Educational web app that explains the principles of microscopy and related topics. Made for my class at UTokyo, where I am teaching the Physics of Microscopy this semester to Physics undergrads. dbkk.github.io/optics-phys-...

OpticsPhysLab

An interactive browser lab for learning optics and microscopy.

dbkk.github.io

Hearts have topological defects. By treating the mouse myocardium as a 3D nematic, we found disclination lines threading through it. In situs inversus hearts, twist must match structural chirality for contraction to work, as found by quantifying the nematic chirality. biorxiv.org/content/10.6...

A paper with Takahiro Kanazawa and Kenta Ishimoto. We approached the question of why many organisms exhibit bilaterally symmetric swimming from the perspective of fluid dynamics. arxiv.org/abs/2603.08444

Hydrodynamic origins of symmetric swimming strategies

Efficient locomotion is important for the evolution of complex life, yet the physical principles selecting specific swimming strokes often remain entangled with biological constraints. In viscous flui...

arxiv.org

New manuscript with Rory Cerbus and Ichiro Hiratani. We analyzed 3D genome data from 247 species to investigate the determinants of the so-called large-scale structure known as compartments. www.biorxiv.org/content/10.6...

Excited to share that our proposal on animal structural colors has been accepted by HFSP. This one is close to my heart, sitting right at the intersection of our lab's diverse interests. So grateful to be working with the dream team: @evolphotonics.bsky.social and Chuong lab (USC)!

Vinod Saranathan, The Evolutionary Photonics Lab@evolphotonics.bsky.social · 5mo ago

Absolutely thrilled and humbled to announce our project proposal led by @kyogok.bsky.social, Cheng-Ming Chuong (@keck.usc.edu), and yours truly, has been awarded a RG. We look forward to integratively pushing the frontiers on the totally tubular physics and biology of animal structural colors.

Absolutely thrilled and humbled to announce our project proposal led by @kyogok.bsky.social, Cheng-Ming Chuong (@keck.usc.edu), and yours truly, has been awarded a RG. We look forward to integratively pushing the frontiers on the totally tubular physics and biology of animal structural colors.

Active quantum flocks Flocks of animals are an archetype of collective behavior in the macroscopic world. Here, we show that flocks can also form at the quantum level with unique quantum features: doi.org/10.1103/rd46... Novel nonequilibrium phase of matter realizable in #Rydberg atomic systems.

Modeling dissipation in quantum active matter https://arxiv.org/pdf/2511.21502 Alexander P. Antonov, Sangyun Lee, Benno Liebchen, Hartmut Löwen, Jannis Melles, Giovanna Morigi, Yehor Tuchkov, Michael te Vrugt.

Published in Science Advances! Looking forward to discussing the implications of our results and their applications with many researchers. www.science.org/doi/10.1126/...

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture

Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.

science.org

Yohsuke T. Fukai@fukaity.bsky.social · 2y ago

Thrilled to share our latest preprint on bioRxiv! 🎉 This collaboration with @kyogok.bsky.social and lab members, Kurumizaka lab(Kujirai-san in particular!) and Umehara lab sheds new light on how histone modification shapes chromatin architecture. 1/5 biorxiv.org/content/10.1...

To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture

Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.

science.org

I’ve released a tool to sketch and edit phylogenetic trees! yawak.jp/PhyloWeaver/ Load a Newick file and intuitively add/remove/resize branches. Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.

PhyloWeaver – Interactive phylogenetic tree editor

Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.

yawak.jp

Call for a research scientist position (indefinite-term) in our group. Deadline: October 15 www.riken.jp/en/careers/r...

Seeking a Research Scientist (Indefinite-term) at Nonequilibrium Physics of Living Matter Laboratory (25-1294)

riken.jp

Exciting new study from Iwasaki lab, led by Kotaro @ktomuro.bsky.social & Yuichi @u1-7no.bsky.social, that I was lucky to be part of! A new method reveals many mRNAs are locally translated. Too much for one tweet—check it out: www.biorxiv.org/content/10.1...

We developed APEX-Ribo-Seq, a method to map subcellular translation with spatial resolution. Using it, we profiled local translation in over 20 conditions!

bioRxivpreprint@biorxivpreprint.bsky.social · last yr.

Sequence grammar and dynamics of subcellular translation revealed by APEX-Ribo-Seq https://www.biorxiv.org/content/10.1101/2025.05.26.656194v1

Call for RIKEN ECL Team / Unit Leaders. In my (biased) opinion, this is probably the best option if you are seeking an independent position in Japan. I will be happy to chat/answer questions via email. www.riken.jp/en/careers/p...

FY 2025 Call for RIKEN ECL Team / Unit Leaders

riken.jp

www.riken.jp/en/careers/p...

FY 2025 Call for RIKEN ECL Team / Unit Leaders

riken.jp

This is a bizarre discovery by Kyosuke. He introduces an active binary mixture model and finds bubbles, typically found in very large MIPS simulations, appearing in smaller setups. Then observes that even the mean-field deterministic ver. of the model also produces bubbles. arxiv.org/abs/2505.08637

Bubble formation in active binary mixture model

Phase separation, the spontaneous segregation of density, is a ubiquitous phenomenon observed across diverse physical and biological systems. Within a crowd of self-propelled elements, active phase se...

arxiv.org

Congrats to our colleague Takahiro Kanazawa, who graduated with honors from U Tokyo Physics! www.s.u-tokyo.ac.jp/ja/info/10714/

令和6年度 総長賞・学修奨励賞・研究奨励賞 - 東京大学 大学院理学系研究科・理学部

東京大学 大学院理学系研究科・理学部の令和6年度 総長賞・学修奨励賞・研究奨励賞情報です。

s.u-tokyo.ac.jp

RIKEN SPDR fellowship, Register basic information by 5 pm April 3, 2025 (Japan Time). Application deadline 5 pm April 10, 2025 (Japan Time). Feel free to contact regarding this, or about opportunities in RIKEN and Japan in general.

