Brownian dynamics simulation and experimental study of colloidal particle deposition in a microchannel flow

This paper reports an analysis of the irreversible deposition of colloidal particles from the pressure-driven flow in a microchannel within the framework of DLVO theory. A theoretical model is presented on the basis of the stochastic Langevin equation, incorporating the random Brownian motion of colloidal particles. Brownian dynamics simulation is used to compute the particle deposition in terms of the surface coverage. To validate the theoretical model, experiments are carried out using the parallel-plate flow cell technique, enabling direct videomicroscopic observation of the deposition kinetics of polystyrene latex particles in NaCl electrolytes. The theoretical predictions are compared with the experimental results, and good agreement is found.     

Coil-to-globule transition by dissipative particle dynamics simulation

The dynamics of a collapsing polymer under a temperature quench in dilute solution is investigated by dissipative particles dynamics. Hydrodynamic interactions and many-body interaction are preserved naturally by incorporating explicit solvent particles in this approach. Our simulation suggests a four-stage collapse pathway: localized clusters formation, cluster coarsening in situ, coarsening involving global backbone conformation change into a crumpled globule, and compaction of the globule. For all the quench depths and chain lengths used in our study, collapse proceeds without the chain getting trapped in a metastable "sausage" configuration, as reported in some earlier studies. We obtain the time scales for each of the first three stages, as well as its scaling with the quench depths ξ and chain lengths N. The total collapse time scales as τ(c) ～ ξ(-0.46 ± 0.04)N(0.98 ± 0.09), with the quench depth and degree of polymerization.     

Dissipative particle dynamics simulation study of the bilayer-vesicle transition

A bilayer structure is an important immediate for the vesicle formation. However,the mechanism for the bilayer-vesicle transition remains unclear. In this work,a dissipative particle dynamics(DPD) simulation method was employed to study the mechanism of the bilayer-vesicle transition. A coarse-grained model was built based on a lipid molecule termed dimyristoylphosphatidylcholine(DMPC). Simulations were performed from two different initial configurations:a random dispersed solution and a tensionless bilayer. It was found that the bilayer-vesicle transition was driven by the minimization of the water-tail hydrophobic interaction energy,and was accompanied with the increase of the position entropy due to the redistribution of water molecules. The bulk pressure was reduced during the bilayer-vesicle transition,suggesting the evolved vesicle morphology was at the relatively low free energy state. The membrane in the product vesicle was a two-dimensional fluid. It can be concluded that the membrane of a vesicle is not interdigitated and most of the bonds in lipid chains are inclined to orient along the radical axis of the vesicle.     

CFD-based simulation and experimental verification of 222Rn distribution in a walk-in type calibration chamber

A walk-in type ²²²Rn calibration chamber (~ 22 m³) is established at the Centre for Advanced Research in Environmental Radioactivity (CARER), Mangalore University, India which is being used by research groups working on ²²²Rn in India and other countries as well. In recent times, computational fluid dynamics (CFD) technique is opted as an alternative approach for the prediction of ²²²Rn concentration profile in the closed domain. CFD simulations were carried out to study the transient build-up and spatial behavior of ²²²Rn concentration in the calibration chamber. Measurements were performed using active ²²²Rn measuring devices and results of the CFD predictions and direct measurements were compared. A good agreement was observed between the simulated and experimental results with deviation between the two entities being ~ 3% in the case of transient build up and ~ 8% in the case of spatial distribution of ²²²Rn concentration.

