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Speed limit effect during lane change in a two-lane lattice model under V2X environment
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作者 金灿 彭光含 聂方彦 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第3期718-722,共5页
Speed limit measures are ubiquitous due to the complexity of the road environment,which can be supplied with the help of vehicle to everything(V2X)communication technology.Therefore,the influence of speed limit on tra... Speed limit measures are ubiquitous due to the complexity of the road environment,which can be supplied with the help of vehicle to everything(V2X)communication technology.Therefore,the influence of speed limit on traffic system will be investigated to construct a two-lane lattice model accounting for the speed limit effect during the lane change process under V2X environment.Accordingly,the stability condition and the mKdV equation are closely associated with the speed limit effect through theory analysis.Moreover,the evolution of density and hysteresis loop is simulated to demonstrate the positive role of the speed limit effect on traffic stability in the cases of strong reaction intensity and high limited speed. 展开更多
关键词 traffic flow lattice model speed limit
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Dark Matter and Dark Energy from Lattice Model of Universe
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作者 Branislav Majerník 《Journal of High Energy Physics, Gravitation and Cosmology》 CAS 2024年第3期1045-1053,共9页
The article considers a conceptual universe model as a periodic lattice (network) with nodes defined by the wave function in a background-independent Hamiltonian based on their relations and interactions. This model g... The article considers a conceptual universe model as a periodic lattice (network) with nodes defined by the wave function in a background-independent Hamiltonian based on their relations and interactions. This model gives rise to energy bands, similar to those in semiconductor solid-state models. In this context, valence band holes are described as dark matter particles with a heavy effective mass. The conducting band, with a spontaneously symmetry-breaking energy profile, contains particles with several times lighter effective mass, which can represent luminous matter. Some possible analogies with solid-state physics, such as the comparison between dark and luminous matter, are discussed. Additionally, tiny dark energy, as intrinsic lattice Casimir energy, is calculated for a lattice with a large number of lattice nodes. 展开更多
关键词 Dark Energy Dark Matter lattice Universe model
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Application of shifted lattice model to 3D compressible lattice Boltzmann method
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作者 黄好雨 金科 +1 位作者 李凯 郑晓静 《Chinese Physics B》 SCIE EI CAS CSCD 2023年第9期312-320,共9页
An additional potential energy distribution function is introduced on the basis of previous D3Q25 model,and the equilibrium distribution function of D3Q25 is obtained by spherical function.A novel three-dimensional(3D... An additional potential energy distribution function is introduced on the basis of previous D3Q25 model,and the equilibrium distribution function of D3Q25 is obtained by spherical function.A novel three-dimensional(3D)shifted lattice model is proposed,therefore a shifted lattice model is introduced into D3Q25.Under the finite volume scheme,several typical compressible calculation examples are used to verify whether the numerical stability of the D3Q25 model can be improved by adding the shifted lattice model.The simulation results show that the numerical stability is indeed improved after adding the shifted lattice model. 展开更多
关键词 lattice Boltzmann method shifted lattice model compressible flow finite volume method
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A novel lattice model integrating the cooperative deviation of density and optimal flux under V2X environment
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作者 彭光含 罗春莉 +1 位作者 赵红专 谭惠丽 《Chinese Physics B》 SCIE EI CAS CSCD 2023年第1期626-633,共8页
A novel lattice hydrodynamic model is proposed by integrating the cooperative deviation of density and optimal flux under vehicle to X(V2X) environment. According to the theoretical analysis, the stability conditions ... A novel lattice hydrodynamic model is proposed by integrating the cooperative deviation of density and optimal flux under vehicle to X(V2X) environment. According to the theoretical analysis, the stability conditions and the mKdV equations affected by the cooperative deviation of traffic information are explored. And the density wave, hysteresis loop and energy consumption of the traffic flow have been investigated via numerical simulation. The results indicate that the cooperative deviation of density and optimal flux can effectively alleviate the traffic congestion. More importantly, our new consideration can reduce fuel consumption and exhaust emission under the V2X environment. 展开更多
关键词 traffic flow lattice hydrodynamic model cooperative deviation
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Coarse-graining Calcium Dynamics on Stochastic Reaction-diffusion Lattice Model 被引量:1
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作者 申传胜 陈含爽 《Chinese Journal of Chemical Physics》 SCIE CAS CSCD 2013年第2期181-184,I0003,I0004,共6页
