Manuscript Topics

Molecular dynamics (MD) simulations and free energy calculations (FEC) have become indispensable tools in biophysics, drug discovery, and materials science. However, despite significant advancements, these methods still face critical challenges—such as sampling limitations, force field inaccuracies, high computational costs, and difficulties in connecting simulations to experimental observables.
This Special Issue aims to highlight cutting-edge approaches to overcome current bottlenecks and explore future breakthroughs in MD and FEC. We welcome original research articles, reviews, and perspectives covering (but not limited to) the following topics:
1.Methodological Advances
Enhanced sampling techniques (e.g., metadynamics, replica-exchange) for rare events.
Machine learning-assisted force fields, coarse-grained models, and hybrid QM/MM methods.
Uncertainty quantification and error reduction in free energy predictions.
2.Computational Efficiency & Scalability
High-performance computing strategies (GPU acceleration, distributed algorithms).
Reduced-order models and AI-driven surrogate potentials.
3.Bridging Theory and Experiment
Validation of MD/FEC results against experimental data (e.g., binding affinities, kinetics).
Applications in drug design (e.g., ΔΔG prediction, allosteric modulation).
Complex systems (membrane proteins, nucleic acids, heterogeneous environments).
4.Emerging Paradigms
Non-equilibrium free energy methods.
Quantum effects in biomolecular simulations.
Integrative modeling combining MD with multi-omics data.

We encourage contributions that address fundamental limitations or propose innovative solutions, including negative results and benchmark studies. By fostering interdisciplinary dialogue, this Special Issue seeks to chart the next frontiers in computational biophysics and chemistry.
Submitted papers should not have been previously published, nor be currently under consideration for publication elsewhere. All manuscripts will be peer-reviewed before their acceptance for publication.

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