Nilay Kumar Email and Phone Number
• I am a PhD candidate with 8 years of research experience in Chemical Engineering and Biological Sciences. Highly skilled in bio-data analysis, developing multi-physics & surrogate models, and designing experiments for their validation. Published over 8+ scientific articles in top-tier journals.• My expertise encompasses a broad range of modeling frameworks for physical systems, including but not limited to Finite Element Modeling (FEM), coarse-grained Molecular Dynamics (MD) simulations, Partial Differential Equations (PDE) modeling of signaling networks, Active Vertex Models of biophysics, numerical models such as Level Set for modeling multiphase flows, as well as surrogate or data-driven modeling approaches.• My familiarity with computer vision and its applications in the field of Systems Bio-engineering is demonstrated through a machine learning-based tool called MAPPER, which automates the analysis of adult fruit fly wings. By combining this tool with bioinformatics analysis, I was able to identify 5 therapeutic targets within a loss-of-function GPCR screening dataset, resulting in 2 publications as first author in peer-reviewed journals.• In addition, I possess a robust domain knowledge of process optimization using machine learning. I developed a Bayesian Optimization framework, employing Gaussian Process Regression models, to estimate parameters for computationally expensive biophysics models of development. This work culminated in the award of a $48,000 pilot grant from Northwestern University's NSF-Simons Center for Quantitative Biology.• As a highly proficient programmer, I am well-versed in multiple programming languages and both commercial and open-source tools for data visualization and machine learning. I have employed these techniques in major scientific projects throughout my career.• I am highly collaborative and skilled in working in a multidisciplinary setting. For instance, I led a team of 10+ individuals in a cross-collaborative project to develop a multiscale mechano-chemical model of epithelial morphogenesis, which resulted in 2 manuscripts being published in peer-reviewed journals.• I've designed a novel simulation to investigate microchannel Taylor flow, showcasing my expertise in microfluidics and computational fluid dynamics. Furthermore, I've engineered a cost-effective microfluidic platform, reducing initial investment costs by 98.5%, and published related work in 3 prestigious peer-reviewed journals.
University Of Notre Dame
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Project: Quantitative Systems Biology And Model SimulationsUniversity Of Notre Dame Aug 2017 - PresentNotre Dame, In, Us• Led a team of 8 people in a cross collaborative project to develop and calibrate a novel, realistic, and multiscale mechano-chemical models of epithelial morphogenesis to infer general design principles that operate across multiple length and time scales (Manuscript in revision at Nature Communications) • Worked towards development and calibration of a subcellular element model for decoupling several factors of cytoskeletal regulation in generation and maintenance of organ shape (Manuscript published at PLOS Computational Biology)• Worked within a mixed team of applied mathematicians and biologists to develop an analytical partial differential equation-based network representation of interactions between morphogens, Rho family of GTPases and regulators of tissue mechanics. (Manuscript in preparation).• Participated in cross-functional teams to develop a cloud computing project for managing 13,000+ image datasets, applying bioinformatics, data processing, and data science methods to identify 4 lead therapeutic candidates using Python and MATLAB (Manuscript under review; arxiv preprint available)• Created a vertex model of epithelial morphogenesis, simulating the biophysical processes regulated by Piezo channels. The model was used to validate the experimental data predicting mechanosensitive Ca2+ channel Piezo's contribution in regulating robustness in organ growth. Developed numerous tools using MATLAB for automated quantitative analysis of large 3D fixed tissue and live imaging datasets. (Manuscript in preparation) -
Project: Computer Vision, Machine Learning And Process OptimizationUniversity Of Notre Dame Aug 2017 - PresentNotre Dame, In, Us• Developed an automated framework using Bayesian optimization and Gaussian process regression for determining optimal physical interactions to create desired organ shape, resulting in a $48,000 pilot grant from Northwestern University's NSF-Simons Center for Quantitative Biology. Manuscript in preparation. • Created a machine learning based tool MAPPER (Github Link) that automates the process of analysis of adult Drosophila wing. Transfer learning was employed to retrain a Convolutional Neural Network (CNN) for the task of segmentation of insect wings. Classification algorithms were applied to classify and extract meaningful geometrical features from the regions of interest within the wing blade. Published in Frontiers in Genetics.• Reviewed advances in AI and data-driven statistical learning algorithms developed for quantitative analysis of multicellular system. The work resulted in a review article published in Journal of Biological Engineering. -
Project: Microfluids And Computational Fluid DynamicsUniversity Of Notre Dame Aug 2017 - Aug 2019Notre Dame, In, Us• Contributed to the development of a low-cost microfluidic platform, capable of studying problems related to mechanobiology, reducing initial investment cost by 98.5% (from $20000 to $300) (Manuscript published in Biomicrofluidics)• Developed a novel simulation to study Taylor flow in micro channels, providing insight into dynamics of heat and mass transfer properties. Published in two prestigious journals, International Journal of Heat & Mass Transfer and Asia Pacific Journal of Chemical Engineering. -
Research FellowshipFeinstein Institute For Medical Research, The Jun 2022 - Jul 2022• Developed a fully trained automated pipeline to track real time mice activity and determine the motion patterns using a deep learning-based tool DeepLabCut• Involved in processing of neural recordings to establish correlations between stimulation of vagus nerve and movements of mouse -
Junior Research FellowDefence Research And Development Organisation (Drdo) May 2016 - May 2017Delhi, New Delhi, In• Worked towards designing a lightweight liquid armor in a Govt. of India sponsored project worth INR 20 million (USD $240,000) funded by the DRDO.• Developed a code in FORTRAN for the project and ideation, fabrication, and installation of experimental setup for results validation . • Used Stokesian Dynamics to study the effect of far field hydrodynamic interactions and frictional coefficient in shear thickening. simulate a system consisting of a mixture of rods and spherical particles and studies its impact on shear thickening.• Worked on device fabrication for flow visualization experiments to observe the microstructure of suspensions exhibiting shear thickening behavior. -
Research AssistantRuhr University Bochum May 2015 - Jul 2015Bochum, Nordrhein-Westfalen, De• Designed the geometry and generated an unstructured mesh using FreeCAD and Gmsh for the studyof the flow through cerebral aneurysms.• Integrated the above generated mesh in complex C++ code, which combines the Lattice Boltzmanmethod for fluid flow with the finite element method and immersed boundary method for the dynamicsof flexible membranes.
Nilay Kumar Education Details
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University Of Notre DameChemical And Biomolecular Engineering -
Indian Institute Of Technology, GuwahatiChemical Engineering
Frequently Asked Questions about Nilay Kumar
What company does Nilay Kumar work for?
Nilay Kumar works for University Of Notre Dame
What is Nilay Kumar's role at the current company?
Nilay Kumar's current role is Systems Biology | Data Science | Machine Learning | Computational Fluid Dynamics | Computer Vision | Unlocking the secrets of life at the intersection of computation and experimentation.
What schools did Nilay Kumar attend?
Nilay Kumar attended University Of Notre Dame, Indian Institute Of Technology, Guwahati.
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