Universal properties of a single polymer chain in slit: Scaling versus molecular dynamics simulations

We revisit the classical problem of a polymer confined in a slit in both of its static and dynamic aspects. We confirm a number of well known scaling predictions and analyze their range of validity by means of comprehensive molecular dynamics simulations using a coarse-grained bead-spring model of a flexible polymer chain. The normal and parallel components of the average end-to-end distance, mean radius of gyration and their distributions, the density profile, the force exerted on the slit walls, and the local bond orientation characteristics are obtained in slits of width D=4/10 (in units of the bead diameter) and for chain lengths N=50/300. We demonstrate that a wide range of static chain properties in normal direction can be described quantitatively by analytic model-independent expressions in perfect agreement with computer experiment. In particular, the observed profile of confinement-induced bond orientation is shown to closely match theory predictions. The anisotropy of confinement is found to be manifested most dramatically in the dynamic behavior of the polymer chain. We examine the relation between characteristic times for translational diffusion and lateral relaxation. It is demonstrated that the scaling predictions for lateral and normal relaxation times are in good agreement with our observations. A novel feature is the observed coupling of normal and lateral modes with two vastly different relaxation times. We show that the impact of grafting on lateral relaxation is equivalent to doubling the chain length.     

Dissipative particle dynamics simulations of polymer melts. I. Building potential of mean force for polyethylene and cis-polybutadiene

We present the derivation of coarse-grained force fields for two types of polymers, polyethylene (PE), and cis-polybutadiene (cis-PB), using the concept of potential of mean force. Coarse-grained force fields were obtained from microscopic simulations for several coarse-graining levels, i.e., different number of monomers lambda per mesoscopic unit called "bead." These force fields are then used in dissipative particle dynamics (DPD) simulations to study structural and dynamical properties of polymer melts of PE and cis-PB. The radial distribution functions g(R), the end-to-end distance R0, the end-to-end vector relaxation time tau, and the chain center of mass self-diffusion D(CM), are computed for different chain lengths at different coarse-graining factor lambda. Scaling laws typical of the Rouse regime are obtained for both polymers for chain lengths ranging from 6 to 50 beads. It is found that the end-to-end distance R0 obtained from DPD simulations agree well with values obtained from both microscopic simulations and experiments. The dependence of the friction coefficient used in DPD simulations versus the coarse-graining level is discussed in view of the overall scaling of the dynamical properties.     

Molecular dynamics simulation study on the phase behavior of the Gay-Berne model with a terminal dipole and a flexible tail

To study the effect of the alkyl tail and the terminal dipole on the stability of the liquid crystalline phase of mesogens, we have carried out molecular dynamics simulations for 1CB(4-methyl-4'-cyanobiphenyl) and 5CB(4-n-pentyl-4'-cyanobiphenyl) by using a coarse-grained model. In the coarse-grained model, a 5CB molecule is divided into the rigid part of 1CB moiety, which is represented by an ellipsoid, and the remaining flexible part which is represented by a chain of united atoms. The nonbonded potential between coarse-grained segments is represented by the generalized Gay-Berne (GB) potential and the potential parameters are determined by directly comparing the GB potential with the atomistic potentials averaged over the rotation of the mesogen around its axis. In addition, a dipole moment is placed at one end of the ellipsoid opposite to the flexible tail. The ordered state obtained in the polar 5CB model was assigned as the nematic phase, and the experimental static and dynamical properties were reproduced well by using this coarse-grained model. Both the dipole-dipole interactions and the thermal fluctuation of the flexible tail increase the positional disorder in the director direction, and stabilize the nematic phase. Thus, the nematic phase in the polar 5CB is induced by a cooperative effect of the flexible tail and the terminal dipole. It is noted that a local bilayer structure with head-to-head association is formed in the nematic phase, as experimentally observed by x-ray diffraction measurements.     

