Emergent or Just Complex?

Understanding Emergent Complexity from a Single-Molecule Perspective

Molecules, with structural, scaling, and interaction diversities, are crucial for the emergence of complex behaviors. Interactions are essential prerequisites for complex systems to exhibit emergent properties that surpass the sum of individual component characteristics. Tracing the origin of complex molecular behaviors from interactions is critical to understanding ensemble emergence, and requires insights at the single-molecule level. Electrical signals from single-molecule junctions enable the observation of individual molecular behaviors, as well as intramolecular and intermolecular interactions. This technique provides a foundation for bottom-up explorations of emergent complexity. This Perspective highlights investigations of various interactions via single-molecule junctions, including intramolecular orbital and weak intermolecular interactions and interactions in chemical reactions. It also provides potential directions for future single-molecule junctions in complex system research.

Harmonic resonance and entrainment of propagating chemical waves by external mechanical stimulation in BZ self-oscillating hydrogels

Smart polymer materials that are nonliving yet exhibit complex "life-like" or biomimetic behaviors have been the focus of intensive research over the past decades, in the quest to broaden our understanding of how living systems function under nonequilibrium conditions. Identification of how chemical and mechanical coupling can generate resonance and entrainment with other cells or external environment is an important research question. We prepared Belousov-Zhabotinsky (BZ) self-oscillating hydrogels which convert chemical energy to mechanical oscillation. By cyclically applying external mechanical stimulation to the BZ hydrogels, we found that when the oscillation of a gel sample entered into harmonic resonance with the applied oscillation during stimulation, the system kept a "memory" of the resonant oscillation period and maintained it post stimulation, demonstrating an entrainment effect. More surprisingly, by systematically varying the cycle length of the external stimulation, we revealed the discrete nature of the stimulation-induced resonance and entrainment behaviors in chemical oscillations of BZ hydrogels, i.e., the hydrogels slow down their oscillation periods to the harmonics of the cycle length of the external mechanical stimulation. Our theoretical model calculations suggest the important roles of the delayed mechanical response caused by reactant diffusion and solvent migration in affecting the chemomechanical coupling in active hydrogels and consequently synchronizing their chemical oscillations with external mechanical oscillations.

Chemical micro-oscillators based on the Belousov–Zhabotinsky reaction

The results of studies on the development of micro-oscillators (MOs) based on the Belousov –Zhabotinsky (BZ) oscillatory chemical reaction are integrated and systematized. The mechanisms of the BZ reaction and the methods of immobilization of the catalyst of the BZ reaction in micro-volumes are briefly discussed. Methods for creating BZ MOs based on water microdroplets in the oil phase and organic and inorganic polymer microspheres are considered. Methods of control and management of the dynamics of BZ MO networks are described, including methods of MO synchronization. The prospects for the design of neural networks of MOs with intelligent-like behaviour are outlined. Such networks present a new area of nonlinear chemistry, including, in particular, the creation of a chemical ‘computer’.

The bibliography includes 250 references.

Delayed Mechanical Response to Chemical Kinetics in Self-Oscillating Hydrogels Driven by the Belousov-Zhabotinsky Reaction

We show experimentally that chemical and mechanical self-oscillations in Belousov–Zhabotinsky hydrogels are inherently asynchronous, that is, there is a detectable delay in swelling–deswelling response after a change in the chemical redox state. This phenomenon is observable in many previous experimental studies and potentially has far-reaching implications for the functionality and response time of the material in future applications; however, so far, it has not been quantified or reported systematically. Here, we provide a comprehensive qualitative and quantitative description of the chemical-to-mechanical delay, and we propose to explain it as a consequence of the slow nonequilibrium swelling–deswelling dynamics of the polymer material. Specifically, standard hydrogel pieces are large enough that transport processes, for example, counterion migration and water diffusion, cannot occur instantaneously throughout the entire gel piece, as opposed to previous theoretical considerations. As a result, the volume response of the polymer to a chemical change may be governed by a characteristic response time, which leads to the emergence of delay in mechanical oscillation. This is supported by our theoretical calculations.

