Nimesh Chahare's CV

Current position

• Postdoctoral Fellow with Dr. Hannah T. Stuart
• Stuart group, Tissue Biology and Disease Modelling
• European Molecular Biology Laboratory (EMBL) Barcelona, Spain

Research Interests

• Epithelial Mechanics.
• Stem cell self-organization and neural tube organoids.
• Neurodevelopmental Biology.
• Mechanobiology.

Contact

nimesh [at] embl.es / nimesh [at] mailbox.org
LinkedIn / Orcid / Google scholar / GitHub / Twitter / Bluesky

Education

Ph.D. in Applied Mathematics
Universitat Politècnica de Catalunya, Barcelona, Spain 2023

Master of Engineering. in Mechanical Engineering
Indian Institute of Science, Bengaluru, India 2016

Bachelor of Technology in Mechanical Engineering
Visvesvaraya National Institute of Technology, Nagpur, India, 2014

Publications

Patents

Chahare, N. R., Le Roux, A., Roca-Cusachs, P., and Trepat, X. Cell Stretchers: microfluidic device for stretching cells and tissues. European patent application EP25383565.6, filed 30 December 2025.

Chahare, N. R., Pullarkat, P., Vishwakarma, R., and Gundiah, N. A microscope-mountable fluid shear device. Indian patent 471468 (application IN201641029893), granted 24 November 2023.

Articles

Chahare, N., Imamura, C., & Nerurkar, N.L. (2026). Morphometric analysis reveals that the chick cranial neural tube expands as an active shell. Biophysical Reports, 100280.

Ouzeri, A., Kale, S., Chahare, N., Torres-Sanchez, A., Santos-Olivan, D., Trepat, X., & Arroyo, M. (2026). Theory of multiscale epithelial mechanics under stretch: from active gels to vertex models. PRX Life, 4(2), 023022.

Golde, T., Pensalfini, M., Chahare, N., Roca-Cusachs, P., Wiche, G., Charras, G., … & Trepat, X. (2026). Dynamics of supracellular keratin bundling and nuclear uncaging in stretched epithelia. Nature Physics

Chahare, N., Ouzeri, A., Wilson, T., Bal, P. K., Golde, T., Vilanova, G., … & Arroyo, M. (2025). Multiscale wrinkling dynamics in epithelial shells. bioRxiv, 2025-06.

Andreu, I. + , Granero-Moya, I. + , Chahare, N. R., Clein, K., Jordàn, M. M., Beedle, A. E., … & Roca-Cusachs, P. (2022). Mechanical force application to the nucleus regulates nucleocytoplasmic transport. Nature Cell Biology, 24(6), 896-905.

Andreu, I. + , Falcones, B. + , Hurst, S., Chahare, N., Quiroga, X., Le Roux, A. L., … & Roca-Cusachs, P. (2021). The force loading rate drives cell mechanosensing through both reinforcement and cytoskeletal softening. Nature communications, 12(1), 4229.

Chatterjee, A., Chahare, N. R., Kondaiah, P., & Gundiah, N. (2021). Role of Fiber Orientations in the Mechanics of Bioinspired Fiber-Reinforced Elastomers. Soft Robotics, 8(6), 640-650.

Kundanati, L., Chahare, N. R., Jaddivada, S., Karkisaval, A. G., Sridhar, R., Pugno, N. M., & Gundiah, N. (2020). Cutting mechanics of wood by beetle larval mandibles. Journal of the Mechanical Behavior of Biomedical Materials, 112, 104027.

Equal contribution is indicated by +

Research software

spatchcocking. Python framework mapping a curved 3D epithelium to a 2D reference frame and quantifying curvature, tissue thickness and mitotic activity across it. Released with Chahare et al., Biophysical Reports 2026.

Nucleocytoplasmic transport analysis tool. Measures nuclear import and export rates from FRAP and FLIP data. Released as supplementary software with Andreu et al., Nature Cell Biology 2022.

Force loading-rate analysis code. Analyzes the atomic force microscopy and optical-tweezer datasets behind the loading-rate dependence. Released as supplementary software with Andreu et al., Nature Communications 2021.

