework for tree selection in urban greening initiatives and offers evidence to guide landscape planning and UHI mitigation strategies through scientifically informed plantation design.展开更多
As a representative insensitive high explosive,3-nitro-1,2,4-triazol-5-one(NTO)has garnered significant attention due to its ability to substantially reduce the risk of accidental detonation in munitions.However,its i...As a representative insensitive high explosive,3-nitro-1,2,4-triazol-5-one(NTO)has garnered significant attention due to its ability to substantially reduce the risk of accidental detonation in munitions.However,its inherent acidity induces severe interfacial corrosion of metal casings,thereby limiting its engineering applications.Based on the micro-corrosion mechanism of NTO on carbon steel(CS),this study designs an arginine-derived corrosion inhibitor,N2-[(phenylamino)thioxomethyl]-arginine(PTA).Electrochemical tests reveal that PTA exhibits an outstanding corrosion inhibition efficiency of 98.0%in NTO solution.Density functional theory(DFT)and molecular dynamics(MD)simulations elucidate the inhibition mechanism of PTA,demonstrating that it not only co-adsorbs with NTO^(−) onto the CS surface to form a dense and stable protective film but also disrupts the strong interactions between NTO^(−) and Fe,thereby suppressing nitro group-induced reduction,decomposition,and excessive surface oxidation.Furthermore,a PTA-loaded mesoporous silica(mSiO_(2))nanoparticles(NPs)-reinforced epoxy resin(EP)composite coating was constructed.Benefiting from the enhanced barrier properties of PTA@mSiO_(2) NPs and the synergistic effect between PTA and NTO^(−),the low-frequency impedance of the composite coating remained as high as 1.29×10^(9)Ω·cm^(2) after 30 days of immersion in NTO solution,exhibiting a two-order-of-magnitude improvement compared to the pure EP coating.This study proposes an effective corrosion control strategy to mitigate NTO-induced corrosion,providing insights into the development of advanced corrosion protection strategies for broader applications.展开更多
Geological CO_(2) storage is a promising strategy for reducing greenhouse gas emissions and has become a growing focus of research and deployment.This paper presents numerical simulations of CO_(2) injection and stora...Geological CO_(2) storage is a promising strategy for reducing greenhouse gas emissions and has become a growing focus of research and deployment.This paper presents numerical simulations of CO_(2) injection and storage in a depleted gas reservoir within the B Depression and evaluates associated CO_(2) trapping mechanisms.In the base case,a constant injection rate of 3500 m^(3)/d over fifteen years resulted in a cumulative injection of 19.2×10^(6) m^(3).The CO_(2) plume expanded radially during injection and subsequently migrated up-dip under buoyancy forces.The final stored mass of CO_(2) in the reservoir was 10.6 million tonnes(Mt),representing less than 10% of its theoretical capacity.The plume was projected to reach the entrapment crest and the top of the reservoir within a century,indicating secure long-term containment.Structural,stratigraphic,and residual trapping dominate in Reservoir A(approximately 90%).Anticlinal closures with thick overlying mudstones in the Zhujiang Formation provide effective seals,further enhancing storage security.Reservoir properties and heterogeneity play a crucial role in controlling CO_(2) storage.However,reservoir heterogeneity exerts only a limited influence when intrinsic properties are favorable.Overall,the study and implementation of CO_(2) capture,utilization,and storage(CCUS)in China's offshore basins show promising prospects.展开更多
Compared to the well-studied two-dimensional(2D)ferroelectricity,the appearance of 2D antiferroelectricity is much rarer,where local dipoles from the nonequivalent sublattices within 2D monolayers are oppositely orien...Compared to the well-studied two-dimensional(2D)ferroelectricity,the appearance of 2D antiferroelectricity is much rarer,where local dipoles from the nonequivalent sublattices within 2D monolayers are oppositely oriented.Using NbOCl_(2) monolayer with competing ferroelectric(FE)and antiferroelectric(AFE)phases as a 2D material platform,we demonstrate the emergence of intrinsic antiferroelectricity in NbOCl_(2) monolayer under experimentally accessible shear strain,along with new functionality associated with electric field-induced AFE-to-FE phase transition.Specifically,the complex configuration space accommodating FE and AFE phases,polarization switching kinetics,and finite temperature thermodynamic properties of 2D NbOCl_(2) are all accurately predicted by large-scale molecular dynamics simulations based on deep learning interatomic potential model.Moreover,room temperature stable antiferroelectricity with low polarization switching barrier and one-dimensional collinear polarization arrangement is predicted in shear-deformed NbOCl_(2) monolayer.The transition from AFE to FE phase in 2D NbOCl_(2) can be triggered by a low critical electric field,leading to a double polarization–electric(P–E)loop with small hysteresis.A new type of optoelectronic device composed of AFE-NbOCl_(2) is proposed,enabling electric“writing”and nonlinear optical“reading”logical operation with fast operation speed and low power consumption.展开更多
ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, unde...ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics simulations of the potential of mean force along the conformational transition pathway [J. Phys. Chem. B 119, 1295(2015)]. However, the occluded conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this work, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1-d2, which are the COM distances between the two sides of the internal(d1)and the external gate(d2). The potential of mean force is thus obtained to identify the transition pathway, along which several outward-facing, inward-facing, and occluded state structures are predicted in good agreement with structural experiments. Our coarse-grained molecular dynamics free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the inward-facing to outward-facing transition and vice versa during the inward-facing to outward-facing transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the previous result, in which both the internal and external gates are open reported in an X-ray experiment [Proc. Natl. Acad. Sci. USA 104,19005(2007)]. Our study sheds light on the molecular mechanism of the state transitions in an ATP-binding cassette exporter.展开更多
We introduce a reaction model for use in coarse-grained simulations to study the chemical reactions in polymer systems at mesoscopic level.In this model,we employ an idea of reaction probability in control of the whol...We introduce a reaction model for use in coarse-grained simulations to study the chemical reactions in polymer systems at mesoscopic level.In this model,we employ an idea of reaction probability in control of the whole process of chemical reactions.This model has been successfully applied to the studies of surface initiated polymerization process and the network structure formation of typical epoxy resin systems.It can be further modified to study different kinds of chemical reactions at mesoscopic scale.展开更多
The micro-capsules used for drug delivery are fabricated using polylactic acid（PLA）,which is a biomedical material approved by the FDA.A coarse-grained model of long-chain PLA was built,and molecular dynamics（MD）s...The micro-capsules used for drug delivery are fabricated using polylactic acid（PLA）,which is a biomedical material approved by the FDA.A coarse-grained model of long-chain PLA was built,and molecular dynamics（MD）simulations of the model were performed using a MARTINI force field.Based on the nonlocal theory,the formula for the initial elastic modulus of polymers considering the nonlocal effect was derived,and the scaling law of internal characteristic length of polymers was proposed,which was used to adjust the cut-off radius in the MD simulations of PLA.The results show that the elastic modulus should be computed using nonlinear regression.The nonlocal effect has a certain influence on the simulation results of PLA.According to the scaling law,the cut-off radius was determined and applied to the MD simulations,the results of which reflect the influence of the molecular weight change on the elastic moduli of PLA,and are in agreement with the experimental outcome.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
Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of dens...Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=1204.10 K, which is in good agreement with experimental results 1104-1 K.展开更多
Protein XPA plays critical roles in nucleotide excision repair pathway.Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site.Her...Protein XPA plays critical roles in nucleotide excision repair pathway.Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site.Here,we investigate the involved dynamical process using extensive coarse-grained molecular simulations at various salt concentrations.The results demonstrated strong salt concentration dependence of the diffusion mechanisms.At low salt concentrations,the one-dimensional diffusion with rotational coupling is the dominant mechanism.At high salt concentrations,the diffusion by three-dimensional mechanism becomes more probable.At wide range of salt concentrations,the residues involved in the DNA binding are similar and the one-dimensional diffusion of XPA along DNA displays sub-diffusive feature.This sub-diffusive feature is tentatively attributed to diverse strengths of XPA-DNA interactions.In addition,we showed that both binding to DNA and increasing salt concentration tend to stretch the conformation of the XPA,which increases the exposure extent of the sites for the binding of other repair proteins.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
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.