Encoding complexity within supramolecular analogues of frustrated magnets

The solid phases of gold(I) and/or silver(I) cyanides are supramolecular assemblies of inorganic polymer chains in which the key structural degrees of freedom-namely, the relative vertical shifts of neighbouring chains-are mathematically equivalent to the phase angles of rotating planar ('XY') spins. Here, we show how the supramolecular interactions between chains can be tuned to mimic different magnetic interactions. In this way, the structures of gold(I) and/or silver(I) cyanides reflect the phase behaviour of triangular XY magnets. Complex magnetic states predicted for this family of magnets-including collective spin-vortices of relevance to data storage applications-are realized in the structural chemistry of these cyanide polymers. Our results demonstrate how chemically simple inorganic materials can behave as structural analogues of otherwise inaccessible 'toy' spin models and also how the theoretical understanding of those models allows control over collective ('emergent') phenomena in supramolecular systems.

Reaction-diffusion processes at the nano- and microscales

The bottom-up fabrication of nano- and microscale structures from primary building blocks (molecules, colloidal particles) has made remarkable progress over the past two decades, but most research has focused on structural aspects, leaving our understanding of the dynamic and spatiotemporal aspects at a relatively primitive stage. In this Review, we draw inspiration from living cells to argue that it is now time to move beyond the generation of structures and explore dynamic processes at the nanoscale. We first introduce nanoscale self-assembly, self-organization and reaction-diffusion processes as essential features of cells. Then, we highlight recent progress towards designing and controlling these fundamental features of life in abiological systems. Specifically, we discuss examples of reaction-diffusion processes that lead to such outcomes as self-assembly, self-organization, unique nanostructures, chemical waves and dynamic order to illustrate their ubiquity within a unifying context of dynamic oscillations and energy dissipation. Finally, we suggest future directions for research on reaction-diffusion processes at the nano- and microscales that we find hold particular promise for a new understanding of science at the nanoscale and the development of new kinds of nanotechnologies for chemical transport, chemical communication and integration with living systems.

CD-MOF: A Versatile Separation Medium

Porous metal-organic frameworks (MOFs) have been studied in the context of a wide variety of applications, particularly in relation to molecular storage and separation sciences. Recently, we reported a green, renewable framework material composed of γ-cyclodextrin (γ-CD) and alkali metal salts--namely, CD-MOF. This porous material has been shown to facilitate the separation of mixtures of alkylaromatic compounds, including the BTEX mixture (benzene, toluene, ethylbenzene, and the regioisomers of xylene), into their pure components, in both the liquid and gas phases, in an energy-efficient manner which could have implications for the petrochemical industry. Here, we report the ability of CD-MOF to separate a wide variety of mixtures, including ethylbenzene from styrene, haloaromatics, terpinenes, pinenes and other chiral compounds. CD-MOF retains saturated compounds to a greater extent than their unsaturated analogues. Also, the location of a double bond within a molecule influences its retention within the extended framework, as revealed in the case of the structural isomers of pinene and terpinine, where the isomers with exocyclic double bonds are more highly retained than those with endocyclic double bonds. The ability of CD-MOF to separate various mono- and disubstituted haloaromatic compounds appears to be controlled by both the size of the halogen substituents and the strength of the noncovalent bonding interactions between the analyte and the framework, an observation which has been confirmed by molecular simulations. Since CD-MOF is a homochiral framework, it is also able to resolve the enantiomers of chiral analytes, including those of limonene and 1-phenylethanol. These findings could lead to cheaper and easier-to-prepare stationary phases for HPLC separations when compared with other chiral stationary phases, such as CD-bonded silica particles.

From chemical systems to systems chemistry: Patterns in space and time

We present a brief, idiosyncratic overview of the past quarter century of progress in nonlinear chemical dynamics and discuss what we view as the most exciting recent developments and some challenges and likely areas of progress in the next 25 years.

