Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session Q19: Focus Session: Theory and Simulations of Macromolecules VII - Chain Conformation |
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Sponsoring Units: DPOLY Chair: Ting Ge, The University of North Carolina at Chapel Hill Room: 404 |
Wednesday, March 5, 2014 2:30PM - 2:42PM |
Q19.00001: Evolution of chain conformation and entanglements as related to the origin of stress overshoot during startup shear of entangled polymer melts Zhen-Gang Wang, Yuyuan Lu, Lijia An, Shi-Qing Wang Using Brownian Dynamics simulation, we determine the chain orientation and stretching and their connection to stress overshoot in an entangled polymer melt undergoing startup shear at rates lower than the reciprocal of the Rouse time yet higher than the reciprocal reptation time. In this regime, the prevailing tube theory envisions little chain stretching and monotonic increase of the radius of gyration to a saturated value, and attributes the stress overshoot to excessive chain orientation. In contrast, our results reveal that there is significant chain stretching which persists well beyond the Rouse time and contributes substantially to the initial stress growth. In particular, stress overshoot is found to be primarily due to chain retraction after considerable stretching rather than chain over-orientation. The coil size shows non-monotonic dependence on the strain. Furthermore, up to many Rouse times, the relaxation of the initial entanglements is slower than that under the quiescent condition. These results point to fundamental deficiencies in the molecular picture of the tube model for startup shear. [Preview Abstract] |
Wednesday, March 5, 2014 2:42PM - 2:54PM |
Q19.00002: Effects of Bond Stiffness on Structural Transitions of Flexible Polymers Tomas Koci, Michael Bachmann Utilizing advanced parallel Monte Carlo simulation methods we examine the structural transitions of a coarse-grained flexible polymer model. In this model, the bond elasticity or effective bond stiffness is considered to be a parameter. Pseudophase diagrams in temperature-stiffness space are constructed by using energy dependent canonical quantities to demonstrate the effects of the changes in the bond flexibility on the liquid and solid structural phases. With increasing bond flexibility we observe the disappearance of the liquid phase and the fusion of the collapse and the freezing transitions. The notoriously difficult sampling of entropically suppressed energetic regions near strong first-order transitions is improved by employing generalized ensemble methods. [Preview Abstract] |
Wednesday, March 5, 2014 2:54PM - 3:06PM |
Q19.00003: Ordering transitions in confined melts of semiflexible polymers: A Monte Carlo simulation Wolfgang Paul, Viktor Ivanov, Marcus Mueller, Kurt Binder Using grand-canonical Monte Carlo simulations of the bond-fluctuation model confined between two hard walls we study the effect of confinement on the isotropic-nematic transition of a melt of semi-flexible chains. The walls have a stiffening effect on the chains in their vicinity leading to an ordering transition at the walls preempting the one in the bulk (surface-induced ordering). For a semi-infinite system the thickness of the ordered nematic layer increases with a complete wetting transition upon approaching bulk coexistence. For a finite extension, D, between the walls, the ordered surfaces induce a shift of the first order isotropic-nematic transition in the bulk of the film (capillary nematization). When D becomes comparable to the extension of a chain, the first order isotropic-nematic transition line ends in a critical point. [Preview Abstract] |
Wednesday, March 5, 2014 3:06PM - 3:18PM |
Q19.00004: Stress-strain relation of K4 phenolic resins by classical MD simulation Katsumi Hagita From viewpoint of collaboration among mathematics, material sciences, and physics, K4 lattice has been much interested. K4 lattice is confirmed to be backbone of Schwarz G surface, which is one of triply periodic minimal surface called Gyroid. Double Gyroid is nested lattice of two single Gyroid. As exploration of new materials inspired from pure mathematics, we proposed K4 Phenolic resins. The resins consist of Phenol and hydrocarbon originated from formaldehyde. The hydrocarbon has a role to connect two phenols. Maximum number of connection from one phenol is 3. Then, as an ideal case, backbone of Phenol resins can be form K4 lattice structure. In the present study, for studying elastic modulus, we performed classical MD simulation with deformation by using LAMMPS packages to estimate stress-strain relation. [Preview Abstract] |
