ReviewFrontiers in molecular biosciences2021
A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.
Review in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- A nanoscale Jitterbug transformer from DNA.Nature communications · 2026Article
- Fitting coarse-grained models to macroscopic experimental data via automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Engineering and Assay of Enzymes for Expanded Genetic Alphabet Replication.Biochemistry · 2025Article
- Nonequilibrium Acceleration and Time Forecasting of Cluster-Mediated Self-Assembly.Journal of chemical theory and computation · 2025Article
- How We Simulate DNA Origami.Small methods · 2025Article
- Article
- Enhancing the speed of DNA walkers through soft confinement.Scientific reports · 2025Article
- Modelling the melting of DNA oligomers with non-inert dangling ends.Frontiers in molecular biosciences · 2025Article
- Nuclease-Resistant L-DNA Tension Probes Enable Long-Term Force Mapping of Single Cells and Cell Consortia.Angewandte Chemie (International ed. in English) · 2024Article
- Density-Nematic Coupling in Isotropic Solution of DNA: Multiscale Model.Macromolecular rapid communications · 2024Article
- Bioinspired designer DNA NanoGripper for virus sensing and potential inhibition.Science robotics · 2024Article
- Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations.Scientific reports · 2024Article
- Encoding signal propagation on topology-programmed DNA origami.Nature chemistry · 2024Article
- A Novel Fractional Brownian Dynamics Method for Simulating the Dynamics of Confined Bottle-Brush Polymers in Viscoelastic Solution.Polymers · 2024Article
- Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies.Nature communications · 2023Article
- Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids.The journal of physical chemistry. B · 2023Article
- Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations.Biophysical journal · 2023Article
- Anomalous Diffusion of Polyelectrolyte Segments on Supported Charged Lipid Bilayers.Entropy (Basel, Switzerland) · 2023Article
- Weak tension accelerates hybridization and dehybridization of short oligonucleotides.Nucleic acids research · 2023Article
- Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization.Molecules (Basel, Switzerland) · 2023Article
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5 authors.
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Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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