Related papers: Coarse-grained Interaction Potentials for Anisotro…
A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach groups of monomers are mapped onto a single pseudoatom (a blob) and the…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…
Soft condensed matter structures often challenge us with complex many-body phenomena governed by collective modes spanning wide spatial and temporal domains. In order to successfully tackle such problems mesoscopic coarse-grained (CG)…
We propose a general coarse-graining method to derive a continuity equation that describes any dissipative system of repulsive particles interacting through short-ranged potentials. In our approach, the effect of particle-particle…
Variational quantum algorithms (VQAs) are increasingly being applied in simulations of strongly-bound (covalently bonded) systems using full molecular orbital basis representations. The application of quantum computers to the weakly-bound…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
Compared to top-down coarse-grained (CG) models, bottom-up approaches are capable of offering higher structural fidelity. This fidelity results from the tight link to a higher-resolution reference, making the CG model chemically specific.…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
Coarse-grained (CG) molecular dynamics simulations extend the length and time scale of atomistic simulations by replacing groups of correlated atoms with CG beads. Machine-learned coarse-graining (MLCG) has recently emerged as a promising…
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low…
Equilibrium aspects of molecular recognition of rigid biomolecules are investigated using coarse-grained lattice models. The analysis is carried out in two stages. First an ensemble of probe molecules is designed with respect to the target…
We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles. The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the…
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…
One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise…
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…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
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 derive a novel formulation for the interaction potential between deformable fibers due to short-range fields arising from intermolecular forces. The formulation improves the existing section-section interaction potential law for in-plane…
We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical…
We systematically studied the validity and transferability of effective, coarse-grained, pair potentials in ultrasoft colloidal systems. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping…