Noise-aided computation within a synthetic gene network through morphable and robust logic gates.

School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287-9709, USA.
Physical Review E (Impact Factor: 2.31). 04/2011; 83(4 Pt 1):041909. DOI: 10.1103/PhysRevE.83.041909
Source: PubMed

ABSTRACT An important goal for synthetic biology is to build robust and tunable genetic regulatory networks that are capable of performing assigned operations, usually in the presence of noise. In this work, a synthetic gene network derived from the bacteriophage λ underpins a reconfigurable logic gate wherein we exploit noise and nonlinearity through the application of the logical stochastic resonance paradigm. This biological logic gate can emulate or "morph" the AND and OR operations through varying internal system parameters in a noisy background. Such genetic circuits can afford intriguing possibilities in the realization of engineered genetic networks in which the actual function of the gate can be changed after the network has been built, via an external control parameter. In this article, the full system characterization is reported, with the logic gate performance studied in the presence of external and internal noise. The robustness of the gate, to noise, is studied and illustrated through numerical simulations.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The logical operations are one of the key issues in today’s computer architecture. Nowadays, there is a great interest in developing alternative ways to get the logic operations by chaos computing. In this paper, a novel implementation method of reconfigurable logic gates based on one-parameter families of chaotic maps is introduced. The special behavior of these chaotic maps can be utilized to provide same threshold voltage for all logic gates. However, there is a wide interval for choosing a control parameter for all reconfigurable logic gates. Furthermore, an experimental implementation of this nonlinear system is presented to demonstrate the robustness of computing capability of chaotic circuits.
    Chaos Solitons & Fractals 12/2014; 69:74–80. DOI:10.1016/j.chaos.2014.08.011 · 1.50 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: We consider the stochastic response of a nonlinear dynamical system towards a combination of input signals. The response can assume binary values if the state of the system is considered to be the output and the system can make transitions between two states separated by an energetic or entropic barrier. We show how the input-output correspondence can be controlled by an external exponentially correlated dichotomous noise optimizing the logical response which exhibits a maximum at an intermediate value of correlation time. This resonance manifests itself as a "logical" resonance correlation effect and sets the condition for performance of the stochastic system as a logic gate. The role of asymmetry of the dichotomous noise is examined and the results on numerical simulations are correlated with a two-state model using a master equation approach.
    Physical Review E 09/2013; 88(3-1):032122. DOI:10.1103/PhysRevE.88.032122 · 2.31 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Four acrylamide polymer flocculants, anionic polyacrylamide P(AA-co-AM), cationic polyacrylamide P(DMB-co-AM), nonionic polyacrylamide P(AM), and hydrophobical polyacrylamide P(OA-co-AM) have been prepared by copolymerizing with acrylic acid, cationic monomer dimethylethyl (acryloxyethyl) ammonium bromide (DMB) and hydrophobical monomer octadecyl acrylate with acrylamide. The interactions between the flocculants with the (012) surface of alumina crystal (Al2O3) have been simulated by molecular dynamics method. All the polymers can bind tightly with Al2O3 crystal, the interaction between the O of polymers and Al of the (012) surface of Al2O3 is significantly strong. The order of binding energy is as follows: P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), implying a better flocculation performance of P(DMB-co-AM) than the others. Analysis indicates that binding energy is mainly determined by Coulomb interaction. Bonds are found between the O atoms of the polymers and the Al atoms of Al2O3. The polymers' structures deform when they combine with Al2O3 crystal, but the deformation energies are low and far less than non-bonding energies. Flocculation experiments in suspension medium of 1%Kaolin show a transmittancy of 90.8% for 6 mg/L P(DMB-co-AM) and 73.0% for P(AM). The sequence of flocculation performance of four polymers is P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), which is in excellent agreement with the simulation results of binding energy.
    Chinese journal of chemical physics 10/2012; 25(5):10-. DOI:10.1088/1674-0068/25/05/571-576 · 0.72 Impact Factor