A review of Monte Carlo simulations of polymers with PERM

In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the $\Theta$ point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011

Conformational changes and dynamics during adsorption of macromolecules with different degree of polymerization studied by Monte Carlo simulations

[EN] Dynamics of multilayer adsorption of macromolecules with different degree of polymerization is studied by coarse¿grained Monte Carlo simulations, focusing on both the interface macromolecule¿surface and chain¿chain interaction in and out of equilibrium conditions. The interfacial interaction between the solid flat surface and the macromolecules is modeled by means of a Lennard¿Jones potential, and inter¿ and intrachain interactions are simulated using bond angle, bond length, and Lennard¿Jones potentials. The results show that local and conformational motions near the glass transition temperature promote configurations with minimal energy, which induce better space efficiency and favor aligned conformations at the interface. In this context, it is also found that restriction of movement, together with the connectivity effect exerted by the partially adsorbed segments, leads to a range of chain lengths that maximizes the molecular groups adsorbed.The support from the Ministry of Economy and Competitiveness-Spain through the Project No. MAT2015-69315-C3-1-R (including the FEDER financial support) is gratefully acknowledged. CIBER-BBN is an initiative funded by the VI National R&D&I Plan 2008 2011, Iniciativa Ingenio 2010, Consolider Program. CIBER Actions are financed by the Instituto de Salud CarlosIII with assistance from the European Regional Development FundSabater I Serra, R.; Torregrosa Cabanilles, C.; Meseguer Dueñas, JM.; Gómez Ribelles, JL.; Molina Mateo, J. (2018). Conformational changes and dynamics during adsorption of macromolecules with different degree of polymerization studied by Monte Carlo simulations. Macromolecular Theory and Simulations. 27(4):1-10. https://doi.org/10.1002/mats.201800012S110274Wiśniewska, M., Chibowski, S., & Urban, T. (2009). Adsorption and thermodynamic properties of the alumina–polyacrylic acid solution system. Journal of Colloid and Interface Science, 334(2), 146-152. doi:10.1016/j.jcis.2009.03.006Roiter, Y., & Minko, S. (2005). AFM Single Molecule Experiments at the Solid−Liquid Interface:  In Situ Conformation of Adsorbed Flexible Polyelectrolyte Chains. Journal of the American Chemical Society, 127(45), 15688-15689. doi:10.1021/ja0558239Chung, Y. S., Yoo, S. H., & Kim, C. K. (2009). Enhancement of Meltdown Temperature of the Polyethylene Lithium-Ion Battery Separator via Surface Coating with Polymers Having High Thermal Resistance. Industrial & Engineering Chemistry Research, 48(9), 4346-4351. doi:10.1021/ie900096zChibowski, S., Wiœniewska, M., & Opala Mazur, E. (2004). The effect of temperature on the adsorption and conformation of polyacrylic acid macromolecules at the ZrO2–polymer solution interface. Powder Technology, 141(1-2), 12-19. doi:10.1016/j.powtec.2004.02.014Kronberg, B., Holmberg, K., & Lindman, B. (2014). Surface Chemistry of Surfactants and Polymers. doi:10.1002/9781118695968Otsuka, H., Nagasaki, Y., & Kataoka, K. (2003). PEGylated nanoparticles for biological and pharmaceutical applications. Advanced Drug Delivery Reviews, 55(3), 403-419. doi:10.1016/s0169-409x(02)00226-0Bhakta, S. A., Evans, E., Benavidez, T. E., & Garcia, C. D. (2015). Protein adsorption onto nanomaterials for the development of biosensors and analytical devices: A review. Analytica Chimica Acta, 872, 7-25. doi:10.1016/j.aca.2014.10.031Goodman, S. B., Yao, Z., Keeney, M., & Yang, F. (2013). The future of biologic coatings for orthopaedic implants. Biomaterials, 34(13), 3174-3183. doi:10.1016/j.biomaterials.2013.01.074Sabater i Serra, R., León-Boigues, L., Sánchez-Laosa, A., Gómez-Estrada, L., Gómez Ribelles, J. L., Salmeron-Sanchez, M., & Gallego Ferrer, G. (2016). Role of chemical crosslinking in material-driven assembly of fibronectin (nano)networks: 2D surfaces and 3D scaffolds. Colloids and Surfaces B: Biointerfaces, 148, 