Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session Z25: Molecular Dynamics: Theory and Simulation |
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Sponsoring Units: DPOLY Chair: Eric Cochran, Iowa State University Room: Baltimore Convention Center 322 |
Friday, March 17, 2006 11:15AM - 11:27AM |
Z25.00001: Application of a Semi-Grand Canonical Monte Carlo (SGMC) Method for the Simulation of Non-Equilibrium Systems Frederick Bernardin, Gregory Rutledge The use of the SGMC as a generalized descriptive tool for interpreting experimental data obtained from non-equilibrium systems will be summarized. The usefulness of the method will be demonstrated specifically by interpreting the orientation distribution functions (odf's) of polymer melts which have been uniaxially oriented. Using SGMC, we identify the thermodynamic variables that serve as chemical potentials in a polydisperse system of orientations, and then generate the ensemble of configurations that minimizes the free energy subject to the constraints set by the odf. In this demonstration, the axial symmetry leads to the use of Legendre polynomials as the basis set for the odf. We apply our approach to obtain molecular ensembles corresponding to different values of P$_{2}$ (the first non-zero Legendre term), which are obtainable through measurements by light scattering or birefringence. Comparisons will be made to a related method by Mavrantzas and Theodorou (Macromolecules, 31, 6310 1998). [Preview Abstract] |
Friday, March 17, 2006 11:27AM - 11:39AM |
Z25.00002: Multiscale modeling of polystyrene dynamics in different environments Roland Faller, Qi Sun, Florence Pon Polystyrene is a very abundant and industrially important polymer. We are modeling its dynamical behavior on multiple length scales and different environments. We start with pure PS where we develop a mesoscale polystyrene model based on atomistic simulations. . The non-bonded effective potential is optimized against the atomistic simulation until the radial distribution function generated from the mesoscale model is consistent with the atomistic simulation. The mesoscale model allows understanding the polymer dynamics of long chains in reasonable computer time. The dynamics of polystyrene melts are investigated at various chain lengths ranging from 15 to 240 monomers and the crossover to entangled dynamics is observed. As computer simulations cannot only address average properties of the system under study but also the distribution over any observable of interest we are study mixtures of polystyrene and polyisoprene by atomistic molecular dynamics and calculate correlation times for all segments in the system. We then identify fast and slow segments and can correlate the segment speed with the local neighborhood and obtain that fast segments have a surplus of the faster component in their neighborhood and vice versa. A coarse grained mixture model will be presented as well. [Preview Abstract] |
Friday, March 17, 2006 11:39AM - 11:51AM |
Z25.00003: Polymer dynamics within a harmonic confinement potential Jeremy Schmit, Joshua Martin, Bulbul Chakraborty, Jan\'{e} Kondev We study the effects of confinement on the Rouse dynamics of polymers inspired by the question of chromosome confinement in the nucleus. We propose a simple model of a polymer diffusing within a three-dimensional harmonic potential. Within this model, the Rouse modes relax as independent particles within the harmonic potential so that the inverse relaxation times increase linearly with the confinement strength. This linear regime is also seen in simulations of phantom chains trapped within a hollow sphere. We also address the effect of self-avoidance using a self-consistent variational approximation to the propagator and compare the results to simulation. [Preview Abstract] |
Friday, March 17, 2006 11:51AM - 12:03PM |
Z25.00004: Monte Carlo simulations of polymer translocation through a nanopore Tapio Ala-Nissila, Kaifu Luo, Ilkka Huopaniemi, See-Chen Ying We investigate the problem of polymer translocation through a nanopore using the fluctuating bond model with single-segment Monte Carlo moves. For non-driven case we study the escape time $\tau_e$ required for a polymer, which is initially placed in the middle of the pore, to completely exit the pore on either end. We find $\tau _e \sim N^{1 + 2\nu }$, where $N$ is the chain length and $\nu $ is the Flory exponent. We also examine the interplay between the pore length $L$ and the radius of gyration $R_{g}$. For driven case we find a crossover scaling for the translocation time $\tau$ with $N$ from $\tau \sim N^{2\nu } $ for relatively short polymers to $\tau \sim N^{1 + \nu }$ for longer chains. This crossover is due to the change of the translocation velocity v from $v \sim N^{ - \nu }$ for relatively short chains to $v \sim N^{ - 1}$ for long polymers. The reason is that a high density of segments near the exit of the pore for long polymer slows down the translocation process due to slow relaxation of the chain. [Preview Abstract] |
Friday, March 17, 2006 12:03PM - 12:15PM |
Z25.00005: Calculating probability distributions for knot sizes and locations Peter Virnau, Yacov Kantor, Mehran Kardar We generate three dimensional random walks and loops with Monte Carlo simulations, and analyze them using various operational definitions of knot sizes and locations. We find that the size of a knot follows a power-law distribution with an exponent of approximately -1.5. As a consequence, knots in open chains are on the average larger when they are located close to the center. [Preview Abstract] |
Friday, March 17, 2006 12:15PM - 12:27PM |
Z25.00006: The Role of Quenched Randomness in the Stereochemical Sequences of Atactic Vinyl Polymers ~ Numan Waheed, Wayne L. Mattice The influence of quenched randomness on the mean square unperturbed
end-to-end distance, $\langle r^{2}\rangle _{0}$, is assessed in
polystyrene, using a rotational isomeric state (RIS) model based on virtual
bonds between the centers of mass of the C$_{6}$ rings. This coarse-grained
model is derived from a conventional RIS model expressed in terms of the C-C
bonds in the main chain and contains bond lengths, angles, and torsions
determined by the stereochemistry and conformations of the underlying
tetrad. The zeroth approximation virtual bond model, which retains only the
most probable conformation(s) of the six stereochemically unique tetrads,
correctly finds $\langle r^{2}\rangle _{0}\sim n $in the limit as
