Related papers: Integrating experimental data with molecular simul…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…
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…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid…
Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene…
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
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 protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations in silico. Recently, generative models has been leveraged as…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
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…
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
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…