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Although the reverse non-equilibrium molecular dynamics (RNEMD) simulation method has been widely employed, the range of applicability is yet to be discussed. In this study, for the first time, we systematically examine the method against an unentangled melt of the Kremer-Grest type chain. The simulation results indicate that as the shear rate increases, the temperature and density become inhomogeneous. However, the average viscosity remains consistent with the results obtained using the SLLOD method under homogeneous temperature and density. We also confirm that the temperature-density inhomogeneity does not significantly affect polymer conformation.

Deep saline aquifers are one of the best options for large-scale and long-term hydrogen storage. Predicting the diffusion coefficient of hydrogen molecules at the conditions of saline aquifers is critical for modelling hydrogen storage. The diffusion coefficient of hydrogen molecules in chloride brine with different cations ($\mathrm{Na}^+$, $\mathrm{K}^+$, $\mathrm{Ca}^{2+}$) containing up to 5 $\mathrm{mol/kg_{H_2O}}$ concentration is numerically investigated using molecular dynamics (MD) simulation. A wide range of pressure (1-218 atm) and temperature (298-648 K) conditions is applied to cover the realistic operational conditions of the aquifers. We find that the temperature, pressure and properties of ions (compositions and concentrations) affect the hydrogen diffusion coefficient. An Arrhenius behavior of the effect of temperature on the diffusion coefficient has been observed with the temperature independent parameters fitted using the ion concentration under constant pressure. However, it is noted that the pressure strongly affects the diffusive behavior of hydrogen at the high temperature ($\geq$ 400 K) regime, indicating the inaccuracy of the Arrhenius model. Hence, we combine the obtained MD results with four models of machine learning (ML), including linear regression (LR), random forest (RF), extra tree (ET) and gradient boosting (GB) to provide effective predictions on the hydrogen diffusion. The resultant combination of GB model with MD data predicts the diffusion of hydrogen more effectively as compared to the Arrhenius model and other ML models. Moreover, a $post hoc$ analysis (feature importance rank) has been performed to extract the correlation between physical descriptors and simulation results from ML models.

A liquid droplet impacting on a solvophobic surface normally rebounds. The rebound is suppressed by a small amount of dissolved polymer. In this work, using multi-body dissipative particle dynamics simulations, two anti-rebound mechanisms, the slow-retraction and the slow-hopping mechanisms, are identified. Which of them dominates depends on the polymer-surface attraction strength. However, these two mechanisms are not excluding each other but may coexist. During the droplet rebound, the surface-adsorbed polymer acts in two ways: the adsorbed beads mediate solvent-surface interactions, and highly stretching unadsorbed polymer segment exerts a retraction force on the liquid. Both actions increase the friction against retraction and the resistance against hopping. We also investigate the effects of the molecular weight and the concentration of the polymer additive, the droplet size, and the impact velocity on the rebound tendency. As the first work to provide a microscopic explanation of the anti-rebound mechanism by polymer additives, this study allows better understanding of wetting behavior by polymer-solution droplets.

A small amount of polymer dissolved in a droplet suppresses droplet rebound when it impinges on a supersolvophobic surface. This work investigates impacting dynamics of a droplet of dilute polymer solution depending on the molecular weight and the concentration of the polymer by using multi-body dissipative particle dynamics simulations. Either the longer polymer or the high polymer concentration suppresses rebound of a droplet although its shear viscosity and the liquid-vapor surface tension are not different from those of a pure solvent droplet. We found a new mechanism of the anti-rebound in which the resistance is applied against the hopping motion, while behavior of the non-rebounding droplet at the earlier spreading and retraction stages is same as for the rebounding droplets. Two polymer contributions to reducing the rebound tendency are quantitatively analyzed: the alteration of the substrate wettability by the polymer adsorption and the polymer elongation force.

