Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session W20: Theory and Simulation III |
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Sponsoring Units: DPOLY Chair: Jack Douglas, National Institute of Standards and Technology Room: 321 |
Thursday, March 19, 2009 11:15AM - 11:27AM |
W20.00001: Conformational Study of Di-Substituted \textit{para-polyphenyleneethylene} (PPE) in Dilute Solutions Sabina Maskey, Flint Pierce, Dvora Perahia, Gary Grest Molecular dynamics (MD) simulations have been used to study the conformation of highly rigid di-substituted \textit{para-polyphenyleneethylenes} (PPEs) polymers, electro-active polymers, in dilute toluene solutions. The conformation of PPEs determines the conjugation of the polymer and their assembly mode which in-turn affect the electro-optical properties. In solution, the conformation is determined by molecular parameters including the length of the polymer and the nature of the side chain, coupled with the interaction of the molecules. The present study investigates the effects of molecular weight and the nature of the side chain in toluene solutions. Toluene is a good solvent for the backbone and a poor solvent for the substituting side chains. Small angle neutron studies have shown that short alkyl PPEs are fully stretched out. With increasing molecular weights they assume a worm like configuration. The current study provides further insight into the factors that determines the conformation of the PPEs. [Preview Abstract] |
Thursday, March 19, 2009 11:27AM - 11:39AM |
W20.00002: Crystal and Rotator Phases of n-alkanes: a Molecular Dynamics Study Nathaniel Wentzel, Scott T. Milner The odd $n$-alkanes exhibit a wide variety of solid phase behavior; experimentally observed phases include an orthorhombic crystal phase, in which the molecules show long range herringbone order, and rotator phases in which the molecules do not diffuse but display various degrees of disorder. The rotator phases are of interest because they are implicated in the nucleation of $n$-alkane and polyethylene crystals. C$_{23}$ has been found experimentally to have two stable rotator phases, orthorhombic $R_{I}$ and hexagonal $R_{II}$, at temperatures between the crystal and melt. The crystal--$R_{I}$ and $R_{I}$--$R_{II}$ phase transitions are observed to be weakly first order. Simulations of C$_{23}$ to date have found the $R_{I}$ phase but not the $R_{II}$ phase, and have not much characterized the phases or the transitions between them. We report our results for local order and pretransitional fluctuations of rotator phases, from our all-atom molecular dynamics simulations of thin layers of C$_{23}$. We also comment on how these properties relate to the experimentally observed phase transitions. [Preview Abstract] |
Thursday, March 19, 2009 11:39AM - 11:51AM |
W20.00003: Computational Modeling of Polymers and the Influence of Molecular Level Structural Features on Mechanical Properties Thomas Clancy, Sarah-Jane Frankland The role of molecular structure on the mechanical properties of polymer based materials is investigated through atomistic based molecular dynamics simulations. Models of crosslinked polymers were built with a range of moisture content in order to study the effect of environmental exposure on mechanical properties. Another key structural parameter, the degree of crosslinking, was also varied. The molecular structural features associated with these parameters are studied for their influence on the mechanical properties. The relative motion of crosslink points and the influence of penetrants such as water are investigated under deformation conditions. The mobility of penetrants within the polymer matrix is studied under equilibrium and deformation conditions in order to assess the role of these structural features on the mechanical properties as well as to assess the influence of deformation on diffusion rates. [Preview Abstract] |
Thursday, March 19, 2009 11:51AM - 12:03PM |
