Related papers: Consistent and transferrable coarse-grained model …
We demonstrate that hierarchical backmapping strategies incorporating generic blob-based models can equilibrate melts of high-molecular-weight polymers, described with chemically specific, atomistic, models. The central idea behind these…
Computer simulations can provide mechanistic insight into ionic liquids (ILs) and predict the properties of experimentally unrealized ion combinations. However, ILs suffer from a particularly large disparity in the time scales of atomistic…
The large time and length scales and, not least, the vast number of particles involved in industrial-scale simulations inflate the computational costs of the Discrete Element Method (DEM) excessively. Coarse grain models can help to lower…
We present a coarse-graining strategy for reducing the number of particle species in mixtures to achieve a simpler system with higher diffusion while preserving the total particle number and characteristic dynamic features. As a system of…
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
This chapter deals with various aspects related to the adsorption of long chain-like macromolecules (polymers) onto solid surfaces. Physical aspects of the adsorption mechanism are elaborated mainly at thermodynamical equilibrium. The basic…
We reconsider the structure-based route to coarse graining in which the coarse-grained model is defined in such a way to reproduce some distributions functions of the original system as accurately as possible. We consider standard…
We use a standard bead-spring model and molecular dynamics simulations to study the static properties of symmetric linear multiblock copolymer chains and their blocks under poor solvent conditions in a dilute solution from the regime close…
Reducing the complexity of cross-linked polymer networks by preserving their main macroscale properties, is key to understanding them, and a crucial issue is to relate individual properties of the polymer constituents to those of the…
Analogous to a model that predicts the linear scaling of the binding energy of a nucleus from the number of nucleons, a simple model was developed to account for the observed linear variation of the quantum-chemically computed total…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
We consider a fully directed self-avoiding walk model on a cubic lattice to mimic the conformations of an infinitely long confined flexible polymer chain; and the confinement condition is achieved by two parallel athermal plates. The…
In this paper we study the shape characteristics of a polymer chain in a good solvent using a mesoscopic level of modelling. The dissipative particle dynamics simulations are performed in the $3D$ space at a range of chain lengths $N$. The…
We present a model for the efficient simulation of generic bilayer membranes. Individual lipids are represented by one head- and two tail-beads. By means of simple pair potentials these robustly self-assemble to a fluid bilayer state over a…
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
We formulate a simple solvation potential based on a coarsed-grain representation of amino acids with two spheres modeling the $C_\alpha$ atom and an effective side-chain centroid. The potential relies on a new method for estimating the…