We investigate the role played by the bidispersity of polymer chains on the local structure and the potential of mean force (PMF) between silica nanoparticles (NPs) in a polystyrene melt. We use the hybrid particle-field molecular dynamics technique which allows to efficiently relax polymer nanocomposites even with high molecular weights.The NPs we investigate are either bare or grafted with polystyrene chains immersed in a melt of free polystyrene chains, whereas the grafted and the free polystyrene chains are either monodisperse or bidisperse. The two-body PMF shows that a bidisperse distribution of free polymer chains increases the strength of attraction between a pair of ungrafted NPs. If the NPs are grafted by polymer chains, the effective interaction crucially depends on bidispersity and grafting density of the polymer chains: for low grafting densities, the bidispersity of both free and grafted chains increases the repulsion between the NPs, whereas for high grafting densities we observe two different effects. An increase of bidispersity in free chains causes the rise of the repulsion between the NPs, while an increase of bidispersity in grafted chains promotes the rise of attraction. Additionally, a proper treatment of multi-body interactions improves the simpler two-body PMF calculations, in both unimodal and bimodal cases. We found that, by properly tuning the bidispersity of both free and grafted chains, we can control the structure of the composite materials, which can be confirmed by experimental observations. As a result, the hybrid particle-field approach is confirmed to be a valid tool for reproducing and predicting microscopic interactions, which determine the stability of the microscopic structure of the composite in a wide range of conditions., Comment: 41 pages, 13 figures, 66 references. To appear in Macromolecules. Supporting Information available

We perform a systematic application of the hybrid particle-field molecular dynamics technique [Milano et al, J. Chem. Phys. 2009, 130, 214106] to study interfacial properties and potential of mean force (PMF) for separating nanoparticles (NPs) in a melt. Specifically, we consider Silica NPs bare or grafted with Polystyrene chains, aiming to shed light on the interactions among free and grafted chains affecting the dispersion of NPs in the nanocomposite. The proposed hybrid models show good performances in catching the local structure of the chains, and in particular their density profiles, documenting the existence of the "wet-brush-to-dry-brush" transition. By using these models, the PMF between pairs of ungrafted and grafted NPs in Polystyrene matrix are calculated. Moreover, we estimate the three-particle contribution to the total PMF and its role in regulating the phase separation on the nanometer scale. In particular, the multi-particle contribution to the PMF is able to give an explanation of the complex experimental morphologies observed at low grafting densities. More in general, we propose this approach and the models utilized here for a molecular understanding of specific systems and the impact of the chemical nature of the systems on the composite final properties., Comment: 16 pages, 11 figures, 80 references. Accepted for publication on Nanoscale

We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true (simulated) distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse-grained an atomistic all-atom model of poly (isoprene) (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes., Comment: 32 pages including 12 figures

Molecular dynamics simulations of diluted (~2.5 weight percent) aqueous solutions of two polyelectrolytes, namely sodium carboxy methyl cellulose (CMC) and sodium poly(acrylate) (PAA) have been performed. Water and counterions were taken into account explicitly. For CMC the substitution pattern and starting conformation is all-important. Two simulations of CMC oligomers resulted in different structures: One molecule takes a stretched conformation, while the second one keeps a globule-like, toroidal one. PAA is stretched during the whole simulation, with an average characteristic ratio of 8.3. On a local atomistic scale CMC and PAA have different hydrogen-bond properties. The COO- groups of PAA can only act as hydrogen bond acceptors, but due to the high negative charge density there are still more water molecules assembled around PAA than around CMC. There are 0.036 bonds/amu respectively 0.029 bonds/amu to water for the two CMC oligomers, but more than twice as many for PAA: 0.083 bonds/amu. Beside intermolecular hydrogen bonding, there is a significant amount of intramolecular H-bonding for CMC, which is influenced by the COO- groups, which act as strong H-acceptor. In contrast to hydroxy- and carboxylic groups, ether oxygens are hardly involved into hydrogen bonding., Comment: 24 pages, 24 Postscript figures, submitted to Macromolecules

