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Publications by Eduardo D. Sontag in year 2020
Articles in journal or book chapters
  1. E.D. Sontag. Input-to-State Stability. In J. Baillieul and T. Samad, editors, Encyclopedia of Systems and Control, pages 1-9. Springer-Verlag, 2020. [PDF] Keyword(s): input to state stability, integral input to state stability, iISS, ISS, input to output stability.
    Abstract:
    The notion of input to state stability (ISS) qualitatively describes stability of the mapping from initial states and inputs to internal states (and more generally outputs). This encyclopedia-style article entry gives a brief introduction to the definition of ISS and a discussion of equivalent characterizations. It is an update of the article in the 2015 edition, including additional citations to recent PDE work.


  2. E.D. Sontag. Scale-invariance in biological sensing. In J. Baillieul and T. Samad, editors, Encyclopedia of Systems and Control, pages S1-. Springer-Verlag, 2020. [PDF] [doi:10.1007/978-1-4471-5102-9_100090-1] Keyword(s): adaptation, biological adaptation, perfect adaptation, fold-change detection.
    Abstract:
    The phenomenon of fold-change detection, or scale-invariance, is exhibited by a variety of sensory systems, in both bacterial and eukaryotic signaling pathways. This encyclopedia-style article gives a brief introduction to the subject.


  3. D.K. Agrawal, E.M. Dolan, N.E. Hernandez, K.M. Blacklock, S.D. Khare, and E.D. Sontag. Mathematical models of protease-based enzymatic biosensors. ACS Synthetic Biology, 9:198-208, 2020. [PDF] Keyword(s): synthetic biology, protease-based circuits, enzymatic circuits, systems biology, Boolean circuits.
    Abstract:
    An important goal of synthetic biology is to build biosensors and circuits with well-defined input-output relationships that operate at speeds found in natural biological systems. However, for molecular computation, most commonly used genetic circuit elements typically involve several steps from input detection to output signal production: transcription, translation, and post-translational modifications. These multiple steps together require up to several hours to respond to a single stimulus, and this limits the overall speed and complexity of genetic circuits. To address this gap, molecular frameworks that rely exclusively on post-translational steps to realize reaction networks that can process inputs at a time scale of seconds to minutes have been proposed. Here, we build mathematical models of fast biosensors capable of producing Boolean logic functionality. We employ protease-based chemical and light-induced switches, investigate their operation, and provide selection guidelines for their use as on-off switches. As a proof of concept, we implement a rapamycin-induced switch in vitro and demonstrate that its response qualitatively agrees with the predictions from our models. We then use these switches as elementary blocks, developing models for biosensors that can perform OR and XOR Boolean logic computation while using reaction conditions as tuning parameters. We use sensitivity analysis to determine the time-dependent sensitivity of the output to proteolytic and protein-protein binding reaction parameters. These fast protease-based biosensors can be used to implement complex molecular circuits with a capability of processing multiple inputs controllably and algorithmically. Our framework for evaluating and optimizing circuit performance can be applied to other molecular logic circuits.


  4. M.A. Al-Radhawi, D. Angeli, and E.D. Sontag. A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks. PLoS Computational Biology, pp 16(2): e1007681, 2020. [PDF] Keyword(s): MAPK cascades, Lyapunov functions, stability, chemical networks, chemical rection networks, systems biology.
    Abstract:
    This paper deals with the analysis of the dynamics of chemical reaction networks, developing a theoretical framework based only on graphical knowledge and applying regardless of the particular form of kinetics. It paper introduces a class of networks that are "structurally (mono) attractive", by which we mean that they are incapable of exhibiting multiple steady states, oscillation, or chaos by the virtue of their reaction graphs. These networks are characterized by the existence of a universal energy-like function which we call a Robust Lyapunov function (RLF). To find such functions, a finite set of rank-one linear systems is introduced, which form the extremals of a linear convex cone. The problem is then reduced to that of finding a common Lyapunov function for this set of extremals. Based on this characterization, a computational package, Lyapunov-Enabled Analysis of Reaction Networks (LEARN), is provided that constructs such functions or rules out their existence. An extensive study of biochemical networks demonstrates that LEARN offers a new unified framework. We study basic motifs, three-body binding, and transcriptional networks. We focus on cellular signalling networks including various post-translational modification cascades, phosphotransfer and phosphorelay networks, T-cell kinetic proofreading, ERK signaling, and the Ribosome Flow Model.