Molecular weight distribution effects on the structure of strongly adsorbed polymers by Monte Carlo simulation

Monte Carlo simulations are reported to study the structure of polymers adsorbed from solution onto strongly attractive, perfectly smooth substrates. Six systems spanning a range of molecular weight distributions are investigated with a coarse-grained united atom model for freely rotating chains. By employing a global replica exchange algorithm and topology altering Monte Carlo moves, a range of monomer-surface attraction from weak (0.27kT) to strong (4kT) is simultaneously explored. Thus for the first time ever, equilibrium polymer adsorption on highly attractive surfaces is studied, with all adsorbed molecules displaying similar properties and statistics. The architecture of the adsorbed layers, including density profiles, bond orientation order parameters, radii of gyration, and distribution of the adsorbed chain fractions, is shown to be highly dependent on the polydispersity of the polymer phase. The homology of polymer chains, and the ergodicity of states explored by the molecules is in contrast to the metastable, kinetically constrained paradigm of irreversible adsorption. The structure of more monodisperse systems is qualitatively similar to experimental results and theoretical predictions, but result from very different chain conformations and statistics. The polydispersity-dependent behavior is explained in the context of the competition between polymers to make contact with the surface.     

Force field dependence of phospholipid headgroup and acyl chain properties: Comparative molecular dynamics simulations of DMPC bilayers

The reliability of molecular simulations largely depends on the quality of the empirical force field parameters. Force fields used in lipid simulations continue to be improved to enhance the agreement with experiments for a number of different properties. In this work, we have carried out molecular dynamics simulations of neat DMPC bilayers using united‐atom Berger force field and three versions of all‐atom CHARMM force fields. Three different systems consisting of 48, 72, and 96 lipids were studied. Both particle mesh Ewald (PME) and spherical cut‐off schemes were used to evaluate the long‐range electrostatic interactions. In total, 21 simulations were carried out and analyzed to find out the dependence of lipid properties on force fields, system size, and schemes to calculate long‐range interactions. The acyl chain order parameters calculated from Berger and the recent versions of CHARMM simulations have shown generally good agreement with the experimental results. However, both sets of force fields deviate significantly from the experimentally observed P‐C dipolar coupling values for the carbon atoms that link the choline and glycerol groups with the phosphate groups. Significant differences are also observed in several headgroup parameters between CHARMM and Berger simulations. Our results demonstrate that when changes were introduced to improve CHARMM force field using PME scheme, all the headgroup parameters have not been reoptimized. The headgroup properties are likely to play a significant role in lipid–lipid, protein–lipid, and ligand–lipid interactions and hence headgroup parameters in phospholipids require refinement for both Berger and CHARMM force fields. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2010     

Developing a coarse-grained force field for the diblock copolymer poly(styrene-b-butadiene) from atomistic simulation

We have developed a coarse-grained force field for the poly(styrene-b-butadiene) diblock copolymer. We describe the computational methods and discuss how they were applied to develop a coarse-grained force field for this diblock copolymer from the atomistic simulation. The new force field contains three different bonds, four angles, five dihedral angles, and three nonbonded terms. We successfully tested this coarse-grained model against the chain properties, including static and dynamic properties, derived from the atomistic simulation; the results suggest that the coarse-grained force field is an effective model.     

A transferable coarse-grained model for hydrogen-bonding liquids

We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effective-potential based approaches. The previous center-of-mass framework (P. A. Golubkov and P. Ren, J. Chem. Phys., 2006, 125, 64103) is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic-level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations.     

Temperature dependence of the properties of simulated PCH5

We present the results of molecular dynamics simulation studies of 4-(trans-4'-pentylcyclohexyl)- benzonitrile (PCH5) at different temperatures in the isotropic and nematic phases within the united atom approach. Special attention is paid to the electrostatic interactions. Different methods of determining point charges are compared and the effect of the electrostatic interactions on the molecular distribution is considered. Their decisive influence on local molecular packing and phase transition temperature is shown. We analyse various static and dynamic properties, being specially interested in the reliability of the simulation results, to check to which extent they are distorted by the confinements adopted during the simulations (and especially the size of the system). Using realistic molecular interaction models in contrast to simple model ellipsoids, we find that the number of molecules and the lengths of the simulation runs have to be increased considerably when studying macroscopic properties like the phase transition temperature and the order parameter. Much easier to access are single particle and local properties such as translational dynamics and local ordering, but also the relative dependence of the order parameters of various ranks.     

