A simulation study was carried out by using dissipative particle dynamics(DPD) method to explore the effects of properties of coating chains, such as length, density, rigidity of polymer chains, as well as the distanc...A simulation study was carried out by using dissipative particle dynamics(DPD) method to explore the effects of properties of coating chains, such as length, density, rigidity of polymer chains, as well as the distance between nanoparticles on bonding reaction of coating chains grafted onto nanoparticles. The results show that bonding ratios of coated chains strongly depend on the length and density of coating chains. For nanoparticles with different coating densities, the optimum chain length for bonding reaction are varied. The rigidity of coating chains exhibits vigorous effects on bonding reaction that highly depends on chain lengths. DPD simulation can be used to study the bonding reaction between coated nanoparticles, which may help experimental synthesis of nanocomposites with excellent properties.展开更多
Flow through arrays of micropillar embedded inside microfluidic chip systems is important for various microfluidic devices. It is critical to accurately predict the mass flow rate through pillar arrays based on the pi...Flow through arrays of micropillar embedded inside microfluidic chip systems is important for various microfluidic devices. It is critical to accurately predict the mass flow rate through pillar arrays based on the pillar design. This work presents a dissipative particle dynamics (DPD) model to simulate a problem of flow across periodic arrays of circular micropillar and investigates the permeability of two types of micropillar arrays. The flow fields including horizontal and vertical velocity fields, the number density field, and the streamline of the flow are analyzed. The predicted solid volumes by the presented DPD simulation of both types of arrays are quite close to the actual counterparts. These quantitative agreements show usefulness and effectiveness of the DPD model in simulating arrays of micropillar. By comparing two types of micropillar arrangement patterns, we find that the arrangement pattern of micropillar does not have significant influence on the permeability of the array.展开更多
We calculate current correlation functions (CCFs) of dissipative particle dy- namics (DPD) and compare them with results of molecular dynamics (MD) and solutions of linearized hydrodynamic equations. In particul...We calculate current correlation functions (CCFs) of dissipative particle dy- namics (DPD) and compare them with results of molecular dynamics (MD) and solutions of linearized hydrodynamic equations. In particular, we consider three versions of DPD, the empirical/classical DPD, coarse-grained (CG) DPD with radial-direction interactions only and full (radial, transversal, and rotational) interactions between particles. To fa- cilitate quantitative discussions, we consider specifically a star-polymer melt system at a moderate density. For bonded molecules, it is straightforward to define the CG variables and to further derive CG force fields for DPD within the framework of the Mori-Zwanzig formalism. For both transversal and longitudinal current correlation functions (TCCFs and LCCFs), we observe that results of MD, DPD, and hydrodynamic solutions agree with each other at the continuum limit. Below the continuum limit to certain length scales, results of MD deviate significantly from hydrodynamic solutions, whereas results of both empirical and CG DPD resemble those of MD. This indicates that the DPD method with Markovian force laws possibly has a larger applicability than the continuum description of a Newtonian fluid. This is worth being explored further to represent gen- eralized hydrodynamics.展开更多
We investigate the behavior of dissipative particle dynamics (DPD) within different scaling regimes by numerical simulations. The paper extends earlier analytical findings of Ripoll, M., Ernst, M. H., and Espafiol, ...We investigate the behavior of dissipative particle dynamics (DPD) within different scaling regimes by numerical simulations. The paper extends earlier analytical findings of Ripoll, M., Ernst, M. H., and Espafiol, P. (Large scale and mesoscopic hy- drodynamics for dissipative particle dynamics. Journal of Chemical Physics, 115(15), 7271-7281 (2001)) by evaluation of numerical data for the particle and collective scaling regimes and the four different subregimes. DPD simulations are performed for a range of dynamic overlapping parameters. Based on analyses of the current auto-correlation functions (CACFs), we demonstrate that within the particle regime at scales smaller than its force cut-off radius, DPD follows Langevin dynamics. For the collective regime, we show that the small-scale behavior of DPD differs from Langevin dynamics. For the wavenumber-dependent effective shear viscosity, universal scaling regimes are observed in the microscopic and mesoscopic wavenumber ranges over the considered range of dynamic overlapping parameters.展开更多
