Ken Halvorsen

We mostly just got rid of all the stuff we didn’t need from a standard gel setup. Turns out you don’t need >200 mL of running buffer, or >100 V between electrodes, or >$1k to spend on a gel box – you just need a 3D printer and a different design. How satisfying!

With a range of designs, we resolved on/off nanoswitches in ~1 minute at 75 volts or in ~45 minutes at 8 volts. We also showed that we could image the gel with a cell phone camera, LED flashlight, and filter paper...

One huge advantage of smaller box is the same voltage gives a larger electric field (closer electrodes), enabling either lower voltage operation or faster separation at the same voltage. 3D printing allowed us to quickly test various inter-electrode distances...

Side note for those interested in electrophoresis – this design is cheap and easy! Prints in <1 hour on a dual-extruder printer for ~30 cents of material (>1000x less than any gel box from lab supply stores). We also printed replacement gel combs which performed identically to the $50+ combs...

Postdoc Lifeng Zhou 3D printed mini boxes and added wire electrodes with early encouraging results that we could eliminate much of the gel apparatus. Later Andrew Hayden found conductive filament, and 3D printed the whole gel box with electrodes. It works as well as our conventional gel system!

It started because: 1) we noticed that typical gel equipment was overkill for our application, and 2) we heard criticisms that DNA nanoswitch sensing could never become “point of care” due to reliance on electrophoresis. This combined two passions - design minimalism and proving critics wrong :)

This dates to ~2019 - we asked whether we could redesign gel electrophoresis to better suit our DNA nanoswitch sensors (which shift migration based on molecular detection). We ended up with a fully 3D printed mini-gel costing ~30 cents, operable with batteries, and capable of detection in minutes…

images of a conventional gel box and 3D printed mini boxes with resulting gel band images

I'm very excited about this new preprint on our work (www.biorxiv.org/content/10.6...). We re-engineered gel electrophoresis for our DNA-base biosensors and came up with a 3D printed mini-gel, complete with electrodes. short thread...

New preprint from our lab, really exited about this one and may post more about it later this weekend

Light‐Guided Molecular Patterning for High‐Throughput Single‐Molecule Mechanical Characterization A light-guided molecular patterning method is presented for high-throughput single-molecule characterization. The approach enables scalable and accessible molecular patterning without specialized lit...

Our light guided molecular patterning method for high-throughput single-molecule studies just published today in Small! Programmable, covalent, multiplexed, accessible.
doi.org/10.1002/smll...

A lot of fun to "get the band back together" so to speak. I realized it's my first "first author" paper in about a decade :)

What better way to start the year then with a deep dive into multiplexed force spectroscopy? It was a lot of fun putting this together with @halvorsenlab.bsky.social. Hope you check it out!

We've got ISSUES. Literally.

We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?

arxiv.org/abs/2601.07563

A 🧵 1/n

We have a PDF on our lab website if people have access limitations here (though I think it's supposed to be open access).

www.halvorsenlab.com/publications

We discuss the history and landscape of multiplexed single-molecule force spectroscopy, including developments in instrumentation, molecular tools, surface chemistry, and analytical methods. We explore emerging applications and outline challenges and opportunities in this evolving field...

Beyond the Single Molecule: Multiplexed Methods in Force Spectroscopy Single-molecule techniques have transformed biological research by enabling direct observation and manipulation of individual molecules. These methods overcome ensemble averaging inherent in bulk meas...

Starting the new year with a review article! (with @wesleywonglab.bsky.social) This feels like a pretty big accomplishment. I remember how much I relied on annual reviews as a grad student to dive into a subject, so its surreal to be on the other side...

www.annualreviews.org/content/jour...

suspect a big reason why many academics and others who work in areas where getting facts RIGHT is key are disinterested in using LLMs for research:

they’ve tried it, they keep noticing major errors in output, and they conclude that having to verify all that doesn’t actually save them time.

thx, looks like the same issue here. I'll reach out to the MIRA staff after the holidays.

