Simulating dynamic crossover behavior of semiflexible linear polymers in solution and in the melt

Coarsening Kinetics of Complex Macromolecular Architectures in Bad Solvent

This study reports a general scenario for the out-of-equilibrium features of collapsing polymeric architectures. We use molecular dynamics simulations to characterize the coarsening kinetics, in bad solvent, for several macromolecular systems with an increasing degree of structural complexity. In particular, we focus on: flexible and semiflexible polymer chains, star polymers with 3 and 12 arms, and microgels with both ordered and disordered networks. Starting from a powerful analogy with critical phenomena, we construct a density field representation that removes fast fluctuations and provides a consistent characterization of the domain growth. Our results indicate that the coarsening kinetics presents a scaling behaviour that is independent of the solvent quality parameter, in analogy to the time-temperature superposition principle. Interestingly, the domain growth in time follows a power-law behaviour that is approximately independent of the architecture for all the flexible systems; while it is steeper for the semiflexible chains. Nevertheless, the fractal nature of the dense regions emerging during the collapse exhibits the same scaling behaviour for all the macromolecules. This suggests that the faster growing length scale in the semiflexible chains originates just from a faster mass diffusion along the chain contour, induced by the local stiffness. The decay of the dynamic correlations displays scaling behavior with the growing length scale of the system, which is a characteristic signature in coarsening phenomena.

Modeling of Entangled Polymer Diffusion in Melts and Nanocomposites: A Review

This review concerns modeling studies of the fundamental problem of entangled (reptational) homopolymer diffusion in melts and nanocomposite materials in comparison to experiments. In polymer melts, the developed united atom and multibead spring models predict an exponent of the molecular weight dependence to the polymer diffusion very similar to experiments and the tube reptation model. There are rather unexplored parameters that can influence polymer diffusion such as polymer semiflexibility or polydispersity, leading to a different exponent. Models with soft potentials or slip-springs can estimate accurately the tube model predictions in polymer melts enabling us to reach larger length scales and simulate well entangled polymers. However, in polymer nanocomposites, reptational polymer diffusion is more complicated due to nanoparticle fillers size, loading, geometry and polymer-nanoparticle interactions.

On the dynamics of molecular self-assembly and the structural analysis of bilayer membranes using coarse-grained molecular dynamics simulations

We present a molecular dynamics simulation study of the self-assembly of coarse-grained lipid molecules from unbiased random initial configurations. Our lipid model is based on a well-tried CG polymer model with an additional potential that mimics the hydrophobic properties of lipid tails. We find that several stages of self-organization of lipid clusters are involved in the dynamics of bilayer formation and that the resulting equilibrium structures sensitively depend on the strength of hydrophobic interactions hc of the lipid tails and on temperature T. The obtained stable lipid membranes are quantitatively analyzed with respect to their local structure and their degree of order. At equilibrium, we obtain self-stabilizing bilayer membrane structures that exhibit a bending stiffness κB and compression modulus KC comparable to experimental measurements under physiological conditions. We present a phase diagram of our lipid model which covers a sol-gel transition, a liquid (or gel-like) phase including stable bilayer structures and vesicle formation, as well as a quasi-crystalline phase. We also determine the exact conditions for temperature T and degree of hydrophobicity hc for stable bilayer formation including closed vesicles.

Scaling of the dynamics of flexible Lennard-Jones chains

The isomorph theory provides an explanation for the so-called power law density scaling which has been observed in many molecular and polymeric glass formers, both experimentally and in simulations. Power law density scaling (relaxation times and transport coefficients being functions of ρ(γ(S)), where ρ is density, T is temperature, and γ(S) is a material specific scaling exponent) is an approximation to a more general scaling predicted by the isomorph theory. Furthermore, the isomorph theory provides an explanation for Rosenfeld scaling (relaxation times and transport coefficients being functions of excess entropy) which has been observed in simulations of both molecular and polymeric systems. Doing molecular dynamics simulations of flexible Lennard-Jones chains (LJC) with rigid bonds, we here provide the first detailed test of the isomorph theory applied to flexible chain molecules. We confirm the existence of isomorphs, which are curves in the phase diagram along which the dynamics is invariant in the appropriate reduced units. This holds not only for the relaxation times but also for the full time dependence of the dynamics, including chain specific dynamics such as the end-to-end vector autocorrelation function and the relaxation of the Rouse modes. As predicted by the isomorph theory, jumps between different state points on the same isomorph happen instantaneously without any slow relaxation. Since the LJC is a simple coarse-grained model for alkanes and polymers, our results provide a possible explanation for why power-law density scaling is observed experimentally in alkanes and many polymeric systems. The theory provides an independent method of determining the scaling exponent, which is usually treated as an empirical scaling parameter.