文摘The oscillation behavior of a two-dimension lattice-gas Brusselator model was investigated. We have adopted a coarse-grained kinetic Monte Carlo （CG-KMC） procedure, where m×m microscopic lattice sites are grouped together to form a CG cell, upon which CG processes take place with well-defined CG rates. Such a CG approach almost fails if the CG rates are obtained by a simple local mean field （s-LMF） approximation, due to the ignorance of correlation among adjcent cells resulting fl＇om the trimolecular reaction in this nonlinear system. By proper incorporating such boundary effects, thus introduce the so-cMled b-LMF CG approach. Extensive numerical simulations demonstrate that the b-LMF method can reproduce the oscillation behavior of the system quite well, given that the diffusion constant is not too small. In addition, the deviation from the KMC results reaches a nearly zero minimum level at an intermediate cell size, which lies in between the effective diffusion length and the minimal size required to sustain a well-defined temporal oscillation.
基金supported by the National Natural Science Foundation of China (Grant No. 11674287)Zhejiang Provincial Natural Science Foundation of China(Grant No. LY19A040009)。
文摘Spectrin, the principal protein of the cytoskeleton of erythrocyte, plays a crucial role in the stability and flexibility of the plasma membrane of erythrocyte. In this work, we investigate the interactions between spectrins and phase-separated lipid bilayers using coarse-grained molecular dynamics simulation. We focus on the preference of spectrins with different lipids, the effects of the anionic lipids and the residue mutation on the interactions between spectrins and the lipid bilayers. The results indicate that spectrins prefer to contact with phosphatidylethanolamine(PE) lipids rather than with phosphatidylcholine(PC) lipids, and tend to contact with the liquid-disordered(Ld) domains enriched in unsaturated PE.Additionally, the anionic lipids, which show specific interaction with the positively charged or polar amino acids on the surface of the spectrins, can enhance the attraction between the spectrins and lipid domains. The mutation leads to the decrease of the structural stability of spectrins and increases the curvature of the lipid bilayer. This work provides some theoretical insights into understanding the erythrocyte structure and the mechanism of some blood diseases.
基金supported by the National Natural Science Foundation of China(22438005,22108117).
文摘Self-assembly of block copolymers(BCPs)is highly intricate and is adsorbing extensive experimental and simulation efforts to reveal it for maximizing structural order and device performances.The coarse-grained(CG)molecular dynamics(MD)simulation offers a microscopic angle to view the self-assembly of BCPs.Although some molecular details are sacrificed during CG processes,this method exhibits remarkable computational efficiency.In this study,a comprehensive CG model for polystyrene-block-poly(2-vinylpyridine),PS-b-P2VP,one of the most extensively studied BCPs for its high Flory-Huggins interaction parameter,is constructed,with parameters optimized using target values derived from all-atom MD simulations.The CG model precisely coincides with various classical self-assembling morphologies observed in experimental studies,matching the theoretical phase diagrams.Moreover,the conformational asymmetry of the experimental phase diagram is also clearly revealed by our simulation results,and the phase boundaries obtained from simulations are highly consistent with experimental results.The CG model is expected to extend to simulate the self-assembly behaviors of other BCPs in addition to PS-b-P2VP,thus increasing understanding of the microphase separation of BCPs from the molecular level.
基金supported by the Advanced Materials-National Science and Technology Major Project(Grant No.2025ZD0618401)the National Natural Science Foundation of China(Grant No.12504285)+1 种基金the Natural Science Foundation of Jiangsu Province(Grant No.BK20250472)NFSG grant from BITS-Pilani,Dubai campus。
文摘The rapid advancement of machine learning based tight-binding Hamiltonian(MLTB)methods has opened new avenues for efficient and accurate electronic structure simulations,particularly in large-scale systems and long-time scenarios.This review begins with a concise overview of traditional tight-binding(TB)models,including both(semi-)empirical and first-principles approaches,establishing the foundation for understanding MLTB developments.We then present a systematic classification of existing MLTB methodologies,grouped into two major categories:direct prediction of TB Hamiltonian elements and inference of empirical parameters.A comparative analysis with other ML-based electronic structure models is also provided,highlighting the advancement of MLTB approaches.Finally,we explore the emerging MLTB application ecosystem,highlighting how the integration of MLTB models with a diverse suite of post-processing tools from linear-scaling solvers to quantum transport frameworks and molecular dynamics interfaces is essential for tackling complex scientific problems across different domains.The continued advancement of this integrated paradigm promises to accelerate materials discovery and open new frontiers in the predictive simulation of complex quantum phenomena.
