Jonathan Doye

University Lecturer, Computational Chemical Physicist

[Jonathan Doye @JonathanDoye]

@DebnathGhosal @Vikram_Alva @OxfordChemistry @buse_isbilir @TBharat_lab @MRC_LMB @MPI_Bio Thanks! You might like this one. It's for a Micrarchaeum (https://t.co/BUSEEOSGY1). Of the SLPs that we've studied it is the closest homologue to that for the Micrarchaeota that you've been studying (https://t.co/s5XdCaKuGk).

[Jonathan Doye @JonathanDoye]

11/11 We can also apply our approach to other 2D protein lattices. Below is our prediction for the exosporium lattice that is part of the outer layer of spores of the pathogenic bacterium Clostridioides difficile.

[Jonathan Doye @JonathanDoye]

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
https://t.co/SbZqHfjrFc

[Jonathan Doye @JonathanDoye]

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.

[Petr Šulc @petr_sulc]

Our new model for DNA and RNA coarse-grained simulations is now out in @JChemPhys :
https://t.co/FapnoqG8ES
It is called #oxNA and includes @ox_DNA and #oxRNA models, and adds support for hybrid DNA:RNA duplexes:
🧵1/4

[Jonathan Doye @JonathanDoye]

And featured in a Scilight:
https://t.co/xZkCcZZWLJ

[Jonathan Doye @JonathanDoye]

Now out in @JChemPhys:
https://t.co/yqnBZd8A91

[Jonathan Doye @JonathanDoye]

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:
https://t.co/wDq8RUKM9q

[Jonathan Doye @JonathanDoye]

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:
https://t.co/wDq8RUKM9q

[Jonathan Doye @JonathanDoye]

Here's the physical copy of the book:

[Jonathan Doye @JonathanDoye]

This tutorial has now been published in the "DNA and RNA Origami: Methods and Protocols" volume of the Methods in Molecular Biology series:
https://t.co/cZyMEX8XNk

[oxDNA and oxRNA @ox_DNA]

A tutorial on how to run oxDNA simulations for DNA origami: https://t.co/KjfFACkfKM

[Jonathan Doye @JonathanDoye]

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:
https://t.co/mADN8YeLrA

[Jonathan Doye @JonathanDoye]

Now out in @PhysRevE:
https://t.co/k8DvwTdK7X

[Jonathan Doye @JonathanDoye]

A new preprint introducing Ian's work designing model reversible molecular mechanical logic gates and their incorporation into simple circuits:
https://t.co/ZkZ44IDdQc