A comprehensive molecular dynamics study of a single polystyrene chain in a good solvent

In this study, molecular characteristics of polystyrene (PS) was calculated measuring its dilute-solution properties in toluene at 288.15 K via molecular dynamics (MD) simulations. The solution models consisted of PS chains with different number of repeating units all of which were in a dilute regime. In order to investigate the compatibility between the polymer and the solvent molecules, interaction energy and Flory-Huggins (FH) interaction parameter were estimated. The simulation results indicate that increasing the chain repeating units enhanced the interaction between the solute and the solvent. Additionally, the chain dimensions were evaluated calculating the radius of gyration (R_g) and end-to-end distance, r0. To determine the dynamic behavior of the chains in the solutions, mean square displacement (MSD) and diffusivity coefficient were calculated. The simulation results indicated that the chain rigidity at low molecular weight and chain flexibility with increasing the molecular weight influenced chains dynamic behavior and diffusivity. Moreover, radial distribution function (RDF) illustrated the effect of steric hindrance of the chains in dilute solution on capturing the solvent molecules. In addition, solution viscosity was calculated by performing non-equilibrium molecular dynamics simulation (NEMD). The obtained results of chain characteristics and viscosity showed a good agreement with experimental results published previously. This agreement confirms the accuracy of the applied simulation method to characterize the dilute solutions and the chains characteristics.     

Structure of a tethered polymer under flow using molecular dynamics and hybrid molecular-continuum simulations

We analyse the structure of a single polymer tethered to a solid surface undergoing a Couette flow. We study the problem using molecular dynamics (MD) and hybrid MD-continuum simulations, wherein the polymer and the surrounding solvent are treated via standard MD, and the solvent flow farther away from the polymer is solved by continuum fluid dynamics (CFD). The polymer represents a freely jointed chain (FJC) and is modelled by Lennard-Jones (LJ) beads interacting through the FENE potential. The solvent (modelled as a LJ fluid) and a weakly attractive wall are treated at the molecular level. At large shear rates the polymer becomes more elongated than predicted by existing theoretical scaling laws. Also, along the normal-to-wall direction the structure observed for the FJC is, surprisingly, very similar to that predicted for a semiflexible chain. Comparison with previous Brownian dynamics simulations (which exclude both solvent and wall potential) indicates that these effects are due to the polymer–solvent and polymer–wall interactions. The hybrid simulations are in perfect agreement with the MD simulations, showing no trace of finite size effects. Importantly, the extra cost required to couple the MD and CFD domains is negligible.     

Hybrid MC/RISM technique for simulation of polymer solutions: Monte Carlo+ RISM integral equations

A new (hybrid) method is reported for modelling complex macromolecular systems. The approach combines the traditional atomistic Monte Carlo (MC) computer simulation of flexible polymer chains with the numerical solution of the site-site Ornstein-Zernike-like (RISM) integral equations. The method is used for calculating properties of a linear polymer in dilute solution. Since the condensed-phase environment of a flexible macromolecule affects the equilibrium configuration probability distribution of the macromolecule, the site-site intramolecular correlation function and the intramolecular potential field are treated in a self-consistent manner. Briefly, the MC method is applied to generate the configurations of a single chain molecule. Using the coordinates of chain beads, the averaged intrapolymer correlation function is obtained. Then, solving the coupled RISM equations for a given density of solvent particles, we find the polymer-solvent correlation functions. This yields the medium-induced intrapolymer potential and the corresponding effective intramolecular energies, which are used in the standard Metropolis MC procedure. The structural properties of the polymer chain are computed by averaging over the statistically representative set of configurations. As a result of many such iterations, the intramolecular structure is determined self-consistently. Using the hybrid MC/RISM method, extensive studies have been made of static properties of flexible polymer chains surrounded by LJ particles with purely repulsive interactions between the particles and chain beads. Also, direct molecular dynamics simulations have been carried out and have demonstrated that the hybrid MC/RISM approach gives a quite accurate prediction for condensed-phase effects.     

