What can molecular assembly learn from catalysed assembly in living organisms?

Molecular assembly is the process of organizing individual molecules into larger structures and complex systems. The self-assembly approach is predominantly utilized in creating artificial molecular assemblies, and was believed to be the primary mode of molecular assembly in living organisms as well. However, it has been shown that the assembly of many biological complexes is "catalysed" by other molecules, rather than relying solely on self-assembly. In this review, we summarize these catalysed-assembly (catassembly) phenomena in living organisms and systematically analyse their mechanisms. We then expand on these phenomena and discuss related concepts, including catalysed-disassembly and catalysed-reassembly. Catassembly proves to be an efficient and highly selective strategy for synergistically controlling and manipulating various noncovalent interactions, especially in hierarchical molecular assemblies. Overreliance on self-assembly may, to some extent, hinder the advancement of artificial molecular assembly with powerful features. Furthermore, inspired by the biological catassembly phenomena, we propose guidelines for designing artificial catassembly systems and developing characterization and theoretical methods, and review pioneering works along this new direction. Overall, this approach may broaden and deepen our understanding of molecular assembly, enabling the construction and control of intelligent assembly systems with advanced functionality.

Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution

In this paper we explore the relevance and integration of system theory and thermodynamics in terms of the Earth system. It is proposed that together, these fields explain the evolution, organization, functionality and directionality of life on Earth. We begin by summarizing historical and current thinking on the definition of life itself. We then investigate the evidence for a single unit of life. Given that any definition of life and its levels of organization are intertwined, we explore how the Earth system is structured and functions from an energetic perspective, by outlining relevant thermodynamic theory relating to molecular, metabolic, cellular, individual, population, species, ecosystem and biome organization. We next investigate the fundamental relationships between systems theory and thermodynamics in terms of the Earth system, examining the key characteristics of self-assembly, self-organization (including autonomy), emergence, non-linearity, feedback and sub-optimality. Finally, we examine the relevance of systems theory and thermodynamics with reference to two specific aspects: the tempo and directionality of evolution and the directional and predictable process of ecological succession. We discuss the importance of the entropic drive in understanding altruism, multicellularity, mutualistic and antagonistic relationships and how maximum entropy production theory may explain patterns thought to evidence the intermediate disturbance hypothesis.

Orbiting Self-Organization of Filament-Tethered Surface-Active Droplets

Dissipative chemical systems hold the potential to enable life-like behavior in synthetic matter, such as self-organization, motility, and dynamic switching between different states. Here, out-of-equilibrium self-organization is demonstrated by interconnected source and drain droplets at an air-water interface, which display dynamic behavior due to a hydrolysis reaction that generates a concentration gradient around the drain droplets. This concentration gradient interferes with the adhesion of self-assembled amphiphile filaments that grow from a source droplet. The chemical gradient sustains a unique orbiting of the drain droplet, which is proposed to be driven by the selective adhesion of the filaments to the front of the moving droplet, while filaments approaching from behind are destabilized upon contact with the hydrolysis product in the trail of the droplet. Potential applications are foreseen in the transfer of chemical signals amongst communicating droplets in rearranging networks, and the implementation of chemical reactions to drive complex positioning routines in life-like systems.

Stability of Pattern Formation in Systems with Dynamic Source Regions

We explain the principles of gene expression pattern stabilization in systems of interacting, diffusible morphogens, with dynamically established source regions. Using a reaction-diffusion model with a step-function production term, we identify the phase transition between low-precision indeterminate patterning and the phase in which a traveling, well-defined contact zone between two domains is formed. Our model analytically explains single- and two-gene domain dynamics and provides pattern stability conditions for all possible two-gene regulatory network motifs.

Self-assembled nanoparticles: A new platform for revolutionizing therapeutic cancer vaccines

Cancer vaccines have had some success in the past decade. Based on in-depth analysis of tumor antigen genomics, many therapeutic vaccines have already entered clinical trials for multiple cancers, including melanoma, lung cancer, and head and neck squamous cell carcinoma, which have demonstrated impressive tumor immunogenicity and antitumor activity. Recently, vaccines based on self-assembled nanoparticles are being actively developed as cancer treatment, and their feasibility has been confirmed in both mice and humans. In this review, we summarize recent therapeutic cancer vaccines based on self-assembled nanoparticles. We describe the basic ingredients for self-assembled nanoparticles, and how they enhance vaccine immunogenicity. We also discuss the novel design method for self-assembled nanoparticles that pose as a promising delivery platform for cancer vaccines, and the potential in combination with multiple therapeutic approaches.