Mono- and poly-disperse melts of oligomers (average length 10 monomers) of trans-1,4-polyisoprene are simulated in full atomistic detail. The force-field is developed by means of a mixture of ab initio quantum-chemistry and an automatic generation of empirical parameters. Comparisons to NMR and scattering experiments validate the model. The local reorientation dynamics shows that for C$-$H vectors there is a two-stage process consisting of an initial decay and a late-stage decorrelation originating from overall reorientation. The atomistic model can be successfully mapped onto a simple model including only beads for the monomers with bond springs and bond angle potentials. End-bridging Monte Carlo as an equilibration stage and molecular dynamics as the subsequent simulation method together prove to be a useful method for polymer simulations., Comment: 25 pages, 15 figures, accepted by Macromolecules

The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse lamellar thickness. Analysis of the single chain conformations in the crystal shows that most chains reenter the same lamella by tight backfolds. Simulations are performed with a mesoscopic bead-spring model including a specific angle bending potential. They demonstrate that chain stiffness alone, without an attractive inter-particle potential, is a sufficient driving force for the formation of chain-folded lamellae., Comment: 4 pages, 5 figures

Atomistic (atom-scale) and coarse-grained (meso-scale) simulations of structure and dynamics of poly-isoprene melts are compared. The local structure and chain packing is mainly determined by the atomistic details of the polymer architecture. The large-time dynamics encountered in NMR experiments can be explained by meso-scale simulations including stiffness. The connecting link between the two scales is the stiffness which, although being a local property, influences strongly even the long-timescale dynamics. The standard reptation scenario fails to explain the observed dynamics. We propose strong reptation as a modified reptation scenario in which the local Rouse motion is absent., Comment: 21 pages, 13 pictures (partially color)

This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how reliable it could possibly be. In a two-dimensional, infinite lattice model system one can calculate exact free energies by exhaustive enumeration. A series of approximations were fitted to exact results to assess the feasibility and utility of pair-wise free energy terms. Approximating the true free energy with pair-wise interactions gives a poor fit with little transferability between systems of different size. Adding extra artificial terms to the approximation yields better fits, but does not improve the ability to generalise from one system size to another. Further, one cannot distinguish folding from non-folding sequences via the approximated free energies. Most usefully, the methodology shows how one can assess the utility of various terms in lattice protein/polymer models., Comment: HTML/GIF-Format, incl. 5 figures, 5 tables - to be published in the The Journal of Chemical Physics

We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered in molecular dynamics simulations is reduced while conserving as many properties of the original substance as possible. We address the problem of finding nonbonded interaction parameters which reproduce structural properties from experiment or atomistic simulations. The approach consists of optimizing automatically nonbonded parameters using the simplex algorithm to fit structural properties like the radial distribution function as target functions. Moreover, any mix of structural and thermodynamic properties can be included in the target function. Different spherically symmetric inter-particle potentials are discussed. Besides demonstrating the method for Lennard--Jones liquids, it is applied to several more complex molecular liquids such as diphenyl carbonate, tetrahydrofurane, and monomers of poly(isoprene)., Comment: 24 pages, 3 tables, 14 figures submitted to the Journal of Chemical Physics (JCP)

We develop coarse-grained force fields for poly (vinyl alcohol) and poly (acrylic acid) oligomers. In both cases, one monomer is mapped onto a coarse-grained bead. The new force fields are designed to match structural properties such as radial distribution functions of various kinds derived by atomistic simulations of these polymers. The mapping is therefore constructed in a way to take into account as much atomistic information as possible. On the technical side, our approach consists of a simplex algorithm which is used to optimize automatically non-bonded parameters as well as bonded parameters. Besides their similar conformation (only the functional side group differs), poly (acrylic acid) was chosen to be in aqueous solution in contrast to a poly (vinyl alcohol) melt. For poly (vinyl alcohol) a non-optimized bond angle potential turns out to be sufficient in connection with a special, optimized non-bonded potential. No torsional potential has to be applied here. For poly (acrylic acid), we show that each peak of the radial distribution function is usually dominated by some specific model parameter(s). Optimization of the bond angle parameters is essential. The coarse-grained forcefield reproduces the radius of gyration of the atomistic model. As a first application, we use the force field to simulate longer chains and compare the hydrodynamic radius with experimental data., Comment: 34 pages, 3 tables, 16 figures