W20.00004: Hydrogen Bonding Structure in Hyperbranched Aliphatic Polyesters Studied by MD Simulations Brian Olson, Mukul Kaushik, Sergei Nazarenko Hyperbranched aliphatic polyesters based on dimethoxy propionic acid (bis-MPA) as the repeating unit and ethoxylated pentaerythritol as the tetrafunctional core gained widespread attention due to their unusual structure and properties. These globular macromolecules possess a large number of hydroxyl functional groups in particular on their periphery. These hydroxyl groups interact readily through hydrogen bonding (HB) and form clusters responsible for many physical properties of this system. The structure of these clusters however remains unclear. Therefore MD simulations have been used to elucidate the structure of these clusters. MD simulations revealed that peripheral hydroxyl groups form linear hydrogen bond clusters (strings) similar to those proposed in hydrofluoric acid (HF) but considerably shorter consisting of 4-10 hydroxyl groups per cluster. Simulations also led to prediction of WAXS pattern for these hyperbranched polyesters in the bulk with the characteristic peak at 2$\theta $ =30\r{ } due to O-O correlations similar to those in water. The predictions were in excellent agreement with the experimental WAXS data. [Preview Abstract] |
Thursday, March 19, 2009 12:03PM - 12:15PM |
W20.00005: Phases of functionalized polymer-inorganic composites in solution studied via molecular dynamics Joshua Anderson, Rastko Sknepnek, Alex Travesset Using self-assembling polymer systems to direct the formation of inorganic crystals, polymer-inorganic composite materials offer new opportunities in materials design. Molecular dynamics simulations allow for an exploration of the wide range of phases in these systems. Amphiphilic ABA triblocks with A hydrophilic, B hydrophobic, and functional ends with an affinity to inorganic particles are modeled to capture the minimum physics needed to describe polymer-inorganc systems currently being investigated by experiment. A number of phases are formed in solution as the attraction strength between the inorganic particles and the affinity of those particles to the functional end beads of the polymer are varied. Some of the phases found include hexagonal, square columnar, lamellar, perforated lamellar, and the gyroid. Polymer stretching plays an important role in each of the phases found, with a characteristic multi-modal behavior in the polymer end to end distance distribution. In the gyroid phase, for instance, the peaks correspond to the polymers being in two preferred conformations: v-shaped with a small end to end distance and fully extended in a line with the largest possible end to end distance. At high interaction strengths, inorganic particles are found to crystallize and form plate-like structures. [Preview Abstract] |
Thursday, March 19, 2009 12:15PM - 12:27PM |
W20.00006: The effect of chain stiffness on the structure and phase behavior of diblock copolymer melts G. Leuty, Mesfin Tsige In block copolymers the covalent bond joining the different immiscible block segments prevents the occurrence of macroscopic phase separation of the different components of a copolymer chain. Instead, the block segments give rise to well-organized periodic domain nanostructures whose size and shape mainly depend on the dimensions of the blocks and the segment-segment interaction parameters. Variations in the stiffness of the different block segments can directly affect the morphology of the system and may result in a very rich phase behavior. To the best of our knowledge, there is no theory at the atomic or molecular level that explains how variations in the stiffness of the different block segments can affect the dynamics and morphology of these systems. We have studied the microphase separation of symmetric diblock copolymers with variable block stiffness and different block chain length using coarse-grained molecular dynamics simulations. The morphology of the diblock systems we studied is found to be strongly dependent on the relative stiffness of the two block segments. [Preview Abstract] |
Thursday, March 19, 2009 12:27PM - 12:39PM |
W20.00007: Rigidity transition with increasing crosslinking of a single macromolecule Jiwu Liu, Phillip Duxbury A nano-particle can be formed by the intramolecular crosslinking of a polymer chain. In this process the rigidity of the system increases with the crosslinking density. We carried out extensive molecular dynamics simulations of the intramolecular crosslinking on six different models to study their rigidity transitions. It was found the crosslinking satisfiablity of the system is greatly affected by its rigidity. A facile analysis of floppy modes of the system was employed to determine the rigidity transition threshold and a good agreement with simulation data was obtained. [Preview Abstract] |
Thursday, March 19, 2009 12:39PM - 12:51PM |