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites tog... We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and deriving CG reaction rates using local mean field approximation, we perform CG kinetic Monte Carlo (kMC) simulations and find the results of CG-kMC simulations are in excellent agreement with that of the microscopic ones. Strikingly, there is an appropriate range of coarse proportion rn, corresponding to the minimal deviation of the phase transition point compared to the microscopic one. For fixed m, the critical point increases monotonously as the system size increases, especially, there exists scaling law between the deviations of the phase transition point and the system size. Moreover, the CG approach provides significantly faster Monte Carlo simulations which are easy to implement and are directly related to the microscopics, so that one can study the system size effects at the cost of reasonable computational time. 展开更多
关键词 Calcium dynamics Kinetic Monte Carlo simulation lattice model Coarse- vgrammg
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A traffic flow lattice model considering relative current influence and its numerical simulation 被引量:1
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作者 孙棣华 田川 刘卫宁 《Chinese Physics B》 SCIE EI CAS CSCD 2010年第8期241-246,共6页
Based on Xue's lattice model, an extended lattice model is proposed by considering the relative current information about next-nearest-neighbour sites ahead. The linear stability condition of the presented model is o... Based on Xue's lattice model, an extended lattice model is proposed by considering the relative current information about next-nearest-neighbour sites ahead. The linear stability condition of the presented model is obtained by employing the linear stability theory. The density wave is investigated analytically with the perturbation method. The results show that the occurrence of traffic jamming transitions can be described by the kink-antikink solution of the modified Korteweg-de Vries (mKdV) equation. The simulation results are in good agreement with the analytical results, showing that the stability of traffic flow can be enhanced when the relative current of next-nearest-neighbour sites ahead is considered. 展开更多
关键词 traffic flow relative current lattice model numerical simulation
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A Backward-Looking Optimal Current Lattice Model
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作者 ZHU Wen-Xing 《Communications in Theoretical Physics》 SCIE CAS CSCD 2008年第9期753-756,共4页
An optimai current lattice model with backward-looking effect is proposed to describe the motion of traffic flow on a single lane highway. The behavior of the new model is investigated anaiytically and numerically. Th... An optimai current lattice model with backward-looking effect is proposed to describe the motion of traffic flow on a single lane highway. The behavior of the new model is investigated anaiytically and numerically. The stability, neutrai stability, and instability conditions of the uniform flow are obtained by the use of linear stability theory. The stability of the uniform flow is strengthened effectively by the introduction of the backward-looking effect. The numerical simulations are carried out to verify the validity of the new model. The outcomes of the simulation are corresponding to the linearly analyticai results. The analytical and numerical results show that the performance of the new model is better than that of the previous models. 展开更多
关键词 backward looking effect lattice model optimal current linear stability theory
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PERSISTENT CURRENT IN A ONE-DIMENSIONAL MESOSCOPIC RING WITH ELECTRON-PHONON INTERACTION IN THE LATTICE MODEL
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作者 李铜忠 《Journal of Shanghai Jiaotong university(Science)》 EI 2001年第2期123-125,130,共4页
A new non-perturbative method is used to discuss the persistent current in a one-dimensional mesoscopic ring threaded by a flux φ with electron-phonon interaction in the lattice model. The current is periodic in φ w... A new non-perturbative method is used to discuss the persistent current in a one-dimensional mesoscopic ring threaded by a flux φ with electron-phonon interaction in the lattice model. The current is periodic in φ with a flux quantum φ 0 and the electron-phonon interaction suppresses the persistent current. By considering the contributions of many-phonon correlations, we could obtain more accurate results. 展开更多
关键词 mesoscopic ring electron-phonon interaction lattice model persistent current
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A Modified Lattice Model of the Reversible Effect of Axial Strain on the Critical Current of Polycrystalline REBa2Cu3O7-δ Films
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作者 苟晓凡 朱光 《Chinese Physics Letters》 SCIE CAS CSCD 2015年第3期128-132,共5页