The DNA sequencing technology has achieved a leapfrog development in recent years. As a new generation of the DNA sequencing technology, nanopore sequenc- ing has shown a broad application prospect and attracted vast ...The DNA sequencing technology has achieved a leapfrog development in recent years. As a new generation of the DNA sequencing technology, nanopore sequenc- ing has shown a broad application prospect and attracted vast research interests since it was proposed. In the present study, the dynamics of the electric-driven translocation of a homopolymer through a nanopore is investigated by the dissipative particle dynam- ics (DPD), in which the homopolymer is modeled as a worm-like chain (WLC). The DPD simulations show that the polymer chain undergoes conformation changes during the translocation process. The different structures of the polymer in the translocation process, i.e., single-file, double folded, and partially folded, and the induced current block- ades are analyzed. It is found that the current blockades have different magnitudes due to the polymer molecules traversing the pore with different folding conformations. The nanoscale vortices caused by the concentration polarization layers (CPLs) in the vicinity of the sheet are also studied. The results indicate that the translocation of the polymer has the effect of eliminating the vortices in the polyelectrolyte solution. These findings are expected to provide the theoretical guide for improving the nanopore sequencing tech- nique.展开更多
The implementation of solid-fluid boundary condition has been a major challenge for dissipative particle dynamics(DPD)method.Current implementations of boundary conditions usually try to approach a uniform density dis...The implementation of solid-fluid boundary condition has been a major challenge for dissipative particle dynamics(DPD)method.Current implementations of boundary conditions usually try to approach a uniform density distribution and a velocity profile close to analytical solution.The density oscillations and slip velocity are intentionally eliminated,and different wall properties disappear in the same analytical solution.This paper develops a new wall model that combines image and frozen particles and a new strategy to emphasize different wall properties especially wettabilities.The strategy first studies the realistic wall-fluid system by molecular dynamics(MD)simulation depending on physical parameters.Then,a DPD simulation is used to match the density and velocity profiles with the new wall model.The obtained DPD parameters can simulate the systems with the same wall and fluid materials.With this method,a simulation of the Poiseuille flow of liquid argon with copper walls is presented.Other walls with super-hydrophilic,hydrophilic,and hydrophobic wettabilities are also simulated.The limitations of the analytical solution and the effect of the wall-fluid interaction are discussed.The results show that the method suggested in this paper can simulate the mesoscale behavior of the microchannel flow related to realistic systems.展开更多
Viscoelastic flows play an important role in numerous engineering fields,and the multiscale algorithms for simulating viscoelastic flows have received significant attention in order to deepen our understanding of the ...Viscoelastic flows play an important role in numerous engineering fields,and the multiscale algorithms for simulating viscoelastic flows have received significant attention in order to deepen our understanding of the nonlinear dynamic behaviors of viscoelastic fluids.However,traditional grid-based multiscale methods are confined to simple viscoelastic flows with short relaxation time,and there is a lack of uniform multiscale scheme available for coupling different solvers in the simulations of viscoelastic fluids.In this paper,a universal multiscale method coupling an improved smoothed particle hydrodynamics(SPH)and multiscale universal interface(MUI)library is presented for viscoelastic flows.The proposed multiscale method builds on an improved SPH method and leverages the MUI library to facilitate the exchange of information among different solvers in the overlapping domain.We test the capability and flexibility of the presented multiscale method to deal with complex viscoelastic flows by solving different multiscale problems of viscoelastic flows.In the first example,the simulation of a viscoelastic Poiseuille flow is carried out by two coupled improved SPH methods with different spatial resolutions.The effects of exchanging different physical quantities on the numerical results in both the upper and lower domains are also investigated as well as the absolute errors in the overlapping domain.In the second example,the complex Wannier flow with different Weissenberg numbers is further simulated by two improved SPH methods and coupling the improved SPH method and the dissipative particle dynamics(DPD)method.The numerical results show that the physical quantities for viscoelastic flows obtained by the presented multiscale method are in consistence with those obtained by a single solver in the overlapping domain.Moreover,transferring different physical quantities has an important effect on the numerical results.展开更多
