Mukund Thattai

@thattai.bsky.social

593 Followers 235 Following

Physicist fascinated by biology, trying to understand how cells work. Also: public engagement, science and culture, puzzles.

Image with three candles. Top: one flame at the end, caption: "How I should be doing it". Middle: flames at both ends, caption: "What the doctor advised against". Bottom: Multiple flames, caption: "Current situation".
Figure showing how cells can synthesise multiple glycan trees simultaneously. A: Examples of two real glycan trees. B: Example reaction pathway to synthesise a desired glycan tree, including off-pathway reactions which lead to errors. C: Abstract setting showing three trees whose synthesis must be simultaneously optimised using a Pareto-optimality framework.
Left: Cellular organelles (nodes) and vesicle traffic flows (edges) represented as a directed graph. Colors represent molecular labels, a type of information. Right: a functional molecule is localized to a specific organelle, due to interactions with labels. The underlying network changes while the funtional molecule remains correctly localized throughout, an example of representational drift in cell biology.
Feynman's handwritten notes from a Thai restaurant, formulating and solving his "Restaurant Problem", preserved by his colleague Ralph Leighton.
Cover of "Evolutionary Cell Biology", a textbook by Michael Lynch.
Internal membranes in the Asgard archaeon Y. umbracryptum. Image credit: MacLeod et al., 2025, An Asgard archaeon with internal membrane compartments.
EM images showing how ESCRT-III proteins from Asgard archaea can tubulate membranes. Image credit: Souza et al., 2025, Asgard archaea reveal the conserved principles of ESCRT-­ III membrane remodeling.
Eukaryotic signature proteins in Asgard archaeal genomes. These include proteins annotated as being involved in "Trafficking" and "Endosomal sorting". Image credit: Eme et al., 2023, Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.
Phases of eukaryote evolution, starting from the archaean-bacterial symbiosis, via a proto-eukaryotic stage with internalized mitochondria and an endomembrane (the nuclear envelope), to the last eukaryotic common ancestor (LECA) which is as complex as a modern protist, with multiple endomembrane compartments exchanging vesicles. Image credit: Thattai, 2023, Molecular and cellular constraints on vesicle traffic evolution.
Archaeal and bacterial contributions to modern eukaryotes. Image credit: Tobiasson et al., 2026, Dominant contribution of Asgard archaea to eukaryogenesis.
Prometheoarchaeum syntrophicum cells, showing surface protrusions. Image credit: Imachi et al., 2020, Isolation of an archaeon at the prokaryote–eukaryote interface.
Inside-out model for the origin of eukaryotes. Image credit: Baum & Baum, 2014, An inside-out origin for the eukaryotic cell.
A robotic submarine at Loki's Castle, near a hydrothermal vent.
Diagram showing the history of different classes of eukaryotic genes. Some are bacterial in origin, some are archaeal in origin. Image credit: Baum & Spang, 2023, On the origin of the nucleus: a hypothesis.
Photograph of Carl Woese. Image credit: IGB.
Photograph of Lynn Margulis on the day of her wedding to Carl Sagan.
Abstract of "The Concept of a Bacterium" by Stanier and van Niel, 1967, where the terms "eukaryotes" and "prokaryotes" were formalized.
Sahana (right) and Kritika (left) who drove the project.
Four directed graphs, whose nodes are compartments (proto-endoplasmic reticulum, plasma membrane, and other intracellular compartments) and whose edges are vesicle flows. The network includes flows that resemble phagocytosis, secretion, and receptor recycling.
Evolutionary landscape of endomembrane systems. Each node is a "motif" representing the functional complexity of the underlying systems. Each edge is a possible transition. At the bottom is the simple proto-eukaryotic starting point. At top are the most complex systems, which are evolutionary endpoints.
A series of endomembrane systems, represented as directed graphs where nodes are compartments, vesicle flows are edges, and compositions are represented by colors. Each graph can transition to the next through basic evolutionary moves: gene duplication, deletion, and simple mutations.
