Related papers: Coarse-Graining Simulation Approaches for Polymer …
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…
We present a dynamic coarse-graining technique that allows to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSM), which we construct from…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
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…
We derive and introduce anisotropic effective pair potentials to coarse-grain solutions of semiflexible rings polymers of various lengths. The system has been recently investigated by means of full monomer-resolved computer simulations,…
Targeting simulations on parallel hardware architectures, this paper presents computational kernels for efficient computations in mortar finite element methods. Mortar methods enable a variationally consistent imposition of coupling…
Coarse Grid Projection (CGP) methodology is used to accelerate the computations of sets of decoupled nonlinear evolutionary and linear static equations. In CGP, the linear equations are solved on a coarsened mesh compared to the nonlinear…
Coarse-grained (CG) molecular dynamics enables simulations of atomic systems such as biomolecules at timescales inaccessible to all-atom (AA) methods, but existing CG neural potentials trained via force matching capture only the gradient of…
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…
We present a promising coarse-graining strategy for linking micro- and mesoscales of soft matter systems. The approach is based on effective pairwise interaction potentials obtained from detailed atomistic molecular dynamics (MD)…
Coarse grain (CG) molecular dynamics (MD) can simulate systems inaccessible to fine grain (FG) MD simulations. A CG simulation decreases the degrees of freedom by mapping atoms from an FG representation into agglomerate CG particles. The FG…
Brute-force simulations for dynamics on very large networks are quite expensive. While phenomenological treatments may capture some macroscopic properties, they often ignore important microscopic details. Fortunately, one may be only…
A versatile and transferable coarse-grained (CG) model was developed to investigate the self-assembly of two ubiquitous methacrylate-based copolymers: poly(ethylene oxide-b-methylmethacrylate) (PEO-b-PMMA) and poly(ethylene…
Coarse-graining (CG) is a systematic reduction of the number of degrees of freedom (DOF) used to describe a system of interest. CG can be thought of as a projection on coarse-grained DOF and is therefore dependent on the functions used to…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
We review a coarse-graining strategy (multiblob approach) for polymer solutions in which groups of monomers are mapped onto a single atom (a blob) and effective blob-blob interactions are obtained by requiring the coarse-grained model to…
The objective of graph coarsening is to generate smaller, more manageable graphs while preserving key information of the original graph. Previous work were mainly based on the perspective of spectrum-preserving, using some predefined…
We study coarse-graining methods for stochastic differential equations. In particular we consider averaging and a type of projection operator method, sometimes referred to as effective dynamic via conditional expectations. The projection…
We propose a systematic coarse-grained representation of block copolymers, whereby each block is reduced to a single ``soft blob'' and effective intra- as well as intermolecular interactions act between centres of mass of the blocks. The…
Stochastic modelling of complex systems plays an essential, yet often computationally intensive role across the quantitative sciences. Recent advances in quantum information processing have elucidated the potential for quantum simulators to…