Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session G20: Focus Session: Theory and Simulations of Macromolecules V |
Hide Abstracts |
Sponsoring Units: DPOLY Chair: Mesfin Tsige, University of Akron Room: 405 |
Tuesday, March 4, 2014 11:15AM - 11:27AM |
G20.00001: Using thermodynamic integration to simulate the free-energy of bicontinuous phases formed by block copolymer/homopolymer blends Poornima Padmanabhan, Francisco Martinez-Veracoechea, Fernando Escobedo AB diblock copolymers can co-assemble with A-type homopolymers to form different bicontinuous phases whose 3D connectivity of both A and B domains is of interest for potential applications in nanolithography, photovoltaic cells and drug delivery. In this work, we use particle-based simulations to study the vicinity of a triple point where three bicontinuous phases (gyroid, double diamond and plumber's nightmare) were predicted to coexist by Self Consistent Field Theory. A key roadblock is that bicontinuous morphologies are highly sensitive to the commensurability of the simulation box size and the a-priori unknown unit cell size. Accurate estimation of free energies is thus crucial to the determination of the stable morphology. In this work, we apply thermodynamic integration over a constructed reversible path to calculate the free energies of these bicontinuous phases relative to a disordered phase and compare the predicted phase stability to results from alternative methods. [Preview Abstract] |
Tuesday, March 4, 2014 11:27AM - 11:39AM |
G20.00002: Binding large globular particles to long polymer chains Anton Souslov, Jennifer E. Curtis, Paul M. Goldbart We present a minimal model that captures the change in conformational properties of long polymer chains as a result of the binding of large suspended globular particles. The large globular particles, which we model as spheres, have a single binding site and interact with each other via excluded volume repulsion, causing the attached chain to swell. This swollen chain in solution can be described as a free chain with an increased effective persistent length at large length scales and as stretched chain at short scales. Within the context of our model, we examine the statistics of these bindings and the structure of dilute and semidilute solutions of such polymer assemblies. We also consider such polymers grafted at an interface with a sufficient surface density to form a brush. We show how this model applies to the macromolecular assemblies found in the synovial fluid and in the pericellular coat of mammalian cells. [Preview Abstract] |
Tuesday, March 4, 2014 11:39AM - 11:51AM |
G20.00003: Depletion induced coil-globule transition of a generic macromolecule: simulations and theory Martin Bertrand, Tyler N. Shendruk, Hendrick de Haan, James L. Harden, Gary W. Slater Entropic depletion forces play a role in the compaction of chromosomal material in simple cells such as bacteria but it remains debatable whether they are sufficient to account for complete chromosome collapse. Using Coarse-Grained Molecular Dynamics simulations we show that depletion induced attractive interactions are sufficient to cause the coil-globule transition of a model chain of supercoiled DNA structural monomers suspended in a bath of smaller generic crowding agents such as proteins. We present a simple theoretical model and quantitatively cast the action of depletants on a generic macromolecular chain as an effective solvent quality: as molecular crowding increases, the radius of gyration goes from its good solvent to globular value via a theta-point and a poor solvent regime. The abrupt collapse of the chain at the predicted volume fraction of depletants is a second-order phase transition. Such coarse-grained simulations may be useful for modelling the effects of molecular crowding on chromosomal DNA in more complex geometries. [Preview Abstract] |
Tuesday, March 4, 2014 11:51AM - 12:03PM |
G20.00004: Coil-globule transition of macromolecules in mixed solvent: A semi-grand canonical molecular dynamics approach Debashish Mukherji, Kurt Kremer Conformational transition of macromolecules in mixed solvents are intimately linked to large local concentration fluctuations of solvent components. The numerical studies in the field are limited to the closed boundary schemes, which, however, suffer from severe system size effects. To overcome this discrepancy, we have developed a semi-grand canonical molecular dynamics scheme for complex fluids [1]. Our method makes use of the adaptive resolution scheme (AdResS) [2] with a metropolis particle exchange criterion. In AdResS, an all-atom region, containing macromolecule, is coupled to a coarse-grained (CG) reservoir. The semi-grand canonical particle exchange is performed in the CG region. As the applications of the method, we study the concentration driven reentrant collapse and swelling transition of poly(N-isopropylacrylamide) (PNIPAm) and poly(N,N-diethylacrylamide) (PDEAm) in aqueous methanol and demonstrate the role of the delicate interplay of the different intermolecular interactions. [1] D. Mukherji and K. Kremer, Macromolecules, DOI:10.1021/ma401877c (2013). [2] M. Praprotnik, L. Delle Site, and K. Kremer, J. Chem. Phys. 123, 224106, (2005). [Preview Abstract] |
Tuesday, March 4, 2014 12:03PM - 12:15PM |