The reorientation dynamics of local tangent vectors of chains in isotropic amorphous melts containing semiflexible model polymers was studied by molecular dynamics simulations. The reorientation is strongly influenced both by the local chain stiffness and by the overall chain length. It takes place by two different subsequent processes: A short-time non-exponential decay and a long-time exponential reorientation arising from the relaxation of medium-size chain segments. Both processes depend on stiffness and chain length. The strong influence of the chain length on the chain dynamics is in marked contrast to its negligible effect on the static structure of the melt. The local structure shows only a small dependence on the stiffness, and is independent of chain length. Calculated correlation functions related to double-quantum NMR experiments are in qualitative agreement with experiments on entangled melts. A plateau is observed in the dependence of segment reorientation on the mean-squared displacement of the corresponding chain segments. This plateau confirms, on one hand, the existence of reptation dynamics. On the other hand, it shows how the reptation picture has to be adapted if, instead of fully flexible chains, semirigid chains are considered., Comment: 29 pages, several figures, accepted by Macromolecules

The reptation concept in polymer dynamics is studied for model chains with added stiffness. The main idea of a chain diffusing inside a tube can be transferred from fully flexible chains. However, the picture, which renormalizes the chain of locally stiff Kuhn segments onto a flexible chain of fewer segments fails. The entanglement length shrinks with increasing persistence length. If entanglement length and persistence length come to the same order of magnitude the picture of a tight tube is better suited, in which chain segments can move only along the contour, any transverse motion being much reduced. Thus, as stiffness increases, the monomers loose their freedom to perform random walks inside the tube, the ``Rouse-like'' part of their dynamics. As a result, for persistence lengths of more than five monomers no length scale can be described by the Rouse model., Comment: 10 pages revtex, 5 figures, partly color

The aim of this study is to understand deeper the thermal diffusion transport process (Ludwig-Soret effect) at the microscopic level. For that purpose, the recently developed reverse nonequilibrium molecular dynamics method was used to calculate Soret coefficients of various systems in a systematic fashion. We studied binary Lennard-Jones (LJ) fluids near the triple point (of one of the components) in which we separately changed the ratio of one of the LJ parameters mass, atomic diameter and interaction strength while keeping all other parameters fixed and identical. We observed that the magnitude of the Soret coefficient depends on all three ratios. Concerning its sign we found that heavier species, smaller species and species with higher interaction strengths tend to accumulate in the cold region whereas the other ones (lighter, bigger or weaker bound) migrate to the hot region of our simulation cell. Additionally, the superposition of the influence of the various parameters was investigated as well as more realistic mixtures. We found that in the experimentally relevant parameter range the contributions are nearly additive and that the mass ratio often is the dominating factor., Comment: 27 pages, 9 figures, submitted to J. Chem. Phys

We demonstrate an automatic method of force field development for molecular simulations. Parameter tuning is taken as an optimization problem in many dimensions. The parameters are automatically adapted to reproduce known experimental data such as the density and the heat of vaporization. Our method is more systematic than guessing parameters and, at the same time saves human labour in parameterization. It was successfully applied to several molecular liquids: As a test, force fields for 2-methylpentane, tetrahydrofurane, cyclohexene and cyclohexane were developed., Comment: 16 pages, 3 figures, final version, forcefields slightly changed

Molecular dynamics simulation of a generic polymer model is applied to study melts of polymers with different types of intrinsic stiffness. Important static observables of the single chain such as gyration radius or persistence length are determined. Additionally we investigate the overall static melt structure including pair correlation function, structure function and orientational correlation function., Comment: 13 pages, 15 figures, PCCP accepted

We investigate mutual local chain order in systems of fully flexible polymer melts in a simple generic bead-spring model. The excluded-volume interaction together with the connectivity leads to local ordering effects which are independent of chain length between 25 and 700 monomers, i.e. in the Rouse as well as in the reptation regime. These ordering phenomena extend to a distance of about 3 to 4 monomer sizes and decay to zero afterwards., Comment: 5 pages, 3 figures