These were the experiments we were trying to explain: www.cell.com/cell-reports...

Low-affinity ligands of the epidermal growth factor receptor are long-range signal transmitters in collective cell migration of epithelial cells

Deguchi et al. find that low-affinity EGFR ligands propagate faster and farther than high-affinity ligands in epithelial cells. They demonstrate that EREG, a low-affinity ligand, contributes to skin w...

cell.com

Purushottam Dixit@pdixit.bsky.social · 2w ago

EGFR signaling breaks this tradeoff: low affinity ligands diffuse farther from the source (expected) but also lead to higher activity (unexpected).We show that kinetic proofreading combined with receptor/ligand degradation explains this phenomena. Work done in collaboration with an undergraduate!

Traditional models of paracrine gradients are constrained by a tradeoff driven by ligand-receptor affinity. High activity implies shorter spatial range and vice versa. Strong binders lead to higher signaling activity but also trigger receptor and ligand degradation and therefore shorter range.

bioRxiv Biophysics@biorxiv-biophys.bsky.social · 2w ago

Kinetic proofreading decouples signal strength and range in paracrine gradient formation https://www.biorxiv.org/content/10.64898/2026.07.17.739274v1

I will be talking about some recent work on using niche theory to model host associated microbiomes in a couple of hours!

International Initiative for Theoretical Ecology@iite-ecotheory.bsky.social · 4mo ago

📣Tomorrow! 📣Purushottam Dixit (Yale Engineering) will present: 'Niche dimensionality drives microbial community structure'

📣Tomorrow! 📣Purushottam Dixit (Yale Engineering) will present: 'Niche dimensionality drives microbial community structure'

How do cells know which way to move in a chemical gradient? 🧭 New work by graduate student Andrew Goetz proposes that receptors can compute direction. This new mechanism for directional sensing was published in PNAS late last year: www.pnas.org/doi/10.1073/...

What if aging isn’t just cellular damage, but a lossy transmission of information? We used single-cell data and physics-based models to show that as cells age, the flow of transcriptional information collapses. Here’s what that means. 👇

bioRxiv SysBio@biorxiv-sysbio.bsky.social · 9mo ago

Decay in transcriptional information flow is a hallmark of cellular aging https://www.biorxiv.org/content/10.1101/2025.10.30.685689v1

Just out: new preprint (with @ralitsamadsen.bsky.social) is now #Reviewed at @eLife! "Non-equilibrium strategies for ligand specificity in signaling networks". We show how cells use non-equilibrium strategies to discriminate between ligands in surprising ways 🔗 elifesciences.org/reviewed-pre...

We have a funding for postdoctoral fellowship that needs to be filled very soon. We are exploring new directions (1) at the interface of non-equilibrium computations and physical learning and (2) in building ecologically motivated machine learning models for microbiomes. Please spread the word!

Just learnt that our collaborative grant proposal on identifying master regulators of T cell metabolism in Lupus will not be reviewed as the study section was indefinitely postponed, along with many other grants that are vital to biomedical research.

Has anybody looked at approximate Bayesian computation (ABC) using stat mech? The formulation used in rejection ABC: rho(S(D),S(D')) < eps (rho is discrepancy function, S is a summary stat, D is data, D' is simulated data) looks an awful lot like the microcanonical ensemble with an energy = S(D).

Our work on computational design of microbiomes with desired host properties using mechanistic models is now out in mSystems: journals.asm.org/doi/10.1128/...

Designing host-associated microbiomes using the consumer/resource model | mSystems

Generative models are extremely popular in modern biology. They have been used to model the variation of protein sequences, entire genomes, and RNA sequencing profiles. Importantly, generative models ...

journals.asm.org

Happy to present our second paper on understanding ligand sensing using non-equilibrium reaction networks. Here, we look at some counterintuitive results on how eukaryotic cells sense extracellular spatial gradients in ligands (e.g. growth factors): www.biorxiv.org/content/10.1...

Receptor polarization through localized activity and global sensitization

Eukaryotic cells chemosense concentration gradients of extracellular ligands using membrane-bound receptors that polarize their activity. Receptors from several chemosensing families are preferentiall...

biorxiv.org

As my first post here, I am really excited to share a new manuscript with @ralitsamadsen.bsky.social on this platform. We looked how non-equilibrium thermodynamics helps ligand discrimination in signaling networks: t.co/ZA6NteUmaS