W20.00008: Spreading of Droplets on Viscous Polymer Liquids Flint Pierce, Dvora Perahia, Gary Grest Significant strides have been made in understanding the spreading of liquid droplets on solid surfaces. However from biological complexes to polymeric interfaces, the surfaces are not ideal; explicitly, the surfaces may dynamically respond as spreading takes place and the droplets may partially penetrate. Molecular dynamic simulations were carried out to investigate the spreading of liquid droplets of short chains on films of viscous polymer melts. Unlike the spreading on solid surfaces, the droplets simultaneously spread and penetrate. The degree of penetration and the magnitude of damping from the film depend on the viscosity of the underlying liquid and the relative interaction of the two constituents. At the interface with viscous films a precursor foot spreads ahead of the droplet whereas on top of less viscous interfaces, the droplets penetrate while spreading with no precursor foot. A kinetic model described the spreading of shorter chain length droplets, while a hydrodynamic model better expresses the spreading of longer chain length liquid. Supported in part under DOE contract No. ER46456. [Preview Abstract] |
Thursday, March 19, 2009 12:51PM - 1:03PM |
W20.00009: Shear rate threshold for the onset of boundary slip in dense polymer films Nikolai Priezjev Molecular dynamics simulations are carried out to investigate the dynamic behavior of the slip length in thin polymer films confined between atomically smooth surfaces. The polymer melt is modeled as a collection of bead-spring chains of 20 Lennard- Jones monomers interacting through the FENE potential. We found that at high melt densities and low shear rates the fluid velocity profiles acquire a pronounced curvature near the walls and the slip length is approximately equal to the thickness of the immobile boundary layer. The linearity of the fluid velocity profiles is restored at higher shear rates where the slip length increases rapidly as a function of shear rate. We will show that the friction coefficient at the interface between a polymer melt and a solid wall follows power law decay as a function of the slip velocity. At large slip velocities the friction coefficient is determined by the product of the value of surface induced peak in the structure factor and the contact density of the first fluid layer near the solid wall. A relation to recent slip flow experiments is discussed. [Preview Abstract] |
Thursday, March 19, 2009 1:03PM - 1:15PM |
W20.00010: Direct Numerical Evaluation of Plateau Modulus of Entangled Polymer Melts via Multi-Scale Molecular Dynamics(MD) Won Bo Lee, Kurt Kremer Plateau modulus and viscosity of entangled polymer melts can be calculated by off-diagonal elements of stress tensor, which are connected by the Green-Kubo relation and tube theory. However, direct numerical evaluation of plateau modulus via stress autocorrelation function (SAF) from MD simulation is a big challenge in a computational point of view due to the following reasons: strong fluctuations, long relaxational times and large spatial scales. In the present work, SAFs of entangled polymer melts are calculated by coarse-grained MD. We find that the use of time-averaged stress helps to reduce strong noise in SAF while capturing most local chain relaxations. Plateau values by SAF are compared with plateau values predicted from the entanglement length evaluated via primitive path analysis (PPA). The importance of well equilibrated melts for such an analysis is shortly discussed. [Preview Abstract] |
Thursday, March 19, 2009 1:15PM - 1:27PM |
W20.00011: Cole-Davidson Glassy Dynamics in Simple Chain Models John McCoy, Joanne Budzien, Taylor Dotson, Douglas Adolf, Jonathan Brown Rotational relaxation functions of the end-to-end vector of short, freely jointed and freely rotating chains were determined from molecular dynamics simulations. The associated response functions were obtained from the one-sided Fourier transform of the relaxation functions. The Cole-Davidson function was used to fit the response functions. For the systems studied, the Cole-Davidson function provided remarkably accurate fits (as compared to the transform of the Kohlrausch-Williams-Watts (KWW) function). The only appreciable deviations from the simulation results were in the high frequency limit and were due to ballistic, or free rotation, effects. The accuracy of the Cole-Davidson function appears to be the result of the transition in the time-domain from stretched exponential behavior at intermediate time to single exponential behavior at long time. [Preview Abstract] |
Thursday, March 19, 2009 1:27PM - 1:39PM |