The strain effect on the critical current is one of the most important properties for polycrystalline YBa2 Cu3O7-δ (REBCO, RE: rare earth) films, in which the reversible effect is intrinsic in the range of strain ... The strain effect on the critical current is one of the most important properties for polycrystalline YBa2 Cu3O7-δ (REBCO, RE: rare earth) films, in which the reversible effect is intrinsic in the range of strain 0 and the irreversible strain εirr. By introducing the applied strain, a modified grain boundaries (GBs) in the REBCO film is developed. lattice model combining the strain and misorientation of A good agreement of the calculation on the lattice model with the experimental data shows that the lattice model is able to well describe the reversible effect of axial strain on the critical current of the REBCO film, and provides a good understanding of the mechanism of the reversible effect of the strain. Moreover, the effects of the crystallographic texture of the REBCO film and the residual strain εr on the variation of the critical current with the applied strain are extensively investigated. Furthermore by using the developed lattice model, the irreversible strain εirr of the REBCO film can be theoretically determined by comparing the calculation of the critical current-strain curve with the experimental data. 展开更多
关键词 REBCO A Modified lattice model of the Reversible Effect of Axial Strain on the Critical Current of Polycrystalline REBa2Cu3O FILMS Cu
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Chiral Current in the Lattice Model of Weyl Semimetal
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作者 孙亮 完绍龙 《Chinese Physics Letters》 SCIE CAS CSCD 2015年第5期129-133,共5页
We demonstrate the existence of the chirai magnetic effect in a simple lattice model of Weyl semimetal, which is a hallmark of chiral anomaly in the Weyl semimetal, by calculating the anomalous charge current directly... We demonstrate the existence of the chirai magnetic effect in a simple lattice model of Weyl semimetal, which is a hallmark of chiral anomaly in the Weyl semimetal, by calculating the anomalous charge current directly. We identify that the uniform external magnetic field can induce a non-dissipative charge current along its direction in Weyl semimetal, even in the absence of an external electric field if the right and left handed Weyl points are separated in energy, and that the anomalous current is proportional to the strength of the magnetic field and the energy separation with a universal coetticient e2/h2, which coincide with the ones predicted on the basis of the field theory treatment. Our results give the possibility to detect these nontrivial electrodynamic phenomena in real materials of Weyl semimetal. 展开更多
关键词 Chiral Current in the lattice model of Weyl Semimetal
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A Theory of Ratio Selection—Lattice Model for Obligate Mutualism
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作者 Kei-Ichi Tainaka Tsuyoshi Hashimoto 《Open Journal of Ecology》 2016年第6期303-311,共9页
Mutualisms are cooperative interactions between members of different species. We focus on obligate mutualism, where each species cannot survive without the other. From a theoretical aspect, obligate mutualism is simil... Mutualisms are cooperative interactions between members of different species. We focus on obligate mutualism, where each species cannot survive without the other. From a theoretical aspect, obligate mutualism is similar to the relationship between male and female. Empirical data indicate a sex-ratio selection: male and female have a specific ratio in their population sizes. In the present paper, we apply lattice model to obligate mutualism between two species, and present a theory of “ratio selection” which is a generalization of sex-ratio selection. Computer simulations are carried out by two methods: local and global interactions. In the former, interactions occur between neighbouring cells, while in the latter they occur between any pair of cells. Simulations in both interactions show the so-called Allee effect: both species can survive, when both densities are large in some extent. However, we find a large difference between local and global simulations. In the case of local interaction, restriction for survival is found to be extremely severe compared to global interaction. Both species require a proper ratio for their sustainability. This result leads to the theory of ratio selection: when interaction occurs locally, the ratio of both species is uniquely determined. We discuss that the ratio selection explains not only the evolution of endosymbionts from free-living ancestors but also the evolution from endosymbionts to organelles. 展开更多
关键词 Obligate Mutualism Population Dynamics Ratio Selection Allee Effect lattice model Sex-Ratio Selection ENDOSYMBIOSIS
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Control Chaos of a Unidirectionally Traffic Coupled Map Lattice Model
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作者 Yaling Fang 《Journal of Applied Mathematics and Physics》 2021年第10期2527-2533,共7页
Spatiotemporal chaos is studied by using the unidirectional traffic coupled lattice model with hyperbolic tangent local map. The coupled map lattice (CML) model can simulate the complex traffic flow phenomenon which i... Spatiotemporal chaos is studied by using the unidirectional traffic coupled lattice model with hyperbolic tangent local map. The coupled map lattice (CML) model can simulate the complex traffic flow phenomenon which is similar to the traditional traffic flow model. The nonlinear feedback method is used to study the control of the chaotic system of the unidirectionally traffic coupled map lattice model. The stability of spatiotemporal chaos in the coupled map lattice is realized. The results of numerical simulation show that there is a relationship between control results and control parameters when controlling spatiotemporal chaos to a uniform stable state in a certain phase space compression parameter region. 展开更多
