We explore fascinating phenomena at the interface of physics, biology, and nanotechnology at the University of Illinois.
Joined December 2019
- Tweets 94
- Following 84
- Followers 1,272
- Likes 105
13 Photos and videos
12 Nov 2024
Happy to see this out! Many thanks to Alan, Philip and the team!
8 Nov 2024
1/5 DNA and DNA/protein conformations at Ångström/millisecond resolution—right in a fluorescence microscope! Check out our new GETvNA paper in @naturemethods :
nature.com/articles/s41592-0…
Want to learn about the science behind GETvNA?
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12 Sep 2024
Great achievement from the Nivala lab! See also in News and Views:
"Thread, read, rewind, repeat: towards using nanopores for protein sequencing" nature.com/articles/d41586-0…
11 Sep 2024
Published today in @Nature, we describe an approach for single-molecule protein reading on @nanopore arrays. By utilizing ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieved single-amino-acid sensitivity. nature.com/articles/s41586-0…
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10 Sep 2024
The variation of the electric field around a DNA duplex is surprisingly complex. Now, a nonlocal electrostatic theory can explain most of the features seen in all-atom MD simulations. Many thanks to Alexei Kornyshev, @JonathanGHedley @KushCoshic and @LeverhulmeTrust
5 Sep 2024
A theoretical analysis of the complex electric field around DNA uncovers the origin of oscillating field patterns and sheds light on the role of the solvent that surrounds the DNA.
Read go.aps.org/47hR1Bn
@JonathanGHedley @KushCoshic @aksimentievLab
#PRXBio, #PRXChem
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AksimentievLab retweeted
30 Jul 2024
Thrilled to share new @NatureNano paper by @FabriniGiacomo introducing genetically encoded condensate-forming RNA nanostructures🧬
doi.org/10.1038/s41565-024-0…
..and the great companion @NatureComms paper by @DrJMStewart @FrancoLabUCLA @pwkrpwkr
doi.org/10.1038/s41467-024-5…
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9 Jul 2024
Have a nanopore but not happy with its ion selectivity or electroosmotic effect? You can easily improve both! Find out how: pubs.acs.org/doi/10.1021/acs…
Thanks to @WanunuLab and Zuzanna Siwy for this great collaboration. Congrats to Behzad on another cover!
#MyACSCover #nanopores
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5 Jun 2024
Well, this project went from "Which molecule moves faster through a nanopore?" to "What is speed? That is, the answer depends on whether you measure translocation speed in base pairs/sec or nm/sec. Many thanks to @Keyserlab and @FilipBoskovic12 for a wonderful collaboration.
3 Jun 2024
_1/n Honestly, it has been an incredible experience to scratch the surface of the physics behind our applied work! Building on the work of nanopore crew, we've uncovered some unexpected clues about the electrophoretic translocation of duplexes and how their form affects velocity!
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5 Jun 2024
Somewhere along the way, we observed a rare event: a nucleic acid duplex biting its own tail! Watch the movie to the end. The A-form RNA/DNA duplex was not so hungry:) #Ouroboros
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AksimentievLab retweeted
3 Jun 2024
In a study led by @FilipBoskovic12 we examined how the electrophoretic transport of RNA:DNA and DNA through nanopores depends on the contour length rather than the number of base pairs. Nice blend of experiments and simulations! @aksimentievLab @acsnano 🧬🕳️⚛️ @Cambridge_Uni
3 Jun 2024
_1/n Honestly, it has been an incredible experience to scratch the surface of the physics behind our applied work! Building on the work of nanopore crew, we've uncovered some unexpected clues about the electrophoretic translocation of duplexes and how their form affects velocity!
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24 May 2024
Many thanks for this collaborative project that has pushed out computational technology to the limit!
24 May 2024
Delighted to see @chalmerscccc work at the interface of nanopore sensing and cell biology published @NatureComms . Great team effort @RadfordLab @ericcells @aksimentievLab
nature.com/articles/s41467-0…
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10 May 2024
We missed you, Kush! @KushCoshic
10 May 2024
Thank you, Sarthak, for the hooding ceremony and for being such a fantastic student! @ksarthak71
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10 May 2024
Thank you, Sarthak, for the hooding ceremony and for being such a fantastic student! @ksarthak71
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9 May 2024
Congratulations to Hemani, our new Beckman Fellow!!!
8 May 2024
Absolutely thrilled to continue my scientific exploration with the amazing @aksimentievLab in collaboration with the Schroeder lab.
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16 Apr 2024
Congratulations to Emad @emadtaj, well deserved and overdue!
15 Apr 2024
Beckman honored three faculty and staff members who show visionary spirit and dedication. 🔶🔷
Emad Tajkhorshid (@emadtaj) won the faculty Vision and Spirit Award.
Teppie Peyton and Michael Marana won the inaugural Staff Spirit and Dedication Award.
▶️bit.ly/3Q2eGhY
ALT Headshots of Emad Tajkhorshid, Teppie Peyton and Michael Marana.
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16 Apr 2024
We are looking for postdoctoral researchers to work on the following topics: computational modeling of viruses and organelles, nanopore protein sequencing, DNA nanotechnology, and synthetic cell development. To apply, visit: my.physics.illinois.edu/subm…
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15 Apr 2024
Many thanks for hosting us!
15 Apr 2024
Prof. Aleksei Aksimentiev @aksimentievLab and Takuya Mabuchi @MabuchiGroup visited and gave excellent talks on MD simulations in our lab. Their presentations were impressive and stimulating.
We also had a great time enjoying a Tempura Soba lunch together!
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AksimentievLab retweeted
28 Mar 2024
It cannot be done, they said.. It's too flexible, they said.. 😁
biorxiv.org/content/10.1101/… #NPC #teamtomo #integrativemodeling by @dgvjayS @neeleshsoni03 @JoshHutchings94 @ig_ech et al. Great collaboration w/ Qiang Guo, Brian Chait, Javi Fernandez-Mtnz, @RoutLab_RU @salilab_ucsf
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20 Mar 2024
Such a beautiful cover!
19 Mar 2024
what a nice bonus:
@NatureNano put our image of a DNA nanoturbine on the front cover to feature our #CDlab paper by @xinshi_d et al: nature.com/articles/s41565-0…
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14 Mar 2024
In partnership with @Sci_Ani, we produced an animation that puts our recent work on genome packaging rdcu.be/dBaXM into a broader perspective. #dna #viruses #highperformancecomputing #tcbguiuc
13 Mar 2024
Unlocking the secrets of #viral genomes through computational microscopy offers new avenues for combating #infections. Supercomputers enable virtual reconstruction of virions, shedding light on their molecular programs.
bit.ly/3Vfz8PG
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6 Mar 2024
In our article published today @Nature , we report complete all-atom structural models of a fully packaged bacteriophage particle. Congratulations to Kush Coshic on his first publication! Many thanks to Chris Maffeo and David Winogradoff for pushing this 6-year project forward.
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6 Mar 2024
Multiple microsecond-long all-atom simulations characterized the effect of the packaged genome on capsid structure, internal pressure, electrostatics and diffusion of water, ions and DNA, and revealed the structural imprints of the capsid onto the genome.
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6 Mar 2024
The packaging process itself was found to occur via a loop-extrusion mechanism, resembling the mechanism implicated in large-scale organization of eucaryotic genomes.
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