W20.00012: Glass transition temperature of PIB, PDMS and PMMA from small-time simulations Solomon Duki, Mesfin Tsige, Philip Taylor We have applied some new techniques to obtain predictions of the glass transition temperatures $T_g$ of poly(isobutylene), poly(dimethyl-siloxane), and poly(methyl methacrylate) from small-time atomistic molecular dynamics simulations. The different fragilities of these materials are reflected in the results of the simulations. One approach involved measurement of the apparent softening of the ``cage'' in which a monomer is bound, while another involved studying autocorrelation of a convolution of the velocity with a smoothing function in order to detect the frequency of escapes from the ``cage.'' To check the accuracy of the short-time methods, the $T_g$ of the polymers was also found using conventional diffusion simulations in which the rate of increase of the root mean squared displacement of an atom, monomer, or molecule is measured at very long times. The economical short-time simulations yielded results for $T_g$ that were identical to those of the computer-intensive long-time simulations. [Preview Abstract] |
Thursday, March 19, 2009 1:39PM - 1:51PM |
W20.00013: Translocation of a Polymer Through a Nanopore in the Presence of Obstacles Hendrick W. de Haan, Gary W. Slater The translocation of a polymer through a nanopore is interesting both as a process of fundamental biological importance and as relevant to the development of next-generation DNA sequencing technology. Due to the time and length scale of typical systems and events, computer simulations are well suited to study this problem and have been used extensively to study different aspects of the translocation process. In this work, we present results from a system in which a polymer and a membrane containing a nanopore are placed in a medium containing obstacles. Using the Espresso Molecular Dynamics simulation package, simulations are performed in which the translocation events are driven by: i) an obstacle concentration gradient and ii) a varying amount of disorder. Results indicating the establishment of a preferential direction and assessing the impact of the system configuration on details such as the translocation time will be given. [Preview Abstract] |
Thursday, March 19, 2009 1:51PM - 2:03PM |
W20.00014: Role of RNA in the self-assembly of virus:A coarse-grained Brownian Dynamics study J.P. Mahalik, Murugappan Muthukumar Assembly of a single viral capsid (Icosahedral T1 type) was studied in the absence and presence of RNA. A coarse-grained rigid body model was used to represent the capsomer units and a flexible polyelectrolyte model was used to represent RNA. Brownian Dynamics simulation was used to study the assembly process. The rate of assembly was found to be enhanced in the presence of RNA. The free energy contribution of the RNA in the self-assembly process was computed using weighted histogram analysis method. [Preview Abstract] |
Thursday, March 19, 2009 2:03PM - 2:15PM |
W20.00015: Probability of adsorption of peptide (CR3-1, S2) chains on clay minerals by coarse-grained Monte Carlo simulation Ras B. Pandey, Hendrik Heinz, Barry L. Farmer, Sharon Jones, Lawrence F. Drummy, Rajesh R. Naik A coarse-grained description is used to study the structure and dynamics of peptide chains (CR3-1, S2) in presence of a clay surface on a cubic lattice. A peptide chain is represented by the specific sequence of amino acids. Specificity of residues is captured via an interaction matrix based on the insight gained from the atomistic simulation, i.e., each residue interacts with surrounding residues, solvent, and the clay surface with a unique interaction potential. We use a standard LJ potential with its coefficient controlled by the interaction matrix. Simulations are performed with a number of peptide chains. Along with the global energy and dynamics of peptides, we keep track of mobility, energy (total and adsorption), and correlation with the local structure from the density profiles of each residue. Based on the analysis of local and global quantities, we are able to assess the probability of adsorption of peptides to clay surface in agreement with experiment. The probability of adsorption of S2 is found to be much higher than that of CR3-1 in which S2 is anchored by Lysine. The procedure is complementary to biopanning experiments since it allows screening a large number of peptides (more than 10E+5) on the surface to estimate their binding potential. [Preview Abstract] |
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