Wednesday, March 5, 2014 3:18PM - 3:30PM |
Q19.00005: Zip-DNA: A Novel DNA Structure Formed Under Mechanical Stress Alexander Balaeff, Ivan Mikhailov, Malakhat Turabekova, Stephen Craig, David Beratan Zip-DNA is a novel DNA structure predicted by molecular dynamics simulations of forced DNA extension. In the zip-DNA form, the Watson-Crick hydrogen bonds are broken and nucleobases from the opposite DNA strands interdigitate with each other, forming a continuous single-base aromatic stack. The B-Zip DNA structural transition is proposed to be responsible for the famous overstretching plateau on the force-extension curve of DNA. The simulations show that zip-DNA may either self-assemble from force-melted DNA strands or evolve from B-DNA through an earlier recognized S-DNA. Zip-DNA is shown to be consistent with multiple experimental observations; notably, the S-DNA transition state is shown to be a highly disordered state consistent with experimentally measured thermodynamic characteristics of DNA extension. We predict that zip-DNA possesses increased molecular conductivity compared to the B-DNA form and, therefore, may find applications in molecular electronics. A conductive state of a stretched non-complementary double-stranded DNA would, if detected, become a ``smoking gun'' experiment validating the existence of zip-DNA. [Preview Abstract] |
Wednesday, March 5, 2014 3:30PM - 3:42PM |
Q19.00006: Excluded-volume interaction induced stiffness of comb polymer with densely grafted side-chains Feng Qiu Excluded-volume interaction has been widely recognized to cause expansion of polymer chain at large length scale. However, its effect on chain conformations at small length scale has been studied to less extent. Here we consider a comb polymer with its backbone densely grafted by side-chains as a model system. The method analogue to solving the electrostatic persistence length problem for either rigid or flexible polyelectrolytes is employed. For comb polymers with rigid backbone near the rod limit, the excluded-volume interaction induced persistence length scales linearly with the volume of the side-chain. While for flexible backbone, the persistence length depends on the side-chain volume more weakly. Field theoretic method that is relevant to address this problem is also explored and discussed. [Preview Abstract] |
Wednesday, March 5, 2014 3:42PM - 3:54PM |
Q19.00007: Effect of bending stiffness and confinement on a polymer chain under tension Peter Poier, Christos N. Likos, Richard Matthews Type II topoisomerase are enzymes that (un)knot DNA. There is experimental evidence that a certain type II topoisomerase preferentially cleaves adenine (A) and thymine (T) rich regions of the DNA. It is believed that AT-rich sequences are more flexible than random ones. This raises the question of whether the flexibility of the preferred cleavage sites of topoisomerase II could play an important role in the regulation of knotting. With this motivation we study the effect of the bending stiffness and confinement on the free-energy cost of a knot in a polymer chain under tension. For the polymer chain we use a coarse-grained model. Via thermodynamic-integration we calculate the change of the free-energy cost of a knot due to modifications of the bending stiffness. The free-energy cost exhibits a minimum at a non-zero value for the bending stiffness. Our simulations suggest that this minimum is related to a suppression of the bending at the points where the strands of the polymer cross in the knotted region. We study how the minimum of the free-energy cost is affected by changing the knot type and introducing a two dimensional confinement for the polymer chain. The results of this work might be of importance for the localization of knots in DNA. [Preview Abstract] |
