Deepak Gupta

Researcher in Statistical Physics.

[Noneq Lab (Tohoku) @TohokuBiophys]

How biological motors achieve maximum efficiency https://t.co/JME6UZl747 via @physorg_com

[Deepak Gupta @PhyDeepak]

Thrilled to see our collaborative work out in @PhysRevLett. @APSphysics @AvHStiftung @SFU @guptadeepak.bsky.social @TohokuBiophys @DavidASivak

[Noneq Lab (Tohoku) @TohokuBiophys]

Our new PRL paper was featured in Physics Magazine by APS. It was a joyful and stimulating collaboration with @DavidASivak group.
https://t.co/9X39uHKsgX
How a Molecular Motor Minimizes Energy Waste
https://t.co/zOX3TAsljc

[Deepak Gupta @PhyDeepak]

Check out our recent work on Thermodynamic Cost of Recurrent Erasure published in @CommsPhys (https://t.co/f0o7FE7KN5)! Fantastic collaboration with
@KristianSOlsen (@HHU_de), and SupriyaK (@Stockholm_Uni). @SoftNordita #research @AvHStiftung

[Deepak Gupta @PhyDeepak]

Check out our recent work showing how environmental fluctuations let biodiversity beat the resource count, with peak diversity at intermediate competition. @_dzanc @SamirSuweis @DFAUnipd @LIPh_Lab @AvHStiftung @tuberlin.bsky.social

[PRX Life @PRX_Life]

A path-integral solution of consumer-resource models shows that #SpeciesDiversity peaks when competitors moderately outnumber resources but collapses when they far exceed them, echoing #biodiversity patterns in real #ecosystems.

Read the paper: https://t.co/kr51072xwi

[Ricard Solé @ricard_sole]

Do ant colonies work like liquid brains? Check this great paper in @pnas, led by @ceabcsic Pol Fernandez-Lopez and @fredbartu, explaining foraging behaviour by modelling ants as mobile neural agents @JordiPinero
https://t.co/Jfshzowq55

[Niko McCarty. @NikoMcCarty]

I’ve always been interested in the stories behind BioNumbers.

Textbooks say DNA polymerase, for example, replicates 220 nucleotides per second. But how do we know this? How can one actually measure the speed of a single enzyme?

A fast typist, for comparison, types ~80 words per minute or ~5-7 characters per second. This means that DNA polymerase (in this case, from T7 phage) “types” letters 30-40 times faster than a skilled typist.

Measuring the speed of a single enzyme is not so simple. In this case, one cannot simply time how long it takes for a cell to divide, say, and then divide that time by the cell's genome length to arrive at an estimate of DNA polymerase speeds. That is because division rates are not bottlenecked by DNA division times, and bacterial cells initiate multiple rounds of DNA replication on their genomes simultaneously.

Therefore, we need another way. Ideally, there would be a “single molecule” way to observe DNA replication happening without relying upon highly indirect measurements. In 2006, a group of Harvard biochemists figured out a way to do exactly that.

Before explaining their experiment, though, it’s important to note that these biochemists took advantage of length differences between single-stranded and double-stranded DNA. Double-stranded DNA has a rigid, helical structure (which we learn about in school) and, therefore, also a consistent length of about 0.34 nanometers per base pair.

Single-stranded DNA, for comparison, is far more flexible and disordered. It doesn’t have stabilizing hydrogen bonds like double-stranded DNA does, so it tends to coil and collapse on itself. Under experimental conditions, and outside of cells, single-stranded DNA has a short length of only about 0.03 nanometers per nucleotide.

Now, here’s how this experiment worked:

First, the researchers took a long, single-stranded thread of DNA and stretched it between a glass surface and a tiny bead, floating in liquid.

Next, they added a short piece of DNA, called a primer, which latched onto the DNA near the glass surface. This gave the enzyme a starting point to begin copying DNA.

Then, they added the T7 DNA polymerase to the liquid. As the enzyme added new nucleotides, it turned the single-stranded DNA into stiff, double-stranded DNA. The DNA began to uncoil and stretch out. And since one end was fixed to the glass and the other to the bead, the bead slowly moved as the DNA extended.

Finally, the researchers watched this movement using a microscope and camera. By tracking the bead’s movements, and measuring its distance further and further from the glass slide, they figured out that polymerase was copying about 220 nucleotides of DNA per second. From this experiment, the researchers could ALSO see that the DNA polymerase enzyme moves in "bursts;" it doesn't copy DNA continuously.