Tunability of Self-Organized Structures Based on Thermodynamic Flux

Nature establishes structures and functions via self-organization of constituents, including ions, molecules, and particles. Understanding the selection rule that determines the self-organized structure formed from many possible alternatives is fundamentally and technologically important. In this study, the selection rule for the self-organization associated with a reaction-diffusion system was explored using the Liesegang phenomenon, by which a periodic precipitation pattern is formed as a model system. Experiments were conducted by systematically changing the mass flux. At low mass fluxes, a vertically periodic pattern was formed, whereas at high mass fluxes, a horizontally periodic pattern was formed. The results inferred that a structural vertical-to-horizontal periodicity transition occurred in the self-organized periodic structure at the crossover flux at which the entropy production rate reversed. Numerical analyses attributed the as-observed flux-dependent structural transition to the selection of the self-organized pattern with a higher entropy production rate. These findings contribute to our understanding of how nature controls self-organized structures and geometry, potentially facilitating the development of novel designs, syntheses, and fabrication processes for well-controlled organized functional structures.

Nonequilibrium thermodynamics of Janus particle self-assembly

We compute the energetic cost of formation of Janus particle structures. Using an approach that couples particle dynamics to the evolution of fuel concentration in the medium, which we consider to be initially inhomogeneous, we show the different types of emerging structures. The energy dissipated in the formation of such structures is obtained from the entropy production rate, which is a non-monotonic function of the fraction of assembled particles and, thus, different in each self-assembly regime. An analysis of the free energy of these particles allows us to establish a thermodynamic criterion of structure formation based on the behavior of chemical potential as a function of the fraction of assembled particles.

Insights into Chemically Fueled Supramolecular Polymers

Supramolecular polymerization can be controlled in space and time by chemical fuels. A nonassembled monomer is activated by the fuel and subsequently self-assembles into a polymer. Deactivation of the molecule either in solution or inside the polymer leads to disassembly. Whereas biology has already mastered this approach, fully artificial examples have only appeared in the past decade. Here, we map the available literature examples into four distinct regimes depending on their activation/deactivation rates and the equivalents of deactivating fuel. We present increasingly complex mathematical models, first considering only the chemical activation/deactivation rates (i.e., transient activation) and later including the full details of the isodesmic or cooperative supramolecular processes (i.e., transient self-assembly). We finish by showing that sustained oscillations are possible in chemically fueled cooperative supramolecular polymerization and provide mechanistic insights. We hope our models encourage the quantification of activation, deactivation, assembly, and disassembly kinetics in future studies.

Light-activated photodeformable supramolecular dissipative self-assemblies

Dissipative self-assembly, one of fundamentally important out-of-equilibrium self-assembly systems, can serve as a controllable platform to exhibit temporal processes for various non-stimulus responsive properties. However, construction of light-fueled dissipative self-assembly structures with transformable morphology to modulate non-photoresponsive properties remains a great challenge. Here, we report a light-activated photodeformable dissipative self-assembly system in aqueous solution as metastable fluorescent palette. Zwitterionic sulfonato-merocyanine is employed as a light-induced amphiphile to co-assemble with polyethyleneimine after light irradiation. The formed spherical nanoparticles spontaneously transform into cuboid ones in the dark with simultaneous variation of the particle sizes. Then the two kinds of nanoparticles can reversibly interconvert to each other by periodical light irradiation and thermal relaxation. Furthermore, after loading different fluorophores exhibiting red, green, blue emissions and their mixtures, all these fluorescent dissipative deformable nanoparticles display time-dependent fluorescence variation with wide range of colors. Owing to the excellent performance of photodeformable dissipative assembly platform, the light-controlled fluorescence has achieved a 358-fold enhancement. Therefore, exposing the nanoparticles loaded with fluorophores to light in a spatially controlled manner allows us to draw multicolored fluorescent images that spontaneously disappeared after a specific period of time.

