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Kyogo Kawaguchi

@kyogok.bsky.social
303 followers 449 following 30 posts

Chief Scientist RIKEN PRI, Assoc Prof Univ Tokyo Department of Physics, Institute for Physics of Intelligence. Biophysics, noneq statphys. noneq-biophys.riken.jp

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Kyogo Kawaguchi @kyogok.bsky.social · 09/07/2026
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-...
dbkk.github.io
OpticsPhysLab
An interactive browser lab for learning optics and microscopy.
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Kyogo Kawaguchi @kyogok.bsky.social · 18/04/2026
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...
biorxiv.org
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Kyogo Kawaguchi @kyogok.bsky.social · 13/04/2026
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
arxiv.org
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...
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Kyogo Kawaguchi @kyogok.bsky.social · 13/04/2026
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...
biorxiv.org
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Kyogo Kawaguchi @kyogok.bsky.social · 21/03/2026
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)!
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Vinod Saranathan, The Evolutionary Photonics Lab @evolphotonics.bsky.social · 21/03/2026
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.
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Heyl Group @heylgroup.bsky.social · 15/12/2025
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.
doi.org
Active Quantum Flocks
Flocks of animals represent a prominent archetype of collective behavior in the macroscopic classical world, where the constituents, such as birds, concertedly perform motions and actions as if being ...
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arXiv bot (quant-ph) @krxiv-quant-ph.bsky.social · 27/11/2025
Modeling dissipation in quantum active matter arxiv.org/pdf/2511.21502 Alexander P. Antonov, Sangyun Lee, Benno Liebchen, Hartmut Löwen, Jannis Melles, Giovanna Morigi, Yehor Tuchkov, Michael te Vrugt.
arxiv.org
https://arxiv.org/abs/2511.21502
arXiv abstract link
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Yohsuke T. Fukai @fukaity.bsky.social · 20/11/2025
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/...
science.org
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.
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Kyogo Kawaguchi @kyogok.bsky.social · 20/11/2025
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/...
science.org
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.
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Yawako @yawaguchi.bsky.social · 18/11/2025
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.
yawak.jp
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.
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Kyogo Kawaguchi @kyogok.bsky.social · 08/09/2025
Call for a research scientist position (indefinite-term) in our group. Deadline: October 15 www.riken.jp/en/careers/r...
riken.jp
Seeking a Research Scientist (Indefinite-term) at Nonequilibrium Physics of Living Matter Laboratory (25-1294)
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Kyogo Kawaguchi @kyogok.bsky.social · 05/06/2025
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...
biorxiv.org
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Kotaro TOMURO @ktomuro.bsky.social · 30/05/2025
We developed APEX-Ribo-Seq, a method to map subcellular translation with spatial resolution. Using it, we profiled local translation in over 20 conditions!
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Kyogo Kawaguchi @kyogok.bsky.social · 23/05/2025
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...
riken.jp
FY 2025 Call for RIKEN ECL Team / Unit Leaders
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Kyogo Kawaguchi @kyogok.bsky.social · 20/05/2025
www.riken.jp/en/careers/p...
riken.jp
FY 2025 Call for RIKEN ECL Team / Unit Leaders
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Kyogo Kawaguchi @kyogok.bsky.social · 15/05/2025
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
arxiv.org
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...
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Kyogo Kawaguchi @kyogok.bsky.social · 28/03/2025
Congrats to our colleague Takahiro Kanazawa, who graduated with honors from U Tokyo Physics! www.s.u-tokyo.ac.jp/ja/info/10714/
s.u-tokyo.ac.jp
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。
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Kyogo Kawaguchi @kyogok.bsky.social · 20/03/2025
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.
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Rosana Collepardo @rcollepardo.bsky.social · 23/01/2025
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)
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Kyogo Kawaguchi @kyogok.bsky.social · 13/03/2025
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...
nature.com
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 ...
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Surya Ganguli @suryaganguli.bsky.social · 07/02/2025
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:
ted.com
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...
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bioRxivpreprint @biorxivpreprint.bsky.social · 01/12/2024
Sequence Composition Dictates Condensate Miscibility www.biorxiv.org/content/10.1101/202…
biorxiv.org
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
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Kyogo Kawaguchi @kyogok.bsky.social · 14/02/2025
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!
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Lisa Heinke @lisaheinke.bsky.social · 10/12/2024
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
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Kyogo Kawaguchi @kyogok.bsky.social · 06/02/2025
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...
journals.aps.org
Universality in the dynamical phase transitions of Brownian motion
We study the dynamical phase transitions (DPTs) appearing for a single Brownian particle without drift. We first explore how first-order DPTs in large deviations can be found even for a single Brownia...
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Kyogo Kawaguchi @kyogok.bsky.social · 04/02/2025
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.
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Miki Ebisuya @ebisuyamiki.bsky.social · 24/01/2025
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...
nature.com
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...
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Kazunari Miyamichi @k-miyamichi.bsky.social · 10/12/2024
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/
nature.com
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...
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Jorge Lázaro @jorgelazaro.bsky.social · 21/11/2024
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/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 30/11/2024
We are seeking a motivated postdoc to join our lab!  Our research focuses on live-cell imaging/analysis to reveal how chromatin behaves in living cells and how its behavior contributes to cellular functions. www.nature.com/articles/s41... www.science.org/doi/10.1126/... Interested? Please DM me!
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Kyogo Kawaguchi @kyogok.bsky.social · 27/11/2024
And our new preprint! "Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture", biorxiv (2024). Led by Yohsuke T Fukai, in collaboration with Kurumizaka lab (U Tokyo) and Umehara lab (RIKEN BDR). www.biorxiv.org/content/10.1...
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Kyogo Kawaguchi @kyogok.bsky.social · 27/11/2024
Recent collaboration: "A Percolation Model of Emergence: Analyzing Transformers Trained on a Formal Language", arXiv:2408.12578 (2024). With Ekdeep Lubana, Robert Dick, and Hidenori Tanaka. arxiv.org/abs/2408.12578
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Kyogo Kawaguchi @kyogok.bsky.social · 26/11/2024
Recent work from our group: "Activity-induced ferromagnetism in one-dimensional quantum many-body systems", Phys. Rev. Research 6, 023096 (2024). With Kazuaki Takasan and Kyosuke Adachi. doi.org/10.1103/Phys...
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Kyogo Kawaguchi @kyogok.bsky.social · 26/11/2024
Recent work from our group: "Dynamical phase transitions in single particle Brownian motion without drift", arXiv:2407.18282 (2014), with Takahiro Kanazawa and Kyosuke Adachi. arxiv.org/abs/2407.18282
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Kyogo Kawaguchi @kyogok.bsky.social · 26/11/2024
Recent work from our group: "Predicting Heteropolymer Interactions: Demixing and Hypermixing of Disordered Protein Sequences", Physical Review X 14, 4902 (2024), with Kyosuke Adachi. doi.org/10.1103/Phys...
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Kyogo Kawaguchi @kyogok.bsky.social · 21/11/2024
Work with Rory Cerbus and Ichiro Hiratani @RIKEN_BDR (no account yet?) out in @PNASNews (not yet?), regarding the new patterns we found in vertebral counts across tetrapods and their relation to Hox cluster sequences. Enjoy! www.pnas.org/doi/10.1073/...
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Kyogo Kawaguchi @kyogok.bsky.social · 20/11/2024
Dear fellow nonequilibrium beings a.k.a. vertebrates on Bluesky, We are a group of (mainly) physicists studying everything interesting in biology. Happy to seek this new platform!
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