Related papers: Coarse-Grained Molecular Dynamics Modeling of A Br…

A polarizable force-field (FF) model for short- and long-alkane chains and amide derivatives was constructed based solely on accurate quantum chemical (QC) calculations. First, the FF model accuracy was accessed by performing molecular…

Sampling equilibrium molecular configurations from the Boltzmann distribution is a longstanding challenge. Boltzmann Generators (BGs) address this by combining exact-likelihood generative models with importance sampling, but practical…

The reaction of $AB_m$ monomers (m=2,3) with a multifunctional B_f-type polymer chain ("hypergrafting") is studied by coarse-grained molecular dynamics simulations. The $AB_m$ monomers are hypergrafted using the slow monomer addition…

Coarse-grained (CG) models play a crucial role in the study of protein structures, protein thermodynamic properties, and protein conformation dynamics. Due to the information loss in the coarse-graining process, backmapping from CG to…

One essential goal of constructing coarse-grained molecular dynamics (CGMD) models is to accurately predict non-equilibrium processes beyond the atomistic scale. While a CG model can be constructed by projecting the full dynamics onto a set…

We present a coarse-graining method applicable to dry scalar active matter with motility regulation. Our approach, based on a multiscale perturbative expansion of the backward Kolmogorov equation, does not rely on any specific microscopic…

We present a quantum mechanical / molecular mechanics (QM/MM) to tackle chemical reactions with substantial molecular reorganization. For this, molecular dynamics simulations with smoothly switched interaction models are used to suggest…

We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…

We introduce a coarse-grained stochastic network dynamics (CGSND) framework for modeling deformation and rupture in polymer networks. The method replaces explicit molecular dynamics (MD) or coarse-grained molecular dynamics (CGMD) with…

Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…

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…

We consider a coarse-grained (CG) model with pairwise interactions, suitable to describe low-density solutions of star-branched polymers of functionality $f$. Each macromolecule is represented by a CG molecule with $(f+1)$ interaction…

Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…

The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…

Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…

The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…

Molecular Dynamics (MD) is crucial in various fields such as materials science, chemistry, and pharmacology to name a few. Conventional MD software struggles with the balance between time cost and prediction accuracy, which restricts its…

We propose a dynamic coarse-graining (CG) scheme for mapping heterogeneous polymer fluids onto extremely CG models in a dynamically consistent manner. The idea is to use as target function for the mapping a wave-vector dependent mobility…

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…