$n\to \infty $ if the probability for a \textit{meso }diad, $p_{m}$, is 0$ |
Friday, March 17, 2006 12:27PM - 12:39PM |
Z25.00007: Effects of Confinement on Tethered Chains John McCoy, Titus Ispirescu, John Curro Density Functional Theory (DFT) is used to analyze tethered Bead-Spring Chains. Previous work has demonstrated the ability of DFT to accurately predict both the density profiles of and colloidal force generated by such chains as compared to the results of computer simulation. In addition, the chains are found to display a collapse transition as a function of either surface coverage or temperature. In the current work, we explore the additional effect of confinement on the collapse transition, and the ability of simple scaling models to describe the behavior. [Preview Abstract] |
Friday, March 17, 2006 12:39PM - 12:51PM |
Z25.00008: Mixtures of Monomer and Dimer Square-well Fluids James Porter, Jane Lipson In previous work, we have used the continuum version of Born-Green-Yvon (BGY) theory, in conjunction with the square-well potential, to model structural and thermodynamic properties of alkanes and, in the case of one-component fluids, have also suggested mappings between the continuum and lattice versions of the theory. Having applied the lattice description to numerous mixtures, we are now interested in determining whether an analogous mapping is possible between the lattice and continuum descriptions when both are used to study mixtures. Towards this end, we present in this talk the first continuum BGY results for monomer/dimer square-well fluid mixtures. Thermodynamic and structural properties are compared with available simulation data, and the effect of changing both monomer diameters and square-well interaction strengths is examined. [Preview Abstract] |
Friday, March 17, 2006 12:51PM - 1:03PM |
Z25.00009: Field-Theoretic Models for Supramolecular Polymers Edward Feng, Won Bo Lee, Glenn Fredrickson Supramolecular polymer systems consist of polymers with bonding groups that can form reversible inter-polymer linkages. These materials have great technological potential since one can use temperature to tune the material properties such as viscosity. Moreover, new methods in synthesizing bonding groups point the way to making supramolecular polymer systems that self-assemble into inhomogeneous phases. To understand these materials, we develop a field-theoretic model for a system in which an A and B homopolymer can reversibly bond to form a diblock copolymer. An energy of bonding governs the strength of this reversible bond. Using computational methods, we calculate a mean-field phase diagram for the symmetric case in which the A and B parts of the system consist of polymers of the same length and occupy the same volume. At low temperatures, we find either a lamellar phase or macrophase separation depending on the strength of the bonding reaction. We are collaborating with experimental groups interested in synthesizing and characterizing these systems. [Preview Abstract] |
Friday, March 17, 2006 1:03PM - 1:15PM |
Z25.00010: Hybrid Two-Chain Simulation and Integral Equation Theory: Application to Polyethylene Liquids Huimin Li, David T. Wu, John G. Curro, John D. McCoy We present results from a hybrid simulation and integral equation approach to the calculation of polymer melt properties. The simulation consists of explicit Monte Carlo (MC) sampling of two polymer molecules, where the effect of the surrounding chains is accounted for by an HNC solvation potential. The solvation potential is determined from the Polymer Reference Interaction Site Model (PRISM) as a functional of the pair correlation function from simulation. This hybrid two-chain MC-PRISM approach was carried out on liquids of polyethylene chains of 24 and 66 $CH_2$ units. The results are compared with MD simulation and self-consistent PRISM-PY theory under the same conditions, revealing that the two-chain calculation is close to MD, and able to overcome the defects of the PRISM-PY closure and predict more accurate structures of the liquid at both short and long range. The direct correlation function, for instance, has a tail at longer range which is consistent with MD simulation and avoids the short-range assumptions in PRISM-PY theory. As a result, the self-consistent two-chain MC-PRISM calculation predicts an isothermal compressibility closer to the MD results. [Preview Abstract] |
Friday, March 17, 2006 1:15PM - 1:27PM |
Z25.00011: Phase coherence in LDOT diblock copolymer films Kwanwoo Shin, Junhan Cho, Kwangsoo Cho, Ji Hyuk Kim, Sushil K. Satija, Du Yeol Ryu, Jin Kon Kim Theoretical and experimental studies of the thin films of LDOT (lower disorder-order transition) diblock copolymers have been studied.~ The recently developed compressible Landau analysis has been applied to the copolymer films to interpret phase-coherent decaying profiles and other thermodynamic aspects of the LDOT films.~ Specific interactions and finite compressibility were considered in a unified way in this compressible Landau approach. The linearized and then nonlinear solutions of the minimized free energy functional under proper constraints were discussed. The neutron reflectivity and the surface topography measurements on the copolymer films were reported here to compare them with the theoretical analysis. [Preview Abstract] |
Friday, March 17, 2006 1:27PM - 1:39PM |
Z25.00012: Relation between cyclization of polymers with different initial conditions Chuck Yeung, Barry Friedman We study cyclization of polymer chains in which the reactive ends of the chains are initially in close proximity (ring initial conditions). We find a surprising general relation between cyclization with ring and equilibrium initial conditions, namely that $\Phi_{ring}(t) \propto d\Phi/dt_{eq}$ where $\Phi(t)$ is the survival fraction. We show that this proportionality is exact for a special type of non-generic ring initial conditions and use an approximate argument to motivate the proportionality for more general ring initial condition. Our analytic results are confirmed by Langevin simulations of Gaussian chains. Earlier work for very long Rouse chains with equilibrium initial conditions show that $d\Phi/dt_{eq} \sim t^{-1/4}$ for times less than the longest polymer relaxation time. Therefore our relation shows that $d\Phi/dt_{ring} \sim t^{-5/4}$ for a ring initial distribution under the same conditions. [Preview Abstract] |
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