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Publications about 'synchronization'
Articles in journal or book chapters
  1. Z. Aminzare and E.D. Sontag. Some remarks on spatial uniformity of solutions of reaction-diffusion PDEs. Nonlinear Analysis, 147:125-144, 2016. [PDF] Keyword(s): contractions, contractive systems, matrix measures, logarithmic norms, synchronization, consensus, reaction-diffusion PDEs, partial differential equations.
    Abstract:
    This paper presents a condition which guarantees spatial uniformity for the asymptotic behavior of the solutions of a reaction diffusion partial differential equation (PDE) with Neumann boundary conditions in one dimension, using the Jacobian matrix of the reaction term and the first Dirichlet eigenvalue of the Laplacian operator on the given spatial domain. The estimates are based on logarithmic norms in non-Hilbert spaces, which allow, in particular for a class of examples of interest in biology, tighter estimates than other previously proposed methods.


  2. E.V. Nikolaev and E.D. Sontag. Quorum-sensing synchronization of synthetic toggle switches: A design based on monotone dynamical systems theory. PLoS Computational Biology, 12:e1004881, 2016. [PDF] Keyword(s): quorum sensing, toggle switches, monotone systems.
    Abstract:
    Synthetic constructs in biotechnology, bio-computing, and proposed gene therapy interventions are often based on plasmids or transfected circuits which implement some form of on-off (toggle or flip-flop) switch. For example, the expression of a protein used for therapeutic purposes might be triggered by the recognition of a specific combination of inducers (e.g., antigens), and memory of this event should be maintained across a cell population until a specific stimulus commands a coordinated shut-off. The robustness of such a design is hampered by molecular (intrinsic) or environmental (extrinsic) noise, which may lead to spontaneous changes of state in a subset of the population and is reflected in the bimodality of protein expression, as measured for example using flow cytometry. In this context, a majority-vote correction circuit, which brings deviant cells back into the required state, is highly desirable. To address this concrete challenge, we have developed a new theoretical design for quorum-sensing (QS) synthetic toggles. QS provides a way for cells to broadcast their states to the population as a whole so as to facilitate consensus. Our design is endowed with strong theoretical guarantees, based on monotone dynamical systems theory, of global stability and no oscillations, and which leads to robust consensus states.


  3. Z. Aminzare, Y. Shafi, M. Arcak, and E.D. Sontag. Guaranteeing spatial uniformity in reaction-diffusion systems using weighted $L_2$-norm contractions. In V. Kulkarni, G.-B. Stan, and K. Raman, editors, A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations, pages 73-101. Springer-Verlag, 2014. [PDF] Keyword(s): contractions, contractive systems, Turing instabilities, diffusion, partial differential equations, synchronization.
    Abstract:
    This paper gives conditions that guarantee spatial uniformity of the solutions of reaction-diffusion partial differential equations, stated in terms of the Jacobian matrix and Neumann eigenvalues of elliptic operators on the given spatial domain, and similar conditions for diffusively-coupled networks of ordinary differential equations. Also derived are numerical tests making use of linear matrix inequalities that are useful in certifying these conditions.


  4. Z. Aminzare and E.D. Sontag. Synchronization of diffusively-connected nonlinear systems: results based on contractions with respect to general norms. IEEE Transactions on Network Science and Engineering, 1(2):91-106, 2014. [PDF] Keyword(s): matrix measures, logarithmic norms, synchronization, consensus, contractions, contractive systems.
    Abstract:
    Contraction theory provides an elegant way to analyze the behavior of certain nonlinear dynamical systems. In this paper, we discuss the application of contraction to synchronization of diffusively interconnected components described by nonlinear differential equations. We provide estimates of convergence of the difference in states between components, in the cases of line, complete, and star graphs, and Cartesian products of such graphs. We base our approach on contraction theory, using matrix measures derived from norms that are not induced by inner products. Such norms are the most appropriate in many applications, but proofs cannot rely upon Lyapunov-like linear matrix inequalities, and different techniques, such as the use of the Perron-Frobenious Theorem in the cases of L1 or L-infinity norms, must be introduced.


