Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session B19: Focus Session: Theory and Simulations of Macromolecules II  From Atomistic to Coarse Grained Models 
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Sponsoring Units: DPOLY Chair: Christoph Junghans, Los Alamos National Laboratory Room: 404 
Monday, March 3, 2014 11:15AM  11:27AM 
B19.00001: Hierarchical Modeling of Polymer/Solid Interfaces: From Abinitio Calculations to Atomistic up to Coarsegrained Simulations Vagelis Harmandaris, Karen Johnston We present a hierarchical simulation approach in order to study nanocomposite systems. Our approach combines quantum calculations, atomistic and coarsegrained (CG) dynamic simulations [12] and allows quantitative modeling of complex hybrid systems over a very broad range of length and time scales. As an example we model the polystyrene/gold system. The proposed scheme consists of the following stages: (1) Abinitio (Density Functional Theory) calculations of a single molecule adsorbed on solid surfaces. (2) Allatom molecular dynamics simulations of short polymer chains/solid systems. We further develop a methodology to obtain rigorous CG models from the atomistic data, for specific polymer/solid systems. (3) CG simulations of more realistic polymer/solid surfaces. Structural, conformational and dynamical properties of systems with longer polymer chains are studied. The width of the interphase region of the polymer films found to be property specific, ranging from about 1.5nm to a distance that is proportional to the square root of the chain length. References [1] K. Johnston and V. Harmandaris, \textit{J. Phys. Chem. C.}, \textbf{115}, (2011) 14707; \textit{Soft Matter}, \textbf{8}, (2012) 6320. [2] K. Johnston and V. Harmandaris, \textit{Macromolecules}, \textbf{2013,} \textit{46}, 5741$$5750. [Preview Abstract] 
Monday, March 3, 2014 11:27AM  11:39AM 
B19.00002: Exploring the Limits of the Iterative Boltzmann Inversion Roland Faller, Beste Bayramoglu We explore the limits of the purely structure based coarsegraining technique, the iterative Boltzmann inversion (IBI), for confined systems using the example of polystyrene solutions. First some technical considerations and challenges encountered in the course of the optimization process are presented. The choice of the initial potentials and the crossdependency of the interactions as well as the order of optimization are discussed in detail. Furthermore, the transferability between different degrees of confinement is examined. We investigate if a CG force field developed for a confined polymer solution by IBI is sensitive to changes in the degree of localization or arrangement of polymers near the surfaces although the concentration is kept constant. The differences in the structure and dynamics of the chains are addressed. Results are compared with those of an unconfined (bulk) system at the same concentration. The chain dimensions and orientations as a function of the distance from the surfaces are also reported. We find that the arrangement of monomers and solvent molecules near the surfaces is an important factor that needs to be paid attention to when considering the application of a CG force field developed by IBI to different degrees of confinement. [Preview Abstract] 
Monday, March 3, 2014 11:39AM  11:51AM 
B19.00003: Coarse graining of atactic polystyrene and its derivatives Anupriya Agrawal, Dvora Perahia, Gary S. Grest Capturing large length scales in polymers and soft matter while retaining atomistic properties is imperative to computational studies of dynamic systems. Here we present a new methodology developing coarsegrain model based on atomistic simulation of atactic polystyrene (PS). Similar to previous work by Fritz et al., each monomer is described by two coarse grained beads. In contrast to this earlier work where intramolecular potentials were based on Monte Carlo simulation of both isotactic and syndiotactic single PS molecule to capture stereochemistry, we obtained intramolecular interactions from a single molecular dynamics simulation of an allatom atactic PS melts. The nonbonded interactions are obtained using the iterative Boltzmann inversion (IBI) scheme. This methodology has been extended to coarse graining of poly(tbutylstyrene) (PtBS). An additional coarsegrained bead is used to describe the tbutyl group. Similar to the process for PS, the intramolecular interactions are obtained from a single all atom atactic melt simulation. Starting from the nonbonded interactions for PS, we show that the IBI method for the nonbonded interactions of PtBS converges relatively fast. A generalized scheme for substituted PS is currently in development. [Preview Abstract] 
Monday, March 3, 2014 11:51AM  12:03PM 
