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Publications of Eduardo D. Sontag jointly with A.P. Tran
Articles in journal or book chapters
  1. A.P. Tran, M. Ali Al-Radhawi, E. Ernst, and E.D. Sontag. Optimization of heuristic logic synthesis by iteratively reducing circuit substructures using a database of optimal implementations. 2021. Note: Submitted. Keyword(s): Heuristic logic minimizer, Boolean circuit reduction, optimal synthesis, logic optimization, synthetic biology.
    Abstract:
    Minimal synthesis of Boolean functions is an NP-hard problem, and heuristic approaches typically give suboptimal circuits. However, in the emergent field of synthetic biology, genetic logic designs that use even a single additional Boolean gate can render a circuit unimplementable in a cell. This has led to a renewed interest in the field of optimal multilevel Boolean synthesis. For small numbers (1-4) of inputs, an exhaustive search is possible, but this is impractical for large circuits. In this work, we demonstrate that even though it is challenging to build a database of optimal implementations for anything larger than 4-input Boolean functions, a database of 4-input optimal implementations can be used to greatly reduce the number of logical gates required in larger heuristic logic synthesis implementations. The proposed algorithm combines the heuristic results with an optimal implementation database and yields average improvements of 5.16% for 5-input circuits and 4.54% for 6-input circuits on outputs provided by the logic synthesis tool extit{ABC}. In addition to the gains in the efficiency of the implemented circuits, this work also attests to the importance and practicality of the field of optimal synthesis, even if it cannot directly provide results for larger circuits. The focus of this work is on circuits made exclusively of 2-input NOR gates but the presented results are readily applicable to 2-input NAND circuits as well as (2-input) AND/NOT circuits. In addition, the framework proposed here is likely to be adaptable to other types of circuits. An implementation of the described algorithm, HLM (Hybrid Logic Minimizer), is available at https://github.com/sontaglab/HLM/.


  2. A.P. Tran, J.H. Meldon, and E.D. Sontag. Transient diffusion into a bi-layer membrane with mass transfer resistance: Exact solution and time lag analysis. Frontiers in Chemical Engineering, 2:25, 2021. [PDF] Keyword(s): Bi-layer membrane, transient diffusion, heat conduction, mass transfer resistance.
    Abstract:
    Exact analytical and closed-form solutions to a problem involving transient diffusion in a bi-layer membrane with external transfer resistance are presented. In addition to the solutions of the transient response, the lead and lag times that are often of importance in the characterization of membranes and arise from the analysis of the asymptotic behavior of the mass permeated through the membrane are also provided. The solutions presented here are also compared to previously derived limiting cases of the diffusion in a bi-layer with an impermeable wall and constant concentrations at the upstream and downstream boundaries. Analysis of the time lag shows that this membrane property is independent of the direction of flow. Finally, an outline is provided of how these solutions, which characterize the response to a step function increase in concentration, can be also used to derive more complex input conditions. Adequately handling boundary layer effects has a wide array of potential applications such as the study of bi-layer undergoing phenomena of heat convection, gas film resistance, and absorption/desorption.


  3. 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.


  4. 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.


Internal reports
  1. A. P. Tran, M. A. 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. Technical report, Cold Spring Harbor Laboratory, 2019. Note: BioRxiv 2019.12.12.874891. Keyword(s): chemotherapy, immunology, immune system, oncology, cancer, metronomic.
    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.



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Last modified: Sat Sep 18 11:53:22 2021
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