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Action and power efficiency in self-organization: The case for growth efficiency as a cellular objective in escherichia coli

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Standard

Action and power efficiency in self-organization : The case for growth efficiency as a cellular objective in escherichia coli. / Georgiev, Georgi Yordanov; Aho, Tommi; Kesseli, Juha; Yli-Harja, Olli; Kauffman, Stuart A.

Evolution, Development and Complexity - Multiscale Evolutionary Models of Complex Adaptive Systems. toim. / Claudio L. Flores Martinez; Georgi Yordanov Georgiev; John M. Smart; Michael E. Price. Springer, 2019. s. 229-244 (Springer Proceedings in Complexity).

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Harvard

Georgiev, GY, Aho, T, Kesseli, J, Yli-Harja, O & Kauffman, SA 2019, Action and power efficiency in self-organization: The case for growth efficiency as a cellular objective in escherichia coli. julkaisussa CL Flores Martinez, GY Georgiev, JM Smart & ME Price (toim), Evolution, Development and Complexity - Multiscale Evolutionary Models of Complex Adaptive Systems. Springer Proceedings in Complexity, Springer, Sivut 229-244, Cancun, Meksiko, 17/09/17. https://doi.org/10.1007/978-3-030-00075-2_8

APA

Georgiev, G. Y., Aho, T., Kesseli, J., Yli-Harja, O., & Kauffman, S. A. (2019). Action and power efficiency in self-organization: The case for growth efficiency as a cellular objective in escherichia coli. teoksessa C. L. Flores Martinez, G. Y. Georgiev, J. M. Smart, & M. E. Price (Toimittajat), Evolution, Development and Complexity - Multiscale Evolutionary Models of Complex Adaptive Systems (Sivut 229-244). (Springer Proceedings in Complexity). Springer. https://doi.org/10.1007/978-3-030-00075-2_8

Vancouver

Georgiev GY, Aho T, Kesseli J, Yli-Harja O, Kauffman SA. Action and power efficiency in self-organization: The case for growth efficiency as a cellular objective in escherichia coli. julkaisussa Flores Martinez CL, Georgiev GY, Smart JM, Price ME, toimittajat, Evolution, Development and Complexity - Multiscale Evolutionary Models of Complex Adaptive Systems. Springer. 2019. s. 229-244. (Springer Proceedings in Complexity). https://doi.org/10.1007/978-3-030-00075-2_8

Author

Georgiev, Georgi Yordanov ; Aho, Tommi ; Kesseli, Juha ; Yli-Harja, Olli ; Kauffman, Stuart A. / Action and power efficiency in self-organization : The case for growth efficiency as a cellular objective in escherichia coli. Evolution, Development and Complexity - Multiscale Evolutionary Models of Complex Adaptive Systems. Toimittaja / Claudio L. Flores Martinez ; Georgi Yordanov Georgiev ; John M. Smart ; Michael E. Price. Springer, 2019. Sivut 229-244 (Springer Proceedings in Complexity).

Bibtex - Lataa

@inproceedings{884013f8045545ad9772e9233f023661,
title = "Action and power efficiency in self-organization: The case for growth efficiency as a cellular objective in escherichia coli",
abstract = "Complex systems of different nature self-organize using common mechanisms. One of those is increase of their efficiency. The level of organization of complex systems of different nature can be measured as increased efficiency of the product of time and energy for an event, which is the amount of physical action consumed by it. Here we apply a method developed in physics to study the efficiency of biological systems. The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used constrained-based metabolic network analysis method for the prediction of cellular phenotypes. The cellular objective may vary depending on the organism and its growth conditions. It is probable that nutritionally scarce conditions are very common in the nature, and, in order to survive in those conditions, cells exhibit various highly efficient nutrient-processing systems like enzymes. In this study, we explore the efficiency of a metabolic network in transformation of substrates to new biomass, and we introduce a new objective function simulating growth efficiency. We are searching for general principles of self-organization across systems of different nature. The objective of increasing efficiency of physical action has been identified previously as driving systems toward higher levels of self-organization. The flow agents in those networks are driven toward their natural state of motion, which is governed by the principle of least action in physics. We connect this to a power efficiency principle. Systems structure themselves in a way to decrease the average amount of action or power per one event in the system. In this particular example, action efficiency is examined in the case of growth efficiency of E. coli. We derive the expression for growth efficiency as a special case of action (power) efficiency to justify it through first principles in physics. Growth efficiency as a cellular objective of E. coli coincides with previous research on complex systems and is justified by first principles in physics. It is expected and confirmed outcome of this work. We examined the properties of growth efficiency using a metabolic model for Escherichia coli. We found that the maximal growth efficiency is obtained at a finite nutrient uptake rate. The rate is substrate dependent and it typically does not exceed 20 mmol/h/gDW. We further examined whether the maximal growth efficiency could serve as a cellular objective function in metabolic network analysis and found that cellular growth in batch cultivation can be predicted reasonably well under this assumption. The fit to experimental data was found slightly better than with the commonly used objective function of maximal growth rate. Based on our results, we suggest that the maximal growth efficiency can be considered a plausible optimization criterion in metabolic modeling for E. coli. In the future, it would be interesting to study growth efficiency as an objective also in other cellular systems and under different cultivation conditions.",
keywords = "Action efficiency, Constraint-based modeling, Metabolism, Microorganism, Principle of least action",
author = "Georgiev, {Georgi Yordanov} and Tommi Aho and Juha Kesseli and Olli Yli-Harja and Kauffman, {Stuart A.}",
note = "jufoid=84878",
year = "2019",
doi = "10.1007/978-3-030-00075-2_8",
language = "English",
isbn = "9783030000745",
series = "Springer Proceedings in Complexity",
publisher = "Springer",
pages = "229--244",
editor = "{Flores Martinez}, {Claudio L.} and Georgiev, {Georgi Yordanov} and Smart, {John M.} and Price, {Michael E.}",
booktitle = "Evolution, Development and Complexity - Multiscale Evolutionary Models of Complex Adaptive Systems",

}

RIS (suitable for import to EndNote) - Lataa

TY - GEN

T1 - Action and power efficiency in self-organization

T2 - The case for growth efficiency as a cellular objective in escherichia coli

AU - Georgiev, Georgi Yordanov

AU - Aho, Tommi

AU - Kesseli, Juha

AU - Yli-Harja, Olli

AU - Kauffman, Stuart A.