基金financially supported by the National Natural Science Foundation of China(Nos.52173020 and 52573023)。
文摘Vitrimers belong to a class of polymeric materials capable of bond exchange reactions,showing great promise for environmental protection and sustainable development.However,studies on the coupling mechanism between the bond exchange kinetics and segmental dynamics near the glass transition temperature(T_(g))remain scarce.Herein,we employed molecular dynamics simulations to investigate the dynamic heterogeneity of the segment motion and bond exchange in vitrimers.The simulation results revealed that the bond exchange energy barrier exerts a much stronger influence on the bond exchange kinetics than on the segmental dynamics.At lower temperatures,slower segmental relaxation further constraind the bond exchange rate.Additionally,increasing the bond exchange energy barrier markedly enhanced the dynamic heterogeneity of segment motion.A close correlation was observed between heterogeneity and bond exchange.This study elucidated the coupling mechanism between bond exchange and segmental dynamics at the molecular scale,thereby providing a theoretical basis for designing vitrimer materials with tunable dynamic properties.
文摘This study develops a surrogate super-resolution(SR)framework that accelerates finite element method(FEM)-based computational fluid dynamics(CFD)using deep learning.High-resolution(HR)FEM-based CFDremains computationally prohibitive for time-sensitive applications,including patient-specific aneurysm hemodynamics where rapid turnaround is valuable.The proposed pipeline learns to reconstruct HR velocity-magnitude fields fromlow-resolution(LR)FEM solutions generated under the same governing equations and boundary conditions.It consistsof three modules:(i)offline pre-training of a residual network on representative vascular geometries;(ii)lightweightfine-tuning to adapt the pretrained model to geometric variability,including patient-specific aneurysm morphologies;and(iii)an unstructured-to-structured sampling strategy with region-of-interest upsampling that concentrates resolution in flow-critical zones(e.g.,the aneurysm sac)rather than the full domain.This targeted reconstruction substantiallyreduces inference and post-processing cost while preserving key HR flow features.Experiments on cerebral aneurysmmodels show that HR velocity-magnitude fields can be recovered with accuracy comparable to direct HR simulationsat less than 1%of the direct HR simulation cost per analysis(LR simulation and SR inference),while adaptation to newgeometries requires only lightweight fine-tuning with limited target-specific HR data.While clinical endpoints andadditional variables(e.g.,pressure or wall-based metrics)are left for future work,the results indicate that the proposedsurrogate SR approach can streamline FEM-based CFD workflows toward near real-time hemodynamic analysis acrossmorphologically similar vascular models.
文摘Urban Heat Island(UHI)effects are exacerbated by the expansion of impervious surfaces and loss of vegetation in urban centers,leading to elevated air and surface temperatures and reduced thermal comfort.Urban trees,through shading and evapotranspiration,are among the most effective Nature-based Solutions(NbS)for passive cooling.This study assesses the cooling potential of selected tree species by analyzing their morphological and physiological traits using a combination of ENVI-met microclimate simulations and multiple regression modeling.A total of 15 urban tree species were selected from the literature and analyzed based on their dependency of their cooling efficacy.Later validated in urban setting by Envi-met simulations.Key traits,such as Leaf Area Index(LAI),canopy density,transpiration rate,tree height,rooting depth,and water availability,were analyzed.Multiple linear regression analysis was conducted to quantify the contribution of each trait to ambient temperature reduction.Results revealed that LAI(R^(2)=0.76,p<0.001)and transpiration rate(R^(2)=0.71,p<0.001)were the most significant predictors of daytime cooling,while canopy openness and tree height were more strongly correlated with nighttime heat dissipation.High-performing species,such as Ficus benghalensis,Azadirachta indica,and Samanea saman,demonstrated a maximum temperature reduction of 2.5-4.2℃,especially in compact,low-rise,and mid-rise zones.The study provides a quantitative trait-based framework for tree selection in urban greening initiatives and offers evidence to guide landscape planning and UHI mitigation strategies through scientifically informed plantation design.
