ArticleThe European physical journal. E, Soft matter2018
Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.
Article in The European physical journal. E, Soft matter, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Tunable Patterning of DNA Origami on Surfaces Using Steric Brushes.Angewandte Chemie (International ed. in English) · 2026Article
- Global Quantitative Analysis of Ligation Reactions in Self-Assembled DNA Nanostructures at the Single-Nick Level.Small (Weinheim an der Bergstrasse, Germany) · 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
- Effects of DNA Origami-Based Nanoagent Design on Apoptosis Induction in a Large 3D Cancer Spheroid Model.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Article
- Topological linking determines elasticity in limited valence networks.Nature materials · 2025Article
- Unzipping of knotted DNA via nanopore translocation.QRB discovery · 2025Article
- Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations.Biophysical journal · 2023Article
- Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions.Journal of the American Chemical Society · 2023Article
- Nanostars planarity modulates the rheology of DNA hydrogels.Soft matter · 2023Article
- Anomalous Diffusion of Polyelectrolyte Segments on Supported Charged Lipid Bilayers.Entropy (Basel, Switzerland) · 2023Article
- Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization.Molecules (Basel, Switzerland) · 2023Article
- The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Heterogeneous migration routes of DNA triplet repeat slip-outs.Biophysical reports · 2022Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- Article
- Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.Journal of molecular biology · 2021Article
- A Versatile DNA Origami-Based Plasmonic Nanoantenna for Label-Free Single-Molecule Surface-Enhanced Raman Spectroscopy.ACS nano · 2021Article
- Design Approaches and Computational Tools for DNA Nanostructures.IEEE open journal of nanotechnology · 2021Article
- A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.Frontiers in molecular biosciences · 2021Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.