Deformation of a tethered polymer in uniform flow

Static properties of a single polymer fixed at one end and subjected to a uniform flow field are investigated for several polymer models: the Gaussian chain, the freely jointed chain, and the FENE (Finitely Extensible Nonlinear Elastic) chain. By taking into account first the excluded-volume interaction and subsequently also the hydrodynamic interaction, the polymer models are gradually completed and the relevance of each effect for the polymer deformation can be identified. Results from computer simulations of these bead spring chains are compared with analytical calculations using either the conformational distribution function or blob models. To this end, in contrast to the blob model with non-draining blobs introduced for a tethered polymer by Brochard-Wyart, we here develop also a model with free-draining blobs. It turns out that a limited extensibility of the polymer – described by nonlinear spring forces in the model – leads to a flow velocity dependence of the end-to-end distance, segment density, etc. which agrees with the power law predictions of the blob model only for very long chains and in a narrow range of flow velocities. This result is important for comparison with recent experiments on DNA molecules which turn out to be still rather short in this respect. The relative importance of finite extensibility, the excluded-volume effect, and hydrodynamic interactions for polymers in flow is not fully understood at present. The simulation of reasonably long chains becomes possible even when fluctuating hydrodynamic interactions are taken into account without employing averaging procedures by introducing efficient numerical approximation schemes. At medium velocity of the uniform flow the polymer is partially uncoiled and simulations show that the effects of excluded-volume and hydrodynamic interactions are position-dependent. Both are stronger near the free end than near the tethered end of the polymer. A crossover from a nearly non-draining polymer at small flow velocities to a free-draining almost uncoiled chain at large velocities is found in the simulations. Accordingly, models assuming the polymer to be composed of either free- or non-draining subunits, like the two blob models, cannot correctly describe the extension and shape of a tethered polymer in flow, and simple power laws for the polymer extension, etc. cannot be expected. Received 21 June 1999     

Importance of hydrodynamic shielding for the dynamic behavior of short polyelectrolyte chains

The dynamic behavior of polyelectrolyte chains in the oligomer range is investigated with coarse-grained molecular dynamics simulation and compared to data obtained by two different experimental methods, namely, capillary electrophoresis and electrophoresis NMR. We find excellent agreement of experiments and simulations when hydrodynamic interactions are accounted for in the simulations. We show that the electrophoretic mobility exhibits a maximum in the oligomer range and for the first time illustrate that this maximum is due to the hydrodynamical shielding between the chain monomers. Our findings demonstrate convincingly that it is possible to model dynamic behavior of polyelectrolytes using coarse-grained models for both the polyelectrolyte chains and the solvent induced hydrodynamic interactions.     

Cross-stream migration of flexible molecules in a nanochannel

Molecular dynamics simulations are used to examine the cross-stream chain migration phenomenon in dilute polymer solutions that are flowing in nanochannels. In particular, both uniform planar shear (Couette) and pressure driven (Poiseuille) flows of a dilute polymer solution are studied using a bead-spring representation of polymer chains and a coarse grained model for the solvent. Our results show that three mechanisms govern the migration of deformable molecules in a nanochannel: (1) chain-wall hydrodynamic interactions, (2) thermal diffusion, and (3) gradient in chain mobility. These results are discussed in the context of recent experimental, numerical and theoretical work.     

GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions

Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute unified device architecture (CUDA) of recent graphics processors (GPUs). Thereby, the simulation of explicit solvent particles is avoided and hydrodynamic interactions can easily be accounted for in already available, highly accelerated molecular dynamics simulations. Special emphasis is put on efficient memory access and numerical stability. The algorithm is applied to the periodic sedimentation of a cluster of four suspended particles. Finally, we investigate the runtime performance of generic memory access patterns of complexity O(N ²) for various GPU algorithms relying on either hardware cache or shared memory.     

An optimised molecular model for ammonia

Based on molecular dynamics (MD) computer simulations we investigate the dynamic behaviour of a model complex fluid suspension consisting of large (A) particles (the ‘solute’) immersed in a bath of smaller ‘solvent’ (B) particles. The goal is to identify the effect of systematic simplifications (coarse-graining) of the solvent on typical microscopic time correlation functions characterizing the single-particle and collective dynamics of the solute. As a reference system we employ a binary Lennard–Jones mixture of spherical particles with significant differences in particle sizes (σ_A>σ_B) and masses (m _A>m _B). We then replace the original B particles step by step by a reduced number of larger and heavier particles such that the mass and volume fraction of B particles is kept constant. At each step of coarse-graining, the intermolecular interactions between A particles are chosen such that the static A–A structure of the reference system is preserved. Our MD results indicate that coarse-graining has a profound influence on both the single-particle dynamics as reflected by the self-diffusion constant and the collective dynamics represented by the distinct part of the van Hove time correlation function. The latter holds only at intermediate packing fractions, whereas the collective dynamics turns out to be essentially insensitive to coarse-graining at high packing fractions.     

