BioRxToolbox: A computational framework to streamline genetic circuit design in molecular data communications

Durmaz, Merve Gorkem; Tulluk, Neval; Aksoy, Recep Deniz; Yilmaz, H Birkan; Yang, Bill; Wipat, Anil; Pusane, Ali Emre; Mısırlı, Göksel; Tugcu, Tuna

Abstract

Developments in bioengineering and nanotechnology have ignited the research on biological and molecular communication systems. Despite potential benefits, engineering communication systems to carry data signals using biological messenger molecules and engineered cells is challenging. Di↵using molecules may fall behind their schedule to arrive at the receiver, interfering with symbols of subsequent time slots and distorting the signal. Existing theoretical molecular communication models often focus solely on the characteristics of a communication channel and fail to provide an end-to-end system response since they assume a simple thresholding process for a receiver cell and overlook how the receiver can detect the incoming distorted molecular signal. In this paper, we present a model-based and computational framework called BioRxToolbox for designing di↵usion-based and end-to-end molecular communication systems coupled with synthetic genetic circuits. We describe a novel framework to encode information as a sequence of bits, each transmitted from the sender as a burst of molecules, control cellular behavior at the receiver, and minimize cellular signal interference by employing equalization techniques from communication theory. This approach allows the encoding and decoding of data bits eciently using two di↵erent types of molecules that act as the data carrier and the antagonist to cancel out the heavy tail of the former. Here, BioRxToolbox is demonstrated using a biological design and computational simulations for various communication scenarios. This toolbox facilitates automating the choice of communication parameters and identifying the best communication scenarios that can produce ecient cellular signals.

Citation

Durmaz, M. G., Tulluk, N., Aksoy, R. D., Yilmaz, H. B., Yang, B., Wipat, A., Pusane, A. E., Mısırlı, G., & Tugcu, T. (in press). BioRxToolbox: A computational framework to streamline genetic circuit design in molecular data communications. Synthetic Biology, https://doi.org/10.1093/synbio/ysae015

• Journal Article Type: Article
• Acceptance Date: Nov 6, 2024
• Online Publication Date: Nov 7, 2024
• Deposit Date: Nov 7, 2024
• Publicly Available Date: Nov 7, 2024
• Journal: Synthetic Biology
• Electronic ISSN: 2397-7000
• Publisher: Oxford University Press (OUP)
• Peer Reviewed: Peer Reviewed
• DOI: https://doi.org/10.1093/synbio/ysae015
• Keywords: Molecular communications; genetic circuits; model-driven design; receiver design, intersymbol interference
• Public URL: https://keele-repository.worktribe.com/output/973458