     

Nanospheres in phase-separating multicomponent fluids: a three-dimensional dissipative particle dynamics simulation

The dynamics of phase separation of three-dimensional fluids containing nanospheres, which interact preferentially with one of the two fluids, is studied by means of large-scale dissipative particle dynamics simulations. We systematically investigated the effect of volume fraction, radius, and mass of the nanoparticles on both kinetics and morphology of the binary mixture. We found that nanospheres lead to a reduction of domain growth which is intensified as their volume fraction is increased for a given radius of nanoparticles, or as the nanoparticles radius is decreased for a given volume fraction. Up to moderate volume fractions of nanoparticles, the growth law, however, is found to be identical to that pure binary fluids, i.e., R(t) approximately t(n), with n=1. For relatively high volume fractions of nanoparticles, a diffusive growth regime was detected. The crossover to the slower growth regime as the nanoparticles volume fraction is increased or their radius is decreased is associated with the crystallization of the nanospheres within the preferred component. These results are qualitatively in good agreement with previous two-dimensional simulations using molecular dynamics [M. Laradji and G. MacNevin, J. Chem. Phys. 119, 2275 (2003)] and a time-dependent Ginzburg-Landau model [M. Laradji, J. Chem. Phys. 120, 9330 (2004)], as well as recent experiments.     

Model simulation and experimental verification of a cation-exchange IgG capture step in batch and continuous chromatography

The cation-exchange capture step of a monoclonal antibody (mAb) purification process using single column batch and multicolumn continuous chromatography (MCSGP) was modeled with a lumped kinetic model. Model parameters were experimentally determined under analytical and preparative conditions: porosities, retention factors and mass transfer parameters of purified mAb were obtained through a systematic procedure based on retention time measurements. The saturation capacity was determined through peak fitting assuming a Langmuir-type adsorption isotherm. The model was validated using linear batch gradient elutions. In addition, the model was used to simulate the start-up, cyclic steady state and shut down behavior of the continuous capture process (MCSGP) and to predict performance parameters. The obtained results were validated by comparison with suitable experiments using an industrial cell culture supernatant. Although the model was not capable of delivering quantitative information of the product purity, it proved high accuracy in the prediction of product concentrations and yield with an error of less than 6%, making it a very useful tool in process development.     

Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations

The generalized Crooks theorem (GCT) for deterministic non-Hamiltonian molecular dynamics simulations [Phys. Rev. E 75, 050101 (2007)] connects the probabilities of nonequilibrium realizations switching the system between two thermodynamic states, to the partition functions of these states. In comparison to the "classical" Crooks nonequilibrium work theorem [J. Stat. Phys. 90, 1481 (1998)], which deals with realizations involving only mechanical work, the GCT also accounts for additional work resulting from changes of the intensive and extensive thermodynamic variables of the system. In this article we present a numerical verification of the GCT using a Lennard-Jones fluid model where two particles are subject to a time-dependent external potential. Moreover, in order to switch the system between different thermodynamic states, the temperature and the pressure (or volume), which are controlled through the Martyna-Tobias-Klein equations of motion [J. Chem. Phys. 101, 4177 (1994)], are also varied externally. The free energy difference between states characterized by different distances of the target particles is evaluated using both a standard methodology (pair radial distribution functions) and the GCT. In order to exploit the various options provided by the GCT approach, i.e., the possibility of temperature/pressure/volume changes during the realizations, the free energy difference is recovered via arbitrary thermodynamic cycles. In all tests, the GCT is quantitatively verified.     

Numerical simulation of bubble dynamics in a micro-channel under a nonuniform electric field

A numerical method is used to simulate the motion and coalescence of air bubbles in a micro-channel under a nonuniform electric field. The channel is equipped with arrays of electrodes embedded in its wall and voltages are applied on the electrodes to generate a specified electric field gradient in the longitudinal direction. In the study, the Navier-Stokes equations are solved by using the level set method handling the deformable/moving interfaces between the bubbles and the ambient liquid. Both the polarization Coulomb force and the dielectrophoresis force are considered as the force source of the Navier-Stokes equations by solving the Maxwell's equations. The flow field equations and the electric field equations are coupled and solved by using the finite element method. The electric field characteristics and the dynamic behavior of a bubble are analyzed by studying the distributions of the electric field and the force, the deformation and the moving velocity of the air bubble. The result suggests that the model of dispersed drops suspended in the immiscible dielectric liquid and driven by a nonuniform electric field is an effective method for the transportation and coalescence of micro-drops.     

