Bioprocess Engineering Lab · Kajita Group

Presented at IIBMP2026, the Annual Meeting of the Japanese Society for Bioinformatics

Wed, 26 Aug 2026 00:00:00 +0000

A second-year master’s student presented a poster at IIBMP2026, the Annual Meeting of the Japanese Society for Bioinformatics (Sagamihara, 26–28 August 2026).

JSPS KAKENHI Grant-in-Aid for Scientific Research (B) awarded (FY2026–2029)

Wed, 01 Apr 2026 00:00:00 +0000

Kajita’s project on mitochondrial ordering by active thermodynamic forces and the optimization of the intracellular ATP distribution received a JSPS KAKENHI Grant-in-Aid for Scientific Research (B) (26K00674, April 2026 – March 2030).

Hosted the Fukui Caravan 2025 of the Japanese Society for Quantitative Biology

Sat, 22 Nov 2025 00:00:00 +0000

We hosted the Fukui Caravan 2025 of the Japanese Society for Quantitative Biology at the University of Fukui, Bunkyo Campus.

Wrote a column for the Encyclopedia of Theoretical Biology

Sat, 01 Nov 2025 00:00:00 +0000

Kajita wrote Column 11, “T cell activation,” in Chapter 6 (Medicine) of Riron Seibutsugaku Jiten [Encyclopedia of Theoretical Biology], edited by Iwasa Y, Ohtsuki H, Satake A, and Mochizuki A (Asakura Publishing, 2025; in Japanese).

Presented at the Oxford-Japan Symposium on Cell Behaviors

Tue, 23 Sep 2025 00:00:00 +0000

Kajita presented “Active thermodynamic force-driven mitochondrial alignment” at the Oxford-Japan Symposium on Cell Behaviors in Simple to Complex Environments.

Presented at the 64th Annual Conference of the Japanese Society for Medical and Biological Engineering

Thu, 05 Jun 2025 00:00:00 +0000

Kajita presented work on how mitochondria control their own arrangement in cells at the 64th Annual Conference of the Japanese Society for Medical and Biological Engineering.

Takeda Science Foundation Life Science Research Grant awarded (FY2025–2029)

Sun, 01 Jun 2025 00:00:00 +0000

Kajita’s project using language models to study how the diversity of immune repertoires is controlled received a Takeda Science Foundation Life Science Research Grant (June 2025 – March 2030).

Joined a JSPS KAKENHI Grant-in-Aid for Scientific Research (C) as co-investigator (FY2025–2028)

Tue, 01 Apr 2025 00:00:00 +0000

Kajita joined a project funded by a JSPS KAKENHI Grant-in-Aid for Scientific Research (C) as a co-investigator (April 2025 – March 2029; principal investigator: Akihiko Sakurai). The project studies the biosynthetic pathway of cordycepin, an adenosine analog produced by Cordyceps.

Gave an invited talk at the 1st India-Japan Workshop on Physical Aspects of Living Systems

Fri, 21 Feb 2025 00:00:00 +0000

Kajita gave an invited talk, “Active thermodynamic force-driven mitochondrial alignment,” at the 1st India-Japan Workshop on Physical Aspects of Living Systems.

Paper published in Physical Review Research (mitochondrial alignment)

Mon, 29 Apr 2024 00:00:00 +0000

The paper “Active thermodynamic force driven mitochondrial alignment” was published as a Letter in Physical Review Research 6, L022024 (2024). doi:10.1103/PhysRevResearch.6.L022024

We showed theoretically that ATP production and ATP-dependent non-directional movement of mitochondria are sufficient for their nearly regular alignment, even without an explicit repulsive force between them or any internal states or memory of the mitochondria.

Organized the 11th Annual Meeting of the Japanese Society for Quantitative Biology

Sat, 06 Jan 2024 00:00:00 +0000

We organized the 11th Annual Meeting of the Japanese Society for Quantitative Biology at the Institute of Industrial Science, the University of Tokyo (6–7 January 2024), and also presented a poster.

Presented at the 7th area meeting of "Information Physics of Living Matters"

Thu, 21 Sep 2023 00:00:00 +0000

Kajita presented work on how mitochondria form equally spaced patterns in neuronal axons at the 7th area meeting (21–22 September 2023, Toki Messe Niigata Convention Center) of the Grant-in-Aid for Scientific Research on Innovative Areas “Information Physics of Living Matters” (area number 8104).

Presented at the 2023 Annual Meeting of the Japanese Society for Mathematical Biology

Wed, 06 Sep 2023 00:00:00 +0000

At the 2023 Annual Meeting of the Japanese Society for Mathematical Biology, Kajita presented work on how an effective repulsion arising from active thermodynamic forces moves and arranges intracellular organelles. A second-year master’s student also presented a poster.