This is just one “Behind the BioNumbers” experiments that I really enjoy. I’ll plan to write more about these in the future if you enjoy them.

[Matt Leighton @MattLeighton5]

Now out in @AnnualReviews of Physical Chemistry: @DavidASivak and I review recent work studying flows of free energy into, out of, and within molecular machines. These nanoscale protein machines convert energy within cells of all living organisms with remarkable efficiencies.

[Deepak Gupta @PhyDeepak]

Our article on Stochastic Resetting, in collaboration with @arnab_non_eqm (@IMScChennai ) and A. Kundu (@ictstifr), has been selected in the JSTAT 20th Anniversary Retrospective collection. @IOPscience #Physics. @LIPh_Lab @DFAUnipd https://t.co/DGRbOW8HVI

[Arnab Pal @arnab_non_eqm]

JSTAT, on its 20th anniversary, has published a spl issue showcasing influential articles since their inception. Our work on Resetting was selected as one of them, moment to cherish. Here's the entire collection: https://t.co/UvOcsbxCri
@IMScChennai
@PhysicsNews @ictstifr

[Ryota IINO 飯野亮太 @ryotaiino]

Akihiro's paper on ATP synthesis of V-ATPase has been published online in @jbiolchem!
We verified that V-ATPase, which functions as active ion pump in the cell, has intrinsic functional reversibility and high thermodynamic efficiency of energy conversion!
https://t.co/Iizlw9UD3x

[Lab of Interdisciplinary Physics @LIPh_Lab]

Check out our latest research! We apply the framework of annealed disorder to ecological modeling 👇

[Deepak Gupta @PhyDeepak]

Our 3-year #research journey has culminated in a #publication in @softmatter, "Dynamics of switching processes: general results and applications to intermittent active motion," is now out. Grateful to co-authors @KristianSOlsen @ionfeeldcharge #Physics
https://t.co/hlMuwHYHfF

[Anjali Sharma - @anjalisharma.bsky.social @anjali_physics]

Science outreach is fun! Thank you! @FnrLux @uni_lu @ESMP_unilu

[Justus Wilhelm Fink @justuswfink]

Why are there so many fitness metrics in microbial ecology? I was confused - with @Michael_Manhart , I developed a framework that unifies existing statistics of relative fitness and shows how they all derive from a few basic principles. Preprint is up! https://t.co/eDFACDlJCP

[Physical Review Research @PhysRevResearch]

Thermodynamic cost of finite-time stochastic resetting, Kristian Stølevik Olsen, Deepak Gupta, Francesco Mori, and Supriya Krishnamurthy @PhyDeepak, @frnc_mori, @KristianSOlsen, @HHU_de, @Stockholm_Uni, @OxfordPhysics @NorditaSweden #StatisticalPhysics https://t.co/8uMxairNAt

[Deepak Gupta @PhyDeepak]

Much-awaited work on the cost of finite-time stochastic reset is now published in the @PhysRevResearch! 🎉 Fantastic collaboration with @KristianSOlsen (@HHU_de), @frnc_mori (@OxfordPhysics), and SupriyaK (@Stockholm_Uni). @SoftNordita #physicsresearch https://t.co/VU7R6kLsAL

[Lab of Interdisciplinary Physics @LIPh_Lab]

💡Research from the lab was just published in Physical Review Letters! Our own Sandro Azaele and Amos Maritan study non-Gaussian disorder in dynamical systems, with applications to ecological modelling: https://t.co/OcnQhri8b3

[ICC @ICC]

𝗜𝗡𝗗𝗜𝗔 𝗔𝗥𝗘 #𝗧𝟮𝟬𝗪𝗼𝗿𝗹𝗱𝗖𝘂𝗽 𝟮𝟬𝟮𝟰 𝗖𝗛𝗔𝗠��𝗜𝗢𝗡𝗦 🏆

Jasprit Bumrah's heroics propels 🇮🇳 to clinch a humdinger in Barbados and create history 👏

#T20WorldCup | #SAvIND | 📝: https://t.co/LlDSkjClGn

[ICC @ICC]

The wait of 17 years comes to an end 🇮🇳

India win their second #T20WorldCup trophy 🏆

[ICC @ICC]

Emotion. Elation. Joy. 🇮🇳😍

#T20WorldCup | #SAvIND

[Valerio Scarani @ValerioScarani]

Fluctuation relations beyond physics: my group's latest numerical experiment finds Crooks in the UNO card game!
https://t.co/jXs0Wn7T03
(Aka what happens when you let your students be creative)