  5. Z. Aminzare and E.D. Sontag. Logarithmic Lipschitz norms and diffusion-induced instability. Nonlinear Analysis: Theory, Methods & Applications, 83:31-49, 2013. [PDF] Keyword(s): contractions, contractive systems, matrix measures, logarithmic norms, Turing instabilities, diffusion, partial differential equations, synchronization.
    Abstract:
    This paper proves that ordinary differential equation systems that are contractive with respect to $L^p$ norms remain so when diffusion is added. Thus, diffusive instabilities, in the sense of the Turing phenomenon, cannot arise for such systems, and in fact any two solutions converge exponentially to each other. The key tools are semi-inner products and logarithmic Lipschitz constants in Banach spaces. An example from biochemistry is discussed, which shows the necessity of considering non-Hilbert spaces. An analogous result for graph-defined interconnections of systems defined by ordinary differential equations is given as well.


  6. G. Russo, M. di Bernardo, and E.D. Sontag. A contraction approach to the hierarchical analysis and design of networked systems. IEEE Transactions Autom. Control, 58:1328-1331, 2013. [PDF] Keyword(s): contractions, contractive systems, matrix measures, logarithmic norms, synchronization, systems biology.
    Abstract:
    This paper studies networks of components, and shows that a contraction property on the interconnection matrix, coupled with contractivity of the individual component subsystems, suffices to insure contractivity of the overall system.


  7. M. Miller, M. Hafner, E.D. Sontag, N. Davidsohn, S. Subramanian, P. E. M. Purnick, D. Lauffenburger, and R. Weiss. Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity. PLoS Computational Biology, 8:e1002579-, 2012. [PDF] Keyword(s): systems biology, homeostasis, stem cells, synthetic biology.
    Abstract:
    Synthetic biology efforts have largely focused on small engineered gene networks, yet understanding how to integrate multiple synthetic modules and interface them with endogenous pathways remains a challenge. Here we present the design, system integration, and analysis of several large scale synthetic gene circuits for artificial tissue homeostasis. Diabetes therapy represents a possible application for engineered homeostasis, where genetically programmed stem cells maintain a steady population of beta-cells despite continuous turnover. We develop a new iterative process that incorporates modular design principles with hierarchical performance optimization targeted for environments with uncertainty and incomplete information. We employ theoretical analysis and computational simulations of multicellular reaction/diffusion models to design and understand system behavior, and find that certain features often associated with robustness (e.g., multicellular synchronization and noise attenuation) are actually detrimental for tissue homeostasis. We overcome these problems by engineering a new class of genetic modules for 'synthetic cellular heterogeneity' that function to generate beneficial population diversity. We design two such modules (an asynchronous genetic oscillator and a signaling throttle mechanism), demonstrate their capacity for enhancing robust control, and provide guidance for experimental implementation with various computational techniques. We found that designing modules for synthetic heterogeneity can be complex, and in general requires a framework for non-linear and multifactorial analysis. Consequently, we adapt a 'phenotypic sensitivity analysis' method to determine how functional module behaviors combine to achieve optimal system performance. We ultimately combine this analysis with Bayesian network inference to extract critical, causal relationships between a module's biochemical rate-constants, its high level functional behavior in isolation, and its impact on overall system performance once integrated.


  8. E.D. Sontag. Contractive systems with inputs. In Jan Willems, Shinji Hara, Yoshito Ohta, and Hisaya Fujioka, editors, Perspectives in Mathematical System Theory, Control, and Signal Processing, pages 217-228. Springer-verlag, 2010. [PDF] Keyword(s): contractions, contractive systems, consensus, synchronization.
    Abstract:
    Contraction theory provides an elegant way of analyzing the behaviors of systems subject to external inputs. Under sometimes easy to check hypotheses, systems can be shown to have the incremental stability property that all trajectories converge to a unique solution. This property is especially interesting when forcing functions are periodic (globally attracting limit cycles result), as well as in the context of establishing synchronization results. The present paper provides a self-contained introduction to some basic results, with a focus on contractions with respect to non-Euclidean metrics.