B19.00004: Coarse Grained Simulations of Entangled Polymer Dynamics Abelardo RamirezHernandez, Marat Andreev, Jay D. Schieber, Juan J. de Pablo We use the Theoretically Informed Entangled Polymer Simulations (TIEPOS) approach for multicomponent polymeric systems to study the linear and nonlinear rheological response of melts. In this manychain model, the topological effect of noncrossability of polymers is described by effective fluctuating interactions, mediated by slipsprings, between neighboring pairs of macromolecules. We explore the effect of different implementations of slipsprings, namely, continuous movement of slipsprings along chains as oposite to discrete jumps between polymer segments, as well as the use of a grandcanonical approach where the total number of slipsprings fluctuates. We perform a comparison between simulation predictions and experimental data for a series of wellcharacterized linear polymeric melts. Our results are shown to be in quantitative agreement both in linear and nonlinear rheology. [Preview Abstract] 
Monday, March 3, 2014 12:03PM  12:15PM 
B19.00005: Systematic coarsegraining of the wormlike chain model for dynamic simulations Elena Koslover, Andrew Spakowitz One of the key goals of macromolecular modeling is to elucidate how macroscale physical properties arise from the microscale behavior of the polymer constituents. For many biological and industrial applications, a direct simulation approach is impractical due to to the wide range of length and time scales that must be spanned by the model, necessitating physically sound and practically relevant procedures for coarsegraining polymer systems. We present a highly general systematic coarsegraining procedure that maps any detailed polymer model onto effective elasticchain models at intermediate and large length scales, and we specifically focus on the wormlike chain model of semiflexible polymers. Our approach defines a continuous flow of coarsegrained models starting from the wormlike chain model, proceeding through an intermediatescale stretchable, shearable wormlike chain, and finally resolving to a Gaussian chain at the longest lengths. Using Brownian dynamic simulations of our coarse grained polymer, we show that this approach to coarse graining the wormlike chain model captures analytical predictions for stress relaxation in a semiflexible polymer. Since we can arbitrarily coarse grain the polymer in these dynamic simulations, our approach greatly accelerates simulations. [Preview Abstract] 
Monday, March 3, 2014 12:15PM  12:27PM 
B19.00006: Multiresolution Modeling of Polymer Solutions: WaveletBased CoarseGraining and ReverseMapping Ahmed Ismail, Carl Simon Adorf, Animesh Agarwal, Christopher R. Iacovella Unlike multiscale methods, which encompass multiple simulation techniques, multiresolution models uses one modeling technique at different length and time scales. We present a combined coarsegraining and reversemapping framework for modeling of semidilute polymer solutions, based on the waveletaccelerated Monte Carlo (WAMC) method, which forms a hierarchy of resolutions to model polymers at length scales that cannot be reached via atomistic or even ``standard'' coarsegrained simulations. A universal scaling function is obtained so that potentials do not need to be recomputed as the scale of the system is changed. We show that coarsegrained polymer solutions can reproduce results obtained from the simulations of the more detailed atomistic system to a reasonable degree of accuracy. Reverse mapping proceeds similarly: using probability distributions obtained from coarsegraining the bond lengths, angles, torsions, and the nonbonded potentials, we can reconstruct a more detailed polymer consistent with both geometric constraints and energetic considerations. Using a ``convergence factor'' within a Monte Carlobased energy optimization scheme, we can successfully reconstruct entire atomistic configurations from coarsegrained descriptions. [Preview Abstract] 

B19.00007: ABSTRACT WITHDRAWN 
Monday, March 3, 2014 12:39PM  12:51PM 
B19.00008: Coarsegraining using the relative entropy and simplexbased optimization methods in VOTCA Victor R\"uhle, Mara Jochum, Konstantin Koschke, N.R. Aluru, Kurt Kremer, S.Y. Mashayak, Christoph Junghans Coarsegrained (CG) simulations are an important tool to investigate systems on larger time and length scales. Several methods for systematic coarsegraining were developed, varying in complexity and the property of interest. Thus, the question arises which method best suits a specific class of system and desired application. The Versatile Objectoriented Toolkit for Coarsegraining Applications (VOTCA) provides a uniform platform for coarsegraining methods and allows for their direct comparison. We present recent advances of VOTCA, namely the implementation of the relative entropy method and downhill simplex optimization for coarsegraining. The methods are illustrated by coarsegraining SPC/E bulk water and a watermethanol mixture. Both CG models reproduce the pair distributions accurately. [Preview Abstract] 