Conferences

Chahare, N. R., Ouzeri, A., Golde, T., Wilson, T., Roca-cusachs, P., Arroyo, M., and Trepat, X. “Harnessing active viscoelasticity for synthetic epithelial morphogenesis.” XIX Jornada de Biologia Molecular, Catalan Society for Biology, Barcelona, Spain. September 2023

Chahare, N. R., Ouzeri, A., Golde, T., Wilson, T., Roca-cusachs, P., Arroyo, M., and Trepat, X. “ Harnessing active viscoelasticity for synthetic epithelial morphogenesis.” German Physics Society, Dresden, Germany. March 26-31, 2023

Chahare, N. R., Ouzeri, A., Golde, T., Wilson, T. Arroyo, M., and Trepat, X. “Shaping epithelia through buckling in pressure-controlled tissue.” World congress of biomechanics, Taipei, Taiwan. July 10-14, 2022

Chahare, N. R., Ouzeri, A., Golde, T., Wilson, T. Arroyo, M., and Trepat, X. “Synthetic epithelial morphogenesis through controlled stretching and buckling.” EMBL-IBEC Conference, Engineering multicellular systems, Barcelona, Spain. June 08-10, 2022

Chahare, N. R., Ouzeri, A., Golde, T., Wilson, T. Arroyo, M., and Trepat, X. “Synthetic epithelial morphogenesis through controlled stretching and buckling.” EMBO-EMBL Symposium, Mechanobiology in development and disease, Heidelberg, Germany. May 15–18, 2022

Chatterjee, A., Chahare, N. R., Kulkarni, A., Kondaiah, P., and Gundiah, N. “Design of adynamic cell stretcher to quantify responses of fibroblasts to cyclic stretching and TGF-β.”5th International Conference on Computational and Mathematical Biomedical Engineering,Pittsburgh, Pennsylvania, USA. April 10–12, 2017

Satone, V., Chahare, N. R., and Padole, P. “Design of pedal operated behda crackingmachine using flywheel motor.” Association for Machines and Mechanisms’ IndustrialProblems on Machines and Mechanisms (IPRoMM), Nagpur, India. Dec 22–23, 2016

Abhijith, K. G., Chahare, N. R., Kundanati, L., and Gundiah, N. “Mechanics of the Cuticleof Wood Boring Insects.” Structural Integrity Conference and Exhibition (SICE), Bengaluru,India. July 4–6, 2016

Invited Talks and Presentations

“What is epithelial mechanics? and Why should we care about it?” Pint of Science talk, New York, USA, May 2025

Multiscale dynamics of epithelial shells, Gulmohar: Indian Society of Developmental Biologists’ postdoc talk series, November 2024

Mechanics of epithelial shells, International Developmental Mechanics Zoom Seminar Series, November 2024

Multiscale buckling of epithelial shells. Indian Institute of Science, Bengaluru, India, March 2024 (link) (archived)

Shaping epithelia through buckling in pressure-control. Princeton University, Princeton, USA, November 2023

Research experience

Postdoctoral fellow, Tissue Biology and Disease Modelling, EMBL Barcelona

Adviser: Dr. Hannah T. Stuart, July 2026- Present

Project: Self-organization of stem cells into neural tube organoids

• Bringing microengineering and tissue mechanics expertise into a newly established stem cell laboratory, and setting it up from scratch.
• Training in pluripotent stem cell biology and the self-organization of neural tube organoids.

Postdoctoral research scientist, Biomedical Engineering, Columbia University

Adviser: Prof. Nandan Nerurkar, May 2024- June 2026

Project: Mechanics of morphogenesis of embryonic brain development

• Characterized chick embryonic brain morphology across developmental stages using optical clearing, confocal imaging, and 3D segmentation of the cranial neural tube.
• Developed spatchcocking a 3D-to-2D morphometric framework to map curvature, tissue thickness, and mitotic activity across the cranial neural tube, revealing that the early embryonic brain expands as an active shell.
• Investigated the relationship between molecular signaling and physical forces, such as pressure and tension, developing lumen-pressure control in the living embryo to alter morphogen patterning.

Published in Biophysical Reports 2026.

PhD student and Postdoctoral researcher, Institute for Bioengineering of Catalonia, and UPC

Adviser: Prof. Xavier Trepat and Prof. Marino Arroyo, Jul 2017– Apr 2024

Thesis: Mechanics of epithelial layers subjected to controlled pressure (Grade: cum laude)

• Developed a microfluidic chip to control epithelial tissue shapes and lumen pressure, enabling investigation of multiscale epithelial mechanics.
• Implemented an innovative approach to pattern epithelial folds through controlled buckling.
• Acquired expertise in cell culture, protein micropatterning, microfluidic device design and fabrication, advanced microscopy, image processing, and cell segmentation.

Published in Nature Physics 2026 and PRX Life 2026; preprint on bioRxiv 2025.

