Related papers: Coarse Graining RNA Nanostructures for Molecular D…
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a…
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…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Constructing atom-resolved states from low-resolution data is of practical importance in many areas of science and engineering. This problem is addressed in this paper in the context of multiscale factorization methods for molecular…
Colloidal synthesis of nanocrystals usually includes complex chemical reactions and multi-step crystallization processes. Despite the great success in the past 30 years, it remains challenging to clarify the correlations between synthetic…
In a recent computational study, we found highly structured ground states for coarse-grained polymers adsorbed to ultrathin nanowires in a certain model parameter region. Those tubelike configurations show, even at a first glance, exciting…
The increasing importance of RNA as a prime player in biology can hardly be overstated. Problems in RNA, such as folding and RNA-RNA interactions that drive phase separation, require cations. Because experiments alone cannot reveal 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…
The dynamics of real magnets is often governed by several interacting processes taking place simultaneously at different length scales. For dynamical simulations the relevant length scales should be coupled, and the energy transfer…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
Cellular automata and other discrete dynamical systems have long been studied as models of emergent complexity. Recently, neural cellular automata have been proposed as models to investigate the emerge of a more general artificial…
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
We present the state-of-the-art theoretical modeling, molecular simulation, and coarse-graining strategies for the transport of gases and liquids in nanoporous materials (pore size 1-100 nm). Special emphasis is placed on the transport of…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…
During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation…
Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…