关键词 Traffic Flow model Coupled Map lattice model Spatiotemporal Chaos Feedback Control
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Lattice models of traffic flow considering drivers' delay in response 被引量:3
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作者 祝会兵 《Chinese Physics B》 SCIE EI CAS CSCD 2009年第4期1322-1327,共6页
This paper proposes two lattice traffic models by taking into account the drivers' delay in response. The lattice versions of the hydrodynamic model are described by the differential-difference equation and differenc... This paper proposes two lattice traffic models by taking into account the drivers' delay in response. The lattice versions of the hydrodynamic model are described by the differential-difference equation and difference-difference equation, respectively. The stability conditions for the two models are obtained by using the linear stability theory. The modified KdV equation near the critical point is derived to describe the traffic jam by using the reductive perturbation method, and the kink-antikink soliton solutions related to the traffic density waves are obtained. The results show that the drivers' delay in sensing headway plays an important role in jamming transition. 展开更多
关键词 lattice hydrodynamic model traffic jams analytical method drivers' delay in response
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Exploration of the coupled lattice Boltzmann model based on a multiphase field model:A study of the solid-liquid-gas interaction mechanism in the solidification process
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作者 朱昶胜 王利军 +2 位作者 高梓豪 刘硕 李广召 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第3期638-648,共11页
A multiphase field model coupled with a lattice Boltzmann(PF-LBM)model is proposed to simulate the distribution mechanism of bubbles and solutes at the solid-liquid interface,the interaction between dendrites and bubb... A multiphase field model coupled with a lattice Boltzmann(PF-LBM)model is proposed to simulate the distribution mechanism of bubbles and solutes at the solid-liquid interface,the interaction between dendrites and bubbles,and the effects of different temperatures,anisotropic strengths and tilting angles on the solidified organization of the SCN-0.24wt.%butanedinitrile alloy during the solidification process.The model adopts a multiphase field model to simulate the growth of dendrites,calculates the growth motions of dendrites based on the interfacial solute equilibrium;and adopts a lattice Boltzmann model(LBM)based on the Shan-Chen multiphase flow to simulate the growth and motions of bubbles in the liquid phase,which includes the interaction between solid-liquid-gas phases.The simulation results show that during the directional growth of columnar dendrites,bubbles first precipitate out slowly at the very bottom of the dendrites,and then rise up due to the different solid-liquid densities and pressure differences.The bubbles will interact with the dendrite in the process of flow migration,such as extrusion,overflow,fusion and disappearance.In the case of wide gaps in the dendrite channels,bubbles will fuse to form larger irregular bubbles,and in the case of dense channels,bubbles will deform due to the extrusion of dendrites.In the simulated region,as the dendrites converge and diverge,the bubbles precipitate out of the dendrites by compression and diffusion,which also causes physical phenomena such as fusion and spillage of the bubbles.These results reveal the physical mechanisms of bubble nucleation,growth and kinematic evolution during solidification and interaction with dendrite growth. 展开更多
关键词 multiphase field model lattice Boltzmann model(LBM) Shan-Chen multiphase flow solidification organization
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Two-dimensional Dirac materials:Tight-binding lattice models and material candidates 被引量:1
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作者 Runyu Fan Lei Sun +2 位作者 Xiaofei Shao Yangyang Li Mingwen Zhao 《ChemPhysMater》 2023年第1期30-42,共13页
The discovery of graphene has led to the devotion of intensive efforts,theoretical and experimental,to produce two-dimensional(2D)materials that can be used for developing functional materials and devices.This work pr... The discovery of graphene has led to the devotion of intensive efforts,theoretical and experimental,to produce two-dimensional(2D)materials that can be used for developing functional materials and devices.This work provides a brief review of the recent developments in the lattice models of 2D Dirac materials and their relevant real material counterparts that are crucial for understanding the origins of 2D Dirac cones in electronic band structures as well as their material design and device applications.We focus on the roles of lattice symmetry,atomic orbital hybridization,and spin-orbit coupling in the presence of a Dirac cone.A number of lattice models,such as honeycomb,kagome,ruby,star,Cairo,and line-centered honeycomb,with different symmetries are reviewed based on the tight-binding approach.Inorganic and organic 2D materials,theoretically proposed or experimentally synthesized to satisfy these 2D Dirac lattice models,are summarized. 展开更多