G20.00005: Unified View on the Mean-Field Order of Coil-Globule Transition Delian Yang, Qiang Wang It is well known that a polymer chain immersed in a small-molecule solvent undergoes the coil-globule transition (CGT) as the solvent quality changes. In the study of CGT, a mean-field theory, either of the Flory-type or the self-consistent field theory, has been commonly used; the transition order predicted by the mean-field theory, however, has been controversial. By examining the first- and second-order derivatives of the Helmholtz free energy with respect to the solvent equality, the continuity of which defines the transition order but has not been reported in the literature, we concluded that the mean-field CGT of a polymer chain of finite length $N$ exhibits the type-I behavior; that is, it is either a first-order phase transition, a critical point, or a crossover depending on the location of the critical point. It becomes a second-order phase transition with respect to the solvent equality characterized by the Flory-Huggins parameter $\chi$ (or equivalently the second virial coefficient $v$ or the temperature $T$) only in the limit of $N\to\infty$. Even in this limit, it still has the type-I behavior with respect to $v N^{1/2}$ (or equivalently $(1-2\chi)N^{1/2}$). [Preview Abstract] |
Tuesday, March 4, 2014 12:15PM - 12:27PM |
G20.00006: Electrophoresis of composite objects: effect of shape, topology and polymer stiffness Mykyta V. Chubynsky, Gary W. Slater In several methods of electrophoretic separation, DNA fragments are conjugated or form complexes with objects of various kinds (linear and branched polymers, globular proteins, gold nanoparticles, micelles) having a different electrophoretic mobility. With these applications in mind, we study the free-solution electrophoresis of various composite objects (diblock copolymers with blocks of different stiffnesses, a polymer attached to a sphere, a branched polymer). We use the approach of Long \textit{et al.} [J. Chem. Phys. 108 (1998) 1234], calculating hydrodynamic interactions within the Kirkwood-Riseman approximation, and we extend the approach to the case where some parts are solid objects, rather than polymers. We find, in particular, that for diblock copolymers the results depend strongly on the relative stiffness of the blocks. If the mobility of the complex is represented as a weighted average of the mobilities of the individual parts, then when a polymer is attached to a sphere or forms a branch the weights are lower for the parts near the attachment point. [Preview Abstract] |
Tuesday, March 4, 2014 12:27PM - 1:03PM |
G20.00007: New perspectives for molecular field simulations of complex fluids Invited Speaker: Friederike Schmid Molecular field simulations have been introduced a while ago as a dynamic extension of the self-consistent field theory, one of the most successful theories for the description of inhomogeneous polymer systems. They build on a continuous free energy functional, which however incorporates details on the structure and architecture of the molecules. In that sense, they bridge between particle-based simulations of complex matter and continuuous simulations based on phase field theories such as the Cahn-Hilliard theory. In the talk I will first very briefly review the basic concept of molecular field simulations, and then present three recent extensions developed in our group. (i) A method to introduce hydrodynamic interactions by coupling molecular fields to a Lattice-Boltzmann fluid model; (ii) A method to deal with permanent crosslinks, i.e., to deal with polymer networks; and (iii) An approach to couple molecular field simulations with particle-based simulations in an adaptive multiscale scheme. \\[4pt] [1] L. Zhang, A. Sevink, F. Schmid, Macromolecules 44, 9434 (2011).\\[0pt] [2] F. Schmid, Phys. Rev. Lett. 111, 028303 (2013).\\[0pt] [3] S. Qi, H. Behringer, F. Schmid, New J. Physics, accepted (2013). [Preview Abstract] |
Tuesday, March 4, 2014 1:03PM - 1:15PM |
G20.00008: Effects of dipolar interactions on thermodynamic stabilities of polymer blends and diblock copolymer melts Rajeev Kumar, M. Muthukumar, Bobby Sumpter We present a generalized theory for studying effects of dipolar interactions on the phase separation in polymer blends and diblock copolymer melts. A new formalism is developed to construct free energy of these polymeric media with inhomogeneous dielectric function, which bears resemblance to the static part of Lifshitz theory for dielectric slabs with sharp interfaces. Using the formalism, effects of continuous dielectric function can be studied. We have applied the formalism to a study of co-existence curves in polymer blends and interfacial tension for a planar interface between the coexisting phases. The same formalism is used to study microphase separation in lamellar forming diblock copolymer melts. Results on the effects of mismatch between the dipole moments on thermodynamics of polymer blends and diblock copolymer melts will be presented in this talk. [Preview Abstract] |
Tuesday, March 4, 2014 1:15PM - 1:27PM |