Computational tool for analyzing nuclear to cytoplasmic transport

• Working in collaboration with Prof. Pere Roca-Cusachs and Ion Andreu, developed a MATLAB script to calculate import and export rate of mechanosensitive protien.
• Developed a fitting algorithm to elucidate protein mobility with Fluorescence recovery after photobleaching (FRAP).
• Utilized an elegant system of differential equations to analyze data from Fluorescence Loss in Photobleaching (FLIP).

Published in Nature Cell Biology 2022.

Analysis of force loading rates associated with cell mechanosensing

• Working in collaboration with Prof. Pere Roca-Cusachs and Victor Gonzalez-Tarrago, developed a MATLAB script for analyzing atomic force microscopy data from JPK software raw data.
• Analyzed timeseries data from AFM experiments to determine detachment force.
• Analyzed optical tweezer experiments by fitting curves piecewise linearly to calculate stiffness of the cells.

Published in Nature Communications 2021.

Project Associate, Biomechanics Lab, Indian Institute of Science

Adviser: Prof. Namrata Gundiah, July 2016–March 2017

Developing constitutive model of Fiber Reinforced Elastomers (FRE)

• Computed stresses and strains from uniaxial and biaxial stretching experiments of Polydimethylsiloxane Fiber Reinforced Elastomer.
• Modeled experimental results using hyperelastic constitutive equation.
• Performed constrained optimization using custom built MATLAB program for fitting the experimental results.

Published in Soft Robotics 2021.

Masters, Mechanical Engineering, Indian Institute of Science

Adviser: Prof. Namrata Gundiah, August 2014–June 2016

Thesis: Design and fabrication of miniature shear device for cell mechanics

• Designed a cost effective system capable of applying uniform shear on culture cells along with real time visualization using fluorescence microscopy.
• Implemented trajectory generation filter based control system in the shear device electronics using MATLAB and Arduino programming.
• Calibrated the device using fluorescence microscopy and traction force microscopy to test for uniform shear flow conditions.

Indian patent 471468, granted 2023.

Finite element analysis of coffee white stem borer (CWSB) mandible

• Created geometry of insect mandible from tomography data using image processing and CAD modeling.
• Stress and displacement distribution on mandible during wood boring were computed using commercial FEA package, ABAQUS.
• Stresses on the mandible were used to examine the morphological adaptations that provide distinct mechanical advantages to the insect for cutting purposes.

Published in J. Mech. Behav. Biomed. Mater. 2020.

Undergraduate, Mechanical Engineering, VNIT

Adviser: Prof. Pramod Padole, May 2013–April 2014

Thesis: Design and Fabrication of a Hirda (Terminalia chebula) Cracking Machine

• The project involved solving problem of Indian tribal population dealing with processing of hirda fruit for medicinal applications.
• Built a machine to separate seed from the fruit called Hirda, by crushing the fruit between two rollers. Use of machine led to lower processing time, higher output and minimal manual labor.

Mentoring experience

Mentored Chieko Imamura, undergraduate student at Columbia Biomedical engineering, for studying mechanobiology of brain development. Co-author on the chick cranial neural tube paper, 2024-2026

Mentored Joseph Yung, undergraduate student at Columbia Biomedical engineering, in finite element analysis, 2026

Mentored Kayla Williamson, undergraduate student at Columbia Biomedical engineering, for designing experimental setups enabling long term imaging of early chick embryo, 2024

Mentored Pau Pujol-Vives, a masters student, in developing algorithms to segment 3D microscopy data. Co-author on the epithelial shells preprint, 2023

Mentored Thomas Wilson, PhD student with Prof. Trepat in developing microfluidic device for light sheet microscopy, 2022-2024

Mentored Gavin McQuarrie, student from University of Glasgow, jointly with Anabel-lise Le Roux to calibrate and develop stretch system, 2021

Undertook Alexandre Garcia-Duran as summer student in University of Barcelona Intership project of characterizing stiffness of PDMS and developing a Microfluidic device for stretching cells/tissues, 2021

Trained two high school students in a project related to 3D epithelia at Institute for Bioengineering of Catalonia through the Parc Científic de Barcelona’s BATX2LAB (Treball de Recerca) program, 2018.

Art Exhibitions

• A=A, B=B, Antoni Tàpies Foundation Museum, Barcelona, Spain. Dec. 2023-Mar. 2024. (archived)
• “Organic Origami” artwork as part of City and Science Biennial 2023, Centre de Cultura Contemporània de Barcelona, Barcelona, Spain. Feb. 2023. (archived)

Professional experience

Project Associate, Biomechanics Lab, Department of Mechanical Engineering, Indian Institute of Science, April 2016- April 2017.

