Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session Q42: Focus Session: Theory and Simulation of Macromolecules I |
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Sponsoring Units: DPOLY DCOMP Chair: Lisa Hall, Ohio State University Room: 214B |
Wednesday, March 4, 2015 2:30PM - 2:42PM |
Q42.00001: Computation of the Gibbs free energy difference between polymorphs Daniel W. Sinkovits, Sanat K. Kumar Semi-crystalline polymers commonly crystallize into several different polymorphs; for example, the alpha and beta phases of isotactic polypropylene. While it is possible to favor particular polymorphs by kinetic means, such as with varying degrees of supercooling or through the use of different solvents in solution casting, we focus on the question of thermodynamic stability; that is, which polymorph possesses the lowest Gibbs free energy for a given temperature and pressure. We implement a version of the Bennett Acceptance Ratio method and find phase diagrams for several polymers. We also demonstrate agreement with phonon analysis in the quasi-harmonic approximation. The advantages and drawbacks of these methods will be discussed. [Preview Abstract] |
Wednesday, March 4, 2015 2:42PM - 2:54PM |
Q42.00002: New Molecular Theory for Dense, Thin Polymer Films Karl Freed The development of a molecular theory for dense polymer systems ranks among the most challenging problems in the statistical mechanics of complex matter. These difficulties become compounded when considering the influence of molecular details on thermodynamic properties of thin polymer films, properties deviating from those of the bulk phases. A new theory of dense polymer films is developed as a significant generalization of methods used to devise the lattice cluster theory, an extension of Flory-Huggins theory that include details of monomer structure and short range correlations (neglected in FH theory) and that has successfully been applied to a wide range of polymer systems. The new theory incorporates the essential ``transport'' constraints of Helfand and focuses on the strict imposition of excluded volume constraints, appropriate to dense polymer systems, rather than the maintenance of chain connectivity as appropriate for lower densities and implemented in self-consistent theories of polymer adsorption at interfaces. The theory is illustrated by presenting examples of the computed density and chain end profiles for free standing films as a function of bulk density, chain length, temperature, and chain semi-flexibility. [Preview Abstract] |
Wednesday, March 4, 2015 2:54PM - 3:06PM |
Q42.00003: Examination of surface nucleation during the growth of long alkane crystals by molecular dynamics simulation Alexander Bourque, Gregory Rutledge Crystal growth from the melt of n-pentacontane (C50) was studied by molecular dynamics simulation using a validated united atom model. By quenching below the melting temperature of C50 (370 K), propagation of the crystal growth front into the C50 melt from a crystalline polyethylene surface was observed. By tracking the location of the midpoint in the orientational order parameter profile between the crystal and melt, crystal growth rates between 0.015-0.040 m/s were observed, for quench depths of 10 to 70 K below the melting point. In this work, surface nucleation is identified with the formation of 2D clusters of crystalline sites within layers parallel to the propagating growth front, by analogy to the formation of 3D clusters in primary, homogeneous nucleation. These surface nucleation events were tracked over several layers and numerous simulations, and a mean first passage time analysis was employed to estimate critical nucleus sizes, induction times and rates for surface nucleation. Based on new insights provided by the detailed molecular trajectories obtained from simulation, the classical theory proposed by Lauritzen and Hoffman is re-examined. [Preview Abstract] |
Wednesday, March 4, 2015 3:06PM - 3:18PM |
Q42.00004: Molecular Dynamics Simulations of Homogeneous Crystallization in Polymer Melt Bin Kong Molecular mechanisms of homogeneous nucleation and crystal growth from the melt of polyethylene-like polymer were investigated by molecular dynamics simulations. The crystallinity was determined by using the site order parameter method (SOP), which described local order degree around an atom. Snapshots of the simulations showed evolution of the nucleation and the crystal growth through SOP images clearly. The isothermal crystallization kinetics was determined at different temperatures. The rate of crystallization, $K_{c}$, and the Avrami exponents, $n$, were determined as a function of temperature. The forming of nucleis was traced to reveal that the nucleis were formed with more ordered cores and less ordered shells. A detailed statistical analysis of the MD snapshots and trajectories suggested conformations of the polymer chains changed smoothly from random coil to chain folded lamella in the crystallization processes. [Preview Abstract] |
Wednesday, March 4, 2015 3:18PM - 3:30PM |