Kyogo Kawaguchi@kyogok.bsky.social · 2y ago

We can host Special Postdoctoral Researchers (SPDR) for FY 2026. This is one of the best postdoc positions you can find in Japan, comparable to departmental or institutional fellowships in the US or Europe. Feel free to reach out if you’re interested! www.riken.jp/en/careers/p...

What is the multiscale structure of chromatin condensates? How does it shape thermodynamic and material properties? We address this at near-atomistic resolution🔥🔥🔥 using cryoET (Rosen & Villa labs, led by H Zhou), a new multiscale model (K Russell) and cryoET-guided sims (J Huertas & J Maristany)

Jan Huertas@janhuemar.bsky.social · 2y ago

Exciting new preprint alert! 🚨 The Collepardo lab, teaming up with Huabin Zhou and the Rosen lab we took a deep, high-resolution look into chromatin condensates! [1/6] #Chromatin #MD @rcollepardo.bsky.social @juliamaristany.bsky.social www.biorxiv.org/content/10.1...

Congratulations to Zihui, Sano-san, and the team on this interesting work! They found that +1 topological defects attract neural progenitors—an observation that seems at odds with expectations for an extensile active nematic. www.nature.com/articles/s41...

Integer topological defects offer a methodology to quantify and classify active cell monolayers - Nature Communications

The orientation of elongated cells often rotates once around the center in tissue. Such structures are called +1 topological defects and play some roles in biological development. By inducing various ...

nature.com

My @TEDAI2024 talk is out! www.ted.com/talks/surya_... I discuss our work, spanning AI, physics, math & neuroscience, to develop a deeper scientific understanding of intelligence, both to understand biological intelligence and make better artificial intelligence. I focus on 5 gaps:

Can AI match the human brain?

AI is evolving into a mysterious new form of intelligence — powerful yet flawed, capable of remarkable feats but still far from human-like reasoning and efficiency. To truly understand it and unlock i...

ted.com

Sequence Composition Dictates Condensate Miscibility https://www.biorxiv.org/content/10.1101/2024.11.29.626135v1

Sequence Composition Dictates Condensate Miscibility https://www.biorxiv.org/content/10.1101/2024.11.29.626135v1

Numerous biomolecular condensates coexist within cells, yet the mechanisms governing their mixing an

biorxiv.org

I feel like this post is becoming even more relevant for our early-career researcher friends in the US—unless it’s already too late. It doesn’t have to be our lab or RIKEN; if you’re interested in coming to Japan, I’m always happy to chat!

Kyogo Kawaguchi@kyogok.bsky.social · 2y ago

We can host Special Postdoctoral Researchers (SPDR) for FY 2026. This is one of the best postdoc positions you can find in Japan, comparable to departmental or institutional fellowships in the US or Europe. Feel free to reach out if you’re interested! www.riken.jp/en/careers/p...

Another of my favourite 2024 #NatRevMCB covers highlights our Review on #somitogenesis by Yuchuan Miao and Olivier Pourquie. We were inspired by the rows of forming somites that resemble rows of seat on a train or plane and their patterning by Hox genes! 🔗 go.nature.com/3Vx3psy

Happy to see this published! This work was led by Takahiro (a talented undergrad@UTokyo) and Kyosuke (a transdisciplinary theoretician@RIKEN). Dynamical phase transitions can occur even for an equilibrium Brownian motion if the dimension is larger than 4. journals.aps.org/prresearch/a...

Starting in April 2025, our RIKEN Hakubi Lab will transition to a Chief Scientist Lab, and we plan to move to Wako in 2026. My affiliation with the IPI, Department of Physics at The University of Tokyo, will continue as before.

Latest from the lab! I've been seeking the ultimate modulator that regulates the tempo of multiple developmental processes simultaneously, and metabolism has been an attractive candidate for such a global tempo modulator. However, I was wrong. 1/ www.nature.com/articles/s41...

Metabolic activities are selective modulators for individual segmentation clock processes - Nature Communications

Metabolism has been considered an attractive candidate as a global modulator of the tempo of multiple developmental processes, including somite segmentation timing. Here they demonstrate that metaboli...

nature.com

The sympathetic nervous system may control selective organs, but how this specificity is achieved is unknown. Our new study @NatureComms www.nature.com/articles/s41...　uncovers a parallel labeled-line organization within the lower thoracic spinal cord. 1/

Parallel labeled-line organization of sympathetic outflow for selective organ regulation in mice - Nature Communications

How individual organs are specifically regulated by the sympathetic neurons at the cellular level remains not fully understood. Here, authors identify two molecularly distinct sympathetic pathways tha...

nature.com

Thorough study comparing the vertebral formula of more than 388 tetrapod species. The relationship between Hox expression and vertebral identity is not trivial, specially in birds. www.pnas.org/doi/10.1073/...