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• Jain, Harish Pruthviraj; Ho, Richard David Jun-Geet & Angheluta, Luiza (2025). Emergent cell migration from cell shape deformations and T1 transitions. Physical Review Research (PRResearch). 7(3). doi: 10.1103/d6qj-775d. Full text in Research Archive Show summary

  T1 transitions—cell neighbor exchanges—are key drivers of tissue remodeling and fluidization in epithelial monolayers. Using a multiphase field (MPF) model that accounts for dynamic cell shapes, alongside an active elastic solid model lacking cell shape degrees of freedom, we study the spatiotemporal organization of T1 transitions. While individual T1 transitions occur as a Poisson process in time, their spatial distribution is strongly influenced by local cell shape deformations. We identify a dual mechanical response: cells losing neighbors tend to relax their shape isotropically, whereas cells gaining neighbors undergo anisotropic elongation. By analyzing successive T1 events in the MPF model, we find asymmetric spatial patterns that depend on whether a cell gains or loses neighbors. These asymmetries lead to persistent, localized directional motion, even in the absence of external cues. Our results suggest an intrinsic mechanism for directed cell migration driven by local topological rearrangements mediated by cell shape dynamics—a process potentially relevant for epithelial flows during development, morphogenesis, and wound healing.

• Ho, Richard David Jun-Geet; Mossige, Joachim; Ponomartcev, Sergei; Natalia, Smirnova,; Sunny, Dai, Keqing & Hu, Xian [Show all 9 contributors for this article] (2025). [2509.08929] Spontaneous elongation of 3D gastruloids from local cell polarity alignment. arXiv. doi: https:/arxiv.org/abs/2509.08929. Full text in Research Archive Show summary

  Gastruloids are 3D stem cell aggregate models for early embryogenesis that provide a unique platform to study how collective cell dynamics drive tissue symmetry breaking and axial elongation. Using 3D light sheet imaging, we show that a pulse of Chiron, a Wnt activator, induces coherent alignment of cell polarity during elongation. While nuclear elongation occurs with or without treatment, only Chiron-treated gastruloids exhibit quasi-long-range alignment of nuclear axes, linking cell polarity coherence to tissue-scale remodeling. A minimal physical model of polarized cells, incorporating alignment-dependent torques and polarity-mediated adhesion, reproduces symmetry breaking and elongation, demonstrating that local cell polarity alignment alone can drive tissue-scale convergence-extension flows.

• Ho, Richard David Jun-Geet; Bøe, Stig Ove; Dysthe, Dag Kristian & Angheluta, Luiza (2024). Role of tissue fluidization and topological defects in epithelial tubulogenesis. Physical Review Research (PRResearch). 6(2), p. 1–10. doi: 10.1103/PhysRevResearch.6.023315. Full text in Research Archive Show summary

  Cellular rearrangements, as primary sources of tissue fluidization, facilitate topological transitions during tissue morphogenesis. We study the role of intrinsic cell properties such as cell polarity and cell-cell adhesion in shaping epithelial tissues using a minimal model of interacting polarized cells. The presence of a vortex in the cell polarization poses the topological constraint that induces an inwards migration with the formation of a conical shape. Local rearrangements at the tip of the cone lead to the onset of tube formation. Switching between collective migration and structural rearrangements is key for balancing the contrasting tendencies, such as the tissue rigidity needed to preserve shape and the tissue fluidity allowing for topological transitions during tissue morphogenesis.

• Nahia, Karim Abu; Sulej, Agata; Migdał, Maciej; Ochocka, Natalia; Ho, Richard David Jun-Geet & Kamińska, Bożena [Show all 8 contributors for this article] (2024). scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation. iScience. 27(6). doi: 10.1016/j.isci.2024.110083. Full text in Research Archive Show summary

  We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. Two previously uncharacterized genes, atp1b3b and colec10, were found to be enriched in the sinoatrial cardiomyocytes. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate, implicating their role in cardiac development and conduction. Additionally, we describe other cardiac cell lineages, including the endothelial and neural cells, providing their expression profiles as a resource. Our results established a detailed atlas of the developing heart, providing valuable insights into cellular and molecular mechanisms, and pinpointed potential new players in heart rhythm regulation.

• Ho, Richard David Jun-Geet; Kishi, Kasumi; Majka, Maciej; Kicheva, Anna & Zagorski, Marcin (2024). Dynamics of morphogen source formation in a growing tissue. PLoS Computational Biology. ISSN 1553-734X. 20(10). doi: 10.1371/journal.pcbi.1012508. Full text in Research Archive Show summary

  A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.

• Ho, Richard David Jun-Geet; Clark, Daniel & Berera, Arjun (2024). Chaotic Measures as an Alternative to Spectral Measures for Analysing Turbulent Flow. Atmosphere. 15(9). doi: 10.3390/atmos15091053. Full text in Research Archive Show summary

  Turbulence has associated chaotic features. In the past couple of decades, there has been growing interest in the study of these features as an alternative means of understanding turbulent systems. Our own input to this effort is in contributing to the initial studies of chaos in Eulerian flow using direct numerical simulation (DNS). In this review, we discuss the progress achieved in the turbulence community in understanding chaotic measures including our own work. A central relation between turbulence and chaos is one by Ruelle that connects the maximum Lyapunov exponent and the Reynolds number. The first DNS studies, ours amongst them, in obtaining this relation have shown the viability of chaotic simulation studies of Eulerian flow. Such chaotic measures and associated simulation methodology provides an alternative means to probe turbulent flow. Building on this, we analyze the finite-time Lyapunov exponent (FTLE) and study its fluctuations; we find that chaotic measures could be quantified accurately even at small simulation box sizes where for comparative sizes spectral measures would be inconclusive. We further highlight applications of chaotic measures in analyzing phase transition behavior in turbulent flow and two-dimensional thin-layer turbulent systems. This work shows that chaotic measures are an excellent tool that can be used alongside spectral measures in studying turbulent flow.

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• Låstad, Silja Borring; Abbasova, Nigar; Ho, Richard David Jun-Geet; Combriat, Thomas Michel Daniel & Dysthe, Dag Kristian (2025). Segmentation-free measurement of cell motion from quantitative phase imaging. Full text in Research Archive

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