Destruction of cancer cells by laser-induced shock waves: recent developments in experimental treatments and multiscale computer simulations

In this emerging area article we review recent progress in the mechanical destruction of cancer cells using laser-induced shock waves. The pure mechanical damaging and destruction of cancer cells associated with this technique possibly opens up a new route to tumor treatments and the corresponding therapies. At the same time progress in multiscale simulation techniques makes it possible to simulate mechanical properties of soft biological matter such as membranes, cytoskeletal networks and even whole cells and tissue. In this way an interdisciplinary approach to understanding key mechanisms in shock wave interactions with biological matter has become accessible. Mechanical properties of biological materials are also critical for many physiological processes and cover length scales ranging from the atomistic to the macroscopic scale. We argue that the latest developments and progress in experimentation enable the investigation of the shock wave interaction with cancer cells on multiple time- and length-scales. In this way the integrated use of experiment and simulation can address key challenges in this field. The exploration of the biological effects of laser-generated shock waves on a fundamental level constitutes an emerging multidisciplinary research area combining scientific methods from the areas of physics, biology, medicine and computer science.

Dynamics of discrete semiflexible chains under dihedral constraints: analytic results

Here we consider the dynamics of semiflexible polymers subject both to angular and to dihedral constraints. We succeed in obtaining analytically the dynamical matrix of such systems by extending the formalism developed by Dolgushev and Blumen [J. Chem. Phys. 131, 044905 (2009)]. This leads to a set of Langevin equations whose eigenvalues determine many dynamical properties. Exemplarily, we display the mechanical relaxation loss moduli [G"(ω)] as a function of several, distinct sets of microscopic stiffness parameters; it turns out that such differences lead to macroscopically distinct patterns.

Static and dynamic contributions to anomalous chain dynamics in polymer blends

By means of computer simulations, we investigate the relaxation of the Rouse modes in a simple bead-spring model for non-entangled polymer blends. Two different models are used for the fast component, namely fully flexible and semiflexible chains. The latter, which incorporate intramolecular barriers with bending and torsion terms, are semiflexible in the sense that static intrachain correlations are strongly non-gaussian at all length scales. The dynamic asymmetry in the blend is strongly enhanced with decreasing temperature, inducing confinement effects on the fast component. The dynamics of the Rouse modes show very different trends for the two models of the fast component. For the fully flexible case, the relaxation times exhibit a progressive deviation from Rouse scaling on increasing the dynamic asymmetry. This anomalous effect has a dynamic origin. It is not related to particular static features of the Rouse modes, which indeed are identical to those of the fully flexible homopolymer, and are not modified by the dynamic asymmetry in the blend. On the contrary, in the semiflexible case the relaxation times approximately exhibit the same scaling behaviour as the amplitudes of the modes. This suggests that the origin of the anomalous dynamic scaling for semiflexible chains confined in the blend is essentially of static nature. We discuss the implications of these observations for the applicability of theoretical approaches to chain dynamics in polymer blends.

A review of computational methods in materials science: examples from shock-wave and polymer physics

This review discusses several computational methods used on different length and time scales for the simulation of material behavior. First, the importance of physical modeling and its relation to computer simulation on multiscales is discussed. Then, computational methods used on different scales are shortly reviewed, before we focus on the molecular dynamics (MD) method. Here we survey in a tutorial-like fashion some key issues including several MD optimization techniques. Thereafter, computational examples for the capabilities of numerical simulations in materials research are discussed. We focus on recent results of shock wave simulations of a solid which are based on two different modeling approaches and we discuss their respective assets and drawbacks with a view to their application on multiscales. Then, the prospects of computer simulations on the molecular length scale using coarse-grained MD methods are covered by means of examples pertaining to complex topological polymer structures including star-polymers, biomacromolecules such as polyelectrolytes and polymers with intrinsic stiffness. This review ends by highlighting new emerging interdisciplinary applications of computational methods in the field of medical engineering where the application of concepts of polymer physics and of shock waves to biological systems holds a lot of promise for improving medical applications such as extracorporeal shock wave lithotripsy or tumor treatment.