  5. M. Ali Al-Radhawi, A.P. Tran, E. Ernst, T. Chen, C.A. Voigt, and E.D. Sontag. Distributed implementation of Boolean functions by transcriptional synthetic circuits. ACS Synthetic Biology, 9:2172-2187, 2020. [PDF] [doi:10.1021/acssynbio.0c00228] Keyword(s): synthetic biology, transcriptional networks, gene networks, boolean circuits, boolean gates, systems biology.
    Abstract:
    Starting in the early 2000s, sophisticated technologies have been developed for the rational construction of synthetic genetic networks that implement specified logical functionalities. Despite impressive progress, however, the scaling necessary in order to achieve greater computational power has been hampered by many constraints, including repressor toxicity and the lack of large sets of mutually-orthogonal repressors. As a consequence, a typical circuit contains no more than roughly seven repressor-based gates per cell. A possible way around this scalability problem is to distribute the computation among multiple cell types, which communicate among themselves using diffusible small molecules (DSMs) and each of which implements a small sub-circuit. Examples of DSMs are those employed by quorum sensing systems in bacteria. This paper focuses on systematic ways to implement this distributed approach, in the context of the evaluation of arbitrary Boolean functions. The unique characteristics of genetic circuits and the properties of DSMs require the development of new Boolean synthesis methods, distinct from those classically used in electronic circuit design. In this work, we propose a fast algorithm to synthesize distributed realizations for any Boolean function, under constraints on the number of gates per cell and the number of orthogonal DSMs. The method is based on an exact synthesis algorithm to find the minimal circuit per cell, which in turn allows us to build an extensive database of Boolean functions up to a given number of inputs. For concreteness, we will specifically focus on circuits of up to 4 inputs, which might represent, for example, two chemical inducers and two light inputs at different frequencies. Our method shows that, with a constraint of no more than seven gates per cell, the use of a single DSM increases the total number of realizable circuits by at least 7.58-fold compared to centralized computation. Moreover, when allowing two DSM's, one can realize 99.995\% of all possible 4-input Boolean functions, still with at most 7 gates per cell. The methodology introduced here can be readily adapted to complement recent genetic circuit design automation software.


  6. T. Chen, M. Ali Al-Radhawi, and E.D. Sontag. A mathematical model exhibiting the effect of DNA methylation on the stability boundary in cell-fate networks. Epigenetics, 15:1-22, 2020. Note: PMID: 32842865. [PDF] [doi:10.1080/15592294.2020.1805686] Keyword(s): methylation, differentiation, epigenetics, pluripotent cells, gene regulatory networks, bistability, bistability, systems biology.
    Abstract:
    Cell-fate networks are traditionally studied within the framework of gene regulatory networks. This paradigm considers only interactions of genes through expressed transcription factors and does not incorporate chromatin modification processes. This paper introduces a mathematical model that seamlessly combines gene regulatory networks and DNA methylation, with the goal of quantitatively characterizing the contribution of epigenetic regulation to gene silencing. The ``Basin of Attraction percentage'' is introduced as a metric to quantify gene silencing abilities. As a case study, a computational and theoretical analysis is carried out for a model of the pluripotent stem cell circuit as well as a simplified self-activating gene model. The results confirm that the methodology quantitatively captures the key role that methylation plays in enhancing the stability of the silenced gene state.


