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Korak Ray @korakray.bsky.social · 23/09/2026

🚨Preprint news!!🚨 Using specifically purified mitotic chromosomes, we show that chromosome mechanics vary based on identity and cell type. Chromosomes from differentiated cells are more compact and stiffer, likely due to increased non-covalent crosslinks within them www.biorxiv.org/content/10.6...

biorxiv.org

Individual mouse mitotic chromosomes exhibit cell type-specific differences in biomechanical properties

Cyclic episodes of chromosome compaction and de-condensation are features of eukaryotic cell division that aid mitotic segregation and help prevent aneuploidy. While biophysical data on mitotic chromo...

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Reposted by Korak Ray

bioRxiv Biophysics @biorxiv-biophys.bsky.social · 28/08/2026

Extending conventional TIRF microscopy to image single molecules in micromolar analyte backgrounds www.biorxiv.org/content/10.64898/20…

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Benjamin Ambrose @single-mole.bsky.social · 01/07/2026

KymoSketch started out as a GUI for our kymotracker script, but after I added DeepDiffusion to it I got suggestions to add more features and it’s since become a more fleshed out analysis platform (1/6)

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Korak Ray @korakray.bsky.social · 30/06/2026

A huge thanks to all the co-authors of the preprint. We'd love to hear your thoughts on these tools. Feel free to reach out about applications and potential collaborations! (4/3)

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Korak Ray @korakray.bsky.social · 30/06/2026

DeepDiffusion is already integrated into KymoSketch, a browser-based analysis platform developed by @single-mole.bsky.social. No installation, no pipeline-building. Just open your browser and start analysing your kymographs! 🔗 KymoSketch: singlemoleculegroup.github.io/kymosketch-a... (3/3)

singlemoleculegroup.github.io

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Korak Ray @korakray.bsky.social · 30/06/2026

Single-molecule experiments reveal protein diffusion on DNA in remarkable detail, but detecting heterogeneous diffusion. has remained a major challenge. DeepDiffusion estimates instantaneous diffusion for a single-molecule trajectory with precision that existing methods cannot access. (2/3)

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Korak Ray @korakray.bsky.social · 18/06/2026

In particular, we show that ANKLE1 prefers cleaving stretched DNA near bubbles or ruptured junctions. This allows it to cleave a whole range of branched DNA substrates and forms the mechanistic basis for its role in processing any remaining chromosomal linkage in the cell during late mitosis. (3/3)

A range of DNA structures found within ultrafine bridges (Holliday junctions, replication forks, overstretched dsDNA, catenations) highlighting stretched junctions that can these structures that can be cleaved by ANKLE1

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Korak Ray @korakray.bsky.social · 18/06/2026

We show that ANKLE1 cuts faster as DNA tension increases. This is critical because when chromosomes are pulled apart, any remaining linkage is put under significant tension. This tension stimulates ANKLE1 activity, allowing it to process these bridges and allow cell divison to proceed. (2/3)

Plot showing increase linear increase in the log of cleavage rate with increasing tension

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Korak Ray @korakray.bsky.social · 18/06/2026

The first paper from my postdoc, looking at how tension activates DNA cleavage by the endonuclease ANKLE1, is out in @narjournal.bsky.social. ANKLE1 processes ultrafine bridges, persisting linkages between chromosomes that can lead to catastrophic DNA ruptures. (1/3) doi.org/10.1093/nar/...

Two panels showing ANKLE1 cleavage of DNA held between optically trapped beads. The left shows slow cleavage at low tension, and the right shows fast cleavage at high tension.

