Related papers: Coarse Graining RNA Nanostructures for Molecular D…
Much of our understanding of complex structures is based on simplification: for example, metal-organic frameworks are often discussed in the context of "nodes" and "linkers", allowing for a qualitative comparison with simpler inorganic…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Quantum nanosystems involve the coupled dynamics of fermions or bosons across multiple scales in space and time. Examples include quantum dots, superconducting or magnetic nanoparticles, molecular wires, and graphene nanoribbons. The number…
We present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and inter-molecular potentials obtained at zero density. We show how this model is able to accurately…
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…
A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific…
The aim of this work is the description of the chain formation phenomena observed in colloidal suspensions of superparamagnetic nanoparticles under high magnetic fields. We propose a new methodology based on an on-the-fly Coarse-Grain (CG)…
A hierarchical model for the growth of planar arch structures for RNA secondary structures is presented, and shown to be equivalent to a tree-growth model. Both models can be solved analytically, giving access to scaling functions for large…
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $\sigma$ are varied over a wide…
We propose GrainGNN, a surrogate model for the evolution of polycrystalline grain structure under rapid solidification conditions in metal additive manufacturing. High fidelity simulations of solidification microstructures are typically…
Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
The structure of polyelectrolytes is highly sensitive to small changes in the interactions between its monomers. In particular, interactions mediated by counterions play a significant role, and are affected by both specific molecular…
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,…
A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a…
We demonstrate how micromagnetic simulations can be employed in order to characterize and analyze the magnetic microstructure of nanocomposites. For the example of nanocrystalline Nd$-$Fe$-$B, which is a potential material for future…
We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by…
We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…