Flux decline in crossflow microfiltration and ultrafiltration: experimental verification of fouling dynamics

The theory of fouling dynamics in crossflow membrane filtration is compared with ultrafiltration experiments with suspensions of 0.12 μm silica colloids. It has been experimentally verified that colloidal fouling in crossflow filtration is a dynamics process from non-equilibrium to equilibrium and that the steady state flux is the limiting flux. With the cake concentration c_g identified from an independent experiment and the specific cake resistance calculated by Carman–Kozeny equation, the time-dependent flux and the time to reach steady state in the experiments of this study are correctly predicted with the theory of fouling dynamics.     

Schmidt number effects in dissipative particle dynamics simulation of polymers

Simulation studies for dilute polymeric systems are presented using the dissipative particle dynamics method. By employing two different thermostats, the velocity-Verlet and Lowe's scheme, we show that the Schmidt number (S(c)) of the solvent strongly affects nonequilibrium polymeric quantities. The fractional extension of wormlike chains subjected to steady shear is obtained as a function of S(c). Poiseuille flow in microchannels for fixed polymer concentration and varying number of repeated units within a chain is simulated. The nonuniform concentration profiles and their dependence on S(c) are computed. We show the effect of the bounce-forward wall boundary condition on the depletion layer thickness. A power law fit of the velocity profile in stratified Poiseuille flow in a microchannel yields wall viscosities different from bulk values derived from uniform, steady plane Couette flow. The form of the velocity profiles indicates that the slip flow model is not useful for the conditions of these calculations.     

Flow-induced translocation of polymers through a fluidic channel: a dissipative particle dynamics simulation study

The dynamics of flow-induced translocation of polymers through a fluidic channel has been studied by dissipative particle dynamics (DPD) approach. Unlike implicit solvent models, the many-body energetic and hydrodynamic interactions are preserved naturally by incorporating explicit solvent particles in this approach. The no-slip wall boundary and the adaptive boundary conditions have been implemented in the modified DPD approach to model the hydrodynamic flow within a specific wall structure of fluidic channel and control the particles' density fluctuations. The results show that the average translocation time versus polymer chain length satisfies a power-law scaling of τ ～N(1.152). The conformational changes and translocation dynamics of polymers through the fluidic channel have also been investigated in our simulations, and two different translocation processes, i.e., the single-file and double-folded translocation events, have been observed in detail. These findings may be helpful in understanding the conformational and dynamic behaviors of such polymer and/or DNA molecules during the translocation processes.     

Comparison between theoretical values and simulation results of viscosity for the dissipative particle dynamics method

In order to investigate the validity of the dissipative particle dynamics method, which is a mesoscopic simulation technique, we have derived an expression for viscosity from the equation of motion of dissipative particles. In the concrete, we have shown the Fokker-Planck equation in phase space, and macroscopic conservation equations such as the equation of continuity and the equation of momentum conservation. The basic equations of the single-particle and pair distribution functions have been derived using the Fokker-Planck equation. The solutions of these distribution functions have approximately been solved by the perturbation method under the assumption of molecular chaos. The expressions of the viscosity due to momentum and dissipative forces have been obtained using the approximate solutions of the distribution functions. Also, we have conducted nonequilibrium dynamics simulations to investigate the influence of the parameters, which have appeared in defining the equation of motion in the dissipative particle dynamics method. The theoretical values of the viscosity due to dissipative forces in the Hoogerbrugge-Koelman theory are in good agreement with the simulation results obtained by the nonequilibrium dynamics method, except in the range of small number densities. There are restriction conditions for taking appropriate values of the number density, number of particles, time interval, shear rate, etc., to obtain physically reasonable results by means of dissipative particle dynamics simulations.     

