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

Conformational, Dynamical. and Tensional Study of Tethered Bilayer Lipid Membranes in Coarse-Grained Molecular Simulations

Tethered bilayer lipid membranes (tBLMs) have attracted great interest recently due to their crucial roles in elucidating fundamental membrane characteristics and the implications in biochemical sensors and pharmaceutical drug carriers. Nevertheless, they have not yet been investigated computationally on the molecular scale. Here, we study tBLMs consisting of DOPCs (1,2-dioleoyl-<i>sn</i>-glycero-3-phosphocholine) as free lipids and pegylated DOPCs (on phosphate group) as tethers in water by a variation of the MARTINI model. By varying grafting densities and tether lengths, distinct conformational changes from planar to undulated bilayers are observed. Lateral diffusivities and lateral pressure profiles show that the dynamical and tensional states are specific to the system configurations. These results suggest that the conformations, fluidity, and elasticity of the tBLMs can be tuned and manipulated to conform to various requirements in theoretical investigations and technological applications

Pressure and Surface Tension Control Self-Assembled Structures in Mixtures of Pegylated and Non-Pegylated Lipids

PEGylated lipid membrane structure and phase behavior are important areas of study because of their potential in various biochemical, biomedical, and pharmaceutical applications. Here, we study mixed bilayers of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) and PEGylated DOPCs (on phosphorus) in water using the MARTINI coarse-grained force field and show that the self-assembled structures can be changed between micelles and bilayers by applying different isotropic and semiisotropic (i.e., surface tension) pressure conditions. Radial distribution functions as well as radii of gyration confirm that structures are distinctly different. The results indicate that environmental conditions can be used to transform, manipulate, and eventually control lipid assemblies

Coarse-Grained Modeling of Polystyrene in Various Environments by Iterative Boltzmann Inversion

We have developed mesoscale models for polystyrene (PS) oligomers in various environments following the Iterative Boltzmann Inversion Technique. Bond, bending angle, torsion angle distributions, and radial distribution functions between PS monomers show that local structures were reproduced very well, while a small discrepancy remained in the reproduction of global structures (radii of gyration and end-to-end distances), which is probably due to end effects. Speedup in polymer dynamics with each model was monitored by scaling factors calculated based on characteristic relaxation times of the end monomers as well as diffusivities of the chains. Results show that coarse-graining is most successful for the highest concentration system (melt) and least for the lowest concentration (dilute solution) due to the stronger slowdown of diffusive and rotational dynamics in atomistic simulations with concentration. The speedup in the confined solution system was found to be greater than in the unconfined solution system due to the same reason except that confinement slows down the dynamics in that situation

Pressure and Surface Tension Control Self-Assembled Structures in Mixtures of Pegylated and Non-Pegylated Lipids

PEGylated lipid membrane structure and phase behavior are important areas of study because of their potential in various biochemical, biomedical, and pharmaceutical applications. Here, we study mixed bilayers of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) and PEGylated DOPCs (on phosphorus) in water using the MARTINI coarse-grained force field and show that the self-assembled structures can be changed between micelles and bilayers by applying different isotropic and semiisotropic (i.e., surface tension) pressure conditions. Radial distribution functions as well as radii of gyration confirm that structures are distinctly different. The results indicate that environmental conditions can be used to transform, manipulate, and eventually control lipid assemblies

Pressure and Surface Tension Control Self-Assembled Structures in Mixtures of Pegylated and Non-Pegylated Lipids

PEGylated lipid membrane structure and phase behavior are important areas of study because of their potential in various biochemical, biomedical, and pharmaceutical applications. Here, we study mixed bilayers of DOPC (1,2-dioleoyl-<i>sn</i>-glycero-3-phosphocholine) and PEGylated DOPCs (on phosphorus) in water using the MARTINI coarse-grained force field and show that the self-assembled structures can be changed between micelles and bilayers by applying different isotropic and semiisotropic (i.e., surface tension) pressure conditions. Radial distribution functions as well as radii of gyration confirm that structures are distinctly different. The results indicate that environmental conditions can be used to transform, manipulate, and eventually control lipid assemblies

