相关论文: GCMe: Efficient implementation of the Gaussian cor…
Colloid models have frequently been used to successfully describe the influence of protein-protein interactions on antibody solution properties, but they suffer from inherent problems due to the anisotropic shape of the particles. The net…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
The study of ion transport in electrochemically active materials for energy storage systems requires simulations on quantum- atomistic- and mesoscales. The methods accessing these scales not only have to be effective but also well…
Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…
Accounting for geometry-induced changes in the electronic distribution in molecular simulation is important for capturing effects such as charge flow, charge anisotropy and polarization. Multipolar force fields have demonstrated their…
Lubricated friction is a multiscale problem where molecular processes dictate the macroscopic response of the system. Traditional lubrication models rely on semi-empirical constitutive relations, which become unreliable under extreme…
In the coarse grained Brownian Dynamics simulation method the many solvent molecules are replaced by random thermal kicks and an effective friction acting on the particles of interest. For Brownian Dynamics the friction has to be so strong…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Microscopic processes on surfaces such as adsorption, desorption, diffusion and reaction of interacting particles can be simulated using kinetic Monte Carlo (kMC) algorithms. Even though kMC methods are accurate, they are computationally…
The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of…
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,…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
We examine the performance of various commonly used integration schemes in dissipative particle dynamics simulations. We consider this issue using three different model systems, which characterize a variety of different conditions often…
Studies of the Gaussian core model (GCM) have shown that it behaves like a mean field model and the properties are quite different from standard glass former. In this work we investigate the entropies, namely the excess entropy ($S_{ex}$)…
Complex fluids exhibit structure on a wide range of length and time scales, and hierarchical approaches are necessary to investigate all facets of their often unusual properties. The study of idealized coarse-grained models at different…
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…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…