Deepak K. Agrawal

Department of Bioengineering, and Electrical and Computer Engineering, 
805 Columbus Ave, Northeastern University,
Boston, MA, 02215, USA
E-mail:  d dot agrawal AT northeastern dot edu 

Google Scholar Profile

About me

I am a postdoc at Northeastern University where I am working with Prof. Eduardo Sontag on dynamic modeling of biological processes and designing new synthetic circuits. In the past, I worked with Prof. Mary Dunlop on a biological control project, and with Prof. Rebecca Schulman on self-assembly and biosensing projects. I got my PhD in Engineering from the University of Cambridge in 2013, under the supervision of Prof. Ashwin Seshia and Prof. Jim Woodhouse.
My education, awards, research, teaching and work experience can be found here in my CV.

Research Interests

My primary research interests are designing and developing new devices and mechanisms that are inspired by feedback driven biological systems. In particular, I am interested in developing self-regulated drug delivery devices and affordable point-of-care diagnostic tools. I also enjoy working on the modeling aspect of a dynamic system, particularly when a complicated set of coupled differential equations could be reduced to a simple analytical expression which is often insightful and compelling.

Tutoring/Teaching Experience

  • Modeling and Statistical Analysis of Data for Chemical and Biomolecular Engineers
  • RF Electronics
  • Integrated Digital Electronics
  • Linear System and Control
  • Communications Fourier Transforms and Signal Data Analysis
  • Wave Propagation and Radiation
  • Optical Engineering

  • Journal Papers

    • D. K. Agrawal, R. Marshall, V. Noireaux, and E. D Sontag, “In vitro Implementation of Robust Gene Regulation in a Synthetic Biomolecular Integral Controller” under review in Nature Communication link.
    • A. Westbrook, X. Tang, R. Marshall, C. Maxwell, J. Chappell, D. K. Agrawal, M. J. Dunlop, V. Noireaux, C. Beisel, J. Lucks, E. Franco, “Distinct Timescales of RNA Regulators Enable the Construction of a Genetic Pulse Generator”, accepted in Biotechnology and Bioengineering link.
    • D. K. Agrawal, X. Tang, A. Westbrook, R. Marshall, C. S. Maxwell, J. Lucks, V. Noireaux, Chase L. Beisel, Mary J. Dunlop, and E. Franco, “Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression”, ACS Synthetic Biology, vol. 7, no. 5, pp. 1219-1228, 2018 link.
    • D. K. Agrawal, R. Jiang, S. Reinhart, A. M. Mohammed, T. D. Jorgenson, and R. Schulman, “Terminating DNA Tile Assembly with Nanostructured Caps”, ACS Nano, vol. 11, no. 10, pp. 9770-9779, 2017 link.
    • T. D. Jorgenson, A. M. Mohammed, D. K. Agrawal, and R. Schulman, “Self-Assembly of Hierarchical DNA Nanotube Architectures with well-defined Geometries”, ACS Nano, vol. 11, no. 2, pp. 1927-1936, 2017 link.
    • D. Agrawal, F. Bizzarri, A. Brambilla, and A. Seshia, “Numerical Verification of an Analytical Model for Phase Noise in MEMS Oscillators”, IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 63, no. 8, pp. 1204-1207, 2016 link.
    • D. K. Agrawal, E. Franco, and R. Schulman,”A Self-regulating Biomolecular Comparator for Processing Oscillatory Signals”, Journal of the Royal Society Interface, vol. 12, no. 111, pp. 20150586, 2015 link.
    • D. K. Agrawal and A. A. Seshia, “An Analytical Formulation for Phase Noise in MEMS Oscillators”, IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 61, no. 12, pp. 1938-1952, 2014 link.
    • D. K. Agrawal, J. Woodhouse, and A. A. Seshia, “Synchronization in a Coupled Architecture of Microelectromechanical Oscillators”, Journal of Applied Physics, vol. 115, no. 16, pp. 164904, 2014 link.
    • D. K. Agrawal, J. Woodhouse, and A. A. Seshia, “Observation of Locked Phase Dynamics and Enhanced Frequency Stability in Synchronized Micromechanical Oscillators”, Physical Review Letters, vol. 111, no. 8, pp. 084101, 2013 link.
    • D. K. Agrawal, J. Woodhouse, and A. A. Seshia, “Modeling Nonlinearities in MEMS Oscillators”, IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 60, no. 8, pp. 1646-1659, 2013 link.
    • D. K. Agrawal and S. Bhattacharya, “Integrated Optical and MEMS Based Design Process for a Variable Optical Attenuator”, Optics and Lasers in Engineering, vol. 49, no. 7, pp. 848-854, 2011 link.

