Related papers: Coarse-Grained Simulation Model for Crystalline Po…
We develop a coarse-grained particle-based model to simulate membranes with nematic liquid-crystal order. The coarse-grained particles form vesicles which, at low temperature, have orientational order in the local tangent plane. As the…
The mechanics of cohesive or cemented granular materials is complex, combining the heterogeneous responses of granular media, like force chains, with clearly defined material properties. Here, we use a discrete element model (DEM)…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
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…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
By mixing glass beads with a curable polymer we create a well-defined cohesive granular medium, held together by solidified, and hence elastic, capillary bridges. This material has a geometry similar to a wet packing of beads, but with an…
The dynamical properties of entangled polymers originate from the dynamic constraints due to the uncrossability between polymer chains. We propose a highly coarse-grained simulation model with transient bonds for such dynamically…
Bio-inspired composites are a great promise for mimicking the extraordinary and highly efficient properties of natural materials. Recent developments in voxel-by-voxel 3D printing have enabled extreme levels of control over the material…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
We present an extension to the iterative Boltzmann inversion method to generate coarse-grained models with three-body intramolecular potentials that can reproduce correlations in structural distribution functions. The coarse-grained…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
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 present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and inter-molecular potentials obtained at zero density. We show how this model is able to accurately…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
In this work, we develop a two-component coarse-grained molecular dynamics (CGMD) model for simulating the erythrocyte membrane. This proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton,…