Monday, March 3, 2014 12:51PM  1:03PM 
B19.00009: Mesoscale simulation of entangled polymers: Part I. CoarseGrained level Tunable DPD Joao Maia, Shagahyegh Khani, Mikio Yamanoi Dissipative Particle Dynamics (DPD) is a coarsegrained molecular dynamics based simulation method that has shown a very good potential in computational modeling of soft matter. However, it is associated with deficiencies in simulating the dynamics of entangled polymer systems. For instance, due to the upper limit of coarsegraining level the method could not be applicable to the whole mesoscopic range. Therefore, our group has proposed a new concept of DPD named CoarseGrained level tunable DPD method in which the level of coarse graining can be tuned by adjusting the simulation parameters considering an energy balance in the system. The unphysical bond crossings that are artifacts of the soft potentials are prevented by applying an entanglement potential between the bonds. The performance of the method in capturing the entanglement effect is investigated by calculating the static and dynamic properties of polymers in entangled state. Linear and nonlinear viscoelastic properties can also be predicted by the CG level tunable DPD method reasonably well. Moreover, this method is able to reproduce the 1.0 to 3.4 transition in power index of the zero shear viscosity with molecular weight which captures the Rouse to reptation behavior in entangled polymer systems. [Preview Abstract] 
Monday, March 3, 2014 1:03PM  1:15PM 
B19.00010: Mesoscale simulation of entangled polymers: Part II. LoweAndersen thermostat Shaghayegh Khani, Mikio Yamanoi, Joao Maia Dissipative Particle Dynamics (DPD), despite its good potential in simulating soft matter, has some limitations when studying the entangled polymer systems. First limitation which arises from utilizing soft potentials in DPD is associated with unphysical bond crossings. The bond crossings can be avoided by introducing a segmental repulsive potential to the bonds. Another deficiency of DPD in simulating fluids is related to the Schmidt number. In standard DPD the momentum and mass transfer at the same rate and thus this dimensionless number takes a gaslike value ($\sim$ 1) when simulating fluids. In order to overcome this problem a LoweAndersen thermostat was used as an alternative method to DPD and the thermostat was found to be more successful in controlling the temperature in equilibrium state (independent from the time step) and over a wide range of shear rates. The ability of the method in capturing the entanglement effect and reproducing the static and dynamic properties of polymer melts and the scaling laws were investigated and the results were compared to the ones from standard DPD. The performance of the method in capturing the main features of the shear flow and reproducing linear and nonlinear viscoelastic properties was also evaluated. [Preview Abstract] 
Monday, March 3, 2014 1:15PM  1:27PM 
B19.00011: Persistent Contacts Along the Primitive Path Scott Milner, Jing Cao In an entangled polymer melt or solution, the uncrossability of the chains effectively restricts a given chain to move perpendicular to its contour path such that the chain is confined in a tube like region. In the present work, we use MD simulations to investigate the dynamics of the tube, represented by the isoconfigurationally averaged primitive path of a selfentangled ring polymer in a melt. A new approach to find entanglement molecular weight is introduced based on identifying close contacts between points along the primitive path, which is in a good agreement with previous work. [Preview Abstract] 
Monday, March 3, 2014 1:27PM  1:39PM 
B19.00012: Viscoelastic hydrodynamic interactions and anomalous CM diffusion in polymer melts Hendrik Meyer, Jean Farago, A.N. Semenov We have recently discovered that anomalous centerofmass (CM) diffusion occurring on intermediate time scales in polymer melts can be explained by the interplay of viscoelastic and hydrodynamic interactions (VHI). The theory has been solved for unentangled melts in 3D [1] and 2D [2] and excellent agreement between theory and simulation is found. The physical mechanism considers that hydrodynamic interactions are time dependent because of increasing viscosity before the terminal relaxation time; it is generally active in melts of any topology. Surprisingly, the effects are relevant for both, momentumconserving and Langevin dynamics [1,2] and this presentation will focus on the differences: The commonly employed Langevin thermostat significantly changes the CM motion on short and intermediate time scales, but approaching the Rouse time, the melt behavior is close to momentumconserving simulations. On the other hand, if momentumconserving simulations are run in too small a simulation box, the result looks as if a Langevin thermostat was used.\\[4pt] [1] PRL 107, 178301 (2011); PRE 85, 051807 (2012).\\[0pt] [2] PRL 109, 248304 (2012); Soft Matter 9, 4249 (2013). [Preview Abstract] 