  7. J.L. Gevertz, J.M. Greene, C Hixahuary Sanchez Tapia, and E D Sontag. A novel COVID-19 epidemiological model with explicit susceptible and asymptomatic isolation compartments reveals unexpected consequences of timing social distancing. Journal of Theoretical Biology, 510:110539, 2020. [WWW] [PDF] Keyword(s): epidemiology, COVID-19, COVID, systems biology.
    Abstract:
    Motivated by the current COVID-19 epidemic, this work introduces an epidemiological model in which separate compartments are used for susceptible and asymptomatic "socially distant" populations. Distancing directives are represented by rates of flow into these compartments, as well as by a reduction in contacts that lessens disease transmission. The dynamical behavior of this system is analyzed, under various different rate control strategies, and the sensitivity of the basic reproduction number to various parameters is studied. One of the striking features of this model is the existence of a critical implementation delay in issuing separation mandates: while a delay of about four weeks does not have an appreciable effect, issuing mandates after this critical time results in a far greater incidence of infection. In other words, there is a nontrivial but tight "window of opportunity" for commencing social distancing. Different relaxation strategies are also simulated, with surprising results. Periodic relaxation policies suggest a schedule which may significantly inhibit peak infective load, but that this schedule is very sensitive to parameter values and the schedule's frequency. Further, we considered the impact of steadily reducing social distancing measures over time. We find that a too-sudden reopening of society may negate the progress achieved under initial distancing guidelines, if not carefully designed.


  8. J. M. Greene, C. Sanchez-Tapia, and E.D. Sontag. Mathematical details on a cancer resistance model. Frontiers in Bioengineering and Biotechnology, 8:501: 1-27, 2020. [PDF] [doi:10.3389/fbioe.2020.00501] Keyword(s): resistance, chemotherapy, phenotype, optimal control, singular controls, cancer, oncology, systems biology.
    Abstract:
    One of the most important factors limiting the success of chemotherapy in cancer treatment is the phenomenon of drug resistance. We have recently introduced a framework for quantifying the effects of induced and non-induced resistance to cancer chemotherapy. In this work, we expound on the details relating to an optimal control problem outlined in our previous paper (Greene et al., 2018). The control structure is precisely characterized as a concatenation of bang-bang and path-constrained arcs via the Pontryagin Maximum Principle and differential Lie algebraic techniques. A structural identifiability analysis is also presented, demonstrating that patient-specific parameters may be measured and thus utilized in the design of optimal therapies prior to the commencement of therapy. For completeness, a detailed analysis of existence results is also included.


  9. E.A. Hernandez-Vargas, G. Giordano, E. D. Sontag, J. G. Chase, H. Chang, and A. Astolfi. First special section on systems and control research efforts against COVID-19 and future pandemics. Annual Reviews in Control, 50:343-344, 2020. [WWW] [doi:https://doi.org/10.1016/j.arcontrol.2020.10.007] Keyword(s): SARS-CoV-2, COVID-19, Modelling, Control, Pandemics.


  10. J. Miller, M.A. Al-Radhawi, and E.D. Sontag. Mediating ribosomal competition by splitting pools. IEEE Control Systems Letters, 5:1555-1560, 2020. [PDF] Keyword(s): systems biology, synthetic biology, ribosomes, RFM.
    Abstract:
    Synthetic biology constructs often rely upon the introduction of "circuit" genes into host cells, in order to express novel proteins and thus endow the host with a desired behavior. The expression of these new genes "consumes" existing resources in the cell, such as ATP, RNA polymerase, amino acids, and ribosomes. Ribosomal competition among strands of mRNA may be described by a system of nonlinear ODEs called the Ribosomal Flow Model (RFM). The competition for resources between host and circuit genes can be ameliorated by splitting the ribosome pool by use of orthogonal ribosomes, where the circuit genes are exclusively translated by mutated ribosomes. In this work, the RFM system is extended to include orthogonal ribosome competition. This Orthogonal Ribosomal Flow Model (ORFM) is proven to be stable through the use of Robust Lyapunov Functions. The optimization problem of maximizing the weighted protein translation rate by adjusting allocation of ribosomal species is formulated and implemented. Note: publsihed Nov 2020, even though journal reprint says "Nov 2021".