Wednesday, March 5, 2014 3:54PM - 4:06PM |
Q19.00008: Molecular mechanics modeling of compressible polymer solutions based on an isobaric-isothermal ensemble. Moeed Shahamat, Alejandro Rey Understanding the thermodynamics and physical properties of polyethylene (PE) in hydrocarbons is significant for its industrial production. Of recent interest are atmostic simulations which provide a detailed molecular level insight without experimental efforts. This paper reports on the density of solutions of PE in hexane using molecular dynamics (MD) simulations at high pressures. The computed densities increase monotonically with raising external pressure and compare quite favorably with experimental and theoretical data. Furthemore, the effect of cut-off distance to density is investigated and it is shown that the density increases with increasing the cut-off radius. It has been revealed that for pressures below 100 bar the mixture density displays a large dependece on cut-offs and for higher pressures solution density and non-bonded interactions demostrate weak sensitivity to cut-off distance. Analysis of the pair distribution function versus pressure shows that the amplitude of the first peak increases and the radial distribution function shifts to shorter separations reflecting structural change of the condensed phase. The implemented MD-NPT approach in this research provides a good insight into the polymer-polymer, polymer-solvent, and solvent-solvent interactions. [Preview Abstract] |
Wednesday, March 5, 2014 4:06PM - 4:18PM |
Q19.00009: Frank elastic constants in LC mesophases of polymeric semiconductors Patrick Gemuenden, Kurt Kremer, Kostas Ch. Daoulas Liquid crystalline (LC) mesophases of polymeric semiconductors [1], e.g. poly(alkylthiophenes), can facilitate processing to obtain morphologies with improved properties. We develop a particle-based modeling approach to study nematic mesophases of such systems. The method uses soft, directional interactions [2] and is inspired by field theoretical approaches to LCs [3]. It enables us to generate large morphologies and calculate Frank elastic constants (FC). Besides interesting theoretical questions related to the behavior of FCs in polymer nematics, they are important when linking particle-based with continuum media descriptions of LCs. We calculate FC related to bend, splay and twist deformations from the fluctuation spectra of the local nematic director. The magnitudes of FC measured in the simulations agree with those reported in experiments on polymer nematics. We discuss their dependence on system parameters, e.g. chain length, and we compare with predictions by analytical field theory [4].\\[4pt] [1] Ho et al., Macromolecules 43, 7895 (2010)\\[0pt] [2] Gem\"{u}nden et al. Macromolecules 46, 5762 (2013)\\[0pt] [3] Pryamitsyn \& Ganesan, J. Chem. Phys. 120, 5824 (2004)\\[0pt] [4] Le Doussal \& Nelson, Europhys. Lett. 15, 161 (1991) [Preview Abstract] |
Wednesday, March 5, 2014 4:18PM - 4:30PM |
Q19.00010: Stability of Polymeric Crystalline Polymorphs Daniel W. Sinkovits, Sanat K. Kumar In the search for polymeric materials with novel properties, such as high dielectric constant and low loss, an important attribute of a material is its crystal structure. Most polymers can crystallize into multiple polymorphs whose properties vary. Therefore, the question of which polymorphs are thermodynamically preferred under what conditions is of great importance. We generate polymorphs using atomistic molecular dynamics simulations and tackle the question of stability using a combination of molecular dynamics and Monte Carlo techniques. [Preview Abstract] |
Wednesday, March 5, 2014 4:30PM - 4:42PM |
Q19.00011: ABSTRACT WITHDRAWN |
Wednesday, March 5, 2014 4:42PM - 4:54PM |
