Nilay Kumar
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Nilay Kumar Email & Phone Number

Systems Biology | Data Science | Machine Learning | Computational Fluid Dynamics | Computer Vision | Unlocking the secrets of life at the intersection of computation and experimentation at University of Notre Dame
Location: Notre Dame, Indiana, United States 6 work roles 2 schools
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Systems Biology | Data Science | Machine Learning | Computational Fluid Dynamics | Computer Vision | Unlocking the secrets of life at the intersection of computation and experimentation
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Notre Dame, Indiana, United States

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Nilay Kumar is listed as Systems Biology | Data Science | Machine Learning | Computational Fluid Dynamics | Computer Vision | Unlocking the secrets of life at the intersection of computation and experimentation at University of Notre Dame, based in Notre Dame, Indiana, United States. AeroLeads shows a matched LinkedIn profile for Nilay Kumar.

Nilay Kumar previously worked as Project: Quantitative Systems Biology and Model Simulations at University Of Notre Dame and Project: Computer Vision, Machine Learning and Process Optimization at University Of Notre Dame. Nilay Kumar holds Doctor Of Philosophy - Phd, Chemical And Biomolecular Engineering from University Of Notre Dame.

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University of Notre Dame

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About Nilay Kumar

• 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.

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University of Notre Dame
University Of Notre Dame
Systems Biology | Data Science | Machine Learning | Computational Fluid Dynamics | Computer Vision | Unlocking the secrets of life at the intersection of computation and experimentation
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6 roles

Nilay Kumar work experience

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Project: Quantitative Systems Biology And Model Simulations

Current

Notre 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.
  • 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.
  • 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.
  • 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.
  • 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.
Aug 2017 - Present

Project: Computer Vision, Machine Learning And Process Optimization

Current

Notre 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.
  • 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.
  • 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.
Aug 2017 - Present

Project: Microfluids And Computational Fluid Dynamics

Notre 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.
  • 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.
Aug 2017 - Aug 2019

Research Fellowship

  • 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
Jun 2022 - Jul 2022

Junior Research Fellow

Delhi, 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.
  • Worked on device fabrication for flow visualization experiments to observe the microstructure of suspensions exhibiting shear thickening behavior.
May 2016 - May 2017

Research Assistant

Bochum, 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.
May 2015 - Jul 2015
2 education records

Nilay Kumar education

Doctor Of Philosophy - Phd, Chemical And Biomolecular Engineering

University Of Notre Dame

Bachelor Of Technology - Btech, Chemical Engineering

Indian Institute Of Technology, Guwahati
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What company does Nilay Kumar work for?

Nilay Kumar works for University of Notre Dame.

What is Nilay Kumar's role at University of Notre Dame?

Nilay Kumar is listed as Systems Biology | Data Science | Machine Learning | Computational Fluid Dynamics | Computer Vision | Unlocking the secrets of life at the intersection of computation and experimentation at University of Notre Dame.

Where is Nilay Kumar based?

Nilay Kumar is based in Notre Dame, Indiana, United States while working with University of Notre Dame.

What companies has Nilay Kumar worked for?

Nilay Kumar has worked for University Of Notre Dame, Feinstein Institute For Medical Research, The, Defence Research And Development Organisation (Drdo), and Ruhr University Bochum.

How can I contact Nilay Kumar?

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What schools did Nilay Kumar attend?

Nilay Kumar holds Doctor Of Philosophy - Phd, Chemical And Biomolecular Engineering from University Of Notre Dame.

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