Artemy Kolchinsky

A remarkable preprint that shows emergence of active protocells from simple starting conditions

If you work on the origins of life / prebiotic chemistry, consider joining OoLEN 🧬🌍

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#OriginOfLife

Launch of new Canada Impact+ Research Training Awards As announced in Budget 2025 -

Interested in the intersection of nonequilibrium thermodynamics and biophysics? Think Canada might be a nice place for your PhD/postdoc? Talk to me! Brand-new funding opportunity has quick deadline (so likely undersubscribed). nserc-crsng.canada.ca/en/news/laun...
SFU internal deadline Feb 11

Nucleation - Wikipedia

Yes, its possible to have local maxima of entropy. Supercooled water is one example, as are other phase transitions that require a "nucleation" event. en.wikipedia.org/wiki/Nucleat...

"Choosing problems is the primary determinant of what one accomplishes in science."
'Now What?' by Nobel Laureate John Hopfield should be required reading for aspiring scientists.
pni.princeton.edu/document/1136

Thermodynamic Geometric Constraint on the Spectrum of Markov Rate Matrices A thermodynamic constraint is placed on the spectrum of Markov rate matrices, allowing for a better understanding of the dynamics of biochemical clocks.

New paper in PRL on the relationship between thermodynamic driving and eigenvalues in Markovian master equations. We prove a weaker version of a beautiful conjecture proposed by Uhl and Seifert. Led by Guo-Hua Xu, with Jean-Charles Delvenne and Sosuke Ito
journals.aps.org/prl/abstract...

Cooperation is a universal feature of complex systems, from the origins of life and microbiomes to societies. What universal patterns can be found in these systems? Here's our new @pnas.org paper. @jordipinero.bsky.social @artemyte.bsky.social @sfiscience.bsky.social www.pnas.org/doi/epdf/10....

The characterization of life as a thermodynamic phenomenon out of equilibrium is usually attributed to Schrödinger.

What if I told you that he wasn't the first (not even the second😶‍🌫️) to reach that famous and influential conclusion?/1

#complexitycat🐈‍⬛

amahury.github.io/posts/reinve...

Philosophical Transactions of the Royal Society B: Biological Sciences: Vol 380, No 1936

It's part of a great special issue on fundamental constraints on the origins of life, organized by
@ricardsole.bsky.social and Chris Kempes royalsocietypublishing.org/toc/rstb/202...

After a long time in the making, my paper on nonequilibrium thermodynamics of Darwinian evolution has been published in Philosophical Transactions B. Updated version: arxiv.org/abs/2112.02809

Philosophical Transactions of the Royal Society B: Biological Sciences: Vol 380, No 1936

How dit life originate in our planet? How can we create it in the lab?Our @royalsocietypublishing.org Theme Issue "Origins of Life: the possible and the actual", coedited with @sfiscience.bsky.social C Kempes and Susan Stepney is out! royalsocietypublishing.org/toc/rstb/202... @manlius.bsky.social

Possible biosignatures detected on Mars
www.nature.com/articles/d41...

Modern aspects of Markov chains: entropy, curvature and the cutoff phenomenon The cutoff phenomenon is an abrupt transition from out of equilibrium to equilibrium undergone by certain Markov processes in the limit where the size of the state space tends to infinity: instead of ...

Reading this beautiful review of the "cutoff timescale" in Markov chains, the timescale over which a system relaxes from nonequilibrium to equilibrium behavior arxiv.org/abs/2508.21055

Center for the Alignment of AI Alignment Centers We align the aligners

This new center strikes the right tone in approaching the AI alignment problem. alignmentalignment.ai

Can a single cell learn? Even without a brain, some microbes show simple forms of cognition. Can this basal cognition be engineered? Check our new paper with @jordiplam.bsky.social on the minimal synthetic circuits & their cognitive limits. @drmichaellevin.bsky.social www.biorxiv.org/content/10.1...

Kyoto Workshop on Quantum Thermodynamics and Stochastic Thermodynamics 2025 Schedule and VenueDecember 8-12, 2025 Panasonic Auditorium, Yukawa Hall, YITP, Kyoto University, JapanScopeRecent advances in physics have increasingly highlighted the need to understand energy conver...

Helping to organize this workshop on quantum and stochastic thermodynamics in Kyoto, Japan, Dec 8-12. Resource theory, optimal transport, and more. Submissions open!

indico.yukawa.kyoto-u.ac.jp/event/68/

Physics of Life: Exploring Information as a Distinctive Feature of Living Systems Living systems are defined by their active acquisition and use of information. This Roadmap surveys current research on life's information processes and their importance for the search for life beyond...

Here is our new paper that we're really excited about. What makes a cell different from a rock? The answer we argue is the USE of information. But information carries meaning and that changes everything if we want to understand the "physics of life".

journals.aps.org/prxlife/abst...

Proud of this preprint with my friends Jonathan Bauermann and @artemyte.bsky.social, about chemical oscillators & phase separation! Main findings:
1. Phase separation controls frequency and amplitude of oscillations
2. If reactions are fast, spirals of droplets emerge!

arxiv.org/abs/2507.16030

How can we build a general theory of mutualistic communities? After five years, we finally completed a new Neutral Theory of Cooperation that is fully solved analytically and displays remarkable properties @jordipinero.bsky.social @artemyte.bsky.social @manlius.bsky.social arxiv.org/abs/2506.09737

We have a new preprint about measuring entropy production in high-dimensional systems, using ideas from information geometry. We successfully infer EP from brain recordings and spin models containing 1000+ degrees of freedom. With
@maguilera.net and Sosuke Ito arxiv.org/abs/2505.10444

How can physics contribute to understanding the evolution of complexity? Although great results have been produced over the last decades, some recent "theories" appear to ignore key ideas from evolutionary theory and are seriously flawed. Check this paper in PNAS www.pnas.org/doi/abs/10.1...

I suspect something like this may be possible, but not give very useful bounds for real organisms. The information gained by a death or replication seems independent from the energy dissipated in creating that organisms, i.e. whether it is a single replicating molecule or a whale

If anyone in the complex systems/computational neuroscience field in Europe is looking to poach an American scientist, I'm interested in what might be out there.
My scholar profile: scholar.google.com/citations?hl...

Joint European Thermodynamics Conference, May 26-30, Belgrade, Serbia. Honored to participate in a mini-symposium on stochastic thermo alongside Sarah Loos and Cai Dieball, and other sessions look fascinating. Abstracts due March 15. www.mi.sanu.ac.rs/JETC2025

TIL that scipost.org publishes several high quality physics journals, all open-access and without any publication fees. Maybe its one way to move beyond the current nightmare of academic publishing....

Maximizing Free Energy Gain Maximizing the amount of work harvested from an environment is important for a wide variety of biological and technological processes, from energy-harvesting processes such as photosynthesis to energy storage systems such as fuels and batteries. Here, we consider the maximization of free energy—and by extension, the maximum extractable work—that can be gained by a classical or quantum system that undergoes driving by its environment. We consider how the free energy gain depends on the initial state of the system while also accounting for the cost of preparing the system. We provide simple necessary and sufficient conditions for increasing the gain of free energy by varying the initial state. We also derive simple formulae that relate the free energy gained using the optimal initial state rather than another suboptimal initial state. Finally, we demonstrate that the problem of finding the optimal initial state may have two distinct regimes, one easy and...

How do systems—biological or technological—maximize energy harvested from their environments? A new study explores how the initial state of a system impacts free energy gain and extractable work and illustrates the findings through a simple information-engine model. https://doi.org/10.3390/e27

Between 2019 and 2023, researchers paid $8.968 billion to make papers open access. Imagine what else could be done with this money if it wasnt paid to for profit publishing companies...
👉 arxiv.org/abs/2407.16551

C'est moi 🍔

Can we design ecosystems? Can synthetic biology help unravel ecological complexity?
In this work, we define the scales of synthetic ecosystems: from test tube to the biosphere. With @ricardsole.bsky.social @jordiplam.bsky.social Dani Amor & Núria Conde. Plus, we got the front cover shorturl.at/1KHe1