关键词 Dirac cones Two-dimensional materials Tight-binding model lattice models
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Uncertainty of concrete strength in shear and flexural behavior of beams using lattice modeling
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作者 Sahand KHALILZADEHTABRIZI Hamed SADAGHIAN Masood FARZAM 《Frontiers of Structural and Civil Engineering》 SCIE EI CSCD 2023年第2期306-325,共20页
This paper numerically studied the effect of uncertainty and random distribution of concrete strength in beams failing in shear and flexure using lattice modeling,which is suitable for statistical analysis.The indepen... This paper numerically studied the effect of uncertainty and random distribution of concrete strength in beams failing in shear and flexure using lattice modeling,which is suitable for statistical analysis.The independent variables of this study included the level of strength reduction and the number of members with reduced strength.Three levels of material deficiency(i.e.,10%,20%,30%)were randomly introduced to 5%,10%,15%,and 20%of members.To provide a database and reliable results,1000 analyses were carried out(a total of 24000 analyses)using the MATLAB software for each combination.Comparative studies were conducted for both shear-and flexure-deficit beams under four-point loading and results were compared using finite element software where relevant.Capability of lattice modeling was highlighted as an efficient tool to account for uncertainty in statistical studies.Results showed that the number of deficient members had a more significant effect on beam capacity compared to the level of strength deficiency.The scatter of random load-capacities was higher in flexure(range:0.680-0.990)than that of shear(range:0.795-0.996).Finally,nonlinear regression relationships were established with coefficient of correlation values(R^(2))above 0.90,which captured the overall load-deflection response and level of load reduction. 展开更多
关键词 lattice modeling shear failure flexural failure UNCERTAINTY DEFICIENCY numerical simulation
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GPU parallel computation of dendrite growth competition in forced convection using the multi-phase-field-lattice Boltzmann model
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作者 高梓豪 朱昶胜 王苍龙 《Chinese Physics B》 SCIE EI CAS CSCD 2023年第7期530-547,共18页
A graphics-processing-unit(GPU)-parallel-based computational scheme is developed to realize the competitive growth process of converging bi-crystal in two-dimensional states in the presence of forced convection condit... A graphics-processing-unit(GPU)-parallel-based computational scheme is developed to realize the competitive growth process of converging bi-crystal in two-dimensional states in the presence of forced convection conditions by coupling a multi-phase field model and a lattice Boltzmann model.The elimination mechanism in the evolution process is analyzed for the three conformational schemes constituting converging bi-crystals under pure diffusion and forced convection conditions,respectively,expanding the research of the competitive growth of columnar dendrites under melt convection conditions.The results show that the elimination mechanism for the competitive growth of converging bi-crystals of all three configurations under pure diffusion conditions follows the conventional Walton-Chalmers model.When there is forced convection with lateral flow in the liquid phase,the anomalous elimination phenomenon of unfavorable dendrites eliminating favorable dendrites occurs in the grain boundaries.In particular,the anomalous elimination phenomenon is relatively strong in conformation 1 and conformation 2 when the orientation angle of unfavorable dendrites is small,and relatively weak in conformation 3.Moreover,the presence of convection increases the tip growth rate of both favorable and unfavorable dendrites in the grain boundary.In addition,the parallelization of the multi-phase-field-lattice Boltzmann model is achieved by designing the parallel computation of the model on the GPU platform concerning the computerunified-device-architecture parallel technique,and the results show that the parallel computation of this model based on the GPU has absolute advantages,and the parallel acceleration is more obvious as the computation area increases. 展开更多
关键词 multi-phase field model GPU grain competition growth lattice Boltzmann model
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Numerical Stability and Accuracy of Contact Angle Schemes in Pseudopotential Lattice Boltzmann Model for Simulating Static Wetting and Dynamic Wetting
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作者 Dongmin Wang Gaoshuai Lin 《Computer Modeling in Engineering & Sciences》 SCIE EI 2023年第10期299-318,共20页
