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

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

Insights into the morphology of multicomponent organic and inorganic aerosols from molecular dynamics simulations

We explore the morphologies of multicomponent nanoparticles through atomistic molecular dynamics simulations under atmospherically relevant conditions. The particles investigated consist of both organic (cis-pinonic acid – CPA, 3-methyl-1,2,3-butanetricarboxylic acid – MBTCA, n-C20H42, n-C24H50, n-C30H62 or mixtures thereof) and inorganic (sulfate, ammonium and water) compounds. The effects of relative humidity, organic mass content and type of organic compound present in the nanoparticle are investigated. Phase separation is predicted for almost all simulated nanoparticles either between organics and inorganics or between hydrophobic and hydrophilic constituents. For oxygenated organics, our simulations predict an enrichment of the nanoparticle surface in organics, often in the form of islands depending on the level of humidity and organic mass fraction, giving rise to core–shell structures. In several cases the organics separate from the inorganics, especially from the ions. For particles containing water-insoluble linear alkanes, separate hydrophobic and hydrophilic domains are predicted to develop. The surface partitioning of organics is enhanced as the humidity increases. The presence of organics in the interior of the nanoparticle increases as their overall mass fraction in the nanoparticle increases, but this also depends on the humidity conditions. Apart from the organics–inorganics and hydrophobics–hydrophilics separation, our simulations predict a third type of separation (layering) between CPA and MBTCA molecules under certain conditions.</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

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

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

Thermodynamically guided nonequilibrium Monte Carlo method for generating realistic shear flows in polymeric systems

A thermodynamically guided atomistic MonteCarlo methodology is presented for simulating systems beyond equilibrium by expanding the statistical ensemble to include a tensorial variable accounting for the overall structure of the system subjected to flow. For a given shear rate, the corresponding tensorial conjugate field is determined iteratively through independent nonequilibrium molecular dynamics simulations. Test simulations for the effect of flow on the conformation of a C50H102 polyethylene liquid show that the two methods (expanded MonteCarlo and nonequilibrium molecular dynamics) provide identical results.open181

Parallel Excluded Volume Tempering for Polymer Melts

We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts which makes use of both parallel tempering and large scale Monte Carlo moves. The method is based upon simulating a set of systems in parallel, each of which has a slightly different repulsive core potential, such that a thermodynamic path from full excluded volume to an ideal gas of random walks is generated. While each system is run with standard stochastic dynamics, resulting in an NVT ensemble, we implement the parallel tempering through stochastic swaps between the configurations of adjacent potentials, and the large scale Monte Carlo moves through attempted pivot and translation moves which reach a realistic acceptance probability as the limit of the ideal gas of random walks is approached. Compared to pure stochastic dynamics, this results in an increased efficiency even for a system of chains as short as $N = 60$ monomers, however at this chain length the large scale Monte Carlo moves were ineffective. For even longer chains the speedup becomes substantial, as observed from preliminary data for $N = 200$