Molecular Dynamics Simulations: Advances and Applications

Dear colleagues,

Molecular dynamics (MD) simulations have led to great advances in many scientific disciplines, such as chemical physics, materials science, and biophysics. This computational methodology has demonstrated high relevance in the detailed characterization of biomolecular systems, including complementarity with experimental data, optimization of the design of experiments, and prediction of relevant properties for chemical systems that are expensive or difficult to handle experimentally. Among many applications, it has been employed to characterize disease development processes and used in the initial stages of drug design and development.

The application of MD simulations to the characterization of biomolecular systems is very broad, encompassing the characterization of membrane structure and organization, membrane permeability, lipid–protein interactions, lipid–drug interactions, protein–ligand interactions, and protein structure and dynamics. In this context, MD simulations have been used to obtain both detailed atomic-scale and coarse-grained level information that can span systems of complexity ranging from a few molecules to an entire organelle.

MD simulations, boosted by an increasing computational power, have evolved to a level that makes them completely suited to the characterization of many properties of molecular and supramolecular systems, such as their preferred organization and free energies of molecular processes. This is accompanied by the emergence of a variety of software packages and tools that were developed to aid parameterization for different force fields. In addition, important manipulation and analysis tools have been developed, increasing the possibilities for building and characterizing new and diverse systems. The development and application of enhanced sampling methods have also been of high importance for the type of information obtained. Knowledge obtained from MD simulations can be of a qualitative or quantitative nature.

In this Special Issue, we invite investigators to contribute original research articles and review articles on all aspects of molecular dynamics simulations. Potential topics include but are not limited to the following:

- Applications of MD simulations to material sciences and chemical engineering;

- Atomistic, coarse-grained, and multiscale MD simulations;

- Characterization of the interaction and permeation of drug-like molecules in lipid membranes;

- Cutting-edge methodologies for the study of biomolecular systems;

- Protein–ligand interactions with implications for disease development and control;

- Quantum mechanics/molecular mechanics approaches to simulations of chemical and biological systems;

- Software, force fields, and diverse tools to deal with biomolecular systems.

Prof. Dr. Luís M.S. Loura
Dr. Hugo A. L. Filipe
Guest Editors

Manuscript Submission Information

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