Logical stochastic resonance with correlated internal and external noises in a synthetic biological logic block

Abstract

Following the advent of synthetic biology, several gene networks have been engineered to emulate digital devices, with the ability to program cells for different applications. In this work, we adapt the concept of logical stochastic resonance to a synthetic gene network derived from a bacteriophage λ. The intriguing results of this study show that it is possible to build a biological logic block that can emulate or switch from the AND to the OR gate functionalities through externally tuning the system parameters. Moreover, this behavior and the robustness of the logic gate are underpinned by the presence of an optimal amount of random fluctuations. We extend our earlier work in this field, by taking into account the effects of correlated external (additive) and internal (multiplicative or state-dependent) noise. Results obtained through analytical calculations as well as numerical simulations are presented.

Emotion: the Self-regulatory Sense

“…(Others have termed this the “sense signal” which is then compared to an inner “reference signal,” triggering the “error signal.” 89 ) These changes are then indeed compared to the desired states and reaction thresholds (basal homeostatic and limiter motifs of negative feedback, shown at right); which triggers a corrective response that reverses the trend, bringing the system back into balance (like the home furnace). While perhaps neglected in cybernetic models of human behavior, this coupled feedback configuration has been noted elsewhere and deemed a biological logic gate or block that can switch from the “and” to the “or” functions, 141 the logic circuitry of the electrical transistors in computer chips.…”

Introduction to Focus Issue: Nonlinear and Stochastic Physics in Biology

“…The inclusion of several studies in this issue applying stochastic dynamics to gene networks and systems biology is indicative of the extent to which stochastic dynamics has extended its reach in recent years. Dari et al 72 offer a genetic module that can perform the AND/OR gate functionalities in the presence of noise, following the logical stochastic resonance paradigm. The effects of connection topology and time-delayed coupling on the dynamics of genetic regulatory small-world networks are studied by Yang et al 73 For a fixed network topology, the phenomenon of delay-induced resonance is revealed.…”

Emotion: The self-regulatory sense

“…89 ) These changes are then indeed compared to the desired states and reaction thresholds (basal homeostatic and limiter motifs of negative feedback, shown at right); which triggers a corrective response that reverses the trend, bringing the system back into balance (like the home furnace). While perhaps neglected in cybernetic models of human behavior, this coupled feedback configuration has been noted elsewhere and deemed a biological logic gate or block that can switch from the "and" to the "or" functions, 141 the logic circuitry of the electrical transistors in computer chips.…”