Fast equilibration protocol for million atom systems of highly entangled linear polyethylene chains.

Equilibrated systems of entangled polymer melts cannot be produced using direct brute force equilibration due to the slow reptationdynamics exhibited by high molecular weight chains. Instead, these dense systems are produced using computational techniques such as Monte Carlo-Molecular Dynamics hybrid algorithms, though the use of soft potentials has also shown promise mainly for coarse-grained polymeric systems. Through the use of soft-potentials, the melt can be equilibrated via molecular dynamics at intermediate and long length scales prior to switching to a Lennard-Jones potential. We will outline two different equilibration protocols, which use various degrees of information to produce the starting configurations. In one protocol, we use only the equilibrium bond angle, bond length, and target density during the construction of the simulation cell, where the information is obtained from available experimental data and extracted from the force field without performing any prior simulation. In the second protocol, we moreover utilize the equilibrium radial distribution function and dihedral angle distribution. This information can be obtained from experimental data or from a simulation of short unentangled chains. Both methods can be used to prepare equilibrated and highly entangled systems, but the second protocol is much more computationally efficient. These systems can be strictly monodisperse or optionally polydisperse depending on the starting chain distribution. Our protocols, which utilize a soft-core harmonic potential, will be applied for the first time to equilibrate a million particle system of polyethylene chains consisting of 1000 united atoms at various temperatures. Calculations of structural and entanglement properties demonstrate that this method can be used as an alternative towards the generation of entangled equilibrium structures.

Computational study of imperfect networks using a coarse-grained model.

The structural and mechanical properties of imperfect entangled polymer networks with various fractions of elastically active chains are studied using a generic coarse-grained model. Network topology is analyzed at various degrees of cross-linking and correlated with the mechanical response under uniaxial deformation at various strain rates. We found excellent agreement between results obtained from the structural analysis and from fitting to stress relaxation data. The relaxation tensile modulus at various engineering strains was also calculated as a function of the fraction of active strands. Results indicate that the mechanical and viscoelastic properties of entangled polymer networks are susceptible to variation in the network structure, where defects can affect the mechanical response especially at low strain rates and the relaxation behavior at long times.

Entangled triblock copolymer gel: morphological and mechanical properties.

The morphological and mechanical properties of entangled ABA triblock copolymer gels, where solvent were selective to the midblock, were studied as a function of polymer concentration using a novel dissipative particle dynamics model which includes a modified segmental repulsive potential that restricts chain crossing. Morphological properties, such as micelle size, distance between micelles, and the bridge fraction, were calculated as a function of concentration. Although the micelle size was shown to have a strong dependence on concentration, the bridge fraction and distance between micelles were shown to plateau at moderate concentrations. Deformation under uni-axial tension was also performed to extract the cross-link and entanglement contribution to the elastic modulus. Scaling results qualitatively agree with other theoretical predications.

Surface orientation of polystyrene based polymers: steric effects from pendant groups on the phenyl ring.

Near edge X-ray absorption fine structure (NEXAFS) coupled with molecular dynamics simulations were utilized to probe the orientation at the exposed surface of the polymer film for polystyrene type polymers with various pendant functional groups off the phenyl ring. For all the polymers, the surface was oriented so that the rings are nominally normal to the film surface and pointing outward from the surface. The magnitude of this orientation was small and dependent on the size of the pendant functional group. Bulky functional groups hindered the surface orientation, leading to nearly unoriented surfaces. Depth dependent NEXAFS measurements demonstrated that the surface orientation was localized near the interface. Molecular dynamics simulations showed that the phenyl rings were not oriented strongly around a particular "average tilt angle". In contrast, simulations demonstrate that the phenyl rings exhibit a broad distribution of tilt angles, and that changes in the tilt angle distribution with pendant functionality give rise to the observed NEXAFS response. The more oriented samples exhibit a higher probability of phenyl ring orientation at angles greater than 60 degrees relative to the plane of the films surface.

Shock Hugoniot calculations of polymers using quantum mechanics and molecular dynamics.

Using quantum mechanics (QM) and classical force-field based molecular dynamics (FF), we have calculated the principle shock Hugoniot curves for numerous amorphous polymers including poly[methyl methacrylate] (PMMA), poly[styrene], polycarbonate, as well as both the amorphous and crystalline forms of poly[ethylene]. In the FF calculations, we considered a non-reactive force field (i.e., polymer consistent FF). The QM calculations were performed with density functional theory (DFT) using dispersion corrected atom centered pseudopotentials. Overall, results obtained by DFT show much better agreement with available experimental data than classical force fields. In particular, DFT calculated Hugoniot curves for PMMA up to 74 GPa are in very good agreement with experimental data, where a preliminary study of chain fracture and association was also performed. Structure analysis calculations of the radius of gyration and carbon-carbon radial distribution function were also carried out to elucidate contraction of the polymer chains with increasing pressure.

Determination of binding energy and solubility parameters for functionalized gold nanoparticles by molecular dynamics simulation.

