Related papers: Martini 3 Coarse-Grained Force Field for Carbohydr…
Electronic structure methods offer in principle accurate predictions of molecular properties, however, their applicability is limited by computational costs. Empirical methods are cheaper, but come with inherent approximations and are…
Monte Carlo simulations are presented for a coarse-grained model of real quadrupolar fluids. Molecules are represented by particles interacting with Lennard-Jones forces plus the thermally averaged quadrupole-quadrupole interaction. The…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
A novel numerical approach to analyze the mechanical behavior within composite materials including the inelastic regime up to final failure is presented. Therefore, a second-gradient theory is combined with phase-field methods to fracture.…
Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN$^-$, K$^+$ and acetamide is improved vis-a-vis experimentally measured properties. Given…
We present a high-fidelity three dimensional computational framework for simulating the bulk mechanical behavior of granular aggregates composed of deformable brittle grains. Departing from classical discrete element methods (DEM), our…
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving…
We present a systematic coarse-graining (CG) strategy for many particle molecular systems based on cluster expansion techniques. We construct a hierarchy of coarse-grained Hamiltonians with interaction potentials consisting of two, three…
The favored phase field method (PFM) has encountered challenges in the finite strain fracture modeling of nearly or truly incompressible hyperelastic materials. We identified that the underlying cause lies in the innate contradiction…
This work presents a novel framework governing the development of an efficient, accurate, and transferable coarse-grained (CG) model of a polyether material. The proposed framework combines the two fundamentally different classical…
The correct description of the ionic interaction and stable equilibrium of the simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model of the monovalent ions is very important. The force field…
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,…
In this study, a coarse-graining framework for discrete models is formulated on the basis of multiscale homogenization. The discrete model considered in this paper is the Lattice Discrete Particle Model (LDPM), which simulates concrete at…
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…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…
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…
Understanding the fracture mechanisms in composite materials across scales, from nano- to micro-scales, is essential for an in-depth understanding of the reinforcement mechanisms and designing the next generation of lightweight,…
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…