There are five most widely used contact angle schemes in the pseudopotential lattice Boltzmann(LB)model for simulating the wetting phenomenon:The pseudopotential-based scheme(PB scheme),the improved virtualdensity sch... There are five most widely used contact angle schemes in the pseudopotential lattice Boltzmann(LB)model for simulating the wetting phenomenon:The pseudopotential-based scheme(PB scheme),the improved virtualdensity scheme(IVD scheme),the modified pseudopotential-based scheme with a ghost fluid layer constructed by using the fluid layer density above the wall(MPB-C scheme),the modified pseudopotential-based scheme with a ghost fluid layer constructed by using the weighted average density of surrounding fluid nodes(MPB-W scheme)and the geometric formulation scheme(GF scheme).But the numerical stability and accuracy of the schemes for wetting simulation remain unclear in the past.In this paper,the numerical stability and accuracy of these schemes are clarified for the first time,by applying the five widely used contact angle schemes to simulate a two-dimensional(2D)sessile droplet on wall and capillary imbibition in a 2D channel as the examples of static wetting and dynamic wetting simulations respectively.(i)It is shown that the simulated contact angles by the GF scheme are consistent at different density ratios for the same prescribed contact angle,but the simulated contact angles by the PB scheme,IVD scheme,MPB-C scheme and MPB-W scheme change with density ratios for the same fluid-solid interaction strength.The PB scheme is found to be the most unstable scheme for simulating static wetting at increased density ratios.(ii)Although the spurious velocity increases with the increased liquid/vapor density ratio for all the contact angle schemes,the magnitude of the spurious velocity in the PB scheme,IVD scheme and GF scheme are smaller than that in the MPB-C scheme and MPB-W scheme.(iii)The fluid density variation near the wall in the PB scheme is the most significant,and the variation can be diminished in the IVD scheme,MPB-C scheme andMPBWscheme.The variation totally disappeared in the GF scheme.(iv)For the simulation of capillary imbibition,the MPB-C scheme,MPB-Wscheme and GF scheme simulate the dynamics of the liquid-vapor interface well,with the GF scheme being the most accurate.The accuracy of the IVD scheme is low at a small contact angle(44 degrees)but gets high at a large contact angle(60 degrees).However,the PB scheme is the most inaccurate in simulating the dynamics of the liquid-vapor interface.As a whole,it is most suggested to apply the GF scheme to simulate static wetting or dynamic wetting,while it is the least suggested to use the PB scheme to simulate static wetting or dynamic wetting. 展开更多
关键词 Pseudopotential lattice Boltzmann model contact angle scheme static wetting dynamic wetting capillary imbibition
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A New Lattice Model of Two-Lane Trafc Flow with the Consideration of the Honk Efect 被引量:1
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作者 彭光含 《Communications in Theoretical Physics》 SCIE CAS CSCD 2013年第10期485-490,共6页
In this paper, a new lattice model of two-lane traffic flow with the honk effect term is proposed to study the influence of the honk effect on wide moving jams under lane changing. The linear stability condition on tw... In this paper, a new lattice model of two-lane traffic flow with the honk effect term is proposed to study the influence of the honk effect on wide moving jams under lane changing. The linear stability condition on two-lane highway is obtained by applying the linear stability theory. The modified Korteweg-de Vries (KdV) equation near the critical point is derived and the coexisting curves resulted from the modified KdV equation can be described, which shows that the critical point, the coexisting curve and the neutral stability line decrease with increasing the honk effect coe^cient. A wide moving jam can be conceivably described approximately in the unstable region. Numerical simulation is performed to verify the analytic results. The results show that the honk effect could suppress effectively the congested traffic patterns about wide moving jam propagation in lattice model of two-lane traffic flow. 展开更多
关键词 traffic flow lattice model honk effect wide moving jam
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Fast Tree Search for A Triangular Lattice Model of Protein Folding
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作者 XiaomeiLi NengchaoWang 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2004年第4期245-252,共8页
Using a triangular lattice model to study the designability of proteinfolding, we overcame the parity problem of previous cubic lattice model and enumerated all thesequences and compact structures on a simple two-dime... Using a triangular lattice model to study the designability of proteinfolding, we overcame the parity problem of previous cubic lattice model and enumerated all thesequences and compact structures on a simple two-dimensional triangular lattice model of size4+5+6+5+4. We used two types of amino acids, hydrophobic and polar, to make up the sequences, andachieved 2^(23)+2^(12) different sequences excluding the reverse symmetry sequences. The totalstring number of distinct compact structures was 219,093, excluding reflection symmetry in theself-avoiding path of length 24 triangular lattice model. Based on this model, we applied a fastsearch algorithm by constructing a cluster tree. The algorithm decreased the computation bycomputing the objective energy of non-leaf nodes. The parallel experiments proved that the fast treesearch algorithm yielded an exponential speed-up in the model of size 4+5+6+5+4. Designabilityanalysis was performed to understand the search result. 展开更多
关键词 triangular lattice model protein folding fast search tree DESIGNABILITY
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