Q42.00005: Molecular dynamics simulation of electromechanical breakdown of polyolefins under a high electric field Mayank Misra, Daniel Sinkovits, Sanat Kumar Polymers are finding increasing use as dielectric materials. Due to their flexibility, polymer dielectrics in the presence of an electric field may undergo large deformations that result in mechanical instability, which leads to detrimental failures. We study this mechanical instability in polyolefins using all-atom molecular dynamics. We vary the simulated external electric field from 0 to 1200 V/$\mu $m to study the effect of high electric fields on polyolefins. At critical conditions, we observe a thinning effect leading to electromechanical breakdown. We also determine the critical voltage using theoretical models and relate it to the thinning effect detected in the molecular dynamics simulations. [Preview Abstract] |
Wednesday, March 4, 2015 3:30PM - 3:42PM |
Q42.00006: Recovery of polymer folding landscapes from univariate time series and its dimensionality reduction using machine learning Jiang Wang, Andrew Ferguson The stable conformations and motions of polymers and macromolecules are governed by their underlying free energy surface. By integrating ideas from dynamical systems theory with nonlinear manifold learning, we have developed an approach to recover single-molecule free energy surfaces from univariate time series of a single system observable. Using the method of delays, we expand the time series into a high dimensional phase space in which, by Takens' Theorem, the dynamics are equivalent to those of the molecule in real space. We then apply nonlinear manifold learning algorithm (diffusion maps and nonliear PCA) to extract a low-dimensional representation of the free energy surface that is diffeomorphic (i.e., a smooth transformation) to that which would have been recovered from a complete knowledge of all system degrees of freedom. We have validated our approach in molecular dynamics simulations of a C$_{24}$H$_{50}$ n-alkane chain, demonstrating that the free energy surface extracted from the atomistic simulation trajectory is geometrically and topologically equivalent to that recovered from a knowledge of only the head-to-tail distance of the chain. Our approach lays the foundations to extract empirical single-molecule free energy surfaces directly from experimental data. [Preview Abstract] |
Wednesday, March 4, 2015 3:42PM - 4:18PM |
Q42.00007: Flow-Induced Crystallization and Nucleation in Isotactic Polypropylenes Invited Speaker: Scott Milner Flow-induced crystallization (FIC) occurs when a brief interval of strong flow precedes a temperature quench; many more nuclei form, resulting in a much more fine-grained solid morphology and better material properties. Common industrial polymer processing (injection molding) depends on FIC, which has been the subject of many experimental studies, most commonly on isotactic polypropylene (iPP). The prevailing hypothesis is that FIC results from flow aligning chains in the melt, increasing the melt free energy with respect to the crystal, hence acting like undercooling. Here, I combine experimental results for FIC and homogeneous nucleation with theoretical estimates for critical nuclei, to assess the prevailing hypothesis. Current best information supports the view that chain stretching (not just alignment) is necessary and sufficient to explain the observed increase in nucleation rate. Important puzzles remain: 1) shear applied at temperatures well above the equilibrium melting temperature Tm = 187 C is effective for FIC, and 2) a sheared sample may be held for hours above Tm, and still crystallize faster when quenched. [Preview Abstract] |
Wednesday, March 4, 2015 4:18PM - 4:30PM |
Q42.00008: Emergent tilt order in zigzagging polymer liquids Benjamin Loewe, Anton Souslov, Paul M. Goldbart We study a liquid of zigzagging two-dimensional polymers that have bending rigidity. These are directed polymers whose conformations lie along the paths followed by pieces on a checkerboard. We observe that in the continuum limit the statistical physics of one such polymer can be described in terms of the Dirac equation for a particle having an imaginary mass. We exploit this observation to investigate a liquid of these polymers by means of quantum many-particle techniques in imaginary-time. We treat hard-core interactions between the polymers via a transmutation of quantum particle statistics, from Bose to Fermi, and we account for additional interactions between polymers by introducing two-body interactions between the fermion particles. A self-consistent approximation predicts a phase of tilted order, i.e., the polymers may develop a spontaneous preference to zig rather than zag (or vice versa). We study this behavior analytically, computing the phase diagram and response functions for the polymer liquid, and comment on the role played by fluctuations. [Preview Abstract] |
Wednesday, March 4, 2015 4:30PM - 4:42PM |
Q42.00009: Aggregation Transitions in Flexible Homopolymer Systems Tomas Koci, Michael Bachmann Ubiquitous in biological systems, aggregation transitions are the key towards understanding a multitude of topics such as the amyloid sheet formation and prionic disease. By means of extensive replica-exchange Monte Carlo simulations of a generic coarse-grained model we examine systems consisting of up to 20 individual polymer chains. The application of powerful microcanonical analysis methods reveals new details about the anatomy of aggregation transitions that were previously inaccessible via conventional canonical analysis. We find evidence for phase separation in the transition region and classify the transition as first order. Finally we show that the aggregation transition consists of a hierarchy of sub-phase transitions and discuss the implications of this finding. [Preview Abstract] |
