title: Physics of metabolic organization.
abstract: We review the most comprehensive metabolic theory of life existing to date. A special focus is given to the thermodynamic roots of this theory and to implications that the laws of physics-such as the conservation of mass and energy-have on all life. Both the theoretical foundations and biological applications are covered. Hitherto, the foundations were more accessible to physicists or mathematicians, and the applications to biologists, causing a dichotomy in what always should have been a single body of work. To bridge the gap between the two aspects of the same theory, we (i) adhere to the theoretical formalism, (ii) try to minimize the amount of information that a reader needs to process, but also (iii) invoke examples from biology to motivate the introduction of new concepts and to justify the assumptions made, and (iv) show how the careful formalism of the general theory enables modular, self-consistent extensions that capture important features of the species and the problem in question. Perhaps the most difficult among the introduced concepts, the utilization (or mobilization) energy flow, is given particular attention in the form of an original and considerably simplified derivation. Specific examples illustrate a range of possible applications-from energy budgets of individual organisms, to population dynamics, to ecotoxicology.
authors.affiliation: Center of Mathematics for Social Creativity, Hokkaido University, 5-8 Kita Ward, Sapporo 060-0808, Japan. Electronic address: mjusup@gmail.com.
authors.forename: Marko
authors.initials: M
authors.lastname: Jusup
authors.affiliation: Maretec, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal.
authors.forename: Tânia
authors.initials: T
authors.lastname: Sousa
authors.affiliation: Maretec, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal.
authors.forename: Tiago
authors.initials: T
authors.lastname: Domingos
authors.affiliation: Department of Physics, University of Rijeka, R. Matejčić 2, 51000 Rijeka, Croatia.
authors.forename: Velimir
authors.initials: V
authors.lastname: Labinac
authors.affiliation: Department for Marine and Environmental Research, Rudjer Boskovic Institute, Bijenička 54, 10000 Zagreb, Croatia.
authors.forename: Nina
authors.initials: N
authors.lastname: Marn
authors.affiliation: Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580, Japan.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department for Marine and Environmental Research, Rudjer Boskovic Institute, Bijenička 54, 10000 Zagreb, Croatia.
authors.forename: Tin
authors.initials: T
authors.lastname: Klanjšček
mesh_terms: D000818:Animals; D001703:Biophysics / Q000379:methods*; D006706:Homeostasis; D006801:Humans; D008660:Metabolism; D008954:Models, Biological
keywords: Conservation laws; DEB theory; Dissipation; Dynamic Energy Budget; Reserve; Structure