  11. E.D. Sontag. Bell-shaped dose response for a system with no IFFLs. bioRxiv, 2020. [PDF] Keyword(s): IFFL, feedforward loops, nonlinear systems, immunology.
    Abstract:
    It is well known that the presence of an incoherent feedforward loop (IFFL) in a network may give rise to a steady state non-monotonic dose response. This note shows that the converse implication does not hold. It gives an example of a three-dimensional system that has no IFFLs, yet its dose response is bell-shaped. It also studies under what conditions the result is true for two-dimensional systems, in the process recovering, in far more generality, a result given in the T-cell activation literature.


  12. A.P. Tran, M. Ali Al-Radhawi, I. Kareva, J. Wu, D.J. Waxman, and E.D. Sontag. Delicate balances in cancer chemotherapy: Modeling immune recruitment and emergence of systemic drug resistance. Frontiers in Immunology, 11:1376-, 2020. [PDF] [doi:10.3389/fimmu.2020.01376] Keyword(s): metronomic chemotherapy, cyclophosphamide, mathematical modeling, immune recruitment, cancer, resistance, oncology, immunology, systems biology.
    Abstract:
    Metronomic chemotherapy can drastically enhance immunogenic tumor cell death. However, the responsible mechanisms are still incompletely understood. Here, we develop a mathematical model to elucidate the underlying complex interactions between tumor growth, immune system activation, and therapy-mediated immunogenic cell death. Our model is conceptually simple, yet it provides a surprisingly excellent fit to empirical data obtained from a GL261 mouse glioma model treated with cyclophosphamide on a metronomic schedule. The model includes terms representing immune recruitment as well as the emergence of drug resistance during prolonged metronomic treatments. Strikingly, a fixed set of parameters, not adjusted for individuals nor for drug schedule, excellently recapitulates experimental data across various drug regimens, including treatments administered at intervals ranging from 6 to 12 days. Additionally, the model predicts peak immune activation times, rediscovering experimental data that had not been used in parameter fitting or in model construction. The validated model was then used to make predictions about expected tumor-immune dynamics for novel drug administration schedules. Notably, the validated model suggests that immunostimulatory and immunosuppressive intermediates are responsible for the observed phenomena of resistance and immune cell recruitment, and thus for variation of responses with respect to different schedules of drug administration.


  13. A.L. Williams, J.E. Fitzgerald, F. Ivich, E.D. Sontag, and M. Niedre. Short-term circulating tumor cell dynamics in mouse xenograft models and implications for liquid biopsy. Frontiers in Oncology, 10:2447-, 2020. [PDF] [doi:10.3389/fonc.2020.601085] Keyword(s): circulating tumor cells, liquid biopsy, cancer, oncology, multiple myeloma, systems biology.
    Abstract:
    Circulating tumor cells (CTCs) are widely studied using liquid biopsy methods that analyze single, fractionally-small peripheral blood (PB) samples. However, little is known about fluctuations in CTC numbers that occur over short timescales in vivo, and how these may affect accurate enumeration from blood samples. Diffuse in vivo flow cytometry (DiFC) developed by the Niedre lab allows continuous, non-invasive counting of rare, green fluorescent protein expressing CTCs in large deeply-seated blood vessels in mice. Here, DiFC is used to study short-term changes in CTC numbers in multiple myeloma and Lewis lung carcinoma xenograft models. Both 35- to 50-minute data sets are analyzed, with intervals corresponding to approximately 1, 5, 10 and 20\% of the PB volume, as well as changes over 24-hour periods. For rare CTCs, the use of short DiFC intervals (corresponding to small PB samples) frequently resulted in no detections. For more abundant CTCs, CTC numbers frequently varied by an order of magnitude or more over the time-scales considered. This variability far exceeded that expected by Poisson statistics, and instead was consistent with rapidly changing mean numbers of CTCs in the PB. Because of these natural temporal changes, accurately enumerating CTCs from fractionally small blood samples is inherently problematic. The problem is likely to be compounded for multicellular CTC clusters or specific CTC subtypes. However, it is also shown that enumeration can be improved by averaging multiple samples, analysis of larger volumes, or development of new methods for enumeration of CTCs directly in vivo.



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Last modified: Thu Jun 3 23:14:07 2021
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