Molecular containers in complex chemical systems

This review discusses recent advances in the use of molecular containers in complex chemical systems, focusing on three aspects: host–guest behaviour, structural transformations and reactivity modulation.

Elastocapillary interaction of particles on the surfaces of ultrasoft gels: a novel route to study self-assembly and soft lubrication

We study the interaction of small hydrophobic particles on the surface of an ultrasoft elastic gel, in which a small amount of elasticity of the medium balances the weights of the particles. The excess energy of the surface of the deformed gel causes them to attract as is the case with the generic capillary interactions of particles on a liquid surface. The variation of the gravitational potential energies of the particles resulting from their descents in the gel coupled with the superposition principle of Nicolson allow a fair estimation of the distance dependent attractive energy of the particles. This energy follows a modified Bessel function of the second kind with a characteristic elastocapillary decay length that decreases with the elasticity of the medium. An interesting finding of this study is that the particles on the gel move toward each other as if the system possesses a negative diffusivity that is inversely proportional to friction. This study illustrates how the capillary interaction of particles is modified by the elasticity of the medium, which is expected to have important implications in the surface force driven self-assembly of particles. In particular, this study points out that the range and the strength of the capillary interaction can be tuned in by appropriate choices of the elasticity of the support and the interfacial tension of the surrounding medium. Manipulation of the particle interactions is exemplified in such fascinating mimicry of the biological processes as the tubulation and phagocytic engulfment and in the assembly of particles that can be used to study nucleation and clustering phenomena in well-controlled settings.

Autonomous viscosity oscillation via metallo-supramolecular terpyridine chemistry of branched poly(ethylene glycol) driven by the Belousov-Zhabotinsky reaction

Herein, we report an autonomous viscosity oscillation of polymer solutions coupled with the metal-ligand association/dissociation between Ru and terpyridine (tpy), driven by the Belousov-Zhabotinsky (BZ) reaction. The tpy ligand for the Ru catalyst was attached to the terminals of poly(ethylene glycol) (PEG) with different numbers of branches (linear-, tetra-, and octa-PEG). It is well known that mono-tpy coordination is stable when Ru is oxidized (Ru(tpy)(3+)), whereas bis-tpy coordination is stable when the Ru centre is reduced (Ru(tpy)2(2+)). In the oxidized state, the three different polymers existed as solutions. In contrast, when the Ru centre was reduced, gels were obtained for the tetra- and octa-PEG owing to the formation of a three-dimensional polymer network through Ru-tpy coordination. Rheological measurements confirmed that the sol-gel transition occurred much more quickly in the octa-PEG system than in the tetra-PEG system, because of the requirement of fewer crosslinking points. The polymer solutions exhibited self-oscillation of absorbance and viscosity when BZ substrates were added to the solutions of Ru(2+)-tpy-modified tetra-/octa-PEG. This indicated that the Ru(tpy)2(2+) attached to the polymer ends could work as a metal catalyst for the BZ reaction. By increasing the number of branches from 4 to 8, the amount of crosslinking changed more remarkably during the oscillation, with a maximum value closer to that necessary for gelation. Thus, viscosity oscillation with a larger amplitude in the region of higher viscosity was achieved by using octa-PEG.

Motility at the origin of life: its characterization and a model

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing replicator-first and metabolism-first approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an ximpoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate time scales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct time scales, which are typically associated with metabolism, motility, development, and evolution. In this view, self-movement, adaptive behavior, and morphological changes could have already been present at the origin of life. In order to illustrate this possibility, we analyze a minimal model of lifelike phenomena, namely, of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis, we suggest that processes on intermediate time scales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced time scales of chemical self-individuation and evolution by natural selection, respectively.

