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Publications about 'Boolean'
Articles in journal or book chapters
  1. 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.


  2. 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, pp A-P, 2020. [PDF] [doi:10.1021/acssynbio.0c00228] Keyword(s): synthetic biology, transcriptional networks, gene networks, boolean circuits, boolean gates.
    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.


  3. A. Dayarian, M. Chaves, E.D. Sontag, and A. M. Sengupta. Shape, Size and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks. PLoS Computational Biology, 5:e10000256, 2009. [PDF] Keyword(s): identifiability, robust, robustness, geometry.
    Abstract:
    The concept of robustness of regulatory networks has received much attention in the last decade. One measure of robustness has been associated with the volume of the feasible region, namely, the region in the parameter space in which the system is functional. In recent work, we emphasized that topology and geometry matter, as well as volume. In this paper, and using the segment polarity gene network to illustrate our approach, we show that random walks in parameter space and how they exit the feasible region provide a rich perspective on the different modes of failure of a model. In particular, for the segment polarity network, we found that, between two alternative ways of activating Wingless, one is more robust. Our method provides a more complete measure of robustness to parameter variation. As a general modeling strategy, our approach is an interesting alternative to Boolean representation of biochemical networks.


  4. A. Maayan, R. Iyengar, and E.D. Sontag. Intracellular Regulatory Networks are close to Monotone Systems. IET Systems Biology, 2:103-112, 2008. [PDF]
    Abstract:
    We find that three intracellular regulatory networks contain far more positive "sign-consistent" feedback and feed-forward loops than negative loops. Negative inconsistent loops can be more easily removed from real regulatory network topologies compared to removing negative loops from shuffled networks. The abundance of positive feed-forward loops and feedback loops in real networks emerges from the presence of hubs that are enriched with either negative or positive links, and from the non-uniform connectivity distribution. Boolean dynamics applied to the signaling network further support the stability of its topology. These observations suggest that the "close-to-monotone" structure of intracellular regulatory networks may contribute to the dynamical stability observed in cellular behavior.


  5. E.D. Sontag, A. Veliz-Cuba, R. Laubenbacher, and A.S. Jarrah. The effect of negative feedback loops on the dynamics of Boolean networks. Biophysical Journal, 95:518-526, 2008. [PDF] Keyword(s): monotone systems, positive feedback systems, Boolean networks, limit cycles.
    Abstract:
    Feedback loops play an important role in determining the dynamics of biological networks. In order to study the role of negative feedback loops, this paper introduces the notion of "distance to positive feedback (PF-distance)" which in essence captures the number of "independent" negative feedback loops in the network, a property inherent in the network topology. Through a computational study using Boolean networks it is shown that PF-distance has a strong influence on network dynamics and correlates very well with the number and length of limit cycles in the phase space of the network. To be precise, it is shown that, as the number of independent negative feedback loops increases, the number (length) of limit cycles tends to decrease (increase). These conclusions are consistent with the fact that certain natural biological networks exhibit generally regular behavior and have fewer negative feedback loops than randomized networks with the same numbers of nodes and connectivity.


  6. M. Chaves, E.D. Sontag, and R. Albert. Methods of robustness analysis for Boolean models of gene control networks. IET Systems Biology, 153:154-167, 2006. [PDF] Keyword(s): systems biology, biochemical networks, boolean systems, identifiability, robust, robustness, geometry, Boolean, segment polarity network, gene and protein networks, hybrid systems.
    Abstract:
    As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states (expressed or not expressed) for each gene or protein in the network as well as a high level of synchronization among the various regulatory processes. In this paper, we discuss and compare two possible methods of adapting qualitative models to incorporate the continuous-time character of regulatory networks. The first method consists of introducing asynchronous updates in the Boolean model. In the second method, we adopt the approach introduced by L. Glass to obtain a set of piecewise linear differential equations which continuously describe the states of each gene or protein in the network. We apply both methods to a particular example: a Boolean model of the segment polarity gene network of Drosophila melanogaster. We analyze the dynamics of the model, and provide a theoretical characterization of the model's gene pattern prediction as a function of the timescales of the various processes.


