Sreejith SanthoshI am a PhD student at the Serra Group, part of the Department of Physics at University of California San Diego, where I work on Dynamical Systems Theory, Biophysics and Developemental Biology. My PhD advisor is Mattia Serra. I have a B.Tech in Engineering Physics from Indian Institute of Technology Madras, where I worked on Active Matter Theory in Sumesh Thampi's lab. I also blog about science, books, movies and personal experiences. |
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ResearchI'm interested in Developemental Biology, Biophysics and Dynamical Systems Theory. |
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A mechanochemical model recapitulates distinct vertebrate gastrulation modesM. Serra , G. S. Najera, M. Chuai, A. Plum, Sreejith Santhosh , V. Spandan, C. J. Weijer, L. Mahadevan Science Advances, 2023 link / free access link / During vertebrate gastrulation, an embryo transforms from a layer of epithelial cells into a multilayered gastrula. This process requires the coordinated movements of hundreds to tens of thousands of cells, depending on the organism. In the chick embryo, patterns of actomyosin cables spanning several cells drive coordinated tissue flows. Here, we derive a minimal theoretical framework that couples actomyosin activity to global tissue flows. Our model predicts the onset and development of gastrulation flows in normal and experimentally perturbed chick embryos, mimicking different gastrulation modes as an active stress instability. Varying initial conditions and a parameter associated with active cell ingression, our model recapitulates distinct vertebrate gastrulation morphologies, consistent with recently published experiments in the chick embryo. Altogether, our results show how changes in the patterning of critical cell behaviors associated with different force-generating mechanisms contribute to distinct vertebrate gastrulation modes via a self-organizing mechanochemical process. |
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Zebrahub - Multimodal Zebrafish Developmental Atlas Reveals the State Transition Dynamics of Late Vertebrate Pluripotent Axial ProgenitorsM. Lange, A. Granados, S. V. Kumar, J. Bragantini, S. Ancheta, Sreejith Santhosh , M. Borja, H. Kobayashi, E. McGeever, Ahmet C. Solak, B. Yang, X. Zhao, Y. Liu, A. Detweiler, S. Paul, H. Mekonen, T. Lao, R. Banks, A. Jacobo, K. Balla, K. Awayan, S. D'souza, R. Haase, A. Dizeux, O. Pourquie, R. Gomez-Sjoberg, G. Huber, M. Serra, N. Neff, A. Pisco and L. A. Royer biorXiv, 2023 link / Elucidating the developmental process of an organism will require the complete cartography of cellular lineages in the spatial, temporal, and molecular domains. We present Zebrahub, a comprehensive dynamic atlas of zebrafish embryonic development that combines single-cell sequencing time course data with light-sheet microscopy-based lineage reconstructions. Zebrahub is a foundational resource to study developmental processes at both transcriptional and spatiotemporal levels. It is publicly accessible as a web-based resource, providing an open- access collection of datasets and tools. Using this resource we shed new light on the pluripotency of Neuro-Mesodermal Progenitors (NMPs). We find that NMPs are pluripotent only during early axis elongation before becoming exclusively mesodermal progenitors. We attribute this restriction in NMP cell fate to emerging morphodynamic features that compartmentalize tissue motion. |
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Spike formation theory in 3D flow separationSreejith Santhosh, Haodong Qin, Bjoern F. Klose, Gustaaf B. Jacobs, Jérôme Vétel, Mattia Serra Journal of Fluid Mechanics, 2023 link / free access link / We develop a frame-invariant theory of material spike formation during flow separation over a no-slip boundary in three-dimensional flows with arbitrary time dependence. Based on the exact evolution of the largest principal curvature on near-wall material surfaces, our theory identifies fixed and moving separation. Our approach is effective over short time intervals and admits an instantaneous limit. As a byproduct, we derive explicit formulas for the evolution of the Weingarten map and the principal curvatures of any surface advected by general three-dimensional flows. The material backbone we identify acts first as a precursor and later as the centerpiece of Lagrangian flow separation. We discover previously undetected spiking points and curves where the separation backbones connect to the boundary and provide wall-based analytical formulas for their locations. We illustrate our results on several steady and unsteady flows. |
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Optimal Locomotion for Limbless CrawlersSreejith Santhosh, Mattia Serra Physical Review E, 2022 link / free access link / Limbless crawling is ubiquitous in biology, from cells to organisms. We develop and analyze a model for the dynamics of one-dimensional elastic crawlers, subject to active stress and deformation-dependent friction with the substrate. We find that the optimal active stress distribution that maximizes the crawler's center of mass displacement given a fixed amount of energy input is a traveling wave. This theoretical optimum corresponds to peristalsis-like extension-contraction waves observed in biological organisms, possibly explaining the prevalence of peristalsis as a convergent gait across species. Our theory elucidates key observations in biological systems connecting the anchoring phase of a crawler to the retrograde and prograde distinction seen in peristaltic waves among various organisms. Using our optimal gait solution, we derive a scaling relation between the crawling speed and body mass, explaining experiments on earthworms with three orders of magnitude body mass variations. Our results offer insights and tools for optimal bioinspired crawling robots design with finite battery capacity. |
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Activity induced nematic order in isotropic liquid crystalsSreejith Santhosh, Mehrana R. Nejad, Amin Doostmohammadi, Julia M Yeomans, Sumesh Thampi Journal of Statistical Physics, 2020 link / free access link / We use linear stability analysis to show that an isotropic phase of elongated particles with dipolar flow fields can develop nematic order as a result of their activity. We argue that ordering is favoured if the particles are flow-aligning and is strongest if the wavevector of the order perturbation is neither parallel nor perpendicular to the nematic director. Numerical solutions of the hydrodynamic equations of motion of an active nematic confirm the results. The instability is contrasted to the well-known hydrodynamic instability of an ordered active nematic. |
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Design and source code from Jon Barron's website |