About this Research Topic
Slow biomolecular dynamics processes (such as protein folding, protein-DNA recognition, RNA folding, membrane transport, etc.) contribute to a wide variety of vital cellular activities, but are often difficult to precisely characterize in experiments due to instrumental limitations. Molecular dynamics (MD) simulation serves as a computational microscope, offering unprecedented high-resolution visualization in inferring the molecular mechanisms for biomolecular dynamics. Since the first MD simulation for protein dynamics was introduced nearly five decades ago, its applications in the field of molecular biology have increased dramatically. MD simulations and computational modeling have become promising approaches and powerful tools for the investigation of biomolecular structure, dynamics, and function, as well as providing mechanistic understanding of biological processes at the molecular level.
However, the conventional MD approaches (limited by current computational abilities) are frequently confronted with one arresting obstacle in practical investigations: the inability to faithfully capture at the spatial and temporal scale of biomolecular processes, which involve the motions of thousands to millions of atoms in the microsecond to second. Various advanced MD approaches have been developed with the aim to overcome the bottleneck of MD simulations. This Research Topic will collect contributions that harness the powers of the promising, novel and recently developed advanced MD simulations in tackling slow and large-scale biomolecular dynamics. We will lend additional focus to two appealing and widely proposed MD approaches termed as “enhanced sampling” and “coarse-grained modeling”. In principle, the enhanced sampling method facilitates the escape of metastable states and crossing barriers, while the coarse-grained model extends the in silico timescale by reducing the system size and is subsequently rationalized with a physical- or empirical-based potential. Although the success of these two methods was well witnessed during the past decades, it is still needed to have a systematic organization as a useful guidance for the future studies in terms of further developments and improvements of the advanced techniques, as well as promoting the applications in biomolecular dynamics.
In this Research Topic we welcome contributors to submit their Original Research articles, concise Reviews or Mini-Reviews, and insightful Perspectives on the developments and applications of state-of-art MD approaches, specially attentive to enhanced sampling and coarse-grained modeling in investigations and understanding of slow and large-scale biomolecular dynamics. Areas to be covered in this Research Topic may include, but are not limited to:
• Enhanced sampling simulation for large-scale biomolecular conformational dynamics
• Design and rational of new sampling techniques
• Kinetic calculation using enhanced sampling methods
• Benchmarking the sampling algorithm with brute-force simulation and/or experimental data
• Development of coarse-grained/hybrid model
• Experimentally-guided/restrained advanced MD simulation
• New theories for enhanced sampling and coarse-grained modeling in biomolecular MD simulation
However, the conventional MD approaches (limited by current computational abilities) are frequently confronted with one arresting obstacle in practical investigations: the inability to faithfully capture at the spatial and temporal scale of biomolecular processes, which involve the motions of thousands to millions of atoms in the microsecond to second. Various advanced MD approaches have been developed with the aim to overcome the bottleneck of MD simulations. This Research Topic will collect contributions that harness the powers of the promising, novel and recently developed advanced MD simulations in tackling slow and large-scale biomolecular dynamics. We will lend additional focus to two appealing and widely proposed MD approaches termed as “enhanced sampling” and “coarse-grained modeling”. In principle, the enhanced sampling method facilitates the escape of metastable states and crossing barriers, while the coarse-grained model extends the in silico timescale by reducing the system size and is subsequently rationalized with a physical- or empirical-based potential. Although the success of these two methods was well witnessed during the past decades, it is still needed to have a systematic organization as a useful guidance for the future studies in terms of further developments and improvements of the advanced techniques, as well as promoting the applications in biomolecular dynamics.
In this Research Topic we welcome contributors to submit their Original Research articles, concise Reviews or Mini-Reviews, and insightful Perspectives on the developments and applications of state-of-art MD approaches, specially attentive to enhanced sampling and coarse-grained modeling in investigations and understanding of slow and large-scale biomolecular dynamics. Areas to be covered in this Research Topic may include, but are not limited to:
• Enhanced sampling simulation for large-scale biomolecular conformational dynamics
• Design and rational of new sampling techniques
• Kinetic calculation using enhanced sampling methods
• Benchmarking the sampling algorithm with brute-force simulation and/or experimental data
• Development of coarse-grained/hybrid model
• Experimentally-guided/restrained advanced MD simulation
• New theories for enhanced sampling and coarse-grained modeling in biomolecular MD simulation
Keywords: Molecular dynamics, Enhanced sampling, Coarse-grained model, Conformational dynamics, Free energy landscape
Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
