Off-lattice Monte Carlo Simulation of Supramolecular Polymer Architectures

We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational changes that exactly preserve fixed-length constraints of all bonds. The algorithm reproduces known end-to-end distance distributions for simple, analytically tractable systems of cross-linked stiff and freely jointed polymers flawlessly, and is used to determine the effective persistence length of short bundles of semi-flexible worm-like chains, cross-linked to each other. It reveals a possible regulatory mechanism in bundled networks: the effective persistence of bundles is controlled by the linker density.Comment: 4 pages, 4 figure

Tension thickening, molecular shape, and flow birefringence of an H-shaped polymer melt in steady shear and planar extension

Despite recent advances in the design of extensional rheometers optimized for strain and stress controlled operation in steady, dynamic, and transient modes, obtaining reliable steady-state elongational data for macromolecular systems is still a formidable task, limiting today's approach to trial-and-error efforts rather than based on a deep understanding of the deformation processes occurring under elongation. Guided, in particular, by the need to understand the special rheology of branched polymers, we studied a model, unentangled H-shaped polyethylene melt using nonequilibrium molecular dynamics simulations based on a recently developed rigorous statistical mechanics algorithm. The melt has been simulated under steady shear and steady planar extension, over a wide range of deformation rates. In shear, the steady-state shear viscosity is observed to decrease monotonically as the shear rate increases; furthermore, the degree of shear thinning of the viscosity and of the first- and second-normal stress coefficients is observed to be similar to that of a linear analog of the same total chain length. By contrast, in planar extension, the primary steady-state elongational viscosity ??1 is observed to exhibit a tension-thickening behavior as the elongation rate ?? increases, which we analyze here in terms of (a) perturbations in the instantaneous intrinsic chain shape and (b) differences in the stress distribution along chain contour. The maximum in the plot of ??1 with ?? occurs when the arm-stretching mode becomes active and is followed by a rather abrupt tension-thinning behavior. In contrast, the second elongational viscosity ??2 shows only a tension-thinning behavior. As an interesting point, the simulations predict the same value for the stress optical coefficient in the two flows, revealing an important rheo-optical characteristic. In agreement with experimental indications on significantly longer systems, our results confirm the importance of chain branching on the unique rheological properties of polymer melts in extension.open5

Monte Carlo algorithm based on internal bridging moves for the atomistic simulation of thiophene oligomers and polymers

We introduce a powerful Monte Carlo (MC) algorithm for the atomistic simulation of bulk models of oligo- and poly-thiophenes by redesigning MC moves originally developed for considerably simpler polymer structures and architectures, such as linear and branched polyethylene, to account for the ring structure of the thiophene monomer. Elementary MC moves implemented include bias reptation of an end thiophene ring, flip of an internal thiophene ring, rotation of an end thiophene ring, concerted rotation of three thiophene rings, rigid translation of an entire molecule, rotation of an entire molecule and volume fluctuation. In the implementation of all moves we assume that thiophene ring atoms remain rigid and strictly co-planar; on the other hand, inter-ring torsion and bond bending angles remain fully flexible subject to suitable potential energy functions. Test simulations with the new algorithm of an important thiophene oligomer, {\alpha}-sexithiophene ({\alpha}-6T), at a high enough temperature (above its isotropic-to-nematic phase transition) using a new united atom model specifically developed for the purpose of this work provide predictions for the volumetric, conformational and structural properties that are remarkably close to those obtained from detailed atomistic Molecular Dynamics (MD) simulations using an all-atom model. The new algorithm is particularly promising for exploring the rich (and largely unexplored) phase behavior and nanoscale ordering of very long (also more complex) thiophene-based polymers which cannot be addressed by conventional MD methods due to the extremely long relaxation times characterizing chain dynamics in these systems

A hybrid kinetic Monte Carlo method for simulating silicon films grown by plasma-enhanced chemical vapor deposition

We present a powerful kinetic Monte Carlo (KMC) algorithm that allows one to simulate the growth of nanocrystalline silicon by plasma enhanced chemical vapor deposition (PECVD) for film thicknesses as large as several hundreds of monolayers. Our method combines a standard n-fold KMC algorithm with an efficient Markovian random walk scheme accounting for the surface diffusive processes of the species involved in PECVD. These processes are extremely fast compared to chemical reactions, thus in a brute application of the KMC method more than 99% of the computational time is spent in monitoring them. Our method decouples the treatment of these events from the rest of the reactions in a systematic way, thereby dramatically increasing the efficiency of the corresponding KMC algorithm. It is also making use of a very rich kinetic model which includes 5 species (H, SiH3, SiH2, SiH, and Si 2H5) that participate in 29 reactions. We have applied the new method in simulations of silicon growth under several conditions (in particular, silane fraction in the gas mixture), including those usually realized in actual PECVD technologies. This has allowed us to directly compare against available experimental data for the growth rate, the mesoscale morphology, and the chemical composition of the deposited film as a function of dilution ratio.open1

Effect of Polymer Concentration on the Structure and Dynamics of Short Poly(N,N-dimethylaminoethyl methacrylate) in Aqueous Solution:A Combined Experimental and Molecular Dynamics Study