Table with 6 columns. Col 1: Number of coats. Col 2: Number of compartments and edges. Col 3: Number of graphs tested, going up to 25 billion. Cols 4-6: The number of graphs consistent with molecular rules only number in the thousands.
Evolutionary landscape of endomembrane systems. On top are two possible endomembrane systems, represented as directed graphs (pER: proto-endoplasmic reticulum; PM: plasma membrane; IC: intracellular compartment). In the layer below, endomembrane graphs are represented as nodes (white dots) connected by evolutionarily viable transitions (red lines). Collectively these dots and lines define an evolutionary landscape. The landscape breaks up into less functional (left) and more functional (right) endomembrane systems, introducing a selective bias.
Representation of spherical harmonics as lobed objects, indexed by l, m.
Diagram showing Asgard ESP homologs involved in the generation of tubular membrane carriers in modern eukaryotes. The left panel lists sequential stages of carrier generation: initiation, cargo loading, tubulation, scission, tethering, and fusion, with associated protein complexes such as Arf GTPases, BAR domain proteins, ESCRTs, and SNAREs. The right panel shows a stylized eukaryotic cell, indicating sites where tubular carriers are found in present-day eukaryotes (ER exit site, endosome/TGN, plasma membrane).
AlphaFold-based structural alignments of Asgard archaeal (red) and eukaryotic (blue) homologs of membrane trafficking proteins. Shown are COPII component Sec24, TRAPP subunit TRAPPC3, AP2 μ and σ subunits, ESCRTIII protein CHMP1B, retromer component VPS29, BAR domain protein Arfaptin, and CORVET/HOPS subunit VPS16. Each pair except CORVET/HOPS show strong structural similarity despite the evolutionary distance.
A simplified evolutionary tree showing how eukaryotes arose from a merger between Asgard archaea (green) and α-proteobacteria (brown). Key nodes include LUCA (last universal common ancestor), FECA (archaeal first eukaryotic common ancestor), FMCA (first mitochondrial common ancestor) and LECA (last eukaryotic common ancestor). The mitochondrial endosymbiosis event is highlighted.
A schematic showing two models for the evolution of the eukaryotic cell plan starting from an archaeal ancestor. The "inside-out" and "outside-in" models both lead to an intermediate stage with internal and plasma membranes connected by tubules. The sequence continues through the formation of an endomembrane lumen, followed by the emergence of membrane contact sites and tubular carriers, and finally coated vesicles and stable compartments.
The solution to the puzzle involves modifying paths in an Nx3 array of squares. First, replace each diagonal step with a special point to its top left. Then associate a minus sign with every edge below that point. The first three columns correspond to X, Y, Z. The image shows examples of this transformation, with the original path on the left and the modified path on the right. Below the modified path is the coordinate of a specific cube in the octahedron, e.g. X-2Z is one positive step in the X direction and two negative steps in the Z direction. The path endpoints correspond to the specific "layer" of each cube in the octahedron (0 is the central cube, and 1, 2, 3 are successive layers). This construction clearly generalises to more dimensions (more columns to the right) and more layers (more rows on top).
Sketch of T. Rex and references to papers regarding possible use of forelimbs. Caption: "My secret hypothesis: Tyrannosaurus Rex had a pouch in which it carried its young. Can you think of ways to test this? Let me know!"
Photo of Jawaharlal Nehru and MIT President James Killian, 1949. Courtesy of the MIT Museum.
Ranu Boppana and Mukund Thattai, with other visitors at the exhibit.
Photo of Jawaharlal Nehru and MIT President James Killian, 1949. Courtesy of the MIT Museum.
Raj Rewal, Untitled Work, circa 1965, coloured ink on paper.
Clam shell with a pattern that resembles a map of continents around the Indian ocean.
Session information text - Light Years in Lines: How Science Speaks. Annapurni Subramaniam, Anil Ananthaswamy, Simon Singh, Venki Ramakrishnan, with Mukund Thattai. Sunday 15 December 4:45 PM. Waterfront, Lalit Ashok. Free Entry. blrlitfest.org.
Participants listen to a lecture on expansion microscopy
Extract from KITP's Fall 2024 Newsletter
Letter from Carl Sagan dated December 5, 1995.