324-332. doi:10.1016/j.colsurfb.2016.08.044Mnatsakanyan, H., Rico, P., Grigoriou, E., Candelas, A. M., Rodrigo-Navarro, A., Salmeron-Sanchez, M., & Sabater i Serra, R. (2015). Controlled Assembly of Fibronectin Nanofibrils Triggered by Random Copolymer Chemistry. ACS Applied Materials & Interfaces, 7(32), 18125-18135. doi:10.1021/acsami.5b05466Appel, E. A., Tibbitt, M. W., Webber, M. J., Mattix, B. A., Veiseh, O., & Langer, R. (2015). Self-assembled hydrogels utilizing polymer–nanoparticle interactions. Nature Communications, 6(1). doi:10.1038/ncomms7295Möddel, M., Bachmann, M., & Janke, W. (2009). Conformational Mechanics of Polymer Adsorption Transitions at Attractive Substrates. The Journal of Physical Chemistry B, 113(11), 3314-3323. doi:10.1021/jp808124vPaul, W., Strauch, T., Rampf, F., & Binder, K. (2007). Unexpectedly normal phase behavior of single homopolymer chains. Physical Review E, 75(6). doi:10.1103/physreve.75.060801Vogel, T., Bachmann, M., & Janke, W. (2007). Freezing and collapse of flexible polymers on regular lattices in three dimensions. Physical Review E, 76(6). doi:10.1103/physreve.76.061803Stillinger, F. H., Head-Gordon, T., & Hirshfeld, C. L. (1993). Toy model for protein folding. Physical Review E, 48(2), 1469-1477. doi:10.1103/physreve.48.1469Hentschke, R. (1997). Molecular modeling of adsorption and ordering at solid interfaces. Macromolecular Theory and Simulations, 6(2), 287-316. doi:10.1002/mats.1997.040060201Lai, C. C., Shieh, J. H., Chiou, B. S., Ho, J. C., & Ku, H. C. (1994). Anisotropic Gd magnetism inTlSr2GdCu2O7−δ, (Pb0.5Cu0.5)Sr2GdCu2O7−δ, andPb2Sr2GdCu3O8+y. Physical Review B, 49(2), 1499-1502. doi:10.1103/physrevb.49.1499Wu, C., & Wang, X. (1998). Globule-to-Coil Transition of a Single Homopolymer Chain in Solution. Physical Review Letters, 80(18), 4092-4094. doi:10.1103/physrevlett.80.4092Paul, W., Rampf, F., Strauch, T., & Binder, K. (2008). Phase transitions in a single polymer chain: A micro-canonical analysis of Wang–Landau simulations. Computer Physics Communications, 179(1-3), 17-20. doi:10.1016/j.cpc.2008.01.005Hodge, I. M. (1994). Enthalpy relaxation and recovery in amorphous materials. Journal of Non-Crystalline Solids, 169(3), 211-266. doi:10.1016/0022-3093(94)90321-2Scherer, G. W. (1990). Theories of relaxation. Journal of Non-Crystalline Solids, 123(1-3), 75-89. doi:10.1016/0022-3093(90)90775-hEuston, S. R. (2010). Molecular Dynamics Simulation of Protein Adsorption at Fluid Interfaces: A Comparison of All-Atom and Coarse-Grained Models. Biomacromolecules, 11(10), 2781-2787. doi:10.1021/bm100857kBarrat, J.-L., Baschnagel, J., & Lyulin, A. (2010). Molecular dynamics simulations of glassy polymers. Soft Matter, 6(15), 3430. doi:10.1039/b927044bTallury, S. S., & Pasquinelli, M. A. (2010). Molecular Dynamics Simulations of Flexible Polymer Chains Wrapping Single-Walled Carbon Nanotubes. The Journal of Physical Chemistry B, 114(12), 4122-4129. doi:10.1021/jp908001dHossain, D., Tschopp, M. A., Ward, D. K., Bouvard, J. L., Wang, P., & Horstemeyer, M. F. (2010). Molecular dynamics simulations of deformation mechanisms of amorphous polyethylene. Polymer, 51(25), 6071-6083. doi:10.1016/j.polymer.2010.10.009Binder, K., Milchev, A., & Baschnagel, J. (1996). Simulation Studies on the Dynamics of Polymers at Interfaces. Annual Review of Materials Science, 26(1), 107-134. doi:10.1146/annurev.ms.26.080196.000543Mańka, A., Nowicki, W., & Nowicka, G. (2013). Monte Carlo simulations of a polymer chain conformation. The effectiveness of local moves algorithms and estimation of entropy. Journal of Molecular Modeling, 19(9), 3659-3670. doi:10.1007/s00894-013-1875-zLi, Y. W., Wüst, T., & Landau, D. P. (2013). Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins. Physical Review E, 87(1). doi:10.1103/physreve.87.012706Glagoleva, A., Erukhimovich, I., & Vasilevskaya, V. (2012). Void Microstructuring in Lamellar Phase of Amphiphilic Macromolecules. Macromolecular Theory and Simulations, 22(1), 31-35. doi:10.1002/mats.201200056Foley, T. T., Shell, M. S., & Noid, W. G. (2015). The impact of resolution upon entropy and information in coarse-grained models. The Journal of Chemical Physics, 143(24), 243104. doi:10.1063/1.4929836Harmandaris, V. A., Adhikari, N. P., van der Vegt, N. F. A., & Kremer, K. (2006). Hierarchical Modeling of Polystyrene: From Atomistic to Coarse-Grained Simulations. Macromolecules, 39(19), 6708-6719. doi:10.1021/ma0606399Karimi-Varzaneh, H. A., & Müller-Plathe, F. (2011). Coarse-Grained Modeling for Macromolecular Chemistry. Topics in Current Chemistry, 295-321. doi:10.1007/128_2010_122Milchev, A., & Binder, K. (1996). Static and Dynamic Properties of Adsorbed Chains at Surfaces:  Monte Carlo Simulation of a Bead-Spring Model. Macromolecules, 29(1), 343-354. doi:10.1021/ma950668bKlushin, L. I., Polotsky, A. A., Hsu, H.-P., Markelov, D. A., Binder, K., & Skvortsov, A. M. (2013). Adsorption of a single polymer chain on a surface: Effects of the potential range. Physical Review E, 87(2). doi:10.1103/physreve.87.022604Li, H., Qian, C.-J., & Luo, M.-B. (2011). Simulation of a flexible polymer tethered to a flat adsorbing surface. Journal of Applied Polymer Science, 124(1), 282-287. doi:10.1002/app.34576Rybicka, J., & Sikorski, A. (2010). Adsorption of Copolymers on Solid Surfaces. Macromolecular Theory and Simulations, 19(2-3), 135-141. doi:10.1002/mats.200900063Pandey, Y. N., & Doxastakis, M. (2012). Detailed atomistic Monte Carlo simulations of a polymer melt on a solid surface and around a nanoparticle. The Journal of Chemical Physics, 136(9), 094901. doi:10.1063/1.3689316Yu, C., Guan, J., Chen, K., Bae, S. C., & Granick, S. (2013). Single-Molecule Observation of Long Jumps in Polymer Adsorption. ACS Nano, 7(11), 9735-9742. doi:10.1021/nn4049039Sabater i Serra, R., Torregrosa-Cabanilles, C., Meseguer Dueñas, J. M., Gómez Ribelles, J. L., & Molina-Mateo, J. (2014). Conformation and dynamics of a diluted chain in the presence of an adsorbing wall: A simulation with the bond fluctuation model. Journal of Non-Crystalline Solids, 402, 7-15. doi:10.1016/j.jnoncrysol.2014.05.009Carmesin, I., & Kremer, K. (1988). The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions. Macromolecules, 21(9), 2819-2823. doi:10.1021/ma00187a030Deutsch, H. P., & Binder, K. (1991). Interdiffusion and self‐diffusion in polymer mixtures: A Monte Carlo study. The Journal of Chemical Physics, 94(3), 2294-2304. doi:10.1063/1.459901Sabater i Serra, R., Torregrosa-Cabanilles, C., Meseguer-Dueñas, J. M., Gómez Ribelles, J. L., & Molina-Mateo, J. (2012). Conformation and segmental mobility of a diluted single polymer chain simulated with bond fluctuation model. Journal of Non-Crystalline Solids, 358(12-13), 1452-1458. doi:10.1016/j.jnoncrysol.2012.03.027Molina-Mateo, J., Meseguer Dueñas, J. M., Gómez Ribelles, J. L., & Torregrosa Cabanilles, C. (2009). The distribution of the relaxation times as seen by bond fluctuation model. Polymer, 50(23), 5618-5622. doi:10.1016/j.polymer.2009.09.039Napolitano, S., Glynos, E., & Tito, N. B. (2017). Glass transition of polymers in bulk, confined geometries, and near interfaces. Reports on Progress in Physics, 80(3), 036602. doi:10.1088/1361-6633/aa5284Brunauer, S., Emmett, P. H., & Teller, E. (1938). Adsorption of Gases in Multimolecular Layers. Journal of the American Chemical Society, 60(2), 309-319. doi:10.1021/ja01269a02

A grazing incidence neutron spin echo study of near surface dynamics in p(MEO2MA-co-OEGMA) copolymer brushes

Surface-attached architectures of p(MEO2MA-co-OEGMA) copolymers are thermoresponsive PEG analogues with potential applications in biotechnology and medicine. In this respect, structure and dynamics of polymer brushes made of these copolymers are of great interest. In this work, the near surface dynamics of a p(MEO2MA-co-OEGMA) brush with a height of 250 nm was investigated with neutron spin echo spectroscopy under grazing incidence (GINSES) conditions. The brush dynamics was studied at two penetration depths of the neutrons. An influence of the distance from the confining surface on the collective diffusion was found. For the first time, the experiment demonstrates the feasibility of studying thermal fluctuations of macromolecules at a single planar liquid/solid interface by neutron spin echo spectroscopy under grazing incidence