oxDNA, oxRNA, oxNA
@oxdna.bsky.social
Coarse-grained models of nucleic acids
Reposted by oxDNA, oxRNA, oxNA
🧪🧬
Our new paper is just out in PNAS:
www.pnas.org/doi/10.1073/...
It is about nucleic acid strand displacement, which is a key reaction in molecular computation, and part of the success of the oxDNA model comes from the fact it can efficiently simulate this process.
1/4🧵
Our new paper is just out in PNAS:
www.pnas.org/doi/10.1073/...
It is about nucleic acid strand displacement, which is a key reaction in molecular computation, and part of the success of the oxDNA model comes from the fact it can efficiently simulate this process.
1/4🧵
Controlling DNA–RNA strand displacement kinetics with base distribution | PNAS
DNA–RNA hybrid strand displacement underpins the function of many natural and engineered
systems. Understanding and controlling factors affecting D...
www.pnas.org
June 7, 2025 at 11:05 AM
🧪🧬
Our new paper is just out in PNAS:
www.pnas.org/doi/10.1073/...
It is about nucleic acid strand displacement, which is a key reaction in molecular computation, and part of the success of the oxDNA model comes from the fact it can efficiently simulate this process.
1/4🧵
Our new paper is just out in PNAS:
www.pnas.org/doi/10.1073/...
It is about nucleic acid strand displacement, which is a key reaction in molecular computation, and part of the success of the oxDNA model comes from the fact it can efficiently simulate this process.
1/4🧵
Reposted by oxDNA, oxRNA, oxNA
Great collaboration with @laklab-tubs.bsky.social , simulations carried out by my student Josh Evans
Very excited to introduce mismatch-assisted toehold exchange (MATE) concept for the first time, our new magnetic diagnostics cascades:
biorxiv.org/content/10.1...
Excellent work by Rebecca, "Metrology4life" 2nd PhD student and Great collaboration with @petrsulc.bsky.social
biorxiv.org/content/10.1...
Excellent work by Rebecca, "Metrology4life" 2nd PhD student and Great collaboration with @petrsulc.bsky.social
Mismatch-Assisted Toehold Exchange Cascades for Magnetic Nanoparticle-Based Nucleic Acid Diagnostics
Sensitive, simple, and rapid detection of nucleic acid sequences at point-of-care (POC) settings is still an unmet quest. Magnetic readout assays combined with toehold-mediated strand displacement (TM...
biorxiv.org
March 17, 2025 at 12:42 PM
Great collaboration with @laklab-tubs.bsky.social , simulations carried out by my student Josh Evans
Reposted by oxDNA, oxRNA, oxNA
🧬 A new tutorial article from our student Sarah, walking step by step through DNA origami simulation using oxDNA model, with the help of oxview.org and oxdna.org free tools. No prior experience assumed, and also accompanied by a video: youtu.be/5-rgMekX8gE
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
How We Simulate DNA Origami
This tutorial provides a detailed step-by-step description on how to import DNA origami designs into the oxDNA model and characterize the origami's properties (such as equilibrium shape and flexibili...
onlinelibrary.wiley.com
February 5, 2025 at 10:57 AM
🧬 A new tutorial article from our student Sarah, walking step by step through DNA origami simulation using oxDNA model, with the help of oxview.org and oxdna.org free tools. No prior experience assumed, and also accompanied by a video: youtu.be/5-rgMekX8gE
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
Reposted by oxDNA, oxRNA, oxNA
🧪 🧬 Can code be evolved? In our collaboration with S. Forrest group, we show that random "mutations" to the code, accepted if they pass unit tests, can actually find changes to CUDA version of oxDNA simulation tool for DNA nanotechnology that lead to a speedup:
doi.org/10.1145/3703...
doi.org/10.1145/3703...
Evolving to find optimizations humans miss: using evolutionary computation to improve GPU code for bioinformatics applications | ACM Transactions on Evolutionary Learning and Optimization
GPUs are used in many settings to accelerate large-scale scientific computation, including
simulation, computational biology, and molecular dynamics. However, optimizing codes
to run efficiently on GP...
doi.org
November 17, 2024 at 12:33 AM
🧪 🧬 Can code be evolved? In our collaboration with S. Forrest group, we show that random "mutations" to the code, accepted if they pass unit tests, can actually find changes to CUDA version of oxDNA simulation tool for DNA nanotechnology that lead to a speedup:
doi.org/10.1145/3703...
doi.org/10.1145/3703...