Structure and mobility of cyclohexane as a solvent for Trans-Polyisoprene

Solutions of {\it trans}$-$polyisoprene in cyclohexane are investigated in atomistic detail at different compositions at two different temperatures. We investigate the influence of polymer concentration on the dynamics of the solvent molecules and the structure of the solvation shell. The double bonds along the polymer backbone are preferentially approached by the solvent molecules. The mobility of cyclohexane molecules decreases with increasing polymer concentration at ambient conditions. The reorientation of molecules becomes more anisotropic with concentration as the polymer hinders the reorientation of the molecular plane. At elevated temperatures the influence of the polymer is weaker and the reorientation of the solvent is more isotropic. Additionally, a fast and efficient way to set up atomistic simulations is shown in detail in which the initial simulations increase in length and in the simulation time-step. The excess energy from initial overlaps is removed by resetting the velocities at regular intervals.Comment: 6 pages, 3 figure

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

Density of states of a binary Lennard-Jones Glass

We calculate the density of states of a binary Lennard-Jones glass using a recently proposed Monte Carlo algorithm. Unlike traditional molecular simulation approaches, the algorithm samples distinct configurations according to self-consistent estimates of the density of states, thereby giving rise to uniform internal-energy histograms. The method is applied to simulate the equilibrium, low-temperature thermodynamic properties of a widely studied glass former consisting of a binary mixture of Lennard-Jones particles. We show how a density-of-states algorithm can be combined with particle identity swaps and configurational bias techniques to study that system. Results are presented for the energy and entropy below the mode coupling temperature.Comment: 6 pages, 3 figures, accepted by J Chem Phy

Constant Pressure Hybrid Molecular Dynamics-Monte Carlo Simulations

New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use the extended-ensemble method of Andersen [H. C. Andersen J. Chem. Phys. {\bf 72},2384 (1980)]. In the second, we arrive at a new constant-pressure Monte Carlo technique based on the reversible generalization of the weak-coupling barostat [H. J. C. Berendsen et. al J. Chem. Phys. {\bf 81}, 3684(1984)]. This latter technique turns out to be highly effective in equilibrating and maintaining a target pressure. It is superior to the extended-ensemble method, which in turn is superior to simple volume-rescaling algorithms. The efficiency of the proposed methods is demonstrated by studying two systems. The first is a simple Lennard-Jones fluid. The second is a mixture of polyethylene chains of 200 monomers.Comment: 10 pages, 4 figure

Local chain ordering in amorphous polymer melts: Influence of chain stiffness

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 accepte

Orientation Correlation in Simplified Models of Polymer Melts

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 figure

Density of States Monte Carlo Method for Simulation of Fluids

A Monte Carlo method based on a density-of-states sampling is proposed for study of arbitrary statistical mechanical ensembles in a continuum. A random walk in the two-dimensional space of particle number and energy is used to estimate the density of states of the system; this density of states is continuously updated as the random walk visits individual states. The validity and usefulness of the method are demonstrated by applying it to the simulation of a Lennard-Jones fluid. Results for its thermodynamic properties, including the vapor-liquid phase coexistence curve, are shown to be in good agreement with high-accuracy literature data.Comment: 5 pages, 3 figures, accepted by J Chem Phy

Local Structure and Dynamics of Trans-polyisoprene oligomers

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 Macromolecule

Modeling of polystyrene under confinement: Exploring the limits of iterative boltzmann inversion

We explore the limits of a purely structure based coarse-graining technique, the iterative Boltzmann inversion (IBI), in the coarse-graining of a confined concentrated polystyrene solution. In the first place, some technical considerations and challenges encountered in the course of the optimization process are represented. The concepts of the choice of the initial potentials and the cross-dependency of the interactions as well as the order of optimization are discussed in detail. Furthermore, the transferability of a previously developed CG confined polystyrene solution model, the "parent CG confined model", to different degrees of confinement at constant concentration and temperature is examined. We investigate if a CG force field developed for a confined polymer solution by IBI is sensitive to changes in the degree of localization or arrangement of polymers near the surfaces although the concentration is kept constant. For this purpose, reference atomistic simulations on systems of different confinement levels have been performed. The differences in the structure and dynamics of the chains are addressed. Results are compared with those of an unconfined (bulk) system at the same concentration. The chain dimensions and orientations as a function of the distance from the surfaces are also reported. To the best of our knowledge, this is the first computational study that investigates the structural behavior of polymers in close proximity of the surfaces in a concentrated polymer solution rather than in a melt. Transferability of the parent CG confined model is tested by employing the parent force field in CG simulations of the reference systems. Results indicate that the degree of arrangement of monomers and solvent molecules near the surfaces is an important factor that needs to be paid attention to when considering the application of a CG force field developed by IBI to different degrees of confinement.U.S. Department of Energy, Office of Science, Basic Energy Sciences (DE-FG02-06ER46340); Scientific and Technological Research Council of Turke