Dissipative self-assembly can serve as a controllable platform to exhibit temporal processes for various non-stimulus responsive properties but construction of light-fueled dissipative self-assembly structures with transformable morphology to modulate non-photoresponsive properties remains a challenge. Here, the authors report a light-activated photodeformable dissipative self-assembly system in aqueous solution as metastable fluorescent platform.

Active Brownian motion of strongly coupled charged grains driven by laser radiation in plasma

The systems of active Brownian grains can be considered as open systems, in which there is an exchange of energy and matter with the environment. The collective phenomena of active Brownian grains can demonstrate analogies with ordinary phase transitions. We study the active Brownian motion of light-absorbing and strongly interacting grains far from equilibrium suspended in gas discharge under laser irradiation when the nature and intensity of the active motion depend on the effect of radiation. Active Brownian motion is caused by photophoresis, i.e., absorption of laser radiation at the metal-coated surface of the grain creates radiometric force, which in turn drives the grains. We experimentally observed the active Brownian motion of charged grains in the transition of the grain monolayer from the solid to liquid state. An analysis of the character of motion, including the mean-square and linear displacement and persistence length at various values of the randomization (coupling parameter) of the grain structure, was presented.

Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials

Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.

Rotation dynamics and internal structure of self-assembled binary paramagnetic colloidal clusters

We study experimentally and theoretically the dynamics of two-dimensional self-assembled binary clusters of paramagnetic colloids of two different sizes and magnetic susceptibilities under a time-varying magnetic field. Due to the continuous energy input by the rotating field, these clusters are at a state of dissipative nonequilibrium. Dissipative viscoelastic shear waves traveling around their interface enable the rotation of isotropic binary clusters. The angular velocity of a binary cluster is much slower than that of the magnetic field; it increases with the concentration of big particles, and it saturates at a concentration threshold. We generalize an earlier theoretical model to successfully account for the observed effect of cluster composition on cluster rotation. We also investigate the evolution of the internal distribution of the two particle types, reminiscent of segregation in a drop of two immiscible liquids, and the effect of this internal structure on rotation dynamics. The binary clusters exhibit short-range order, which rapidly vanishes at a larger scale, consistent with the clusters' viscoelastic liquid behavior.

Unravelling the antimicrobial activity of peptide hydrogel systems: current and future perspectives

The use of hydrogels has garnered significant interest as biomaterial and drug delivery platforms for anti-infective applications. For decades antimicrobial peptides have been heralded as a much needed new class of antimicrobial drugs. Self-assembling peptide hydrogels with inherent antimicrobial ability have recently come to the fore. However, their fundamental antimicrobial properties, selectivity and mechanism of action are relatively undefined. This review attempts to establish a link between antimicrobial efficacy; the self-assembly process; peptide-membrane interactions and mechanical properties by studying several reported peptide systems: β-hairpin/β-loop peptides; multidomain peptides; amphiphilic surfactant-like peptides and ultrashort/low molecular weight peptides. We also explore their role in the formation of amyloid plaques and the potential for an infection etiology in diseases such as Alzheimer's. We look briefly at innovative methods of gel characterization. These may provide useful tools for future studies within this increasingly important field.

Peptide-Based Supramolecular Systems Chemistry

Peptide-based supramolecular systems chemistry seeks to mimic the ability of life forms to use conserved sets of building blocks and chemical reactions to achieve a bewildering array of functions. Building on the design principles for short peptide-based nanomaterials with properties, such as self-assembly, recognition, catalysis, and actuation, are increasingly available. Peptide-based supramolecular systems chemistry is starting to address the far greater challenge of systems-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated. We discuss key features relevant to systems-level design, including regulating supramolecular order and disorder, development of active and adaptive systems by considering kinetic and thermodynamic design aspects and combinatorial dynamic covalent and noncovalent interactions. Finally, we discuss how structural and dynamic design concepts, including preorganization and induced fit, are critical to the ability to develop adaptive materials with adaptive and tunable photonic, electronic, and catalytic properties. Finally, we highlight examples where multiple features are combined, resulting in chemical systems and materials that display adaptive properties that cannot be achieved without this level of integration.