Experimental assessment of the sensitiveness of an electrochemical oscillator towards chemical perturbations

In this study we address the problem of the response of a (electro)chemical oscillator towards chemical perturbations of different magnitudes. The chemical perturbation was achieved by addition of distinct amounts of trifluoromethanesulfonate (TFMSA), a rather stable and non-specifically adsorbing anion, and the system under investigation was the methanol electro-oxidation reaction under both stationary and oscillatory regimes. Increasing the anion concentration resulted in a decrease in the reaction rates of methanol oxidation and a general decrease in the parameter window where oscillations occurred. Furthermore, the addition of TFMSA was found to decrease the induction period and the total duration of oscillations. The mechanism underlying these observations was derived mathematically and revealed that inhibition in the methanol oxidation through blockage of active sites was found to further accelerate the intrinsic non-stationarity of the unperturbed system. Altogether, the presented results are among the few concerning the experimental assessment of the sensitiveness of an oscillator towards chemical perturbations. The universal nature of the complex chemical oscillator investigated here might be used for reference when studying the dynamics of other less accessible perturbed networks of (bio)chemical reactions.

On emergence: a neo-psychoanalytic essay on change and science

The neo-psychoanalytic paradigm re-establishes the connection between psychodynamics and evolution. This allows us to transcend the limitations of dualistic metapsychology, and to make seminal contributions to traditional science. The new paradigm employs the concept of emergence, the potential for change in the evolutionary and clinical process. Emergence is described as originating with the Big Bang, but also is reflected at much higher levels, for example, biochemistry, or the capacity of the evolved mind to produce insights in psychotherapy. The constraints of dualistic theories are examined. A neuron-based view of change illustrates the evolution of traditional science as well as the neuron, itself. The new mind paradigm recognizes individual, familial, communitarian, and global reciprocal influences mediated by culture and illustrated by the extended mind and the democratic spirit. Thus both traditional and psychodynamic sciences are undergoing revolutionary changes in their common efforts to better understand the mechanisms of knowledge, relationship and consciousness. The boundaries of the self and the consultation suite are also expanded in this view. Following a survey of invagination, the work is concluded by an application of emergence theory to the creationist controversy and Freud's views of religion.

Dynamic combinatorial chemistry at the phospholipid bilayer interface

Background

Molecular recognition at the environment provided by the phospholipid bilayer interface plays an important role in biology and is subject of intense investigation. Dynamic combinatorial chemistry is a powerful approach for exploring molecular recognition, but has thus far not been adapted for use in this special microenvironment.

Results

Thioester exchange was found to be a suitable reversible reaction to achieve rapid equilibration of dynamic combinatorial libraries at the egg phosphatidyl choline bilayer interface. Competing thioester hydrolysis can be minimised by judicial choice of the structure of the thioesters and the experimental conditions. Comparison of the library compositions in bulk solution with those in the presence of egg PC revealed that the latter show a bias towards the formation of library members rich in membrane-bound building blocks. This leads to a shift away from macrocyclic towards linear library members.

Conclusions

The methodology to perform dynamic combinatorial chemistry at the phospholipid bilayer interface has been developed. The spatial confinement of building blocks to the membrane interface can shift the ring-chain equilibrium in favour of chain-like compounds. These results imply that interfaces may be used as a platform to direct systems to the formation of (informational) polymers under conditions where small macrocycles would dominate in the absence of interfacial confinement.

Emergent, collective oscillations of self-mobile particles and patterned surfaces under redox conditions

We have discovered that silver chloride (AgCl) particles in the presence of UV light and dilute hydrogen peroxide exhibit both single-particle and collective oscillations in their motion which arise due to an oscillatory, reversible conversion of AgCl to silver metal at the particle surface. This system exhibits several of the hallmarks of nonlinear oscillatory reactions, including bistability, reaction waves, and synchronized collective oscillations at high particle concentrations. However, unlike traditional oscillatory reactions that take place among dispersed solute species in solution or near a fixed electrode surface, this system of self-mobile catalytic particles evinces a new dynamical length scale: the interparticle spacing, which appears to control wave propagation. The collective motions of these powered nanoparticles self-organize into clumped oscillators with significant spatiotemporal correlations between clumps. A variant of this system using a regular array of lithographically patterned silver disks supports the propagation of binary "On/Off" Ag/AgCl waves through the lattice.