Properties of simple models of polymer networks. A Monte Carlo simulation

A model polymer network was constructed from branched chains. Each chain was built on a simple cubic lattice forming a star-branched polymer consisting of f = 3 arms of equal lengths. The fragment of network under consideration consisted of 1, 2 and 3 star polymers with different topology of connections. The only potential used was excluded volume (athermal chains). The properties of the network were determined by the means of computer simulations using the classical Metropolis sampling algorithm (local micromodifications of chain conformation). The behaviour of linear chains of the same molecular weight was also studied as a state of reference. The influence of attaching the next star-branched chain to the network on its static and dynamic properties was studied. The short-time dynamic behaviour of chain fragments was determined and discussed.     

Effective thermostat induced by coarse graining of simple point charge water

We investigate how the transport properties of a united atom fluid with a dissipative particle dynamics thermostat depend on the functional form and magnitude of both the conservative and the stochastic interactions. We demonstrate how the thermostat strongly affects the hydrodynamics, especially diffusion, viscosity, and local escape times. As model system we use simple point charge (SPC) water, from which projected trajectories are used to determine the effective interactions in the united atom model. The simulation results support our argument that the thermostat should be viewed as an integral part of the coarse-grained dynamics rather than a tool for approaching thermal equilibrium. As our main result we show that the united atom model with the adjusted effective interactions approximately reproduces the diffusion constant and the viscosity of the underlying detailed SPC water model.     

Mesoscale model of polymer melt structure: self-consistent mapping of molecular correlations to coarse-grained potentials

Development and application of coarse-graining methods to condensed phases of macromolecules is an active area of research. Multiscale modeling of polymeric systems using coarse-graining methods presents unique challenges. Here we apply a coarse-graining method that self-consistently maps structural correlations from detailed molecular dynamics (MD) simulations of alkane oligomers onto coarse-grained potentials using a combination of MD and inverse Monte Carlo methods. Once derived, the coarse-grained potentials allow computationally efficient sampling of ensemble of conformations of significantly longer polyethylene chains. Conformational properties derived from coarse-grained simulations are in excellent agreement with experiments. The level of coarse graining provides a control over the balance of computational efficiency and retention of chemical identity of the underlying polymeric system. Challenges to extension and application of this and similar structure-based coarse-graining methods to model dynamics and phase behavior in polymeric systems are briefly discussed.     

Dynamic and static interactions between bitumen droplets in water

In the commercial bitumen extraction operation, dynamic and static interaction forces between bitumen drops in water determine the likelihood of desirable bitumen coalescence at different process stages. These dynamic and static forces were measured using colloidal particle scattering and hydrodynamic force balance techniques, respectively. In the former technique, dynamic interactions are studied through droplet-droplet collision trajectory measurement. In the latter technique, the static attractive forces between droplets are determined when a doublet is separated with a known and adjustable hydrodynamic force. The dynamic force measurement implies the presence of rigid chains on bitumen surfaces. The mean chain lengths for deasphalted bitumen at pH 7, whole bitumen at pH 7, and whole bitumen at pH 8.5 are 50, 78, and 41 nm, respectively. However, the static force measurement indicates much shorter mean chain lengths (<9 nm) in these three bitumen systems. Shorter chain length indicates weaker repulsive force. This finding of a much weaker repulsion between bitumen droplets under static conditions has important implications on the commercial bitumen extraction operation.     

Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations

A multiscale method is presented to bridge between the atomistic and mesoscopic membrane systems. The atomistic model in this case is the united atom dimyristoylphosphatidylcholine membrane system, although the method is completely general. Atomistic molecular dynamics provides the expansion modulus which is used to parametrize a mesoscopic elastic membrane model. The resulting elastic membrane model, including explicit mesoscopic solvent, shows appropriate static and dynamic undulation behaviors. Large membranes of approximately 100 nm in length can then be easily simulated using the mesoscopic membrane system. The critical feedback from the mesoscopic system back down to the atomistic-scale system is accomplished by bridging the stress (or surface tension) of a small region in the mesoscopic membrane to the corresponding atomistic membrane system. Because of long length-scale modes of membranes such as undulation and buckling, the local tension responds differently from the frame tension, when subjected to external perturbations. The effect of these membrane modes is shown for the stress response of a local membrane region and therefore the atomistic membrane system. In addition, certain equilibrium static and dynamic properties of stand-alone and multiscale coupled systems are presented for several different membrane sizes. Although static properties such as two-dimensional pair-correlation function and order parameters show no noticeable discrepancy for the different systems, lipid self-diffusion and the rotational relaxation of lipid dipoles have a strong dependence on the membrane size (or long-wavelength membrane motions), which is properly modeled by the present multiscale method.     