文摘As a representative insensitive high explosive,3-nitro-1,2,4-triazol-5-one(NTO)has garnered significant attention due to its ability to substantially reduce the risk of accidental detonation in munitions.However,its inherent acidity induces severe interfacial corrosion of metal casings,thereby limiting its engineering applications.Based on the micro-corrosion mechanism of NTO on carbon steel(CS),this study designs an arginine-derived corrosion inhibitor,N2-[(phenylamino)thioxomethyl]-arginine(PTA).Electrochemical tests reveal that PTA exhibits an outstanding corrosion inhibition efficiency of 98.0%in NTO solution.Density functional theory(DFT)and molecular dynamics(MD)simulations elucidate the inhibition mechanism of PTA,demonstrating that it not only co-adsorbs with NTO^(−) onto the CS surface to form a dense and stable protective film but also disrupts the strong interactions between NTO^(−) and Fe,thereby suppressing nitro group-induced reduction,decomposition,and excessive surface oxidation.Furthermore,a PTA-loaded mesoporous silica(mSiO_(2))nanoparticles(NPs)-reinforced epoxy resin(EP)composite coating was constructed.Benefiting from the enhanced barrier properties of PTA@mSiO_(2) NPs and the synergistic effect between PTA and NTO^(−),the low-frequency impedance of the composite coating remained as high as 1.29×10^(9)Ω·cm^(2) after 30 days of immersion in NTO solution,exhibiting a two-order-of-magnitude improvement compared to the pure EP coating.This study proposes an effective corrosion control strategy to mitigate NTO-induced corrosion,providing insights into the development of advanced corrosion protection strategies for broader applications.
基金funded by the National Natural Science Foundation of China(Grant No.42102169)the Shaanxi Province key Research and Development Project(Grant No.2023-ZDLSF-64)+1 种基金the Scientific Research and Technological Development Project of China National Logging Corporation(Grant No.25ZYCJSG013-2504)the Youth Science and Technology Special Fund of PetroChina(Grant No.2024DQ03172)。
文摘Geological CO_(2) storage is a promising strategy for reducing greenhouse gas emissions and has become a growing focus of research and deployment.This paper presents numerical simulations of CO_(2) injection and storage in a depleted gas reservoir within the B Depression and evaluates associated CO_(2) trapping mechanisms.In the base case,a constant injection rate of 3500 m^(3)/d over fifteen years resulted in a cumulative injection of 19.2×10^(6) m^(3).The CO_(2) plume expanded radially during injection and subsequently migrated up-dip under buoyancy forces.The final stored mass of CO_(2) in the reservoir was 10.6 million tonnes(Mt),representing less than 10% of its theoretical capacity.The plume was projected to reach the entrapment crest and the top of the reservoir within a century,indicating secure long-term containment.Structural,stratigraphic,and residual trapping dominate in Reservoir A(approximately 90%).Anticlinal closures with thick overlying mudstones in the Zhujiang Formation provide effective seals,further enhancing storage security.Reservoir properties and heterogeneity play a crucial role in controlling CO_(2) storage.However,reservoir heterogeneity exerts only a limited influence when intrinsic properties are favorable.Overall,the study and implementation of CO_(2) capture,utilization,and storage(CCUS)in China's offshore basins show promising prospects.
基金supported by the National Natural Science Foundation of China (Grant No.11574244 for G.Y.G.)the XJTU Research Fund for AI Science (Grant No.2025YXYC011 for G.Y.G.)the Hong Kong Global STEM Professorship Scheme (for X.C.Z.)。
文摘Compared to the well-studied two-dimensional(2D)ferroelectricity,the appearance of 2D antiferroelectricity is much rarer,where local dipoles from the nonequivalent sublattices within 2D monolayers are oppositely oriented.Using NbOCl_(2) monolayer with competing ferroelectric(FE)and antiferroelectric(AFE)phases as a 2D material platform,we demonstrate the emergence of intrinsic antiferroelectricity in NbOCl_(2) monolayer under experimentally accessible shear strain,along with new functionality associated with electric field-induced AFE-to-FE phase transition.Specifically,the complex configuration space accommodating FE and AFE phases,polarization switching kinetics,and finite temperature thermodynamic properties of 2D NbOCl_(2) are all accurately predicted by large-scale molecular dynamics simulations based on deep learning interatomic potential model.Moreover,room temperature stable antiferroelectricity with low polarization switching barrier and one-dimensional collinear polarization arrangement is predicted in shear-deformed NbOCl_(2) monolayer.The transition from AFE to FE phase in 2D NbOCl_(2) can be triggered by a low critical electric field,leading to a double polarization–electric(P–E)loop with small hysteresis.A new type of optoelectronic device composed of AFE-NbOCl_(2) is proposed,enabling electric“writing”and nonlinear optical“reading”logical operation with fast operation speed and low power consumption.