Mesoscopic simulation of self-assembly in surfactant oligomers by dissipative particle dynamics

Self-assembling properties of surfactant oligomers in an aqueous medium is simulated by dissipative particle dynamics (DPD). The critical micellar concentration (CMC) of dimeric (oligomerization = 2) and trimeric (oligomerization = 3) surfactant is much lower than their single-chain counterpart. All surfactants form spherical micelles at the concentration not far above their CMC. The transition from spherical to cylindrical micelles exhibits with increasing surfactant concentration. Lamellar micelles will appear with further increasing the surfactant concentration. For dimeric and trimeric surfactants, cylindrical micelles transform into extremely long “wormlike” or “threadlike” micelles before the transition to lamellar micelles. These results are in qualitative agreement with laboratory experiment. Average aggregation numbers (AN) of micelles increase with a power law of AN  c when the surfactant concentration c CMC. The self-diffusion coefficients will drop with a power law of D  c⁻ when wormlike micelles are formed.     

A molecular dynamics simulation of lithium fluoride: Volume phase and nanosized particle

The PC GAMESS package was used to obtain interionic pair potentials for lithium fluoride. A molecular dynamics simulation of the volume phase and nanosized LiF particle was performed. The temperatures of fusion and self-diffusion coefficients of the volume phase and lithium fluoride nanoparticle were found; for the volume phase, they were close to the experimental data. The temperature of fusion of a particle ～2 Å in diameter decreased by ～600 K. The possibility of a considerable increase in ionic conductivity over the temperature range 520–1122 K was demonstrated for nanosized LiF.     

IBIsCO: a molecular dynamics simulation package for coarse-grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors.     

基于甲酸和氢氧化钠的衍生移动反应界面的数值计算与实验验证(英文)

在甲酸（α相）和氢氧化钠（γ相）缓冲液形成的移动反应界面的基础上,提出了一种衍生移动反应界面模型。模型表明在α相和γ相之间会形成一个新的β相,β相和α相形成衍生移动反应界面,β相和γ相形成移动界面。为了验证该模型的有效性,该文给出了相关理论及数值推导过程。此外,基于毛细管电泳和自制装置进行了相关实验。结果表明,若使用以前的移动反应界面,实验结果与理论计算存在较大误差,而采用该文提出的衍生移动反应界面,实验数据与理论计算结果高度一致。该文提出的衍生移动反应界面理论及模型对于电泳,特别是毛细管电泳中样品的分离与富集具有重要的意义。     

Dissipative particle dynamics simulation of microphase separation behaviors in graft-diblock copolymer films

Dependence of the microphase separation behaviors of graft-diblock copolymers (A _x )g(B _y ) in thin films on composition fraction, thickness of film and A–B repulsing strength is investigated preliminarily by dissipative particle dynamics. Several kinds of ordered mesostructures have been observed and the simulated phase diagrams show evident asymmetries, besides, the center of lamellas region shifts away from f _A = 0.5. Some of the mesostructures in the film can correspond to those in bulk. Decreasing the thickness of film as well as strengthening the A–B repulsion help the mesostructures enhance the degree of order.     

Progressive failure numerical simulation and experimental verification of carbon-fiber composite corrugated beams under dynamic impact

To explore the axial impact energy absorption capacity of bidirectional carbon pre-impregnated (prepreg) composite corrugated beams, a solid 3D finite element model with different trigger mechanism settings and different ply designs was established. Numerical simulation of dynamic impact was performed on the model. An in-plane damage model considering shear failure was created based on continuum damage mechanics and Hashin's criteria, and a stiffness degradation model of damage failure for G803/5224 is proposed. The cohesive zone model is used and the bilinear traction-separation constitutive model is considered to simulate inter-laminar delamination failure, thereby accurately reflecting the anisotropic progressive damage characteristics of bidirectional carbon-fiber prepreg composite corrugated beams. The results show that progressive failure and damage occur under impact loading of corrugated beams. The energy-absorbing load-displacement curve and specific energy absorption were obtained through simulation. Simulation results were validated by comparison with test results. With the maximum relative error of its average crushing load less than 11%, the damage morphology and test results of the beam has improved in uniformity. Furthermore, the validity of 3D finite element models considering inter-laminar delamination damage has been validated.