Combined Monte Carlo and molecular dynamics simulation of hydrated 18:0 sphingomyelin-cholesterol lipid bilayers

We have carried out atomic level molecular dynamics and Monte Carlo simulations of hydrated 18:0 sphingomyelin (SM)-cholesterol (CHOL) bilayers at temperatures of 20 and 50 degrees C. The simulated systems each contained 266 SM, 122 CHOL, and 11861 water molecules. Each simulation was run for 10 ns under semi-isotropic pressure boundary conditions. The particle-mesh Ewald method was used for long-range electrostatic interactions. Properties of the systems were calculated over the final 3 ns. We compare the properties of 20 and 50 degrees C bilayer systems with each other, with experimental data, and with experimental and simulated properties of pure SM bilayers and dipalmitoyl phospatidyl choline (DPPC)-CHOL bilayers. The simulations reveal an overall similarity of both systems, despite the 30 degrees C temperature difference which brackets the pure SM main phase transition. The area per molecule, lipid chain order parameter profiles, atom distributions, and electron density profiles are all very similar for the two simulated systems. Consistent with simulations from our lab and others, we find strong intramolecular hydrogen bonding in SM molecules between the phosphate ester oxygen and the hydroxyl hydrogen atoms. We also find that cholesterol hydroxyl groups tend to form hydrogen bonds primarily with SM carbonyl, methyl, and amide moieties and to a lesser extent methyl and hydroxyl oxygens.     

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.     

Development of intermolecular potentials for predicting transport properties of hydrocarbons

We explore the ability of a modified form of an n-6 potential to represent transport property data of n-paraffins over a range of temperatures, pressures, and chain lengths. General features of the relationship between the potential form and resulting properties are investigated for methane, where it is shown that the tunable softness of the potential function allows for adjustment of transport properties, through modulation of the magnitude of the density fluctuations, while leaving thermodynamic properties such as liquid density and vapor-liquid coexistence properties essentially unchanged. We tune potential parameters of a united atom model for n-paraffins to viscosity and density data of low molecular weight (C4-C10) species and demonstrate the robust predictive capability of viscosity-temperature-pressure relationships for species up to n-C36.     

Molecular dynamics simulation of the glass transition temperature of fullerene filled cis-1,4-polybutadiene nanocomposites

t In this work,the effect of the fullerene (C60) weight fraction and PB-C60 interaction on the glass transition temperature (Tg) of polymer chains has been systemically investigated by adopting the united atom model of cis-1,4-poly(butadiene) (cis-PB).Various chain dynamics properties,such as atom translational mobility,bond/segment reorientation dynamics,torsional dynamics,conformational transition rate and dynamic heterogeneity of the cis-PB chains,are analyzed in detail.It is found that Tg could be affected by the C60 weight fraction due to its inhibition effect on the mobility of the cis-PB chains.However,Tg is different,which depends on different dynamics scales.Among the chain dynamics properties,Tg is the lowest from atom translational mobility,while it is the highest from the dynamic heterogeneity.In addition,Tg can be more clearly distinguished from the dynamic heterogeneity;however,the conformational transition rate seems to be not very sensitive to the C60 weight fraction compared with others.For pure cis-PB chains,Tg and the activation energy in this work can be compared with those of other polymers.In addition,the temperature dependence of the dynamic properties has different Arrhenius behaviors above and below Tg.The activation energy below Tg is lower than that above Tg.This work can help to understand the effect of the C60 on the dynamic properties and glass transition temperature of the cis-PB chains from different scales.