基金supported by the National Natu-ral Science Foundation of China(No.21073170 and No.21273209).
文摘ATP-binding cassette exporters transport many substrates out of cellular membranes via alternating between inward-facing and outward-facing conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics simulations of the potential of mean force along the conformational transition pathway [J. Phys. Chem. B 119, 1295(2015)]. However, the occluded conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this work, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1-d2, which are the COM distances between the two sides of the internal(d1)and the external gate(d2). The potential of mean force is thus obtained to identify the transition pathway, along which several outward-facing, inward-facing, and occluded state structures are predicted in good agreement with structural experiments. Our coarse-grained molecular dynamics free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the inward-facing to outward-facing transition and vice versa during the inward-facing to outward-facing transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the previous result, in which both the internal and external gates are open reported in an X-ray experiment [Proc. Natl. Acad. Sci. USA 104,19005(2007)]. Our study sheds light on the molecular mechanism of the state transitions in an ATP-binding cassette exporter.
基金the support of the National Natural Science Foundation of China(Grant Nos.21025416,20974040,50930001)China Postdoctoral Science Foundation(Grant No.20110491295).
文摘We introduce a reaction model for use in coarse-grained simulations to study the chemical reactions in polymer systems at mesoscopic level.In this model,we employ an idea of reaction probability in control of the whole process of chemical reactions.This model has been successfully applied to the studies of surface initiated polymerization process and the network structure formation of typical epoxy resin systems.It can be further modified to study different kinds of chemical reactions at mesoscopic scale.
基金Project supported by the National Natural Science Foundation of China(no.11272360)the Natural Science Foundation of Guangdong Province(no.2014A030313793)+1 种基金the Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund(the second phase)National Supercomputer Center in Guangzhou
文摘The micro-capsules used for drug delivery are fabricated using polylactic acid（PLA）,which is a biomedical material approved by the FDA.A coarse-grained model of long-chain PLA was built,and molecular dynamics（MD）simulations of the model were performed using a MARTINI force field.Based on the nonlocal theory,the formula for the initial elastic modulus of polymers considering the nonlocal effect was derived,and the scaling law of internal characteristic length of polymers was proposed,which was used to adjust the cut-off radius in the MD simulations of PLA.The results show that the elastic modulus should be computed using nonlinear regression.The nonlocal effect has a certain influence on the simulation results of PLA.According to the scaling law,the cut-off radius was determined and applied to the MD simulations,the results of which reflect the influence of the molecular weight change on the elastic moduli of PLA,and are in agreement with the experimental outcome.
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.
文摘Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=1204.10 K, which is in good agreement with experimental results 1104-1 K.
基金supported by the National Natural Science Foundation of China(Grant Nos.11974173 and 11774158)the HPC center of Nanjing University。
文摘Protein XPA plays critical roles in nucleotide excision repair pathway.Recent experimental work showed that the functional dynamics of XPA involves the one-dimensional diffusion along DNA to search the damage site.Here,we investigate the involved dynamical process using extensive coarse-grained molecular simulations at various salt concentrations.The results demonstrated strong salt concentration dependence of the diffusion mechanisms.At low salt concentrations,the one-dimensional diffusion with rotational coupling is the dominant mechanism.At high salt concentrations,the diffusion by three-dimensional mechanism becomes more probable.At wide range of salt concentrations,the residues involved in the DNA binding are similar and the one-dimensional diffusion of XPA along DNA displays sub-diffusive feature.This sub-diffusive feature is tentatively attributed to diverse strengths of XPA-DNA interactions.In addition,we showed that both binding to DNA and increasing salt concentration tend to stretch the conformation of the XPA,which increases the exposure extent of the sites for the binding of other repair proteins.
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℃.
