Multiscale Simulation of DNA: From Atoms to Chromosomes
A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Biochemistry, Biophysics and Computational Biology".
Deadline for manuscript submissions: closed (26 December 2021) | Viewed by 2760
Special Issue Editors
2. Institute Pasteur of Montevideo, 11400 Montevideo, Uruguay
Interests: multiscale modeling; nucleic acids; computational methods
Special Issue Information
Dear Colleagues,
In the past few years, there has been a renewed interest in modeling and simulating the structure, conformation, and dynamical behavior of biological systems containing DNA, a key molecule of life. Boosted by recent developments in refined all-atom force fields (parmbsc1, ol15, c36), the standardization and universalization of genome-wide experiments (deep sequencing, 3C technologies, etc.), and advances in high-resolution microscopy coupled to gene-painting techniques, dozens of new models and hundreds of new applications have come to light. Given the intrinsically multiscale nature of DNA, the new models and applications published to date range from atomistic molecular dynamics (MD) approaches analyzing the sequence-dependent structural properties of DNA oligomers alone or in complexes with proteins, to mesoscopic simulations of chromatin fibers using polymer physics to unveil the conformation and dynamics of entire chromosomes. Fueled by the increasing computational power available, simulations of nucleosomes at atomic resolution have reached the microsecond timescale. Simultaneously, several coarse-grained models of chromatin derived from first principles (bottom-up) have reached maturity, allowing the simulation of chromatin fibers in different epigenetic states. Finally, a huge variety of top-down mesoscopic models have emerged based on constrained simulations that leverage spatial information derived from the experiments mentioned above.
With this remarkable thrust on DNA simulations in mind, we are calling for contributions on new theoretical developments or applications of modeling and simulation techniques for a Special Issue of the Biochemistry, Biophysics and Computational Biology section of the journal Life. Original works from the whole spectrum of scales will be considered: from the simulation of short DNA oligomers in atomic detail to mesoscopic models of chromosome folding.
Dr. Pablo D. Dans
Dr. Marco Pasi
Guest Editors
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Keywords
- Molecular dynamics
- Force fields
- Coarse-grained models
- Mesoscopic models
- Monte Carlo
- Nucleosomes
- Chromatin
- Chromosomes
- DNA oligomers
- Physical properties
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