G20.00009: Confined ring polymers as a model nucleoid Bae-Yeun Ha, C. Jeon, J. Kim, H. Jeong, S. Jun, Y. Jung The bacterial chromosome is tightly packed in an intracellular space called the nucleoid with its loci linearly and precisely positioned. Here we propose a model nucleoid: a ring polymer confined in a cylindrical space. When the cylinder-ring parameters are chosen properly, our model describes the observed locus distributions of the {\it E. coli} chromosome surprisingly well. Our results illustrate how the geometry and function of the nucleoid are interrelated. [Preview Abstract] |
Tuesday, March 4, 2014 1:27PM - 1:39PM |
G20.00010: The influence of topology on the free energy and metric properties of ring polymer confined in a slit Zhao-Yan sun, Bing Li, Li-Jia An, Zhen-Gang Wang An off-lattice model with no excluded volume is used to study the effect of topological constraint on the free energy and metric properties of ring polymer confined in a slit with height $d$. The topological state is conserved by forbidding bond crossing. This model was applied to ring polymers with chain length up to $N=10^{3}$. Umbrella sampling and weighted histogram analysis method (WHAM) are used to calculate the free energy and the radius of gyration. In the strong confinement limit, free energy of linear chain in our model scales as $d^{-2}$ and the in-plane radius of gyration $R_{||}$ is independent of confinement, which agrees with the theoretical prediction very well. However, unlike the linear chain, the scaling behavior of ring polymer shows a different trend. This abnormal scaling behavior is thought to be caused by the topological constraint: the knotting probability of ring polymer increases with decreasing the slit height, and in this case, ring polymer is forced to expand itself to conserve its topological unknotted state. [Preview Abstract] |
Tuesday, March 4, 2014 1:39PM - 1:51PM |
G20.00011: Shear-induced desorption of isolated polymer molecules from a planar wall Sarit Dutta, Kevin Dorfman, Satish Kumar Shear-induced desorption of isolated polymer molecules is studied using Brownian dynamics simulations. The polymer molecules are modeled as freely jointed bead-spring chains interacting with a planar wall via a short-range potential. The simulations include both intrachain and chain-wall hydrodynamic interactions. Shear flow is found to cause chain flattening, resulting at low shear rates in an increased fraction of chain segments bound to the wall. However, above a critical shear rate the chains desorb completely. The desorption process is nucleated by random protrusions in the shear gradient direction which evolve under the combined effect of drag, hydrodynamic interaction, and vorticity-induced rotation, and subsequently lead to recapture. Above the critical shear rate, these protrusions grow in length until the entire chain is peeled off the wall. For free-draining chains, the protrusions are not sustained and no desorption is observed even at shear rates much higher than the critical value. These simulations can help in interpreting experiments on shear-induced desorption of polymer films and brushes. [Preview Abstract] |
Tuesday, March 4, 2014 1:51PM - 2:03PM |
G20.00012: Evidence of random copolymer adsorption at fluctuating selective interfaces from Monte-Carlo simulation studies Igor Gazuz, Jens-Uwe Sommer We performed Monte Carlo simulations of a binary, strongly separated mixture of A- and B-type homopolymers with some amount of random AB copolymers added. We show that the copolymers tend to localize at the interface between A and B species. We also simulated random copolymers in a one-component surrounding and compared the free energy to the case of copolymers at the interface. The result shows that interface adsorption is energetically clearly favored compared to bulk micellization, contrary to the conclusion made previously in the literature. We calculate the reduction of the interface tension due to copolymers and check the theoretical predictions for the adsorption mechanism and scaling laws made in the previous works, where ideal interfaces were considered. [Preview Abstract] |
Tuesday, March 4, 2014 2:03PM - 2:15PM |
G20.00013: Adsorption of Polymers on Rough Surfaces Abishek Venkatakrishnan, Vikram Kuppa Most of the surfaces encountered in nature display irregularity and self-similarity at certain length scales. Such real surfaces can be mimicked via fractal surfaces using an algorithm that produces random surfaces. The problem of polymer chains adsorbed on smooth surfaces has been well understood whereas adsorption on rough surfaces still remains unclear due to the complexity involved in equilibration and sampling of molecules in such systems. The enthalpic interactions between the monomers and the entropic penalty arising due to adsorption on rough surfaces are significantly different from smooth surfaces. In this study, we investigate the adsorption of freely rotating polymer chains on fractal surfaces by Monte-Carlo molecular simulations. Random fractal surfaces are generated using the diamond-square algorithm for different values of the Hurst parameter. Properties like monomer-surface interaction, density profiles, chain orientation profiles and distribution of adsorbed chain fractions are investigated. We also demonstrate the significant effect of fractal dimension on adsorption of polymers on rough surfaces. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2023 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
1 Research Road, Ridge, NY 11961-2701
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700