自扩散泳微观转动马达的介观模拟

转动的微尺度马达是一类重要的微流器件.近年来,因为其重要的应用及理论价值引起了学术界的广泛关注.本文提出了一种新型的自扩散泳驱动的微观转动马达模型.通过介观动力学模拟,验证了该模型的有效性.模拟结果表明,该自扩散泳微观转动马达可以单向地自驱动转动,并且转动速度和马达表面发生的催化化学反应速率(即自产生的浓度梯度场强弱)、以及液体分子与马达之间的相互作用有关.此外,研究了两个转动马达共存时的运动行为,重点考察了马达之间的流体力学相互作用和浓度梯度场效应对马达转动的影响.该自扩散泳微观转动马达为设计实用的微流器件提供了新的思路和参考,也为研究活性胶体系统的集体行为提供了理想模型.     

The compression of polymer brushes under shear: the friction coefficient as a function of compression,shear rate and the properties of the solvent

We present a study of the compression of polymer-grafted surfaces using the dissipative particle dynamics (DPD) method at constant chemical potential. We demonstrate the importance of performing simulations of compression at fixed chemical potential of the solvent by comparing the simulated force-compression curves at constant chemical potential and density with the experimental profile determined for poly(ethylene-propylene) chains grafted onto mica surfaces in a cyclohexane solvent. The simulated force-distance and friction profiles are presented as a function of the polymer grafting density, the shear rate and the nature of the solvent. We also study the influence of the steepness of conservative potential between polymer segments and the size of the solvent elements (particles) on the form of the force-compression and friction-compression profiles.     

Polymer-decorated tethered membranes under good- and poor-solvent conditions

We study tethered membranes grafted by polymer chains on one side. Mean-field and scaling arguments predicting a spontaneous curvature are compared to the results of lattice-based Monte Carlo simulations using the Bond Fluctuation Model, which are carried out for various grafting densities and chain lengths. We show that already slightly overlapping chains bend the membrane significantly. This proves the entropic origin for the bending stiffness, which is of order kT . To understand the membrane curvature under conditions of very small bending stiffness we apply a geometrical model which takes into account the state of chains at the overlap threshold. Applying a thermal solvent model for the grafted chains, we demonstrate that the bending direction of the membrane can be triggered by variation of the solvent quality. This indicates that polymer-decorated membranes may serve as switchable nanoscale devices.     

Atomistic hybrid DSMC/NEMD method for nonequilibrium multiscale simulations

A multiscale hybrid method for coupling the direct simulation Monte Carlo (DSMC) method to the nonequilibrium molecular dynamics (NEMD) method is introduced. The method addresses Knudsen layer type gas flows within a few mean free paths of an interface or about an object with dimensions of the order of a few mean free paths. It employs the NEMD method to resolve nanoscale phenomena closest to the interface along with coupled DSMC simulation of the remainder of the Knudsen layer. The hybrid DSMC/NEMD method is a particle based algorithm without a buffer zone. It incorporates a new, modified generalized soft sphere (MGSS) molecular collision model to improve the poor computational efficiency of the traditional generalized soft sphere GSS model and to achieve DSMC compatibility with Lennard-Jones NEMD molecular interactions. An equilibrium gas, a Fourier thermal flow, and an oscillatory Couette flow, are simulated to validate the method. The method shows good agreement with Maxwell–Boltzmann theory for the equilibrium system, Chapman–Enskog theory for Fourier flow, and pure DSMC simulations for oscillatory Couette flow. Speedup in CPU time of the hybrid solver is benchmarked against a pure NEMD solver baseline for different system sizes and solver domain partitions. Finally, the hybrid method is applied to investigate interaction of argon gas with solid surface molecules in a parametric study of the influence of wetting effects and solid molecular mass on energy transfer and thermal accommodation coefficients. It is determined that wetting effect strength and solid molecular mass have a significant impact on the energy transfer between gas and solid phases and thermal accommodation coefficient.     