I may be reading this wrong, but there seems to be conflict between the PAR-26-121 instructions and new biosketch instructions. In particular the "contributions to science" which MIRA calls for with citations and new biosketch which doesn't allow citations. Anybody resolved this yet?

imagining a NSF PO handing a VC bro the stack of 10-to-15 proposals they'll have to be ready to discuss, then explaining that they'll be paid $600 for the three days of the panel meeting

Oh wow great, thanks for sharing - been waiting with some anxiety for this

‘A huge rupture in everything’: US science faced major upheaval in 2025 Amid enormous shifts, many scientists pushed back and risked dismissal from their jobs even as federal agencies fired thousands of employees

Excited to be featured in this @cenmag.bsky.social piece with @standupforscience.bsky.social friend @jeremymberg.bsky.social

❤️✊

cen.acs.org/policy/nih-n...

large crates packed with science equipment

Christmas came early! New science toy from @lumicks.bsky.social for @thernainstitute.bsky.social - very excited to get this all set up and operational.

Investigating Polarity Effects in DNA Base Stacking Nucleic acid structures are stabilized by both base pairing and base stacking. While energetics of base pairing interactions are relatively well established, our understanding of the energetic contributions of base stacking remain incomplete. Here, we use a combination of single-molecule and computational biophysics approaches to investigate the effect of strand polarity on base-stacking energetics. We designed pairs of DNA constructs with reversed stacking polarities at nick sites, along with corresponding no-stack controls to isolate stacking contributions. Performing single-molecule force-clamp assays with a Centrifuge Force Microscope (CFM), we observed polarity-dependent differences in stacking energetics. These differences were most pronounced in purine–purine and certain purine–pyrimidine interactions. Notably, a 5′ purine stacked on a 3′ pyrimidine was generally more stable than the reverse polarity. We employed molecular dynamics (MD) simulations to observe stacking interfaces in the DNA constructs. The simulations were qualitatively consistent with our experiments, and showed positional differences between opposite polarity stacking pairs, giving some insight into the origin of these polarity differences. Overall, these results demonstrate that base polarity can modulate stacking stability and should be considered when designing short duplex regions such as overhangs in molecular biology and biotechnology applications.

Our latest lab paper (and last for @jibinpunnoose.bsky.social) is out! We look at strand polarity in base stacking interactions, with single-molecule measurements and MD simulations with collaborators in Chen and Vangaveti labs @thernainstitute.bsky.social pubs.acs.org/doi/10.1021/...

Figure 1 from a paper published in Nature (linked in post). The figure purports to be an infographic depiction of the "Overall working of the framework" for 'explainably' diagnosing autism spectrum disorder. The infographic is plainly nonsense, containing many spelling errors, nonsense words, meaningless images and graphs. Clearly created using generative AI and (crucially) NEVER CHECKED AT ANY STEP OF THE WRITING OR PUBLICATION PROCESS.

Hey @nature.com, have you got an explanation for how the hell THIS happened? & especially why you accepted a paper with such a bizarre piece of genAI slop in it?!
& more to the point, why we should take you seriously at all going forward?
www.nature.com/articles/s41...

Dang, hard disagree. The best papers to write and read are works of art, not merely a list of data and statements.

Don’t let LLMs take this away too, for gods sake.

This is sad...we should allow some fun and levity in our papers. That was a great intro...

Gov. Hochul Announces $50M Life Sciences Expansion for RNA Institute research The Life Sciences Research Building, which is home to cutting-edge labs where researchers from the RNA Institute blend bench science with AI to help accelerate the development of RNA-based treatments ...

ICYMI: #UAlbany's Life Sciences Research Building will get a $50M state-funded expansion to support The RNA Institute.

The funding will advance the Institute's research, training & workforce development, including its use of AI to guide drug discovery.
www.albany.edu/news-center/...

And importantly to celebrate your compliance lol

November Ballot Measure: Prop 1 Proposal 1 would officially authorize that use while securing thousands of acres of new protected land in return.

This is the best plain description I've seen adk.org/november-bal...