  9. L. Scardovi, M. Arcak, and E.D. Sontag. Synchronization of interconnected systems with applications to biochemical networks: an input-output approach. IEEE Transactions Autom. Control, 55:1367-1379, 2010. [PDF]
    Abstract:
    This paper provides synchronization conditions for networks of nonlinear systems, where each component of the network itself consists of subsystems represented as operators in the extended L2 space. The synchronization conditions are provided by combining the input-output properties of the subsystems with information about the structure of network. The paper also explores results for state-space models as well as biochemical applications. The work is motivated by cellular networks where signaling occurs both internally, through interactions of species, and externally, through intercellular signaling.


  10. 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, 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.


Conference articles
  1. Z. Aminzare and E.D. Sontag. Contraction methods for nonlinear systems: A brief introduction and some open problems. In Proc. IEEE Conf. Decision and Control, Los Angeles, Dec. 2014, pages 3835-3847, 2014. [PDF] Keyword(s): contractions, contractive systems, stability, reaction-diffusion PDE's, synchronization, contractive systems, stability.
    Abstract:
    Contraction theory provides an elegant way to analyze the behaviors of certain nonlinear dynamical systems. Under sometimes easy to check hypotheses, systems can be shown to have the incremental stability property that trajectories converge to each other. The present paper provides a self-contained introduction to some of the basic concepts and results in contraction theory, discusses applications to synchronization and to reaction-diffusion partial differential equations, and poses several open questions.


  2. Z. Aminzare and E.D. Sontag. Remarks on diffusive-link synchronization using non-Hilbert logarithmic norms. In Proc. IEEE Conf. Decision and Control, Los Angeles, Dec. 2014, pages 6086-6091, 2014. Keyword(s): contractions, contractive systems, stability, reaction-diffusion PDE's, synchronization.
    Abstract:
    In this paper, we sketch recent results for synchronization in a network of identical ODE models which are diffusively interconnected. In particular, we provide estimates of convergence of the difference in states between components, in the cases of line, complete, and star graphs, and Cartesian products of such graphs.


  3. Y. Shafi, Z. Aminzare, M. Arcak, and E.D. Sontag. Spatial uniformity in diffusively-coupled systems using weighted L2 norm contractions. In Proc. American Control Conference, pages 5639-5644, 2013. [PDF] Keyword(s): contractions, contractive systems, matrix measures, logarithmic norms, Turing instabilities, diffusion, partial differential equations, synchronization.
    Abstract:
    We present conditions that guarantee spatial uniformity in diffusively-coupled systems. Diffusive coupling is a ubiquitous form of local interaction, arising in diverse areas including multiagent coordination and pattern formation in biochemical networks. The conditions we derive make use of the Jacobian matrix and Neumann eigenvalues of elliptic operators, and generalize and unify existing theory about asymptotic convergence of trajectories of reaction-diffusion partial differential equations as well as compartmental ordinary differential equations. We present numerical tests making use of linear matrix inequalities that may be used to certify these conditions. We discuss an example pertaining to electromechanical oscillators. The paper's main contributions are unified verifiable relaxed conditions that guarantee synchrony.


  4. G. Russo, M. di Bernardo, and E.D. Sontag. Stability of networked systems: a multi-scale approach using contraction. In Proc. IEEE Conf. Decision and Control, Atlanta, Dec. 2010, pages FrB14.3, 2010. Keyword(s): contractive systems, contractions, systems biology, biochemical networks, synchronization.
    Abstract:
    Preliminary conference version of ''A contraction approach to the hierarchical analysis and design of networked systems''.


  5. L. Scardovi, M. Arcak, and E.D. Sontag. Synchronization of interconnected systems with an input-output approach. Part I: Main results. In Proc. IEEE Conf. Decision and Control, Shanhai, Dec. 2009, pages 609-614, 2009. Note: First part of conference version of journal paper.Keyword(s): passive systems, secant condition, biochemical networks, systems biology.
    Abstract:
    See abstract and link to pdf in entry for Journal paper.


  6. L. Scardovi, M. Arcak, and E.D. Sontag. Synchronization of interconnected systems with an input-output approach. Part II: State-Space result and application to biochemical networks. In Proc. IEEE Conf. Decision and Control, Shanhai, Dec. 2009, pages 615-620, 2009. Note: Second part of conference version of journal paper.Keyword(s): passive systems, secant condition, biochemical networks, systems biology.
    Abstract:
    See abstract and link to pdf in entry for Journal paper.



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Last modified: Thu Nov 23 10:40:57 2017
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