research.md

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Research

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Computational approaches to RNA dynamics

RNA molecules are highly dynamic, with functions often influenced by multiple structures. Our computational tools complement experimental approaches to reveal these dynamics and their biological implications.

Enhanced Sampling and Integrative Approaches

We develop enhanced sampling methods to improve the precision of molecular dynamics (MD) simulations. Additionally, we employ integrative approaches to align computational results with experimental data, including force-field improvements, ensemble refinement, and other advanced techniques.

Applications of Molecular Dynamics

Using molecular dynamics simulations, we characterize the structures and dynamics of RNA molecules, as well as their interactions with ions, proteins, and small molecules, providing insights into their biological roles.

Bioinformatics for Large Systems

To scale our studies to larger RNA systems, we utilize bioinformatics tools like secondary structure prediction, enabling us to integrate computational insights into complex biological contexts.

PLUMED

We are involved in the development PLUMED, an open-source software widely used for enhanced sampling and integrative methods in molecular dynamics simulations. PLUMED integrates seamlessly with various MD engines, enabling advanced methodologies that are central to our research.