Wednesday, March 4, 2015 4:42PM - 4:54PM |
Q42.00010: Scaling properties of the free energy of a wormlike chain in confinement Jeff Z.Y. Chen We discuss the free energy and conformational properties of a wormlike chain in spherical, cylindrical, and slit confinements. We show that in the weak-confinement limit, the wormlike chain model exactly reproduces the confinement properties of a Gaussian chain. In such a case the confinement entropy dominates the free energy. In the strong-confinement limit, the free energy is dominated by the bending energy of the chain, or the Odijk scaling behavior. The crossover region between the weak and strong asymptotic limits is examined. [Preview Abstract] |
Wednesday, March 4, 2015 4:54PM - 5:06PM |
Q42.00011: Parallel framework for wormlike chains using self consistent field theory David Ackerman, Baskar Ganapathysubramanian The Gaussian chain model commonly used in Self Consistent Field Theory (SCFT) has enabled study of a wide range of macromolecule systems; however, the flexible nature of the model makes it unsuitable for many biomolecules and systems such as liquid crystals where alignment effects are critical. The orientations accounted for in a wormlike chain model can correctly capture the physics of these systems. The primary problem with a wormlike chain model is the computational cost of implementation, which far exceeds that of the Gaussian chain model. We address this problem though a parallel SCFT framework for wormlike chains incorporating orientation interactions. The framework can scale to 10s of thousands of processors using an efficient finite element (FE) approach. Orientations are treated with an FE in FE method which overlays a surface orientation mesh on top of the spatial geometry mesh. The finite element approach allows use of arbitrarily shaped systems and is ideal for studying confinement effects. We explore how this framework works on a few examples for polymers confined to a sphere. [Preview Abstract] |
Wednesday, March 4, 2015 5:06PM - 5:18PM |
Q42.00012: Structure and dynamics of highly adsorbed semiflexible polymer melts Jan-Michael Carrillo, Shiwang Cheng, Rajeev Kumar, Monojoy Goswami, Alexie Sokolov, Bobby Sumpter We present a detailed analysis of coarse-grained molecular dynamics simulations of melts of semi-flexible polymer chains in the presence of an adsorbing substrate. For polymer chains located far from the substrate the chain conformations follow the worm-like chain model, in contrast to the reflected Gaussian conformation near the substrate. This is demonstrated in the chain center-of-mass distribution normal to the substrate and the probability of a polymer chain ends to be the closest to the substrate. Both quantities agree with Silberberg's derivation for an ideal chain in the presence of a reflecting wall. We characterized the adsorbed chains and counted the number of loops and tails. For stiff chains, a tail and an adsorbed segment dominate the chain conformation of the adsorbed layer. Also, the mean-square end-to-end distance normal to the substrate is proportional to the normal component of the mean-square end-to-end distance of the tails. The tails do not follow the worm-like chain model and exhibit a stretched conformation. This picture for the adsorbed layer is akin to the ``polydisperse pseudobrush'' envisioned by Guiselin. We probe the dynamics of the segments by calculating the layer (z-)resolved intermediate coherent collective dynamics structure factor, S(q,t,z), for q values equivalent to the bond length. The segment dynamics is slower for stiffer chains. In the adsorbed layer, dynamics is slowed down and can be described by two relaxation times. [Preview Abstract] |
Wednesday, March 4, 2015 5:18PM - 5:30PM |
Q42.00013: Polymer segregation under confinement: Free energy calculations and segregation dynamics simulations James Polson, Logan Montgomery Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. We measure the free energy $F$ as a function of the separation of the centers of mass of the polymers $\lambda$, and examine the effects of varying the tube diameter $D$ and length $L$, as well as the polymer length $N$ and persistence length $P$. For long tubes and fully flexible chains, $F$ monotonically increases with decreasing $\lambda$ while the chains overlap. The scaling of the free energy barrier height with $D$ and $N$ is close to a prediction using the de~Gennes blob scaling model. For finite $L$, the free energy barrier height increases with increasing $L/D$ at fixed volume fraction $\phi$, and it decreases with increasing $\phi$ at fixed $L/D$. Increasing the polymer stiffness reduces the overlap free energy. For strongly confined systems, the observed scaling of $F(\lambda)$ with $D$ and $P$ is close to that predicted using a simple analytical model. Finally, MC dynamics simulations are used to study polymer segregation dynamics for fully flexible chains. We find that segregation rates increase with increasing entropic force. In addition, the polymers are not conformationally relaxed at later times during segregation. [Preview Abstract] |
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