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      Perspectives on Natural Philosophy

      Philosophies
      MDPI AG

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          Abstract

          This paper presents a viewpoint on natural philosophy focusing on the organization of substance, as well as its changes as invited by the Second Law of thermodynamics. Modes of change are pointed to as definitive of levels of organization; these include physical, chemical, and biological modes of change. Conceptual uses of the subsumptive hierarchy format are employed throughout this paper. Developmental change in dissipative structures is examined in some detail, generating an argument for the use of final causality in studies of natural systems. Considerations of ‘internalism’ in science are presented along the way.

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          Physical foundations of evolutionary theory

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            Hierarchical Structures

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              Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase.

              The molecular origin of the action of the F(0) proton gradient-driven rotor presents a major puzzle despite significant structural advances. Although important conceptual models have provided guidelines of how such systems should work, it has been challenging to generate a structure-based molecular model using physical principles that will consistently lead to the unidirectional proton-driven rotational motion during ATP synthesis. This work uses a coarse-grained (CG) model to simulate the energetics of the F(0)-ATPase system in the combined space defined by the rotational coordinate and the proton transport (PTR) from the periplasmic side (P) to the cytoplasmic side (N). The model establishes the molecular origin of the rotation, showing that this effect is due to asymmetry in the energetics of the proton path rather than only the asymmetry of the interaction of the Asp on the c-ring helices and Arg on the subunit-a. The simulation provides a clear conceptual background for further exploration of the electrostatic basis of proton-driven mechanochemical systems.
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                Author and article information

                Journal
                Philosophies
                Philosophies
                MDPI AG
                2409-9287
                September 2018
                August 28 2018
                : 3
                : 3
                : 23
                Article
                10.3390/philosophies3030023
                1cc1763e-022d-42e9-83ab-e31963d9c0aa
                © 2018

                https://creativecommons.org/licenses/by/4.0/

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