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Alexis Barr @alexisbarr.bsky.social · 21/05/2026

We're looking for a new Roving Research @mrc-lms.bsky.social A unique post for those who love research, learning new techniques & working across different teams. Must be a great communicator & well organised! Apply by 21 June: fa-evzn-saasfaukgovprod1.fa.ocs.oraclecloud.com/hcmUI/Candid...

fa-evzn-saasfaukgovprod1.fa.ocs.oraclecloud.com

Investigator Scientist Roving Researcher

Investigator Scientist (Roving Researcher) (LMS 2369) Salary £42,159 – 44,801 plus London Allowance (£5,560) per annum | 2 years fixed term | Full time | Closing Date: 21 June

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Quentin Smith @qmsmith.bsky.social · 25/03/2026

1/11 In our story out today in @nature.com , we showcase the molecular mechanisms that enable Cas9 to bind and cleave negatively supercoiled ((-)SC) off-targets! 🧬🧵 🔗 www.nature.com/articles/s41... #CRISPR #Cas9 #DNATopology #AFM #CryoEM #SingleMolecule #Biophysics

nature.com

Structural basis of supercoiling-induced CRISPR–Cas9 off-target activity - Nature

Cas9 structures explain topology sensing and off-target activation.

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Quentin Smith @qmsmith.bsky.social · 22/01/2026

🔬 Calling all early-career researchers (ECRs) for the GRS Single Molecule Approaches to Biology! 🌎 Location: Les Diablerets, Switzerland 📆 Save the date: June 27-28, 2026 🔗 More information: www.grc.org/single-molec... #biology #biophysics #single-molecule #microscopy #ECR

Visual advertisement providing details for the 2026 Single Molecule Approaches to Biology GRS in Les Diablerets, Switzerland in June 27-28, 2026. Two-day event for early-career single-molecule biophysicists, with a keynote session, 12 selected talks, 2 poster sessions, and mentorship component. For more information contact Alba or Quentin or see the official GRS website.

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Ruben Gonzalez @rubenlgonzalez.bsky.social · 05/01/2026

Slightly overdue article highlight! In PNAS, we use smFRET to reveal how polypeptide release factor 2 (RF2) undergoes a cascade of structural changes to catalyze polypeptide release during translation termination and ArfA-mediated ribosome rescue. 🧵⬇️ doi.org/10.1073/pnas...

Energy-landscape model of RF2 activation. Comparison of termination complexes (TC), wild-type ArfA-bound nonstop elongation complexes (nsECs), and loss-of-function ArfA mutant-bound nsECs reveals that wild-type ArfA promotes RF2 docking to nsECs by reshaping the conformational cascade.

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Korak Ray @korakray.bsky.social · 31/07/2025

A bit of good news! Part of my PhD work in collaboration with @ssjang.bsky.social and David Lynall is out in @narjournal.bsky.social! We uncover a surprising mechanism by which an ultrastable RNA stem-loop tunes its flexibility, enabling it to both fold rapidly and resist unfolding.

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Korak Ray @korakray.bsky.social · 10/06/2025

Congratulations, John! Great to see this out!

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Anita Meier @anitafmeier.bsky.social · 18/02/2025

Are you at #bps2025 and want to hear about: HSV-1 DNA replication, DNA looping, #smFRET, TIRF, optical tweezers or cryoEM? Come and talk to me at my poster B175 on Wed, 10.30am!

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MRC Laboratory of Medical Sciences @mrc-lms.bsky.social · 10/01/2025

Exciting new research from the Cellular Stress and Single Molecule Imaging groups has created a new technique for transfecting cells that could pave the way for new gene therapies! We'll be recapping some of the highlights from the article in this thread. 🧵1/6

sciencedirect.com

Precise intracellular uptake and endosomal release of diverse functional mRNA payloads via glutathione-responsive nanogels

We present a novel, highly customizable glutathione-responsive nanogel (NG) platform for efficient mRNA delivery with precise mRNA payload release con…

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Korak Ray @korakray.bsky.social · 10/02/2024

Also make sure you have the latest version of the software for your analysis needs. The software is always being updated. You can find the latest updates at the website gonzalezbiophysicslab.github.io/tmaven/ Also, please follow and take part in the discussions at github.com/GonzalezBiop...

github.com

GonzalezBiophysicsLab tmaven · Discussions

Explore the GitHub Discussions forum for GonzalezBiophysicsLab tmaven. Discuss code, ask questions & collaborate with the developer community.