Presented at the Life Science Innovation Center research meeting (FY2023), University of Fukui

Tue, 22 Aug 2023 00:00:00 +0000

Kajita presented work on the alignment of intracellular organelles by an effective repulsion arising from active thermodynamic forces at the research exchange meeting of the Life Science Innovation Center, University of Fukui. A second-year master’s student also gave a talk.

Poster presented at CoPhEE2023

Sat, 12 Aug 2023 00:00:00 +0000

Kajita presented the poster “Active thermodynamic force driven mitochondrial alignment” at Collective Phenomena in complex systems: problems inspired by Ecology and Evolution (CoPhEE2023).

Poster presented at STATPHYS28

Mon, 07 Aug 2023 00:00:00 +0000

Kajita presented the poster “Noise-induced receptor clustering as a functional role of noise for reducing errors in target ligand detection” at the 28th International Conference on Statistical Physics (STATPHYS28).

Preprint posted on arXiv (mitochondrial alignment)

Tue, 09 May 2023 00:00:00 +0000

The preprint “Active thermodynamic force driven mitochondrial alignment” was posted on arXiv. arXiv:2305.05553

It was later published as a Letter in Physical Review Research 6, L022024 (2024). doi:10.1103/PhysRevResearch.6.L022024 (news)

The work is also described on the Research page.

Presented at the 2023 Spring Meeting of the Physical Society of Japan

Sat, 25 Mar 2023 00:00:00 +0000

Kajita presented work on the movement of intracellular organelles driven by entropic forces at the 2023 Spring Meeting of the Physical Society of Japan.

Presented at the 7th Workshop on Theoretical Immunology

Tue, 21 Mar 2023 00:00:00 +0000

Kajita presented work on estimating disease progression from patients’ gene expression data, and its applications, at the 7th Workshop on Theoretical Immunology.

Presented posters at the 10th Annual Meeting of the Japanese Society for Quantitative Biology

Thu, 15 Dec 2022 00:00:00 +0000

At the 10th Annual Meeting of the Japanese Society for Quantitative Biology, Kajita presented a poster on a mathematical model of the spatial dynamics of transcription. A second-year master’s student also presented a poster.

Paper published in npj Systems Biology and Applications (CML treatment response)

Thu, 13 Oct 2022 00:00:00 +0000

The paper “Early dynamics of chronic myeloid leukemia on nilotinib predicts deep molecular response” was published in npj Systems Biology and Applications 8, 39 (2022). doi:10.1038/s41540-022-00248-3

Patients with different responses to nilotinib could be classified by parameters of a simple dynamical model estimated from two routinely measured laboratory values. Data from only three initial time points identified, with high accuracy, patients who failed to reach the treatment goal.

Paper published in Cancers

Thu, 22 Sep 2022 00:00:00 +0000

The paper “Time-series clustering of single-cell trajectories in collective cell migration” was published in Cancers 14 (19), 4587 (2022). doi:10.3390/cancers14194587

This is joint work with the group of Satoshi Fujita in our department. Cells that had undergone epithelial–mesenchymal transition were cultured together with cells that had not, and their collective migration on fibrous scaffolds was recorded by time-lapse microscopy. From these movies we extracted the trajectory of each cell and presented a method that uses time-series clustering to group cells with similar migration patterns. The same cluster contained both epithelial and mesenchymal cells, and how cells were grouped was related to their location and to cell division.

Presented at a workshop at the 94th Annual Meeting of the Genetics Society of Japan

Thu, 15 Sep 2022 00:00:00 +0000

In a workshop at the 94th Annual Meeting of the Genetics Society of Japan, Kajita presented on how to start mathematical and data-science research in the life and medical sciences.

Presented at the Life Science Innovation Center research meeting (FY2022), University of Fukui

Wed, 24 Aug 2022 00:00:00 +0000

Kajita presented work on inferring biological networks from multivariate data with machine learning at the research exchange meeting of the Life Science Innovation Center, University of Fukui.

Presented at the 6th Workshop on Theoretical Immunology

Mon, 14 Mar 2022 00:00:00 +0000

Kajita presented work on early, patient-specific prediction of treatment response in chronic myeloid leukemia from disease dynamics at the 6th Workshop on Theoretical Immunology.

Paper published in Molecular and Cellular Neuroscience (mitochondria in axons)

Fri, 04 Feb 2022 00:00:00 +0000

The paper “Intermitochondrial signaling regulates the uniform distribution of stationary mitochondria in axons” was published in Molecular and Cellular Neuroscience 119, 103704 (2022). doi:10.1016/j.mcn.2022.103704

Stationary mitochondria were observed to be distributed relatively uniformly along axons. Local inactivation of mitochondria by light reduced the motility of nearby mitochondria, suggesting that functional mitochondria enhance the motility of other mitochondria in their vicinity. A mathematical model showed that the ATP gradient generated by mitochondria and ATP-dependent regulation of their motility can produce a uniform distribution. The work was a collaboration with experimentalists; Kajita developed the model.