The binding energy, density, and solubility of functionalized gold nanoparticles in a vacuum are computed using molecular dynamics simulations. Numerous parameters including surface coverage fraction, functional group (-CH(3), -OH, -NH(2)), and nanoparticle orientation are considered. The analysis includes computation of minimum interparticle binding distances and energies and an analysis of mechanisms that may contribute to changes in system potential energy. A number of interesting trends and results are observed, such as increasing binding distance with higher terminal group electronegativity and a minimum particle-particle binding energy (solubility parameter) based upon surface coverage. These results provide a fundamental understanding of ligand-coated nanoparticle interactions required for the design and processing of high-density polymer composites. The computational model and results are presented as support for these conclusions.

Spectral collocation methods for polymer brushes.

We provide an in-depth study of pseudo-spectral numerical methods associated with modeling the self-assembly of molten mixed polymer brushes in the framework of self-consistent field theory (SCFT). SCFT of molten polymer brushes has proved numerically challenging in the past because of sharp features that arise in the self-consistent pressure field at the grafting surface due to the chain end tethering constraint. We show that this pressure anomaly can be reduced by smearing the grafting points over a narrow zone normal to the surface in an incompressible model, and/or by switching to a compressible model for the molten brush. In both cases, we use results obtained from a source (delta function) distribution of grafting points as a reference. At the grafting surface, we consider both Neumann and Dirichlet conditions, where the latter is paired with a masking method to mimic a confining surface. When only the density profiles and relative free energies of two comparison phases are of interest, either source or smeared distributions of grafting points can be used, but a smeared distribution of grafting points exhibits faster convergence with respect to the number of chain contour steps. Absolute free energies converge only within the smeared model. In addition, when a sine basis is used with the masking method and a smeared distribution, fewer iterations are necessary to converge the SCFT fields for the compressible model. The numerical methods described here and investigated in one-dimension will provide an enabling platform for computationally more demanding three-dimensional SCFT studies of a broad range of mixed polymer brush systems.

Self-consistent field theory simulations of block copolymer assembly on a sphere.

Recently there has been a strong interest in the area of defect formation in ordered structures on curved surfaces. Here we explore the closely related topic of self-assembly in thin block copolymer melt films confined to the surface of a sphere. Our study is based on a self-consistent field theory (SCFT) model of block copolymers that is numerically simulated by spectral collocation with a spherical harmonic basis and an extension of the Rasmussen-Kalosakas operator splitting algorithm [J. Polym. Sci. Part B: Polym. Phys. 40, 1777 (2002)]. In this model, we assume that the composition of the thin block copolymer film varies only in longitude and colatitude and is constant in the radial direction. Using this approach we are able to study the formation of defects in the lamellar and cylindrical phases, and their dependence on sphere radius. Specifically, we compute ground-state (i.e., lowest-energy) configurations on the sphere for both the cylindrical and lamellar phases. Grain boundary scars are also observed in our simulations of the cylindrical phase when the sphere radius surpasses a threshold value R_{c} approximately 5d , where d is the natural lattice spacing of the cylindrical phase, which is consistent with theoretical predictions [Bowick, Phys. Rev. B 62, 8738 (2000); Bausch, Science 299, 1716 (2003)]. A strong segregation limit approximate free energy is also presented, along with simple microdomain packing arguments, to shed light on the observed SCFT simulation results.

Highly Transparent and Toughened Poly(methyl methacrylate) Nanocomposite Films Containing Networks of Cellulose Nanofibrils.

Cellulose nanofibrils (CNFs) are a class of cellulosic nanomaterials with high aspect ratios that can be extracted from various natural sources. Their highly crystalline structures provide the nanofibrils with excellent mechanical and thermal properties. The main challenges of CNFs in nanocomposite applications are associated with their high hydrophilicity, which makes CNFs incompatible with hydrophobic polymers. In this study, highly transparent and toughened poly(methyl methacrylate) (PMMA) nanocomposite films were prepared using various percentages of CNFs covered with surface carboxylic acid groups (CNF-COOH). The surface groups make the CNFs interfacial interaction with PMMA favorable, which facilitate the homogeneous dispersion of the hydrophilic nanofibrils in the hydrophobic polymer and the formation of a percolated network of nanofibrils. The controlled dispersion results in high transparency of the nanocomposites. Mechanical analysis of the resulting films demonstrated that a low percentage loading of CNF-COOH worked as effective reinforcing agents, yielding more ductile and therefore tougher films than the neat PMMA film. Toughening mechanisms were investigated through coarse-grained simulations, where the results demonstrated that a favorable polymer-nanofibril interface together with percolation of the nanofibrils, both facilitated through hydrogen bonding interactions, contributed to the toughness improvement in these nanocomposites.

Simultaneous detection of double-stranded RNA-induced protein kinase and its specific mRNA by single cell analysis.

Fluorescent in situ hybridization was combined with flow cytometry to detect the expression of the double-stranded-RNA-induced protein kinase (PKR) in single cells. Labeled anti-sense oligonucleotide was used to target the specific mRNA while the protein was targeted with an antibody. It was demonstrated that the PKR-mRNA signal could be protected through a lengthy immunostaining procedure. The expression pattern of the PKR-mRNA with respect to DNA content was shown to be comparable to that of 18S ribosomal RNA.