Properties of Poly (isoprene) - Model Building in the Melt and in Solution

Properties of 1,4-\textit{trans} poly (isoprene) at ambient conditions are determined by simulations on two length scales based on two different models: a full-atomistic and a mesoscopic one. The models are linked via a mapping scheme such that one mesoscopic bead represents one chemical repeat unit. Melts as well as solutions of several chain lengths were investigated and mapped individually to the meso-scale. The resulting models are compared to each other. The meso-scale models could be simulated over a large variety of chain lengths and time-scales relevant for experimental comparison. Concerning static properties, we determined the persistence length of our systems and the scaling behavior of the radius of gyration. The latter was compared to experiments and the agreement is satisfactory. Furthermore, we find deviations from Rouse dynamics at all chain lengths at ambient conditions.Comment: 11 pictures 7 figure

Mapping atomistic to coarse-grained polymer models using automatic simplex optimization to fit structural properties

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 figure

Corrections to Scaling in the Hydrodynamic Properties of Dilute Polymer Solutions

We discuss the hydrodynamic radius $R_H$ of polymer chains in good solvent, and show that the leading order correction to the asymptotic law $R_H \propto N^\nu$ ($N$ degree of polymerization, $\nu \approx 0.59$) is an ``analytic'' term of order $N^{-(1 - \nu)}$, which is directly related to the discretization of the chain into a finite number of beads. This result is further corroborated by exact calculations for Gaussian chains, and extensive numerical simulations of different models of good--solvent chains, where we find a value of $1.591 \pm 0.007$ for the asymptotic universal ratio $R_G / R_H$, $R_G$ being the chain's gyration radius. For $\Theta$ chains the data apparently extrapolate to $R_G / R_H \approx 1.44$, which is different from the Gaussian value 1.5045, but in accordance with previous simulations. We also show that the experimentally observed deviations of the initial decay rate in dynamic light scattering from the asymptotic Benmouna--Akcasu value can partly be understood by similar arguments.Comment: 13 pages, 10 figures. submitted to J. Chem. Phy

Mapping atomistic to coarse-grained polymer models using automatic simplex optimization to fit structural properties

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 figure

On the nature of Thermal Diffusion in binary Lennard-Jones liquids

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. Phy

How does the chain extension of poly (acrylic acid) scale in aqueous solution? A combined study with light scattering and computer simulation

This work adresses the question of the scaling behaviour of polyelectrolytes in solution for a realistic prototype: We show results of a combined experimental (light scattering) and theoretical (computer simulations) investigation of structural properties of poly (acrylic acid) (PAA). Experimentally, we determined the molecular weight (M_W) and the hydrodynamic radius (R_H) by static light scattering for six different PAA samples in aqueous NaCl-containing solution (0.1-1 mol/L) of polydispersity D_P between 1.5 and 1.8. On the computational side, three different variants of a newly developed mesoscopic force field for PAA were employed to determine R_H for monodisperse systems of the same M_W as in the experiments. The force field effectively incorporates atomistic information and one coarse-grained bead corresponds to one PAA monomer. We find that R_H matches with the experimental data for all investigated samples. The effective scaling exponent for R_H is found to be around 0.55, which is well below its asymptotic value for good solvents. Additionally, data for the radius of gyration (R_G) are presented.Comment: 17 pages, 3 figures, submitted to Macromolecule

Coarse Graining of Nonbonded Inter-particle Potentials Using Automatic Simplex Optimization to Fit Structural Properties

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

Deriving effective mesoscale potentials from atomistic simulations

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 figure

Reaction behavior modeling of metal hydride based on FeTiMn using numerical simulations

In this contribution, we perform computer simulations to expedite the development of hydrogen storages based on metal hydride. These simulations enable in-depth analysis of the processes within the systems which otherwise could not be achieved. That is, because the determination of crucial process properties require measurement instruments in the setup which are currently not available. Therefore, we investigate the reliability of reaction values that are determined by a design of experiments. Specifically, we first explain our model setup in detail. We define the mathematical terms to obtain insights into the thermal processes and reaction kinetics. We then compare the simulated results to measurements of a 5-gram sample consisting of iron-titanium-manganese (FeTiMn) to obtain the values with the highest agreement with the experimental data. In addition, we improve the model by replacing the commonly used Van’t-Hoff equation by a mathematical expression of the pressure-composition-isotherms (PCI) to calculate the equilibrium pressure. Finally, the parameters’ accuracy is checked in yet another with an existing metal hydride system. The simulated results demonstrate high concordance with experimental data, which advocate the usage of approximated kinetic reaction properties by a design of experiments for further design studies. Furthermore, we are able to determine process parameters like the entropy and enthalpy

Fine-tuning property domain weighting factors and the objective function in force-field parameter optimization

Force field (FF) based molecular modeling is an often used method to investigate and study structural and dynamic properties of (bio-)chemical substances and systems. When such a system is modeled or refined, the force-field parameters need to be adjusted. This force-field parameter optimization can be a tedious task and is always a trade-off in terms of errors regarding the targeted properties. To better control the balance of various properties’ errors, in this study we introduce weighting factors for the optimization objectives. Different weighting strategies are compared to fine-tune the balance between bulk-phase density and relative conformational energies (RCE), using n-octane as a representative system. Additionally, a non-linear projection of the individual property-specific parts of the optimized loss function is deployed to further improve the balance between them. The results show that the combined error for the reproduction of the properties targeted in this optimization is reduced. Furthermore, the transferability of the force field parameters (FFParams) to chemically similar systems is increased. One interesting outcome is a large variety in the resulting optimized FFParams and corresponding errors, suggesting that the optimization landscape is multi-modal and very dependent on the weighting factor setup. We conclude that adjusting the weighting factors can be a very important feature to lower the overall error in the FF optimization procedure, giving researchers the possibility to fine-tune their FFs