The Gay-Berne (GB) model has been proved to be highly successful in the simulation of liquid crystal phases via both molec- ular dynamics (MD) and nonequilibrium molecular dynamics (NEMD). However, the conventio...The Gay-Berne (GB) model has been proved to be highly successful in the simulation of liquid crystal phases via both molec- ular dynamics (MD) and nonequilibrium molecular dynamics (NEMD). However, the conventional thermostats used in the simulations of GB systems, such as Nose-Hoover and Langevin thermostats, have serious shortcomings especially in NEMD simulations. Recently, dissipative particle dynamics (DPD) has established itself as a useful thermostat for soft matter simulations, whereas the application of DPD thermostat in (NE)MD simulations is limited to the spherically isotropic potential models, such as the Lennard-Jones model. Considering the virtues of the DPD thermostat, that is, local, momentum conserved, and Galilean invariant, we extend the DPD thermostat to the non-spherical GB model. It is interesting to find that the translational DPD and rotational DPD thermostats can be used in the GB system independently and both can achieve the thermostatting effects. Also, we compared the performance of the DPD thermostat with other commonly used thermostats in NEMD simulations by investigating the streaming velocity profiles and the dynamics of phase separation in a typical but simple binary GB mixture under shear field. It is revealed that the known virtues of DPD thermostats, such as Galilean invariant, shear velocity profile-unbiased, and unscreened hydrodynamic interactions, are still intact when applying to GB systems. Finally, the appro- priate parameters for the DPD thermostat in the GB system are identified for future investigations.展开更多
Chemical flooding is one of the effective technologies to increase oil recovery of petroleum reservoirs after water flooding.Above the scale of representative elementary volume(REV), phenomenological modeling and nume...Chemical flooding is one of the effective technologies to increase oil recovery of petroleum reservoirs after water flooding.Above the scale of representative elementary volume(REV), phenomenological modeling and numerical simulations of chemical flooding have been reported in literatures,but the studies alike are rarely conducted at the pore-scale,at which the effects of physicochemical hydrodynamics are hardly resolved either by experimental observations or by traditional continuum-based simulations.In this paper,dissipative particle dynamics(DPD),one of mesoscopic fluid particle methods,is introduced to simulate the pore-scale flow in chemical flooding processes.The theoretical background,mathematical formulation and numerical approach of DPD are presented.The plane Poiseuille flow is used to illustrate the accuracy of the DPD simulation,and then the processes of polymer flooding through an oil-wet throat and a water-wet throat are studies, respectively.The selected parameters of those simulations are given in details.These preliminary results show the potential of this novel method for modeling the physicochemical hydrodynamics at the pore scale in the area of chemical enhanced oil recovery.展开更多
A simple model, i.e. sodium di(2-ethylhexyl) sulfosuccinate (AOT) represented by one-head and two-tail beads tied together by a harmonic spring and water or isooctane by one bead, was put forward via Dissipative Parti...A simple model, i.e. sodium di(2-ethylhexyl) sulfosuccinate (AOT) represented by one-head and two-tail beads tied together by a harmonic spring and water or isooctane by one bead, was put forward via Dissipative Particles Dynamics (DPD) simulation method. Using the changes of interfacial tension between water and oil phase, a ternary phase diagram of AOT/water/isooctane system was drawn. From the simulation, one conclusion is shown that DPD simulation can be considered as an adjunct to experiments.展开更多
An overview of the smoothed dissipative particle dynamics (SDPD) method is presented in a format that tries to quickly answer questions that often arise among users and newcomers. It is hoped that the status of SDPD...An overview of the smoothed dissipative particle dynamics (SDPD) method is presented in a format that tries to quickly answer questions that often arise among users and newcomers. It is hoped that the status of SDPD is clarified as a mesoscopic particle model and its potentials and limitations are highlighted, as compared with other methods.展开更多
