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Research

We focus on developing and applying the mathematical methods of control & dynamical systems. Applications are to complex systems in engineering and nature, especially for design of biomolecular circuits. Our approach uses both theoretical models and laboratory experiments.

Publications

  • Sen S, Patel A, Gola KK, “Design of a Toolbox of RNA Thermometers”, Riboregulator Design and Analysis, Methods in Molecular Biology, Springer (submitted), 2021.

  • Joshi SK, Sen S, Kar IN, “Synchronization of Coupled Benchmark Oscillators: Analysis and Experiments”, International Journal of Dynamics and Control, 10.1007/s40435-021-00827-y, 2021.

  • Banerjee S, Shah K, Sen S, “On the length scale dependence of DNA conformational change under local perturbation”, BioSystems, 198, 10.1016/j.biosystems.2020.104228, 2020.

  • Patel A, Murray RM, Sen S, “Assessment of Robustness to Temperature in a Negative Feed- back Loop and a Feedforward Loop”, ACS Synthetic Biology, 9(7), Pages 1581-1590, 10.1021/acssynbio.0c00023, 2020. bioRxiv preprint server, 10.1101/774042, 2020.

  • Patel A, Sen S, “Experimental Evidence for Constraints in Amplitude-Timescale Co-variation of a Biomolecular Pulse Generating Circuit Design”, IET Systems Biology, 14(5), Pages 217-220, 10.1049/iet-syb.2019.0123, 2020. bioRxiv preprint server, 10.1101/756049, 2019.

  • Patel A, Sen S, “Computational Framework for Design of a Pulse Generating Biomolecular Circuit”, IFAC International Conference on Advances in Control and Optimization of Dynamical Systems, Chennai, 2020.

  • Joshi SK, Sen S, Kar IN, “Synchronization of Master-Slave Oscillators: Analysis and Experimental Results”, IFAC International Conference on Advances in Control and Optimization of Dynamical Systems, Chennai, 2020.

  • Banerjee S, Sen S, “Robustness of a Biomolecular Oscillator to Pulse Perturbations”, IET Systems Biology, 14(3), Pages 127-132, 10.1049/iet-syb.2019.0029, 2020.

  • Dey A, Bokka V, Sen S, “Dependence of Bacterial Growth Rate on Dynamic Temperature Changes”, IET Systems Biology, 14(2), Pages 68-74, 10.1049/iet-syb.2018.5125, 2019.

  • Dey A, Chakrabarti K, Gola KK, Sen S, “A Kalman Filter Approach for Biomolecular Systems with Noise Covariance Updating”, Sixth Indian Control Conference, 2019. arXiv preprint server: 1712.02150 [q-bio.QM].

  • Relan R, Dey A, Sen S, “The Best Linear Approximation of Biomolecular Systems”, Fifth Indian Control Conference, IIT Delhi, 2019.

  • Patel A, Sen S, “Non-normality Can Facilitate Pulsing in Biomolecular Circuits”, IET Systems Biology, 12(5), Pages 199-204, 10.1049/iet-syb.2018.0008, 2018.

  • Bokka V, Dey A, Sen S, “Period-Amplitude Co-variation in Biomolecular Oscillators”, IET Systems Biology, 12(4), Pages 190-198, 10.1049/iet-syb.2018.0015, 2018.

  • Agarwal A, Dey A, Relan R, Sen S, “Nonparametric Analysis of Nonlinear Distortions for Biomolecular Systems”, Third IFAC International Conference on Advances in Control and Optimization of Dynamical Systems, Hyderabad, 2018.

  • Banerjee S, Bokka V, Sen S, “Attentuation of Pulse Disturbances in Biomolecular Oscillators”, Third IFAC International Conference on Advances in Control and Optimization of Dynamical Systems, Hyderabad, 2018.

  • Patel A, Sen S, “On Amplitude-Timescale Constraints in a Pulse Generating Biomolecular Circuit”, Indian Control Conference, IIT Kanpur, 2018.

  • Dey A, Sen S, “Describing function-based Approximations of Biomolecular Systems”, IET Systems Biology, 12(3), Pages 93-100, 10.1049/iet-syb.2017.0026, 2017.

  • Sen S, Apurva D, Satija R, Siegal D, Murray RM, “Design of a Toolbox of RNA Thermometers”, ACS Synthetic Biology, 6(8), 1461-1470, 10.1021/acssynbio.6b00301, 2017. Synthetic Biology: Engineering, Evolution & Design Conference, 2015, oral presentation; biorxiv preprint server, 10.1101/017369, 2015. Updated version - bioRxiv preprint server, 10.1101/017269, 2016.

  • Joshi SK, Sen S, Kar IN, “Synchronization of Ring Coupled Four Oscillators”, Indian Control Conference, IIT Guwahati, 2017.

  • Joshi SK, Sen S, Kar IN, “Synchronization of Coupled Oscillator Dynamics”, 4th International Conference on Advances in Control and Optimization of Dynamical Systems, 2016.

  • Sen S, “Transient Response Characteristics in a Biomolecular Integral Controller”, IET Systems Biology, 10(2), Pages 57-63, 10.1049/iet-syb.2015.0004, 2016.

  • Dey A, Sen S, “Describing Function-based Approximations of Biomolecular Signalling Systems”, European Control Conference, Pages 2292-2297, 10.1109/ECC.2015.7330880, 2015.

  • Sen S, Murray RM, “Negative Feedback Facilitates Temperature Robustness in Biomolecular Circuit Dynamics”, bioRxiv preprint server, 10.1101/007385, 2014.

  • Sen S, Kim J, Murray RM, “Designing Robustness to Temperature in a Feedforward Loop Circuit”, 53rd IEEE Conference on Decision and Control, Pages 4629-4634, 10.1109/CDC.2014.7040112, 2014.

  • Kim J, Khetarpal I, Sen S, Murray RM, “Synthetic Circuit for Exact Adaptation and Fold-Change Detection”, Nucleic Acids Research, 42(9), Pages 6078-6089, 10.1093/nar/gku233, 2014.

  • Bokka V, Sen S, “Sensitivity Analysis of Oscillatory Circuits”, 3rd International Conference on Advances in Control and Optimization of Dynamical Systems, 10.3182/20140313-3-IN-3024.00220, 2014.

  • Sen S, “Characterization of Tradeoffs in Biomolecular Signaling”, BioSystems, 114(3), Pages 261-268, 10.1016/j.biosystems.2013.09.006, 2013.

  • Sen S, Murray RM, “Temperature Dependence of Biomolecular Circuit Designs”, 52nd IEEE Conference on Decision and Control, Pages 1398-1403, 10.1109/CDC.2013.6760078, 2013.

  • Sen S, Murray RM, “Performance Metrics for a Biomolecular Step Response”, 51st IEEE Conference on Decision and Control, Pages 5536-5541, 10.1109/CDC.2012.6425892, 2012.

  • Sen S, “Tradeoffs in Simple Biomolecular Signaling Systems”, Systems & Control Letters, 61(8), Pages 834-838, 10.1016/j.sysconle.2012.04.011, 2012.

  • Sen S, García-Ojalvo J, Elowitz MB, “Dynamical Consequences of Bandpass Feedback Loops in a Bacterial Phosphorelay”, PLoS ONE 6(9): e25102, doi:10.1371/journal.pone.0025102, 2011.

  • Sen S, “Regulatory Consequences of Bandpass Feedback in a Bacterial Phosphorelay”, Ph.D. Dissertation, California Institute of Technology.