Presented at the 39th Chromosome Workshop

Wed, 22 Dec 2021 00:00:00 +0000

At the 39th Chromosome Workshop and the 20th Nuclear Dynamics Meeting, Kajita presented work on combining a mathematical model of RNA polymerase II movement along genes with experimental data.

Gave an invited talk at the Life Science Innovation Center research meeting (FY2021), University of Fukui

Tue, 21 Sep 2021 00:00:00 +0000

Kajita gave an invited talk on data-driven mathematical modeling of disease dynamics toward personalized medicine at the research exchange meeting of the Life Science Innovation Center, University of Fukui.

Presented at the 2021 Annual Meeting of the Japanese Society for Mathematical Biology

Mon, 13 Sep 2021 00:00:00 +0000

Kajita presented a mathematical model of the spatial distribution of mitochondria in axons at the 2021 Annual Meeting of the Japanese Society for Mathematical Biology.

Presented at the joint Moonshot projects workshop

Fri, 13 Aug 2021 00:00:00 +0000

Kajita presented a mathematical approach to immune and neural functions arising from changes in intracellular localization at the joint workshop of the Aihara and Murakami Moonshot projects.

JSPS KAKENHI Grant-in-Aid for Early-Career Scientists awarded (FY2021–2025)

Thu, 01 Apr 2021 00:00:00 +0000

Kajita’s project on a cell-differentiation model based on the dynamics of transcriptional enzymes along genes, and on testing it against measured data, received a JSPS KAKENHI Grant-in-Aid for Early-Career Scientists (April 2021 – March 2026).

Preprint posted on bioRxiv (CML treatment response)

Wed, 17 Feb 2021 00:00:00 +0000

The preprint “Early dynamics of chronic myeloid leukemia on nilotinib predicts deep molecular response” was posted on bioRxiv. doi:10.1101/2021.02.17.431221

It was later published in npj Systems Biology and Applications 8, 39 (2022). doi:10.1038/s41540-022-00248-3 (news)

Paper published in JRNAL

Wed, 20 May 2020 00:00:00 +0000

The paper “An error correction mechanism for reliable chemical communication systems” was published in the Journal of Robotics, Networking and Artificial Life 7 (1), 52–57 (2020). doi:10.2991/jrnal.k.200512.011

Moved to the University of Fukui

Sun, 01 Mar 2020 00:00:00 +0000

Kajita moved from the Institute of Industrial Science, the University of Tokyo, to the University of Fukui as an assistant professor in the Department of Applied Chemistry and Biotechnology, Faculty of Engineering.

Paper published in Chaos (ligand detection by receptor clusters)

Fri, 24 Jan 2020 00:00:00 +0000

The paper “Reliable target ligand detection by noise-induced receptor cluster formation” was published in Chaos 30 (1), 011104 (2020). doi:10.1063/1.5140714

Although intracellular reactions are stochastic, cells detect target molecules reliably among many similar molecules. We showed that, through ligand-induced stochastic clustering of receptors, noise can enhance both sensitivity and specificity. The effect arises when the target ligand promotes the cooperative reaction by which a cluster recruits receptors. Detection performance is maintained as nontarget ligands increase if the noise intensity is adjusted.

Review published in Seisan Kenkyu (antigen discrimination by T cells)

Sat, 30 Mar 2019 00:00:00 +0000

The review “Quantitative biology of ligand discrimination by immune T cells” was published in Seisan Kenkyu 71 (2), 125–132 (2019) (in Japanese). doi:10.11188/seisankenkyu.71.125

Using our work on antigen discrimination as an example, it describes how hypotheses built on quantitative data and mathematical models have helped explain immune phenomena.

Paper published in Physical Review E (zero-order ultraspecificity)

Fri, 14 Jul 2017 00:00:00 +0000

The paper “Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity” was published in Physical Review E 96, 012405 (2017). doi:10.1103/PhysRevE.96.012405

To distinguish target ligands from many structurally similar nontarget ligands, cells must amplify small differences in affinity. In multistep kinetic proofreading, higher specificity comes at the cost of sensitivity and speed. We showed that combining kinetic proofreading with amplification by saturated zero-order reactions (zero-order ultraspecificity) balances specificity, sensitivity, and speed with few steps. An extension of the model also adds insensitivity to large amounts of nontarget ligands.

Review published in Biophysics (antigen discrimination by T cells)

Thu, 26 Mar 2015 00:00:00 +0000

The review “Experimental and theoretical bases for mechanisms of antigen discrimination by T cells” was published in Biophysics 11, 85–92 (2015). doi:10.2142/biophysics.11.85

It reviews experimental and theoretical work on antigen discrimination by T cells, focusing on four properties: specificity, sensitivity, speed, and concentration compensation.