V. Mlynsky

Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

This study benchmarks force-field performance for DNA/RNA hybrid duplexes, finding no force field accurately reproduces all structural features and highlighting parameter conflicts.

Mechanical stability and unfolding pathways of parallel tetrameric G-quadruplexes probed by pulling simulations

This study uses pulling simulations to analyze the mechanical stability and unfolding pathways of tetrameric parallel G-quadruplexes, identifying key factors like vertical force components and unfolding transitions.

Simple Adjustment of Intra-nucleotide Base-phosphate Interaction in OL3 AMBER Force Field Improves RNA Simulations

The paper adjusts the AMBER OL3 force field to improve RNA simulations by fixing intra-nucleotide steric clashes in base-phosphate interactions.

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations

The paper uses atomistic simulations to study how human telomeric GQs unfold under different mechanical forces and identifies factors influencing their unfolding mechanisms.

Towards Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Corrections

This study compares enhanced sampling techniques and force field corrections for RNA tetraloop folding simulations, finding that combining REST2 with ST-MetaD improves sampling efficiency and that force field modifications stabilize native states.

W-RESP: Well-Restrained Electrostatic Potential Derived Charges. Revisiting the Charge Derivation Model.

The paper improves the RESP charge model to better describe electrostatic potentials around molecules, particularly for aromatic heterocyclic compounds, enhancing nucleic acid force field performance.

UNCG RNA tetraloop as a formidable force-field challenge for MD simulations

This study analyzes MD simulations of the UNCG RNA tetraloop, identifying force field deficiencies that contribute to its instability in simulations.

Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides

The paper improves RNA force field simulations by adding two terms, gHBfix and tHBfix, to better model terminal nucleotide interactions and enhance accuracy for RNA tetranucleotides.

IMPROVING THE PERFORMANCE OF THE AMBER RNA FORCE FIELD BY TUNING THE HYDROGEN-BONDING INTERACTIONS

This paper improves the AMBER RNA force field by tuning hydrogen-bonding interactions to better match experimental data in RNA folding simulations.