Monday, March 3, 2014 1:39PM  1:51PM 
B19.00013: Molecular simulation investigation of the nanorheology of an entangled polymer melt Mir Karim, Rajesh Khare, Tsutomu Indei, Jay Schieber Knowledge of the ``local rheology'' is important for viscoelastic systems that contain significant structural and dynamic heterogeneities, such as cellular and extracellular crowded environments. For homogeneous viscoelastic media, a study of probe particle motion provides information on the microstructural evolution of the medium in response to the probe particle motion. Over the last two decades, probe particle rheology has emerged as a leading experimental technique for capturing local rheology of complex fluids. In recent work [\textit{M. Karim, S. C. Kohale, T. Indei, J. D. Schieber, and R. Khare, Phys. Rev. E }\textbf{\textit{86}}\textit{, 051501 (2012)}], we showed that this approach can be used in molecular dynamics (MD) simulations to study the nanoscale viscoelastic properties of an unentangled polymer melt; an important conclusion of that work was that medium and particle inertia play a crucial role in analysis of the particle rheology simulation data. MD simulations have a natural advantage that they enable study of deformation and dynamics over a small length scale around the moving probe particle. In this work, the approach is extended to compare the motion of a nanoscale probe in melts of entangled and unentangled chains. The simulations will be used to elucidate the differences between the local responses of these media to the probe particle motion. In particular, results will be presented for the differences in the resultant velocity and stress fields as well as any possible structural asymmetry developed around the moving probe particle in the entangled and unentangled cases. [Preview Abstract] 
Monday, March 3, 2014 1:51PM  2:03PM 
B19.00014: Estimation of Linear Viscoelasticity of Polymer Melts in Molecular Dynamics Simulations Based on Relaxation Mode Analysis Nobuyuki Iwaoka, Katsumi Hagita, Hiroshi Takano On the basis of relaxation mode analysis (RMA), we present an efficient method to estimate the linear viscoelasticity of polymer melts in a molecular dynamics (MD) simulation. Slow relaxation phenomena appeared in polymer melts cause a problem that a calculation of the stress relaxation function in MD simulations, especially in the terminal time region, requires large computational efforts. Relaxation mode analysis is a method that systematically extracts slow relaxation modes and rates of the polymer chain from the time correlation of its conformations. We show the computational cost may be drastically reduced by combining a direct calculation of the stress relaxation function based on the GreenKubo formula with the relaxation rates spectra estimated by RMA. [Preview Abstract] 
Monday, March 3, 2014 2:03PM  2:15PM 
B19.00015: Finding the Missing Physics: Simulating Polydisperse Polymer Melts Nichoals Rorrer, John Dorgan A Monte Carlo algorithm has been developed to model polydisperse polymer melts. For the first time, this enables the specification of a predetermined molecular weight distribution for lattice based simulations. It is demonstrated how to map an arbitrary probability distributions onto a discrete number of chains residing on an fcc lattice. The resulting algorithm is able to simulate a wide variety of behaviors for polydisperse systems including confinement effects, shear flow, and parabolic flow. The dynamic version of the algorithm accurately captures Rouse dynamics for short polymer chains, and reptationlike dynamics for longer chain lengths.$^{\mathrm{1}}$ When polydispersity is introduced, smaller Rouse times and broadened the transition between different scaling regimes are observed. Rouse times also decrease under confinement for both polydisperse and monodisperse systems and chain length dependent migration effects are observed. The steadystate version of the algorithm enables the simulation of flow and when polydisperse systems are subject to parabolic (Poiseulle) flow, a migration phenomenon based on chain length is again present. These and other phenomena highlight the importance of including polydispersity in obtaining physically realistic simulations of polymeric melts. 1. Dorgan, J.R.; Rorrer, N.A.; Maupin, C.M., \textit{Macromolecules }\textbf{2012}, \textit{45 }(21), 88338840. [Preview Abstract] 
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