Consultant, Macrophysiology Lab, Indian Institute of Science: April–May 2017

• Developing a lizard bite force sensor.
• Fabricated the device with miniature load cell as a force sensor to measure bite force of the lizards.

Intern, Tata Motors, May–June 2012 Department of Safety, Tata Indica plant, Pune, India

Accomplishments

Awards and Honors

Won the best poster prize at 15th IBEC SYMPOSIUM on Bioengineering for Active Ageing, Barcelona, Spain 2022.

All India Rank 362 (99.8 percentile) out of 185,578 in Graduate Aptitude Test in Engineering in 2014.

Received second prize for Best paper presentation in Association for Machines and Mechanisms’ Industrial Problems on Machines and Mechanisms (IPRoMM), Nagpur, India, 2016.

Bagged 22nd position in national level presentation competition for future transportation solution, TATA MOTORS’ MIND ROVER, 2013.

Grants

International travel grant for EMBO workshop on computational modeling of multicellular systems in Barcelona, Spain, 2025

International travel grant for attending winter school on Quantitative Systems Biology at International Centre for Theoretical Sciences (ICTS), Bengaluru, India 2019.

Junior Research Fellowship, CSIR–UGC, Indian Institute of Science, Bengaluru, 2017.

Awarded scholarship by Ministry of Human resource and development, India for M.E. 2014-16.

In press

2025 The International Epithelial Mechanics Fan Club profiled by FocalPlane, The Company of Biologists link (archived)

2023 Invited to be on panel discussion on subject of “Why scientists should care about art?” Roundtable discussion was in Catalan link (video) (participant page, archived)

2022 Interviewed for European Commision funded project, Mechanocontrol, Talked about the inventing novel microfluidic devices. link (archived)

Key Proficiencies

Biology

Chick embryology including ex vivo culture (HH3-21) and surgical perturbations of the neural tube (HH11-21), cryosectioning, mammalian cell culture, human pluripotent stem cell culture at BSL-2 and neural tube organoid differentiation, immunofluorescence stainings, protein micropatterning (microcontact printing and photopatterning), hydrogel preparation, 3DISCO clearing, Handling epithelial cell lines in the context of in vitro 2D/3D experiments.

Microscopy

Advanced microscopy techniques, including light/fluorescence microscopy and 2 photon, spinning disk/laser scanning confocal microscopy, and SPIM lightsheet microscopy. Utilized photobleaching techniques (FRAP, FLIP), along with local photoactivation for optogenetics, and long-term live imaging of deforming tissue.

Mechanical measurement

Traction force microscopy, monolayer stress microscopy, and controlled-pressure and controlled-stretch actuation of living tissue.

Microfluidics

Experienced in working within microfabrication facilities, involving designing photomasks, photolithography, plasma bonding, 3D printing with a DLP projector, elastomer (PDMS) preparation, and fabrication of frugal microfluidic devices using a desktop cutting machine.

Design and Analysis

Programming: Python, MATLAB, R, FIJI macro, Markdown, LaTeX. Image Processing: Automated segmentation including SAM-family models fine-tuned on own annotated stacks, Napari, Vedo, and 3D analysis pipeline development for large datasets. Modeling: Continuum mechanics and finite-element modeling. 3D modeling: FreeCAD, SolidWorks, Inkscape, Blender, and Keyshot.

Soft Skills

Strong collaboration and teamwork abilities, confident in public speaking, self-motivated quick learner, adept at trouble-shooting, and adaptable to dynamic challenges.

Leadership and Service Activities

• Elected as Co-Vice President at Columbia University Postdoctoral Society (CUPS). 2025-2026. (archived)
• Elected as Steward at Columbia Postdoctoral Workers, UAW Local 4100, representing the ~200-member Mudd building unit. 2024-2026. (election results)
• Mentored undergraduate students at Columbia University. 2024-2026.
• Founder and convenor of the International Epithelial Mechanics Fan Club, with 51 named delegates across 14 countries and an audience of over 3,000. 2023-Present.
• Organized the New York mobilisation of Stand Up for Science. 2025.
• Invited to be a panelist in a discussion on the topic of ‘Why Scientists Should Care About Art?’ organized by the Barcelona City Government. 2023. (video)
• Active participation in organizing March for Science events in Barcelona. 2018, 2023.
• Managed data servers (synology and magnetic tape drive system) serving 40 researchers at Prof. Trepat’s lab. 2018-2024.
• Member of the PhD committee at Institute for Bioengineering of Catalonia. 2017-2019.

Languages

Native   : Marathi, Hindi, and English
B1.2      : Catalan
A1         : Spanish