Applications of Molecular Dynamics to Biological Systems
A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Biochemistry, Biophysics and Computational Biology".
Deadline for manuscript submissions: 26 August 2025 | Viewed by 1357
Special Issue Editor
Interests: computer simulations; computational biophysics; membranes; membrane permeation; conformational transitions of proteins; molecular dynamics; reaction pathways; long time dynamics; RNA folding
Special Issues, Collections and Topics in MDPI journals
Special Issue Information
Dear Colleagues,
Molecular Dynamics (MD) simulations have become a standard tool in investigating biomolecular systems. While experiments are indispensable and simulations must be verified by experiments, atomistic information supplants wet laboratory data with highly detailed spatial and temporal molecular information. The atomically detailed mechanisms revealed by computer simulations lead to a better understanding of fundamental processes. The simulations are synergetic with experiments and suggest new measurements and directions of investigation. While significant challenges in using MD continue to attract considerable research attention (achieving long-time dynamics, efficient sampling of confirmational space, the accuracy of force fields, etc.), the field is sufficiently mature such that meaningful experiment-guiding predictions are made by simulating the corresponding systems. Biological systems investigated by physics-based computer simulations are highly diverse in size, time scale, and general complexity. Computational investigations vary from relatively small molecules, such as peptides and nucleotides, to large assemblies, such as chromatin and biological membranes. Different spatial and temporal scales are necessary to understand the biological behavior of signaling, reactions, structure formation, and flexibility. Processes of individual biological molecules are simulated with high accuracy (e.g., peptide and protein folding in aqueous solutions). Conformational transitions and activations of proteins and protein complexes have long been a focus of simulations and experimental interactions, and the two provide an invaluable exchange of complementing views. Complex assemblies with multiple phases are also of significant interest and include phospholipid membranes, their interactions with embedded proteins, and peptide permeation. Another field that MD significantly impacts is chromatin modeling, with extremely large length scales at the molecular scale. In summary, molecular biophysics structures and events with exceptionally long time scales (from femtoseconds to hours) and spatial scales (from angstrom to micrometers) are revealed by the tools of MD.
Dr. Ron Elber
Guest Editor
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Keywords
- computer simulation
- biophysical modeling
- molecular dynamics
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