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The structure of polymer networks, defined by chain lengths and connectivity patterns, fundamentally influences their bulk properties. While existing polymer network models connect chain properties to emergent network behavior, they are…
We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
We revisit a model of semiflexible Gaussian chains proposed by Winkler \textit{et al}, solve the dynamics of the discrete description of the model and derive exact algebraic expressions for some of the most relevant dynamical observables,…
Building on the results of our computer simulation (ArXiv cond-mat/0503573)we develop a theoretical description of the motion of a bead, embedded in a network of semiflexible polymers, and responding to an applied force. The theory reveals…
An efficient numerical framework is presented for modeling viscoelasticity and permanent set of polymers. It is based on the hereditary integral form of transient network theory, in which polymer chains belong to distinct networks each with…
We develop a general analysis of the diffusive dynamics of polydisperse polymers in the presence of chemical potential gradients, within the context of the tube model (with all species entangled). We obtain a set of coupled dynamical…
Coarse-grained (CG) molecular dynamics (MD) simulations can simulate large molecular complexes over extended timescales by reducing degrees of freedom. A critical step in CG modeling is the selection of the CG mapping algorithm, which…
We consider a general discrete model for heterogeneous semiflexible polymer chains. Both the thermal noise and the inhomogeneous character of the chain (the disorder) are modeled in terms of random rotations. We focus on the quenched…
Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the dynamics of the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
The diffusion of small molecular penetrants through polymeric materials represents an important fundamental problem, relevant to the design of materials for applications such as coatings and membranes. Polymer networks hold promise in these…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
We use an off - lattice bead - spring model of a self - avoiding polymer chain immersed in a 3-dimensional quenched random medium to study chain dynamics by means of a Monte - Carlo (MC) simulation. The chain center of mass mean-squared…
The endpoint distribution and dynamics of semiflexible fibers is studied by numerical simulation. A brief overview is given over the analytical theory of flexible and semiflexible polymers. In particular, a closed expression is given for…
Networks of coupled phase oscillators are one of the most studied dynamical systems with numerous applications in physics, chemistry, biology, and engineering. Their behaviour is often characterized by the emergence of various partially…
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…
We propose a novel and systematic method for coarse-graining oscillator networks described by phase equations. Our coarse-graining method enables us to obtain the closed coarse-grained equations for a few effective eigenmodes, which is…
We investigate the behaviour of randomly cross-linked (co)polymer blends using a combination of replica theory and large-scale molecular dynamics simulations. In particular, we derive the analogue of the random phase approximation for…
The structure of polyelectrolytes is highly sensitive to small changes in the interactions between its monomers. In particular, interactions mediated by counterions play a significant role, and are affected by both specific molecular…