In this work, by using coarse-grained molecular dynamics simulations, we found that poly(2-metha-cryloyloxyethyl phosphorylcholine)(PMPC) showed a strong solubility and a so-called antipolyelectrolyte effect(APE...In this work, by using coarse-grained molecular dynamics simulations, we found that poly(2-metha-cryloyloxyethyl phosphorylcholine)(PMPC) showed a strong solubility and a so-called antipolyelectrolyte effect(APE)in water. In contrast, obvious aggregations but no APE were found in n-butyl-substituted choline phosphatepolymers(PMBP) solutions. The underlying mechanisms for different solution behaviors of PMPC and PMBP wereinvestigated in detail. Our results indicate that the presence of butyl groups in PMBP enhances both the electrostaticinteractions and the hydrophobicity of PMBP molecules in the system. Both factors were found to contribute to theformations of aggregates in the PMBP system. Further researches revealed that hydrophobicity arising from the butylgroup plays a more important role than electrostatic interactions in inducing the PMBP aggregation. In addition, thestrong hydrophobicity in PMBP was found to be responsible for the absence of APE. These results are expected tocontribute to a better understanding and a better design of the solution properties of polyzwitterions.展开更多
基金Funded by the National Natural Science Foundation of China(Nos.20974001,21174001,51273001,and 51403001)
文摘A simulation study was carried out by using dissipative particle dynamics(DPD) method to explore the effects of properties of coating chains, such as length, density, rigidity of polymer chains, as well as the distance between nanoparticles on bonding reaction of coating chains grafted onto nanoparticles. The results show that bonding ratios of coated chains strongly depend on the length and density of coating chains. For nanoparticles with different coating densities, the optimum chain length for bonding reaction are varied. The rigidity of coating chains exhibits vigorous effects on bonding reaction that highly depends on chain lengths. DPD simulation can be used to study the bonding reaction between coated nanoparticles, which may help experimental synthesis of nanocomposites with excellent properties.
基金Project supported by the National Natural Science Foundation of China(Nos.31370953,10942004,and 91230203)
文摘Flow through arrays of micropillar embedded inside microfluidic chip systems is important for various microfluidic devices. It is critical to accurately predict the mass flow rate through pillar arrays based on the pillar design. This work presents a dissipative particle dynamics (DPD) model to simulate a problem of flow across periodic arrays of circular micropillar and investigates the permeability of two types of micropillar arrays. The flow fields including horizontal and vertical velocity fields, the number density field, and the streamline of the flow are analyzed. The predicted solid volumes by the presented DPD simulation of both types of arrays are quite close to the actual counterparts. These quantitative agreements show usefulness and effectiveness of the DPD model in simulating arrays of micropillar. By comparing two types of micropillar arrangement patterns, we find that the arrangement pattern of micropillar does not have significant influence on the permeability of the array.
基金funding support of the U.S.Army Research Laboratory with Cooperative Agreement No.W911NF-12-2-0023
文摘We calculate current correlation functions (CCFs) of dissipative particle dy- namics (DPD) and compare them with results of molecular dynamics (MD) and solutions of linearized hydrodynamic equations. In particular, we consider three versions of DPD, the empirical/classical DPD, coarse-grained (CG) DPD with radial-direction interactions only and full (radial, transversal, and rotational) interactions between particles. To fa- cilitate quantitative discussions, we consider specifically a star-polymer melt system at a moderate density. For bonded molecules, it is straightforward to define the CG variables and to further derive CG force fields for DPD within the framework of the Mori-Zwanzig formalism. For both transversal and longitudinal current correlation functions (TCCFs and LCCFs), we observe that results of MD, DPD, and hydrodynamic solutions agree with each other at the continuum limit. Below the continuum limit to certain length scales, results of MD deviate significantly from hydrodynamic solutions, whereas results of both empirical and CG DPD resemble those of MD. This indicates that the DPD method with Markovian force laws possibly has a larger applicability than the continuum description of a Newtonian fluid. This is worth being explored further to represent gen- eralized hydrodynamics.
文摘We investigate the behavior of dissipative particle dynamics (DPD) within different scaling regimes by numerical simulations. The paper extends earlier analytical findings of Ripoll, M., Ernst, M. H., and Espafiol, P. (Large scale and mesoscopic hy- drodynamics for dissipative particle dynamics. Journal of Chemical Physics, 115(15), 7271-7281 (2001)) by evaluation of numerical data for the particle and collective scaling regimes and the four different subregimes. DPD simulations are performed for a range of dynamic overlapping parameters. Based on analyses of the current auto-correlation functions (CACFs), we demonstrate that within the particle regime at scales smaller than its force cut-off radius, DPD follows Langevin dynamics. For the collective regime, we show that the small-scale behavior of DPD differs from Langevin dynamics. For the wavenumber-dependent effective shear viscosity, universal scaling regimes are observed in the microscopic and mesoscopic wavenumber ranges over the considered range of dynamic overlapping parameters.
基金supported by the National Natural Science Foundation of China(Nos.11272197 and11372175)the Innovation Program of Shanghai Municipality Education Commission,China(No.14ZZ095)
文摘The DNA sequencing technology has achieved a leapfrog development in recent years. As a new generation of the DNA sequencing technology, nanopore sequenc- ing has shown a broad application prospect and attracted vast research interests since it was proposed. In the present study, the dynamics of the electric-driven translocation of a homopolymer through a nanopore is investigated by the dissipative particle dynam- ics (DPD), in which the homopolymer is modeled as a worm-like chain (WLC). The DPD simulations show that the polymer chain undergoes conformation changes during the translocation process. The different structures of the polymer in the translocation process, i.e., single-file, double folded, and partially folded, and the induced current block- ades are analyzed. It is found that the current blockades have different magnitudes due to the polymer molecules traversing the pore with different folding conformations. The nanoscale vortices caused by the concentration polarization layers (CPLs) in the vicinity of the sheet are also studied. The results indicate that the translocation of the polymer has the effect of eliminating the vortices in the polyelectrolyte solution. These findings are expected to provide the theoretical guide for improving the nanopore sequencing tech- nique.
文摘The implementation of solid-fluid boundary condition has been a major challenge for dissipative particle dynamics(DPD)method.Current implementations of boundary conditions usually try to approach a uniform density distribution and a velocity profile close to analytical solution.The density oscillations and slip velocity are intentionally eliminated,and different wall properties disappear in the same analytical solution.This paper develops a new wall model that combines image and frozen particles and a new strategy to emphasize different wall properties especially wettabilities.The strategy first studies the realistic wall-fluid system by molecular dynamics(MD)simulation depending on physical parameters.Then,a DPD simulation is used to match the density and velocity profiles with the new wall model.The obtained DPD parameters can simulate the systems with the same wall and fluid materials.With this method,a simulation of the Poiseuille flow of liquid argon with copper walls is presented.Other walls with super-hydrophilic,hydrophilic,and hydrophobic wettabilities are also simulated.The limitations of the analytical solution and the effect of the wall-fluid interaction are discussed.The results show that the method suggested in this paper can simulate the mesoscale behavior of the microchannel flow related to realistic systems.
基金Project supported by the National Natural Science Foundation of China(No.52109068)the Water Conservancy Technology Project of Jiangsu Province of China(No.2022060)。
文摘Viscoelastic flows play an important role in numerous engineering fields,and the multiscale algorithms for simulating viscoelastic flows have received significant attention in order to deepen our understanding of the nonlinear dynamic behaviors of viscoelastic fluids.However,traditional grid-based multiscale methods are confined to simple viscoelastic flows with short relaxation time,and there is a lack of uniform multiscale scheme available for coupling different solvers in the simulations of viscoelastic fluids.In this paper,a universal multiscale method coupling an improved smoothed particle hydrodynamics(SPH)and multiscale universal interface(MUI)library is presented for viscoelastic flows.The proposed multiscale method builds on an improved SPH method and leverages the MUI library to facilitate the exchange of information among different solvers in the overlapping domain.We test the capability and flexibility of the presented multiscale method to deal with complex viscoelastic flows by solving different multiscale problems of viscoelastic flows.In the first example,the simulation of a viscoelastic Poiseuille flow is carried out by two coupled improved SPH methods with different spatial resolutions.The effects of exchanging different physical quantities on the numerical results in both the upper and lower domains are also investigated as well as the absolute errors in the overlapping domain.In the second example,the complex Wannier flow with different Weissenberg numbers is further simulated by two improved SPH methods and coupling the improved SPH method and the dissipative particle dynamics(DPD)method.The numerical results show that the physical quantities for viscoelastic flows obtained by the presented multiscale method are in consistence with those obtained by a single solver in the overlapping domain.Moreover,transferring different physical quantities has an important effect on the numerical results.