    • Conference Publications, Talks and Posters

    • D. K. Agrawal, S. D. Khare, and E. D Sontag, “Designing Protease Based Logic Gates”, The 1st Annual NEU Bioengineering Research Symposium, Boston, MA, USA, Jun. 20, 2018.
    • X. Tang, D. K. Agrawal, M. J. Dunlop, and E. Franco, “RNA-based PID Controllers for Regulation of Gene Expression”, 23rd International Conference on DNA Computing and Molecular Programming (DNA23), Austin, TX, USA, Sept. 24-28, 2017.
    • D. K. Agrawal and M. J. Dunlop, “Constructing Mathematical Models of RNA based Biomolecular Controllers”, EBRC Fall 2017 Retreat, Atlanta, GA, USA, Sep. 22-23, 2017.
    • D. K. Agrawal and M. J. Dunlop, “Designing Biomolecular PID Control”, 11th Annual q-bio Conference, New Brunswick, NJ, USA, Jul. 25-28, 2017.
    • D. K. Agrawal and M. J. Dunlop, “Designing RNA based PI Control”, EBRC Spring 2017 Retreat, Evanston, IL, USA, Mar. 24-25, 2017.
    • D. K. Agrawal, A. M. Mohammed, S. Reinhart, T. Jorgenson, and R. Schulman, “Dynamic Control of DNA Tile Nanotube Nucleation and Elongation”, 21st International Conference on DNA Computing and Molecular Programming (DNA21), Boston, MA, USA, Aug. 17-21, 2015.
    • D. K. Agrawal, E. Franco, and R. Schulman, “Designing a Self-regulating Biomolecular Comparator”, American Control Conference (ACC), IEEE 2015, Chicago, IL, USA, Jul. 1-3, 2015 (oral presentation).
    • D. K. Agrawal, and A. A. Seshia, “Designing MEMS Resonator-based Oscillators”, 2011 UK-India Education and Research Initiative workshop, IISC Bangalore, India, (invited presentation).
    • D. K. Agrawal, J. Woodhouse, and A. A. Seshia, “Modelling Nonlinearities in a MEMS Square Wave Oscillator”, 2012 IEEE Frequency Control Symposium, Baltimore, MD, USA, May 21-24, 2012 (oral presentation).
    • D. K. Agrawal, P. Thiruvenkatanathan, J. Yan, and A. A. Seshia, “Electrically Coupled MEMS Oscillators”, 2011 Joint conference of the IEEE Frequency Control Symposium and the European Frequency and Time Forum, San Francisco, CA, USA, May 1-5, 2011.
    • D. K. Agrawal and S. Bhattacharya, “Design and Realization of a MEMS Based Variable Optical Attenuator”, International Workshop on Physics of Semiconductor Devices, Mumbai, India, 695-698, 2007 (oral presentation).

    • Manuscripts to be submitted/in preparation

    • D. K. Agrawal, and R. Schulman, “Modular Protein-oligonucleotide Signal Exchange” to be submitted (Nucleic Acid Research).
    • D. K. Agrawal, S. D. Khare, and E. D Sontag, “Constructing Mathematical Models of Protease Based Enzymatic Logic Gates for Biosensing”, in preparation.
    • D. K. Agrawal, and R. Schulman, “Dynamic Control Over Nanotube Nucleation”, in preparation.
    • N. E. Hernandez, W. A. Hansen, D. K. Agrawal, N. A. Inoa, B. J. Yachnin, E. D. Sontag, S. D. Khare, “Exploiting Latent Promiscuity and Epistasis to Improve Biodegradation of a Herbicide”, in preparation.