Q19.00012: \textit{A priori }Determination of the Rheological Properties and Slip Phenomena of Polymer Melts John Dorgan, Nicholas Rorrer This work builds on previous studies...$^{\mathrm{1,\thinspace 2}}$ done utilizing a coarse grained Dynamic Monte Carlo algorithm. The algorithm is able to capture the molecular scale details of flowing polymer melts in nanoscopic geometries. In shear flow all of the known observable viscoelastic behavior associated with polymer melts is predicted in a completely \textit{a priori }manner. For example, the correct scaling of the zero shear viscosity with molecular weight is observed. When polydispersity is introduced, the viscosity curves demonstrate a broadening behavior, exhibiting the same zero shear viscosity but lower viscosities at higher shear rates. Slip phenomena has been investigated under both shear (Couette) and parabolic (Poiseulle) flow. These two different flow cases are demonstrated to be profoundly different in their molecular scale details. All of the predicted results are in \textit{post facto} agreement with many experiments and help shed fundamental insight into the molecular scale behavior of polymer fluid dynamics. .1. Dorgan, J. R.; Rorrer, N. A.; Maupin, C. M., \textit{Macromolecules }\textbf{2012,} \textit{45} (21), 8833-8840. 2. Dorgan, J. R.; Rorrer, N. A., \textit{Physical Review Letters }\textbf{2013,} \textit{110} (17) [Preview Abstract] |
Wednesday, March 5, 2014 4:54PM - 5:06PM |
Q19.00013: Autocorrelation study for a coarse-grained polymer model Kai Qi, Michael Bachmann By means of Metropolis Monte Carlo simulations of a coarse-grained model for flexible polymers, we investigate how the integrated autocorrelation times of different energetic and structural quantities depend on the temperature. We show that, due to critical slowing down, an extremal autocorrelation time can also be considered as an indicator for the collapse transition that helps to locate the transition point. This is particularly useful for finite systems, where response quantities do not necessarily exhibit clear indications for pronounced thermal activity. [Preview Abstract] |
Wednesday, March 5, 2014 5:06PM - 5:18PM |
Q19.00014: The Configuration and Dynamics of Self-Attractive Flexible and Semi-Flexible Polymers Ronald Larson, Indranil Saha Dalal, Miqiu Kong We study ``bead-rod'' chains containing stiff Fraenkel springs with nearly fixed Kuhn length, but with varying numbers of rods representing each Kuhn length, N$_{\mathrm{r,K}}$, modeled by incorporating a bending potential between consecutive rods. We find converged results as we increase the number of rods per Kuhn step. We find that at high $\varepsilon ^{\mathrm{\ast }}$N$_{\mathrm{r,K}}$, where $\varepsilon^{\mathrm{\ast }}$ is the attractive interaction strength per bead normalized by kT, collapsed globules are produced at moderate dimensionless chain diameter $\sigma^{\mathrm{\ast }}=$1/4, while for $\sigma^{\mathrm{\ast }}=$1, helices are formed, and for $\sigma^{\mathrm{\ast }}=$1/16, tori, folded bundles, and finally globules, are formed as $\varepsilon ^{\mathrm{\ast }}$N$_{\mathrm{r,K}}$ increases. Under shear, a universal tumbling state is found where chain width in the shear gradient direction is independent of chain length and proportion to shear rate to the fourth power. [Preview Abstract] |
Wednesday, March 5, 2014 5:18PM - 5:30PM |
Q19.00015: Floquet-Bloch theory for polymers in a periodic Ricardo Pablo Pedro, David Tempel, Alfredo Alexander-Katz Anderson localization in disordered systems predicts the localization of electronic wave functions and the resulting absence of diffusion. The phenomenon is much more general and has been observed in a variety of systems. In the case of the polymer, the behavior of it in a periodic potential is equivalent to the behavior of a quantum-machanicial particle in a periodic potential. According to this mapping our results for polymers in a periodic potential ara valid for localization of a quantum-mechanical particle in a periodic potential. Besides, one of our motivations for studying polymers in a periodic potential is because it reveals interesting aspects of a self-organization of the adsorbed polymers onto a surface with periodic potential. In order to describe the properties of time-periodic polymer system, we consider the potential time dependent which is periodic in time and space and we evaluate the solutions using the powerful nonperturbative Floquet-Bloch theory which is formulated for linear systems. Finally, we also consider a more interesting problem of when disorder is included in the time-periodic system, where localization of the wave function can occur. [Preview Abstract] |
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