A dissipative pathway for the structural evolution of DNA fibres

Biochemical networks interconnect, grow and evolve to express new properties as different chemical pathways are selected during a continuous cycle of energy consumption and transformation. In contrast, synthetic systems that push away from equilibrium usually return to the same self-assembled state, often generating waste that limits system recyclability and prevents the formation of adaptable networks. Here we show that annealing by slow proton dissipation selects for otherwise inaccessible morphologies of fibres built from DNA and cyanuric acid. Using single-molecule fluorescence microscopy, we observe that proton dissipation influences the growth mechanism of supramolecular polymerization, healing gaps within fibres and converting highly branched, interwoven networks into nanocable superstructures. Just as the growth kinetics of natural fibres determine their structural attributes to modulate function, our system of photoacid-enabled depolymerization and repolymerization selects for healed materials to yield organized, robust fibres. Our method provides a chemical route for error-checking, distinct from thermal annealing, that improves the morphologies and properties of supramolecular materials using out-of-equilibrium systems.

Thermodynamics of structure-forming systems

Structure-forming systems are ubiquitous in nature, ranging from atoms building molecules to self-assembly of colloidal amphibolic particles. The understanding of the underlying thermodynamics of such systems remains an important problem. Here, we derive the entropy for structure-forming systems that differs from Boltzmann-Gibbs entropy by a term that explicitly captures clustered states. For large systems and low concentrations the approach is equivalent to the grand-canonical ensemble; for small systems we find significant deviations. We derive the detailed fluctuation theorem and Crooks' work fluctuation theorem for structure-forming systems. The connection to the theory of particle self-assembly is discussed. We apply the results to several physical systems. We present the phase diagram for patchy particles described by the Kern-Frenkel potential. We show that the Curie-Weiss model with molecule structures exhibits a first-order phase transition.

Out-of-Equilibrium Colloidal Assembly Driven by Chemical Reaction Networks

Transient assembled structures play an indispensable role in a wide variety of processes fundamental to living organisms including cellular transport, cell motility, and proliferation. Typically, the formation of these transient structures is driven by the consumption of molecular fuels via dissipative reaction networks. In these networks, building blocks are converted from inactive precursor states to active (assembling) states by (a set of) irreversible chemical reactions. Since the activated state is intrinsically unstable and can be maintained only in the presence of sufficient fuel, fuel depletion results in the spontaneous disintegration of the formed superstructures. Consequently, the properties and behavior of these assembled structures are governed by the kinetics of fuel consumption rather than by their thermodynamic stability. This fuel dependency endows biological systems with unprecedented spatiotemporal adaptability and inherent self-healing capabilities. Fascinated by these unique material characteristics, coupling the assembly behavior to molecular fuel or light-driven reaction networks was recently implemented in synthetic (supra)molecular systems. In this invited feature article, we discuss recent studies demonstrating that dissipative assembly is not limited to the molecular world but can also be translated to building blocks of colloidal dimensions. We highlight crucial guiding principles for the successful design of dissipative colloidal systems and illustrate these with the current state of the art. Finally, we present our vision on the future of the field and how marrying nonequilibrium self-assembly with the functional properties associated with colloidal building blocks presents a promising route for the development of next-generation materials.

Self-Assembled Nanoparticles: Exciting Platforms for Vaccination

Vaccination is successfully advanced to control several fatal diseases and improve human life expectancy. However, additional innovations are required in this field because there are no effective vaccines to prevent some infectious diseases. The shift from the attenuated or inactivated pathogens to safer but less immunogenic protein or peptide antigens has led to a search for effective antigen delivery carriers that can function as both antigen vehicles and intrinsic adjuvants. Among these carriers, self-assembled nanoparticles (SANPs) have shown great potential to be the best representative. For the nanoscale and multiple presentation of antigens, with accurate control over size, geometry, and functionality, these nanoparticles are assembled spontaneously and mimic pathogens, resulting in enhanced antigen presentation and increased cellular and humoral immunity responses. In addition, they may be applied through needle-free routes due to their adhesive ability, which gives them a great future in vaccination applications. This review provides an overview of various SANPs and their applications in prophylactic vaccines.