Pressure and Surface Tension Control Self-Assembled Structures in Mixtures of Pegylated and Non-Pegylated Lipids

PEGylated lipid membrane structure and phase behavior are important areas of study because of their potential in various biochemical, biomedical, and pharmaceutical applications. Here, we study mixed bilayers of DOPC (1,2-dioleoyl-<i>sn</i>-glycero-3-phosphocholine) and PEGylated DOPCs (on phosphorus) in water using the MARTINI coarse-grained force field and show that the self-assembled structures can be changed between micelles and bilayers by applying different isotropic and semiisotropic (i.e., surface tension) pressure conditions. Radial distribution functions as well as radii of gyration confirm that structures are distinctly different. The results indicate that environmental conditions can be used to transform, manipulate, and eventually control lipid assemblies

Aggregation and pressure effects of asphaltene and resin molecules at oil–water interfaces: a coarse-grained molecular dynamics and free energy study

Coarse-grained molecular dynamics simulations were used to investigate the aggregation of asphaltene and resin molecules in oils and their deposition to oil–water interfaces. Resin, “interfacially-active” asphaltenes, and “bulk-like” asphaltenes are considered as solutes in organic phases consisting of aromatics or saturates. Resins and asphaltenes formed aggregates with a spacing of 0.46 nm between stacked polycyclic sheets. Whether in the aromatic or saturated solvent, resin molecules did not interact with the interface, but its aggregates remained in the bulk. The degree of surface activity of asphaltenes was found to increase with the polarity of their chemical groups, and decrease with the aromatics content of the solvent. Axial stress profiles were measured to calculate the interfacial tension of each system. The tension of interfaces of crude oil with water was found to depend on aromatics content. The free energy of deposition of asphaltenes and resin molecules to the interface was measured using well-tempered metadynamics, in which it was found that “interfacially-active” asphaltenes possess greater stability at the oil-water interface than “bulk-like” asphaltenes, and the organic solvent influences the favorability of deposition.</p

Parallel Optimization of a Reactive Force Field for Polycondensation of Alkoxysilanes

We have optimized a reactive force field (ReaxFF) in order to model the gelation of alkoxysilanes in bulk precursor solutions. The force field parameter set was refined using a parallelized local search algorithm. Using this approach, each processor is assigned a small list of parameters. At the end of every iteration, all parameters are updated simultaneously after being independently evaluated. In comparison to the serial evaluation of parameters, this results in faster parametrization of ReaxFF, as well as helps to prevent entrapment in local minima. The resulting model is found to reproduce hydrolysis and condensation reaction energies well. By applying the model to the condensation of silicic acid monomers at several temperatures, the activation energy of silane condensation is determined. The expected behavior, a gradual depletion of hydrolyzed silicon and growth of condensed silica clusters is observed over timescales of a few nanoseconds. The new model is also verified by modeling the early stages of clusterization in an alkoxysilane precursor solution. Both hydrolysis and condensation reactions are observed in a system containing a mixture of tetramethoxysilane, methanol, and water

Pressure and Surface Tension Control Self-Assembled Structures in Mixtures of Pegylated and Non-Pegylated Lipids

PEGylated lipid membrane structure and phase behavior are important areas of study because of their potential in various biochemical, biomedical, and pharmaceutical applications. Here, we study mixed bilayers of DOPC (1,2-dioleoyl-<i>sn</i>-glycero-3-phosphocholine) and PEGylated DOPCs (on phosphorus) in water using the MARTINI coarse-grained force field and show that the self-assembled structures can be changed between micelles and bilayers by applying different isotropic and semiisotropic (i.e., surface tension) pressure conditions. Radial distribution functions as well as radii of gyration confirm that structures are distinctly different. The results indicate that environmental conditions can be used to transform, manipulate, and eventually control lipid assemblies