基金support of the National Natural Science Foundation of China(20674093)
文摘The Gay-Berne (GB) model has been proved to be highly successful in the simulation of liquid crystal phases via both molec- ular dynamics (MD) and nonequilibrium molecular dynamics (NEMD). However, the conventional thermostats used in the simulations of GB systems, such as Nose-Hoover and Langevin thermostats, have serious shortcomings especially in NEMD simulations. Recently, dissipative particle dynamics (DPD) has established itself as a useful thermostat for soft matter simulations, whereas the application of DPD thermostat in (NE)MD simulations is limited to the spherically isotropic potential models, such as the Lennard-Jones model. Considering the virtues of the DPD thermostat, that is, local, momentum conserved, and Galilean invariant, we extend the DPD thermostat to the non-spherical GB model. It is interesting to find that the translational DPD and rotational DPD thermostats can be used in the GB system independently and both can achieve the thermostatting effects. Also, we compared the performance of the DPD thermostat with other commonly used thermostats in NEMD simulations by investigating the streaming velocity profiles and the dynamics of phase separation in a typical but simple binary GB mixture under shear field. It is revealed that the known virtues of DPD thermostats, such as Galilean invariant, shear velocity profile-unbiased, and unscreened hydrodynamic interactions, are still intact when applying to GB systems. Finally, the appro- priate parameters for the DPD thermostat in the GB system are identified for future investigations.
基金supported by the National Basic Research Program of China(2005CB221307 & 2005CB221304)China Postdoctoral Science Foundation(20090460391 & 201003138)PetroChina RIPED Innovations Foundation.
文摘Chemical flooding is one of the effective technologies to increase oil recovery of petroleum reservoirs after water flooding.Above the scale of representative elementary volume(REV), phenomenological modeling and numerical simulations of chemical flooding have been reported in literatures,but the studies alike are rarely conducted at the pore-scale,at which the effects of physicochemical hydrodynamics are hardly resolved either by experimental observations or by traditional continuum-based simulations.In this paper,dissipative particle dynamics(DPD),one of mesoscopic fluid particle methods,is introduced to simulate the pore-scale flow in chemical flooding processes.The theoretical background,mathematical formulation and numerical approach of DPD are presented.The plane Poiseuille flow is used to illustrate the accuracy of the DPD simulation,and then the processes of polymer flooding through an oil-wet throat and a water-wet throat are studies, respectively.The selected parameters of those simulations are given in details.These preliminary results show the potential of this novel method for modeling the physicochemical hydrodynamics at the pore scale in the area of chemical enhanced oil recovery.
文摘A simple model, i.e. sodium di(2-ethylhexyl) sulfosuccinate (AOT) represented by one-head and two-tail beads tied together by a harmonic spring and water or isooctane by one bead, was put forward via Dissipative Particles Dynamics (DPD) simulation method. Using the changes of interfacial tension between water and oil phase, a ternary phase diagram of AOT/water/isooctane system was drawn. From the simulation, one conclusion is shown that DPD simulation can be considered as an adjunct to experiments.
基金Project supported by the Ministerio de Economia y Competitividad od Spain(No.FIS2013-47350-C5-3-R)
文摘An overview of the smoothed dissipative particle dynamics (SDPD) method is presented in a format that tries to quickly answer questions that often arise among users and newcomers. It is hoped that the status of SDPD is clarified as a mesoscopic particle model and its potentials and limitations are highlighted, as compared with other methods.
文摘In this work, by using coarse-grained molecular dynamics simulations, we found that poly(2-metha-cryloyloxyethyl phosphorylcholine)(PMPC) showed a strong solubility and a so-called antipolyelectrolyte effect(APE)in water. In contrast, obvious aggregations but no APE were found in n-butyl-substituted choline phosphatepolymers(PMBP) solutions. The underlying mechanisms for different solution behaviors of PMPC and PMBP wereinvestigated in detail. Our results indicate that the presence of butyl groups in PMBP enhances both the electrostaticinteractions and the hydrophobicity of PMBP molecules in the system. Both factors were found to contribute to theformations of aggregates in the PMBP system. Further researches revealed that hydrophobicity arising from the butylgroup plays a more important role than electrostatic interactions in inducing the PMBP aggregation. In addition, thestrong hydrophobicity in PMBP was found to be responsible for the absence of APE. These results are expected tocontribute to a better understanding and a better design of the solution properties of polyzwitterions.