Related papers: Development and applications of Coarse Grained mod…
We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
More than twenty coarse-grained (CG) DNA models have been developed for simulating the behavior of this molecule under various conditions, including those required for nanotechnology. However, none of these models reproduces the DNA…
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA,…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
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 introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate…
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…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…
The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a…
The emerging field of hybrid DNA - protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with versatility of protein interactions. However, the design and…
Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
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…
Coarse-graining is a molecular modeling technique in which an atomistic system is represented in a simplified fashion that retains the most significant system features that contribute to a target output, while removing the degrees of…