A combined experimental and molecular dynamics (MD) study is performed to investigate the effect of polymer concentration on the zero shear rate viscosity η0 of a salt-free aqueous solution of poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA), a flexible thermoresponsive weak polyelectrolyte with a bulky 3-methyl-1,1-diphenylpentyl unit as the terminal group. The study is carried out at room temperature (T = 298 K) with relatively short PDMAEMA chains (each containing N = 20 monomers or repeat units) at a fixed degree of ionization (α+ = 100%). For the MD simulations, a thorough validation of several molecular mechanics force fields is first undertaken for assessing their capability to accurately reproduce the experimental observations and established theoretical laws. The generalized Amber force field in combination with the restrained electrostatic potential charge fitting method is eventually adopted. Three characteristic concentration regimes are considered: the dilute (from 5 to 10 wt %), the semidilute (from 10 to 20 wt %), and the concentrated (from 20 to 29 wt %); the latter two are characterized by polymer concentrations cp higher than the characteristic overlap concentration cp*. The structural behavior of the PDMAEMA chains in the solution is assessed by calculating the square root of their mean-square radius of gyration «Rg 2»0.5, the square root of the average square chain end-to-end distance «Ree 2»0.5, the ratio «Ree 2»/«Rg 2», and the persistence length Lp. It is observed that at low polymer concentrations, PDMAEMA chains adopt a stiffer and slightly extended conformation because of excluded-volume effects (a good solvent is considered in this study) and electrostatic repulsions within the polymer chains. As the polymer concentration increases above 20 wt %, the PDMAEMA chains adopt more flexible conformations, as the excluded-volume effects seize and the charge repulsion within the polymer chains subsides. The effect of total polymer concentration on PDMAEMA chain dynamics in the solution is assessed by calculating the orientational relaxation time τc of the chain, the center-of-mass diffusion coefficient D, and the zero shear rate viscosity η0; the latter is also measured experimentally here and found to be in excellent agreement with the MD predictions.</p

Energetic and Entropic Elasticity of Nonisothermal Flowing Polymers: Experiment, Theory, and Simulation

The thermodynamical aspects of polymeric liquids subjected to nonisothermal flow are examined from the complementary perspectives of theory, experiment, and simulation. In particular, attention is paid to the energetic effects, in addition to the entropic ones, that occur under conditions of extreme deformation. Comparisons of experimental measurements of the temperature rise generated under elongational flow at high strain rates with macroscopic finite element simulations offer clear evidence of the persistence and importance of energetic effects under severe deformation. The performance of various forms of the temperature equation are evaluated with regard to experiment, and it is concluded that the standard form of this evolution equation, arising from the concept of purely entropic elasticity, is inadequate for describing nonisothermal flow processes of polymeric liquids under high deformation. Complete temperature equations, in the sense that they possess a direct and explicit dependence on the energetics of the microstructure of the material, provide excellent agreement with experimental data

Dynamic Heterogeneity in Ring-Linear Polymer Blends

We present results from a direct statistical analysis of long molecular dynamics (MD) trajectories for the orientational relaxation of individual ring molecules in blends with equivalent linear chains. Our analysis reveals a very broad distribution of ring relaxation times whose width increases with increasing ring/linear molecular length and increasing concentration of the blend in linear chains. Dynamic heterogeneity is also observed in the pure ring melts but to a lesser extent. The enhanced degree of dynamic heterogeneity in the blends arises from the substantial increase in the intrinsic timescales of a large subpopulation of ring molecules due to their involvement in strong threading events with a certain population of the linear chains present in the blend. Our analysis suggests that the relaxation dynamics of the rings are controlled by the different states of their threading by linear chains. Unthreaded or singly-threaded rings exhibit terminal relaxation very similar to that in their own melt, but multiply-threaded rings relax much slower due to the long lifetimes of the corresponding topological interactions. By further analyzing the MD data for ring molecule terminal relaxation in terms of the sum of simple exponential functions we have been able to quantify the characteristic relaxation times of the corresponding mechanisms contributing to ring relaxation both in their pure melts and in the blends, and their relative importance. The extra contribution due to ring-linear threadings in the blends becomes immediately apparent through such an analysis

Atomistic Simulation of Energetic and Entropic Elasticity in Short-chain Polyethylenes

The thermodynamical aspects of polymeric liquids subjected to uniaxial elongational flow are examined using atomistically detailed nonequilibrium Monte Carlo simulations. In particular, attention is paid to the energetic effects, in addition to the entropic ones, which occur under conditions of extreme deformation. Atomistic nonequilibrium Monte Carlo simulations of linear polyethylene systems, ranging in molecular length from C24 to C78 and for temperatures from 300 to 450 K, demonstrate clear contributions of energetic effects to the elasticity of the system. These are manifested in a conformationally dependent heat capacity, which is significant under large deformations. Violations of the hypothesis of purely entropic elasticity are evident in these simulations, in that the free energy of the system is demonstrated to be composed of significant energetic effects under high degrees of orientation. These arise mainly from favorable intermolecular side-to-side interactions developing in the process of elongation due to chain uncoiling and alignment in the direction of extension