TY - GEN
T1 - End-to-end molecular communication channels in cell metabolism
T2 - 4th ACM International Conference on Nanoscale Computing and Communication, NanoCom 2017
AU - Sakkaf, Zahmeeth
AU - Catlett, Jennie L.
AU - Cashman, Mikaela
AU - Pierobon, Massimiliano
AU - Buan, Nicole R.
AU - Cohen, Myra B.
AU - Kelley, Christine A.
N1 - Funding Information:
We have applied our methodology to two important microorganisms present in the human gut, whose behavior has been liked to obesity. Our results demonstrate that different chemical compounds present in the environment are associated with different amounts of information propagated through the aforementioned channels, and therefore their variations result in different consequences on cell behavior. In future work we plan to realize a complete communication model of these channels, by taking into account their dynamic behaviors and associated noise. ACKNOWLEDGMENTS This work was supported by the US NSF through grants MCB-1449014, EPSCoR EPS-1004094, and CCF-1161767, and the NIH through grant 1-P20-GM113126-01. We also thank Aditya Immaneni for providing constrictive feedback for the data analysis and coding. REFERENCES
PY - 2017/9/27
Y1 - 2017/9/27
N2 - The opportunity to control and fine-tune the behavior of biological cells is a fascinating possibility for many diverse disciplines, ranging from medicine and ecology, to chemical industry and space exploration. While synthetic biology is providing novel tools to reprogram cell behavior from their genetic code, many challenges need to be solved before it can become a true engineering discipline, such as reliability, safety assurance, reproducibility and stability. This paper aims to understand the limits in the controllability of the behavior of a natural (non-engineered) biological cell. In particular, the focus is on cell metabolism, and its natural regulation mechanisms, and their ability to react and change according to the chemical characteristics of the external environment. To understand the aforementioned limits of this ability, molecular communication is used to abstract biological cells into a series of channels that propagate information on the chemical composition of the extracellular environment to the cell's behavior in terms of uptake and consumption of chemical compounds, and growth rate. This provides an information-theoretic framework to analyze the upper bound limit to the capacity of these channels to propagate information, which is based on a well-known and computationally efficient metabolic simulation technique. A numerical study is performed on two human gut microbes, where the upper bound is estimated for different environmental compounds, showing there is a potential for future practical applications.
AB - The opportunity to control and fine-tune the behavior of biological cells is a fascinating possibility for many diverse disciplines, ranging from medicine and ecology, to chemical industry and space exploration. While synthetic biology is providing novel tools to reprogram cell behavior from their genetic code, many challenges need to be solved before it can become a true engineering discipline, such as reliability, safety assurance, reproducibility and stability. This paper aims to understand the limits in the controllability of the behavior of a natural (non-engineered) biological cell. In particular, the focus is on cell metabolism, and its natural regulation mechanisms, and their ability to react and change according to the chemical characteristics of the external environment. To understand the aforementioned limits of this ability, molecular communication is used to abstract biological cells into a series of channels that propagate information on the chemical composition of the extracellular environment to the cell's behavior in terms of uptake and consumption of chemical compounds, and growth rate. This provides an information-theoretic framework to analyze the upper bound limit to the capacity of these channels to propagate information, which is based on a well-known and computationally efficient metabolic simulation technique. A numerical study is performed on two human gut microbes, where the upper bound is estimated for different environmental compounds, showing there is a potential for future practical applications.
KW - Cell metabolism
KW - Information theory
KW - Molecular communication
UR - http://www.scopus.com/inward/record.url?scp=85034734722&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85034734722&partnerID=8YFLogxK
U2 - 10.1145/3109453.3109474
DO - 10.1145/3109453.3109474
M3 - Conference contribution
AN - SCOPUS:85034734722
T3 - Proceedings of the 4th ACM International Conference on Nanoscale Computing and Communication, NanoCom 2017
BT - Proceedings of the 4th ACM International Conference on Nanoscale Computing and Communication, NanoCom 2017
PB - Association for Computing Machinery, Inc
Y2 - 27 September 2017 through 29 September 2017
ER -