N1 - jufoid=84878

PY - 2019

Y1 - 2019

N2 - Complex systems of different nature self-organize using common mechanisms. One of those is increase of their efficiency. The level of organization of complex systems of different nature can be measured as increased efficiency of the product of time and energy for an event, which is the amount of physical action consumed by it. Here we apply a method developed in physics to study the efficiency of biological systems. The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used constrained-based metabolic network analysis method for the prediction of cellular phenotypes. The cellular objective may vary depending on the organism and its growth conditions. It is probable that nutritionally scarce conditions are very common in the nature, and, in order to survive in those conditions, cells exhibit various highly efficient nutrient-processing systems like enzymes. In this study, we explore the efficiency of a metabolic network in transformation of substrates to new biomass, and we introduce a new objective function simulating growth efficiency. We are searching for general principles of self-organization across systems of different nature. The objective of increasing efficiency of physical action has been identified previously as driving systems toward higher levels of self-organization. The flow agents in those networks are driven toward their natural state of motion, which is governed by the principle of least action in physics. We connect this to a power efficiency principle. Systems structure themselves in a way to decrease the average amount of action or power per one event in the system. In this particular example, action efficiency is examined in the case of growth efficiency of E. coli. We derive the expression for growth efficiency as a special case of action (power) efficiency to justify it through first principles in physics. Growth efficiency as a cellular objective of E. coli coincides with previous research on complex systems and is justified by first principles in physics. It is expected and confirmed outcome of this work. We examined the properties of growth efficiency using a metabolic model for Escherichia coli. We found that the maximal growth efficiency is obtained at a finite nutrient uptake rate. The rate is substrate dependent and it typically does not exceed 20 mmol/h/gDW. We further examined whether the maximal growth efficiency could serve as a cellular objective function in metabolic network analysis and found that cellular growth in batch cultivation can be predicted reasonably well under this assumption. The fit to experimental data was found slightly better than with the commonly used objective function of maximal growth rate. Based on our results, we suggest that the maximal growth efficiency can be considered a plausible optimization criterion in metabolic modeling for E. coli. In the future, it would be interesting to study growth efficiency as an objective also in other cellular systems and under different cultivation conditions.

AB - Complex systems of different nature self-organize using common mechanisms. One of those is increase of their efficiency. The level of organization of complex systems of different nature can be measured as increased efficiency of the product of time and energy for an event, which is the amount of physical action consumed by it. Here we apply a method developed in physics to study the efficiency of biological systems. The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used constrained-based metabolic network analysis method for the prediction of cellular phenotypes. The cellular objective may vary depending on the organism and its growth conditions. It is probable that nutritionally scarce conditions are very common in the nature, and, in order to survive in those conditions, cells exhibit various highly efficient nutrient-processing systems like enzymes. In this study, we explore the efficiency of a metabolic network in transformation of substrates to new biomass, and we introduce a new objective function simulating growth efficiency. We are searching for general principles of self-organization across systems of different nature. The objective of increasing efficiency of physical action has been identified previously as driving systems toward higher levels of self-organization. The flow agents in those networks are driven toward their natural state of motion, which is governed by the principle of least action in physics. We connect this to a power efficiency principle. Systems structure themselves in a way to decrease the average amount of action or power per one event in the system. In this particular example, action efficiency is examined in the case of growth efficiency of E. coli. We derive the expression for growth efficiency as a special case of action (power) efficiency to justify it through first principles in physics. Growth efficiency as a cellular objective of E. coli coincides with previous research on complex systems and is justified by first principles in physics. It is expected and confirmed outcome of this work. We examined the properties of growth efficiency using a metabolic model for Escherichia coli. We found that the maximal growth efficiency is obtained at a finite nutrient uptake rate. The rate is substrate dependent and it typically does not exceed 20 mmol/h/gDW. We further examined whether the maximal growth efficiency could serve as a cellular objective function in metabolic network analysis and found that cellular growth in batch cultivation can be predicted reasonably well under this assumption. The fit to experimental data was found slightly better than with the commonly used objective function of maximal growth rate. Based on our results, we suggest that the maximal growth efficiency can be considered a plausible optimization criterion in metabolic modeling for E. coli. In the future, it would be interesting to study growth efficiency as an objective also in other cellular systems and under different cultivation conditions.

KW - Action efficiency

KW - Constraint-based modeling

KW - Metabolism

KW - Microorganism

KW - Principle of least action

U2 - 10.1007/978-3-030-00075-2_8

DO - 10.1007/978-3-030-00075-2_8

M3 - Conference contribution

SN - 9783030000745

T3 - Springer Proceedings in Complexity

SP - 229

EP - 244

BT - Evolution, Development and Complexity - Multiscale Evolutionary Models of Complex Adaptive Systems

A2 - Flores Martinez, Claudio L.

A2 - Georgiev, Georgi Yordanov

A2 - Smart, John M.

A2 - Price, Michael E.

PB - Springer

ER -