  7. M. Chaves, R. Albert, and E.D. Sontag. Robustness and fragility of Boolean models for genetic regulatory networks. J. Theoret. Biol., 235(3):431-449, 2005. [PDF] Keyword(s): systems biology, biochemical networks, boolean systems, gene and protein networks.
    Abstract:
    Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or logical approaches. Here we propose a framework for gene regulatory networks that combines the intuitive appeal of a qualitative description of gene states with a high flexibility in incorporating stochasticity in the duration of cellular processes. We apply our methods to the regulatory network of the segment polarity genes, thus gaining novel insights into the development of gene expression patterns. For example, we show that very short synthesis and decay times can perturb the wild type pattern. On the other hand, separation of timescales between pre- and post-translational processes and a minimal prepattern ensure convergence to the wild type expression pattern regardless of fluctuations.


  8. W. Maass, G. Schnitger, and E.D. Sontag. A comparison of the computational power of sigmoid and Boolean threshold circuits. In V. P. Roychowdhury, Siu K. Y., and Orlitsky A., editors, Theoretical Advances in Neural Computation and Learning, pages 127-151. Kluwer Academic Publishers, 1994. [PDF] Keyword(s): neural networks, boolean systems.
    Abstract:
    We examine the power of constant depth circuits with sigmoid threshold gates for computing boolean functions. It is shown that, for depth 2, constant size circuits of this type are strictly more powerful than constant size boolean threshold circuits (i.e. circuits with linear threshold gates). On the other hand it turns out that, for any constant depth d, polynomial size sigmoid threshold circuits with polynomially bounded weights compute exactly the same boolean functions as the corresponding circuits with linear threshold gates.


  9. E.D. Sontag. Feedforward nets for interpolation and classification. J. Comput. System Sci., 45(1):20-48, 1992. [PDF] [doi:http://dx.doi.org/10.1016/0022-0000(92)90039-L] Keyword(s): neural networks, VC dimension, boolean systems.
    Abstract:
    This paper deals with single-hidden-layer feedforward nets, studying various aspects of classification power and interpolation capability. In particular, a worst-case analysis shows that direct input to output connections in threshold nets double the recognition but not the interpolation power, while using sigmoids rather than thresholds allows doubling both. For other measures of classification, including the Vapnik-Chervonenkis dimension, the effect of direct connections or sigmoidal activations is studied in the special case of two-dimensional inputs.


  10. E.D. Sontag. Sigmoids distinguish more efficiently than Heavisides. Neural Computation, 1:470-472, 1989. [PDF] Keyword(s): neural networks, boolean systems.
    Abstract:
    Every dichotomy on a 2k-point set in Rn can be implemented by a neural net with a single hidden layer containing k sigmoidal neurons. If the neurons were of a hardlimiter (Heaviside) type, 2k-1 would be in general needed.


Conference articles
  1. M. Chaves, E.D. Sontag, and R. Albert. Structure and timescale analysis in genetic regulatory networks. In Proc. IEEE Conf. Decision and Control, San Diego, Dec. 2006, pages 2358-2363, 2006. IEEE. [PDF] Keyword(s): genetic regulatory networks, Boolean systems, hybrid systems.
    Abstract:
    This work is concerned with the study of the robustness and fragility of gene regulation networks to variability in the timescales of the distinct biological processes involved. It explores and compares two methods: introducing asynchronous updates in a Boolean model, or integrating the Boolean rules in a continuous, piecewise linear model. As an example, the segment polarity network of the fruit fly is analyzed. A theoretical characterization is given of the model's ability to predict the correct development of the segmented embryo, in terms of the specific timescales of the various regulation interactions.


  2. W. Maass, G. Schnitger, and E.D. Sontag. On the computational power of sigmoid versus Boolean threshold circuits (extended abstract). In Proceedings of the 32nd annual symposium on Foundations of computer science, Los Alamitos, CA, USA, pages 767-776, 1991. IEEE Computer Society Press. Keyword(s): neural networks, theory of computing and complexity.


  3. E.D. Sontag. Comparing sigmoids and heavisides. In Proc. Conf. Info. Sci. and Systems, Princeton, 1990, pages 654-659, 1990. Keyword(s): neural networks, boolean systems.



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