University Lecturer, Computational Chemical Physicist
Oxford
Joined October 2013
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I am excited to share our new preprint on the structure of S-layers. The work is a collaboration between @OxfordChemistry (Ed Johnston and myself) and @buse_isbilir and @TBharat_lab at @MRC_LMB and @Vikram_Alva at @MPI_Bio. 🧵 1/11
biorxiv.org/content/10.1101/…
10/11 By contrast S-layers in bacteria are a part of a more complex cell envelope architecture and play a less critical structural role. The different types of S-layers represent local islands in sequence space that have arisen through multiple independent evolutionary events.
Jonathan Doye retweeted
Our new model for DNA and RNA coarse-grained simulations is now out in @JChemPhys :
doi.org/10.1063/5.0199558
It is called #oxNA and includes @ox_DNA and #oxRNA models, and adds support for hybrid DNA:RNA duplexes:
🧵1/4
Now out in @JChemPhys:
doi.org/10.1063/5.0199558
This preprint introduces a new member of the @ox_DNA family of coarse-grained nucleic acid models that allows RNA-DNA hybrids to be modelled:
doi.org/10.48550/arXiv.2311.…
This preprint introduces a new member of the @ox_DNA family of coarse-grained nucleic acid models that allows RNA-DNA hybrids to be modelled:
doi.org/10.48550/arXiv.2311.…
This tutorial has now been published in the "DNA and RNA Origami: Methods and Protocols" volume of the Methods in Molecular Biology series:
doi.org/10.1007/978-1-0716-3…
And here is a follow-on preprint analysing some of the challenges in creating larger circuits from these molecular mechanical logic gates, particularly considering the effects on reversibility:
doi.org/10.48550/arXiv.2306.…
Now out in @PhysRevE:
doi.org/10.1103/PhysRevE.107…
A new preprint introducing Ian's work designing model reversible molecular mechanical logic gates and their incorporation into simple circuits:
arxiv.org/abs/2205.01563
Jonathan Doye retweeted
Some folks asked for more info on this work. Thanks! It pictures molecules (or other structures) as objects built out of smaller components, and asks how much information is necessary to describe the assembly process for a given structure. 1/
It doesn't connect with related work in the way that science often does. In 2010 we published a complexity measure that explicitly quantifies the simplest possible assembly process needed to build a molecule journals.aps.org/pre/abstrac… (preprint arxiv.org/abs/0912.3464). 6/
