Related papers: A nucleotide-level coarse-grained model of RNA
We explore a systematic approach to studying the dynamics of evolving networks at a coarse-grained, system level. We emphasize the importance of finding good observables (network properties) in terms of which coarse grained models can be…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
It is well-established that many physical properties of DNA at sufficiently long length scales can be understood by means of simple polymer models. One of the most widely used elasticity models for DNA is the twistable worm-like chain…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…
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…
The increasing importance of well-controlled ordered nanostructures on surfaces represents a challenge for existing metrology techniques. To develop such nanostructures and monitor complex processing constraints fabrication, both a…
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Integrative biomolecular modeling of RNA relies on structural refined collections and accurate experimental data that reflect binding and folding behavior. However, the prediction of such collections remains challenging due to the rugged…
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently…
We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles. The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the…
Simulations of condensed matter systems often focus on the dynamics of a few distinguished components but require integrating the dynamics of the full system. A prime example is a molecular dynamics simulation of a (macro)molecule in…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
The paper constructs a coarse-grained model to investigate dry sliding friction of the body-centered-cubic Fe micron-scale system by smoothed particle hydrodynamics simulations and examines influences of the spring force on the characters…
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
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 derive a coarse-grained description of the dynamics of a nanoparticle immersed in an isothermal simple fluid by performing a systematic coarse graining of the underlying microscopic dynamics. As coarse-grained or relevant variables we…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…