[en] We present the results of molecular dynamics simulations of very long model polymer chains analyzed by various experimentally relevant techniques. The segment motion of the chains is found to be in very good agreement with the reptation model. We also calculated the plateau modulus G⁰_N. The predictions of the entanglement length N_e from G⁰_N and from the mean square displacement of the chain segments disagree by a factor of about 2.2(2), indicating an error in the prefactor in the standard formula for G⁰_N. We show that recent neutron spin echo measurements were carried out for chain lengths which are too small to allow for a correct determination of N_e

[en] This set of view graphs outline the simulation of the behavior of polyelectrolytes

[en] The non-linear stress-strain relation for crosslinked polymer networks is studied using molecular dynamics simulations. Previously we demonstrated the importance of trapped entanglements in determining the elastic and relaxational properties of networks. Here we present new results for the stress versus strain for both dry and swollen networks. Models which limit the fluctuations of the network strands like the tube model are shown to describe the stress for both elongation and compression. For swollen networks, the total modulus is found to decrease like (V(sub o)/V)(sup 2/3) and goes to the phantom model result only for short strand networks

[en] We show how the idea of fractal dimensions of phase space variables can be employed to develop a concept of adaptive resolution treatment of a molecular liquid. The resulting theoretical framework allows for calculation of statistical averages of thermodynamic quantities in multiresolution computer simulation algorithms where the molecular degrees of freedom change on the fly. (fast track communication)

[en] We develop a hybrid Monte Carlo approach for modelling nematic liquid crystals of homopolymer melts. The polymer architecture is described with a discrete worm-like chain model. A quadratic density functional accounts for the limited compressibility of the liquid, while an additional quadratic functional of the local orientation tensor of the segments captures the nematic ordering. The approach can efficiently address large systems parametrized according to volumetric and conformational properties, representative of real polymeric materials. The results of the simulations regarding the influence of the molecular weight on the isotropic-nematic transition are compared to predictions from a Landau-de Gennes free energy expansion. The formation of the nematic phase is addressed within Rouse-like dynamics, realized using the current model. (paper)

[en] Highlights: • The potential of mean force describes the insertion of a compound in a membrane. • Multiscaling speeds up the calculation of atomistic potentials of mean force. • The method requires a large configurational overlap between different resolutions. The determination of potentials of mean force for solute insertion in a lipid membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. Recently, a multiscale method has been proposed to leverage the conformational ensemble of a lower-resolution model as starting point for higher resolution simulations. In this work, we analyze the efficiency of this method by comparing its predictions for propanol insertion into a lipid membrane against conventional atomistic umbrella sampling simulation results. The multiscale approach is confirmed to provide accurate results with a gain of one order of magnitude in computational time. We then investigate the role of the coarse-grained representation. We find that the accuracy of the results is tightly connected to the presence of a good configurational overlap between the coarse-grained and atomistic models—a general requirement when developing multiscale simulation methods.

[en] Topologically constrained molecular systems are relevant to many areas of physics and biology, from the collapse of a polymer gel to the existence of chromosome territories. As a model system for the study of such unusual interactions, we simulated melts of unconcatenated polymer rings, where topology directly influences not only dynamic properties, as is the case for linear chains, but also the statics. In order to access the relatively large chain lengths required to observe significant effects, we implemented an efficient, on-lattice Monte Carlo model allowing for fast relaxation thanks to non-local moves which randomly displace kinks along the polymer contour. The sufficiently long rings are shown to behave as compact objects, their size scaling as N^1/3 for large chain length N; this observation is supported by measurements of several other static properties. The entanglement length of the rings' linear counterparts is used to characterize the topological constraints, allowing for an estimate of the onset of the regime where rings are compact

[en] In this work we discuss two mirror but distinct phenomena of polymer paradoxical properties in mixed solvents: co-non-solvency and co-solvency. When a polymer collapses in a mixture of two miscible good solvents the phenomenon is known as co-non-solvency, while co-solvency is a phenomenon that is associated with the swelling of a polymer in poor solvent mixtures. A typical example of co-non-solvency is provided by poly(N-isopropylacrylamide) in aqueous alcohol, while poly(methyl methacrylate) in aqueous alcohol shows co-solvency. We discuss these two phenomena to compare their microscopic origins and show that both can be understood within generic universal concepts. A broad range of polymers is therefore expected to exhibit these phenomena where specific chemical details play a lesser role than the appropriate combination of interactions between the trio of molecular components. (paper)

[en] Understanding properties of polymer alloys with computer simulations frequently requires equilibration of samples comprised of microscopically described long molecules. We present the extension of an efficient hierarchical backmapping strategy, initially developed for homopolymer melts, to equilibrate high-molecular-weight binary blends. These mixtures present significant interest for practical applications and fundamental polymer physics. In our approach, the blend is coarse-grained into models representing polymers as chains of soft blobs. Each blob stands for a subchain with N _b microscopic monomers. A hierarchy of blob-based models with different resolution is obtained by varying N _b. First the model with the largest N _b is used to obtain an equilibrated blend. This configuration is sequentially fine-grained, reinserting at each step the degrees of freedom of the next in the hierarchy blob-based model. Once the blob-based description is sufficiently detailed, the microscopic monomers are reinserted. The hard excluded volume is recovered through a push-off procedure and the sample is re-equilibrated with molecular dynamics (MD), requiring relaxation on the order of the entanglement time. For the initial method development we focus on miscible blends described on microscopic level through a generic bead-spring model, which reproduces hard excluded volume, strong covalent bonds, and realistic liquid density. The blended homopolymers are symmetric with respect to molecular architecture and liquid structure. To parameterize the blob-based models and validate equilibration of backmapped samples, we obtain reference data from independent hybrid simulations combining MD and identity exchange Monte Carlo moves, taking advantage of the symmetry of the blends. The potential of the backmapping strategy is demonstrated by equilibrating blend samples with different degree of miscibility, containing 500 chains with 1000 monomers each. Equilibration is verified by comparing chain conformations and liquid structure in backmapped blends with the reference data. Possible directions for further methodological developments are discussed. (paper)

[en] A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations