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1. Functional Interdependence in Coupled Dissipative Structures: Physical Foundations of Biological Coordination

   https://doi.org/10.3390/e23050614  

   De Bari, Benjamin ; Paxton, Alexandra ; Kondepudi, Dilip K. ; Kay, Bruce A. ; Dixon, James A. ( May 2021 , Entropy)

   null (Ed.)

   Coordination within and between organisms is one of the most complex abilities of living systems, requiring the concerted regulation of many physiological constituents, and this complexity can be particularly difficult to explain by appealing to physics. A valuable framework for understanding biological coordination is the coordinative structure, a self-organized assembly of physiological elements that collectively performs a specific function. Coordinative structures are characterized by three properties: (1) multiple coupled components, (2) soft-assembly, and (3) functional organization. Coordinative structures have been hypothesized to be specific instantiations of dissipative structures, non-equilibrium, self-organized, physical systems exhibiting complex pattern formation in structure and behaviors. We pursued this hypothesis by testing for these three properties of coordinative structures in an electrically-driven dissipative structure. Our system demonstrates dynamic reorganization in response to functional perturbation, a behavior of coordinative structures called reciprocal compensation. Reciprocal compensation is corroborated by a dynamical systems model of the underlying physics. This coordinated activity of the system appears to derive from the system’s intrinsic end-directed behavior to maximize the rate of entropy production. The paper includes three primary components: (1) empirical data on emergent coordinated phenomena in a physical system, (2) computational simulations of this physical system, and (3) theoretical evaluation of the empirical and simulated results in the context of physics and the life sciences. This study reveals similarities between an electrically-driven dissipative structure that exhibits end-directed behavior and the goal-oriented behaviors of more complex living systems. 

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2. Assembly of a patchy protein into variable 2D lattices via tunable multiscale interactions

   https://doi.org/10.1038/s41467-020-17562-1  

   Zhang, Shuai ; Alberstein, Robert G. ; De Yoreo, James J. ; Tezcan, F. Akif ( July 2020 , Nature Communications)

   Self-assembly of molecular building blocks into higher-order structures is exploited in living systems to create functional complexity and represents a powerful strategy for constructing new materials. As nanoscale building blocks, proteins offer unique advantages, including monodispersity and atomically tunable interactions. Yet, control of protein self-assembly has been limited compared to inorganic or polymeric nanoparticles, which lack such attributes. Here, we report modular self-assembly of an engineered protein into four physicochemically distinct, precisely patterned 2D crystals via control of four classes of interactions spanning Ångström to several-nanometer length scales. We relate the resulting structures to the underlying free-energy landscape by combining in-situ atomic force microscopy observations of assembly with thermodynamic analyses of protein-protein and -surface interactions. Our results demonstrate rich phase behavior obtainable from a single, highly patchy protein when interactions acting over multiple length scales are exploited and predict unusual bulk-scale properties for protein-based materials that ensue from such control.

    

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3. Activity-controlled annealing of colloidal monolayers

   https://doi.org/10.1038/s41467-019-11362-y  

   Ramananarivo, Sophie ; Ducrot, Etienne ; Palacci, Jeremie ( July 2019 , Nature Communications)

   Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium.

    

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4. Prebiotic Geochemical Automata at the Intersection of Radiolytic Chemistry, Physical Complexity, and Systems Biology

   https://doi.org/10.1155/2018/9376183  

   Adam, Zachary R. ; Fahrenbach, Albert C. ; Kacar, Betul ; Aono, Masashi ( June 2018 , Complexity)

   The tractable history of life records a successive emergence of organisms composed of hierarchically organized cells and greater degrees of individuation. The lowermost object level of this hierarchy is the cell, but it is unclear whether the organizational attributes of living systems extended backward through prebiotic stages of chemical evolution. If the systems biology attributes of the cell were indeed templated upon prebiotic synthetic relationships between subcellular objects, it is not obvious how to categorize object levels below the cell in ways that capture any hierarchies which may have preceded living systems. In this paper, we map out stratified relationships between physical components that drive the production of key prebiotic molecules starting from radiolysis of a small number of abundant molecular species. Connectivity across multiple levels imparts the potential to create and maintain far-from-equilibrium chemical conditions and to manifest nonlinear system behaviors best approximated using automata formalisms. The architectural attribute of “information hiding” of energy exchange processes at each object level is shared with stable, multitiered automata such as digital computers. These attributes may indicate a profound connection between the system complexity afforded by energy dissipation by subatomic level objects and the emergence of complex automata that could have preceded biological systems. 

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5. Precise Control of Dissipative Self‐assembly by Light and Electricity

   https://doi.org/10.1002/chem.202300347  

   Chen, Chunfeng ; Guan, Zhibin ( March 2023 , Chemistry – A European Journal)

   Nature‐inspired synthetic dissipative self‐assemblies have attracted much attention recently. However, it remains a major challenge to achieve precise control over dissipative supramolecular assembly structures and functions of self‐contained systems. Here we combine light and electricity as two clean, and spatiotemporally addressable fuels to provide precise control over the morphology for dissipative self‐assembly of a perylene bisimide glycine (PBIg) building block in a self‐contained solution. In this design, electrochemical oxidation provides the positive fuel to activate PBIg self‐assembly while photoreduction supplies the negative fuel to deactivate the system for disassembly. Through programming the two counteracting fuels, we demonstrated the control of PBIg self‐assembly into a variety of assembly morphologies in a self‐contained system. In addition, by exerting light and electrical dual fuels simultaneously, we could create an active homeostasis exhibiting dynamic instability, leading to morphological change to asymmetric assemblies with curvatures. Such precise control over self‐assembly of self‐contained systems may find future applications in programming complex active materials as well as formulating pharmaceutical reagents with desired morphologies.

    

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