Conformational fluctuations of a tethered polymer in uniform flow

The decay of correlations in the conformational fluctuations of a tethered polymer subjected to a uniform flow is analyzed in terms of relaxation times and associated normal modes. These quantities are calculated numerically from Brownian dynamics simulations of several bead spring polymer models. In this way, the influence of different effects like a finite extensibility of the springs and excluded-volume as well as hydrodynamic interactions between the beads on the decay of fluctuations is identified. Moreover, by comparison of the simulation results to analytically tractable blob models with corresponding assumptions, the capability of the tensile-blob picture to predict relaxation times and modes is assessed. For excluded-volume and hydrodynamic interactions a crossover to Rouse-like behavior occurs when the flow velocity and hence the polymer deformation exceeds a certain value. For finitely extensible springs, in contrast, the relaxation times decrease monotonically with increasing polymer deformation. This latter behavior differs from assumptions often used in rheological modeling by dumbbells and is not captured by the blob model.Received: 4 April 2003, Published online: 12 August 2003PACS: 83.80.Rs Polymer solutions - 83.10.Mj Molecular dynamics, Brownian dynamics - 36.20.Ey Conformation (statistics and dynamics) - 47.50. + d Non-Newtonian fluid flows     

Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones （LJ） or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.     

Influence of Solvent-Solvent and Solute-Solvent Interaction Properties on Solvent-Mediated Potential

A recently proposed universal calculational recipe for solvent-mediated potential is applied to calculate excess potential of mean force between two large Lennard-Jones (LJ) or hard core attractive Yukawa particles immersed in small LJ solvent bath at supercritical state. Comparison between the present prediction with a hypernetted chain approximation adopted for solute-solute correlation at infinitely dilute limit and existing simulation data shows high accuracy for the region with large separation, and qualitative reliability for the solute particle contact region. The calculational simplicity of the present recipe allows for a detailed investigation on the effect of the solute-solvent and solvent-solvent interaction details on the excess potential of mean force. The resultant conclusion is that gathering of solvent particles near a solute particle leads to repulsive excess PMF, while depletion of solvent particles away from the solute particle leads to attractive excess PMF, and minor change of the solvent-solvent interaction range has large influence on the excess PMF.     

Molecular-dynamics simulations with explicit hydrodynamics I: On the friction coefficients of deformed polymers

We implement large-scale Molecular-Dynamics (MD) simulations which incorporate hydrodynamic interactions via the inclusion of explicit Lennard-Jones solvent to examine the behaviour of polymer chains in sieving media. We begin by examining the friction coefficients of polymers in long-lived states responsible for inducing length-dependent mobility, i.e., allowing separation of polymers (or polyelectrolytes) by molecular weight. In particular, the conformations we examine occur in devices which utilize arrays of molecular obstacles or dilute solutions of polymers. We compare the results from our MD simulations with expressions from macroscopic hydrodynamics for four specific cases: i) a random coil excluded-volume Zimm polymer, ii) a rigid polymer moving perpendicular to its major axis iii) a rigid polymer moving parallel to its major axis and iv) a rigid polymer, folded at different points along its contour. We also examine the behaviour of the friction coefficient of a fully flexible molecule pulled by its middle monomer as a function of an applied force F and show that there are several distinct frictional regimes.PACS: 83.10.Mj Molecular dynamics, Brownian dynamics - 61.41. + e Polymers, elastomers, and plastics - 82.20.Wt Computational modeling; simulation     

Dynamics of a tethered polymer in shear flow

The dynamics of a single polymer tethered to a solid surface in a shear flow was observed using fluorescently labeled DNA chains. Dramatic shear enhanced temporal fluctuations in the chain extension were observed. The rate of these fluctuations initially decreased for increasing shear rate gamma; and increased above a critical gamma;. Simulations revealed that these anomalous dynamics arise from a continual recirculating motion of the chain or cyclic dynamics. These dynamics arise from a coupling of the chain velocity in the flow direction to thermally driven fluctuations of the chain in the shear gradient direction.