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Korak Ray @korakray.bsky.social · 10/02/2024

tMAVEN, our open-source comprehensive platform for single-molecule data analysis, is finally here! Check out our article describing the platform and how we use it to investigate the use of kinetic models to extract mechanistic info from data, out in Biophys J. www.sciencedirect.com/science/arti...

sciencedirect.com

Increasing the accuracy of single-molecule data analysis using tMAVEN

Time-dependent single-molecule experiments contain rich kinetic information about the functional dynamics of biomolecules. A key step in extracting th…

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Reposted by Korak Ray

Mikko Jimenez @mikkojimenez.bsky.social · 23/10/2023

Spooky season reminder that, at its core, The Monster Mash is a cautionary tale about working in the lab late one night and, ultimately, the dangers of poor work/life balance under late capitalism.

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Korak Ray @korakray.bsky.social · 21/10/2023

That sounds really interesting and definitely something to try out. Thank you for the suggestion!

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Korak Ray @korakray.bsky.social · 20/10/2023

The meta-analysis is complicated because a) different software were historically used with other equipment that confound the software's effect. b) metadata on software in PDB files had inconsistent reporting. So, our analysis is purely descriptive. With those caveats in mind however, yes, there is

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Korak Ray @korakray.bsky.social · 20/10/2023

(6/6) Our method, which we call HARP, is open-source and freely available as a downloadable application which you can use to test the local resolution and map-to-model agreement of your favourite (or your own!) cryoEM structure! Give it a try! github.com/bayes-shape-...

github.com

GitHub - bayes-shape-calc/HARP: Hierarchical Atomic Resolution Perception

Hierarchical Atomic Resolution Perception. Contribute to bayes-shape-calc/HARP development by creating an account on GitHub.

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Korak Ray @korakray.bsky.social · 20/10/2023

(5/6) We also see how sensitive this framework is to local chemical changes, with specific amino acids that are known to appear distorted in cryoEM maps (Glu, Asp, Cys), showing lower levels of atomic information than similarly sized residues.

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Korak Ray @korakray.bsky.social · 20/10/2023

(4/6)...revealing, e.g., how the cryoEM resolution revolution has lead to increased atomic resolution over the years, and, surprisingly, a seasonal trend in atomic resolution (based on when structures are deposited in the PDB) that seems to correlate with the academic calendar.

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Korak Ray @korakray.bsky.social · 20/10/2023

(3/6) Comparison between the atomic and residue models in particular reveals the extent of local atomic resolution at individual residues. As expected, on average, this local atomic resolution measure correlates with the standard FSC resolution of maps, but yields richer info...

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Korak Ray @korakray.bsky.social · 20/10/2023

(2/6) We utilise the hierarchical nature of biomolecular structure to define models of cryoEM density at different structural levels, which can be used to select the level that agrees best with experimental data, revealing the extent of structural information present in the data.

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Korak Ray @korakray.bsky.social · 20/10/2023

🚨 Preprint news!! 🚨 The collaboration with @ckinzthompson on a novel definition of resolution and how it can be used to calculate the local atomic resolution and map-to-model correspondence in cryoEM structures is finally on bioRxiv!!!! www.biorxiv.org/content/10.1... 🧵(1/6)

biorxiv.org

Scale-dependent hierarchical resolution: applications to atomic resolution and model validation in c...

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Korak Ray @korakray.bsky.social · 20/10/2023

github.com

GitHub - bayes-shape-calc/HARP: Hierarchical Atomic Resolution Perception

Hierarchical Atomic Resolution Perception. Contribute to bayes-shape-calc/HARP development by creating an account on GitHub.

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Korak Ray @korakray.bsky.social · 20/10/2023

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Korak Ray @korakray.bsky.social · 20/10/2023

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Korak Ray @korakray.bsky.social · 20/10/2023

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Korak Ray @korakray.bsky.social · 20/10/2023

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C&EN (Chemical & Engineering News) @cenmag.bsky.social · 04/10/2023

BREAKING NEWS: Three scientists have won the 2023 #NobelPrize in Chemistry for their research on the discovery and synthesis of quantum dots. Moungi G. Bawendi, Louis E. Brus and Alexei I. Ekimov share prize for research that added color to nanotechnology: cen.acs.org/people/nobel...

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