I. Andricioaei

A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software

The paper provides advanced tutorials for WESTPA 2.0, demonstrating new features for rare-events sampling in molecular simulations.

Force Field Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA

This paper investigates how different force field models affect the WC to HG base pair transition in DNA, finding that enthalpic stabilization and entropy balance determine conformational stability.

Point Mutations in SARS-CoV-2 Variants Induce Long-Range Dynamical Perturbations in Neutralizing Antibodies

This study shows how point mutations in SARS-CoV-2 variants alter the dynamics of neutralizing antibodies, affecting their binding affinity and structure.

Markovian Weighted Ensemble Milestoning (M-WEM): Long-time Kinetics from Short Trajectories

This paper introduces M-WEM, a method to calculate long-timescale biomolecular kinetics from short simulations, showing high accuracy and low computational cost.

Distant Residues Modulate Conformational Opening in SARS-CoV-2 Spike Protein

This paper identifies non-RBD residues in SARS-CoV-2 spike protein that modulate conformational changes critical for receptor binding, offering targets for broad-spectrum therapeutics.

Free Energy Landscape and Conformational Kinetics of Hoogsteen Base-Pairing in DNA vs RNA

This study uses simulations to analyze the free energy and kinetics of Hoogsteen base pairing in DNA and RNA, revealing distinct transition pathways and intermediates.