Photochemical Control over Oscillations in Chemical Reaction Networks

Choreographing Oscillatory Hydrodynamics with DNA-Coated Gold Nanoparticles

Periodic responses to nonperiodic energy inputs, such as oscillations, are hallmarks of living systems. Nanoparticle-based systems have largely remained unexplored in the generation of oscillatory features. Here, we demonstrate a nanosystem featuring hierarchical response to light, where thermoplasmonic effects and reversible DNA-hybridization generate thermal convective forces and ultimately, oscillatory hydrodynamic flows. The slow aggregation of gold nanoparticles (AuNPs) serves as a positive feedback, while fast photothermal disassembly acts as negative feedback. These asymmetric feedback loops, combined with thermal hysteresis for time-delay, are essential ingredients for orchestrating an oscillating response.

Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises

Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.

A Peptide-Based Oscillator

Living organisms are replete with rhythmic and oscillatory behavior at all levels, to the extent that oscillations have been termed as a defining attribute of life. Recent studies of synthetic oscillators that mimic such functions have shown decayed cycles in batch-mode reactions or sustained oscillatory kinetics under flow conditions. Considering the hypothesized functionality of peptides in early chemical evolution and their central role in current bio-nanotechnology, we now reveal a peptide-based oscillator. Oscillatory behavior was achieved by coupling coiled-coil-based replication processes as positive feedback to controlled initiation and inhibition pathways in a continuously stirred tank reactor (CSTR). Our results stress that assembly into the supramolecular structure and specific interactions with the replication substrates are crucial for oscillations. The replication-inhibition processes were first studied in batch mode, which produced a single damped cycle. Thereafter, combined experimental and theoretical characterization of the replication process in a CSTR under different flow and environmental (pH, redox) conditions demonstrated reasonably sustained oscillations. We propose that studies in this direction might pave the way to the design of robust oscillation networks that mimic the autonomous behavior of proteins in cells (e.g., in the cyanobacterial circadian clock) and hence hint at feasible pathways that accelerated the transition from simple peptides to extant enzymes.

Directing Uphill Strand Displacement with an Engineered Superhelicase

The ability to finely tune reaction rates and binding energies between components has made DNA strand displacement circuits promising candidates to replicate the complex regulatory functions of biological reaction networks. However, these circuits often lack crucial properties, such as signal turnover and the ability to transiently respond to successive input signals that require the continuous input of chemical energy. Here, we introduce a method for providing such energy to strand displacement networks in a controlled fashion: an engineered DNA helicase, Rep-X, that transiently dehybridizes specific DNA complexes, enabling the strands in the complex to participate in downstream hybridization or strand displacement reactions. We demonstrate how this process can direct the formation of specific metastable structures by design and that this dehybridization process can be controlled by DNA strand displacement reactions that effectively protect and deprotect a double-stranded complex from unwinding by Rep-X. These findings can guide the design of active DNA strand displacement regulatory networks, in which sustained dynamical behavior is fueled by helicase-regulated unwinding.

Cascade nanozymatic network mimicking cells with selective and linear perception of H2O2

A single stimulus leading to multiple responses is an essential function of many biological networks, which enable complex life activities. However, it is challenging to duplicate a similar chemical reaction network (CRN) using non-living chemicals, aiming at the disclosure of the origin of life. Herein, we report a nanozyme-based CRN with feedback and feedforward functions for the first time. It demonstrates multiple responses at different modes and intensities upon a single H₂O₂ stimulus. In the two-electron cascade oxidation of 3,3',5,5'-tetramethylbenzidine (TMB), the endogenous product H₂O₂ competitively inhibited substrates in the first one-electron oxidation reaction on a single-atom nanozyme (Co-N-CNTs) and strikingly accelerated the second one-electron oxidation reaction under a micellar nanozyme. As a proof-of-concept, we further confined the nanozymatic network to a microfluidic chip as a simplified artificial cell. It exhibited remarkable selectivity and linearity in the perception of H₂O₂ stimulus against more than 20 interferences in a wide range of concentrations (0.01-100 mM) and offered an instructive platform for studying primordial life-like processes.

Mechanosensitive non-equilibrium supramolecular polymerization in closed chemical systems

Chemical fuel-driven supramolecular systems have been developed showing out-of-equilibrium functions such as transient gelation and oscillations. However, these systems suffer from undesired waste accumulation and they function only in open systems. Herein, we report non-equilibrium supramolecular polymerizations in a closed system, which is built by viologens and pyranine in the presence of hydrazine hydrate. On shaking, the viologens are quickly oxidated by air followed by self-assembly of pyranine into micrometer-sized nanotubes. The self-assembled nanotubes disassemble spontaneously over time by the reduced agent, with nitrogen as the only waste product. Our mechanosensitive dissipative system can be extended to fabricate a chiral transient supramolecular helix by introducing chiral-charged small molecules. Moreover, we show that shaking induces transient fluorescence enhancement or quenching depending on substitution of viologens. Ultrasound is introduced as a specific shaking way to generate template-free reproducible patterns. Additionally, the shake-driven transient polymerization of amphiphilic naphthalenetetracarboxylic diimide serves as further evidence of the versatility of our mechanosensitive non-equilibrium system.

Transient Host-Guest Complexation To Control Catalytic Activity

Signal transduction mechanisms are key to living systems. Cells respond to signals by changing catalytic activity of enzymes. This signal responsive catalysis is crucial in the regulation of (bio)chemical reaction networks (CRNs). Inspired by these networks, we report an artificial signal responsive system that shows signal-induced temporary catalyst activation. We use an unstable signal to temporarily activate an out of equilibrium CRN, generating transient host–guest complexes to control catalytic activity. Esters with favorable binding toward the cucurbit[7]uril (CB[7]) supramolecular host are used as temporary signals to form a transient complex with CB[7], replacing a CB[7]-bound guest. The esters are hydrolytically unstable, generating acids and alcohols, which do not bind to CB[7], leading to guest reuptake. We demonstrate the feasibility of the concept using signal-controlled temporary dye release and reuptake. The same signal controlled system was then used to tune the reaction rate of aniline catalyzed hydrazone formation. Varying the ester structure and concentration gave access to different catalyst liberation times and free catalyst concentration, regulating the overall reaction rate. With temporary signal controlled transient complex formation we can tune the kinetics of a second chemical reaction, in which the signal does not participate. This system shows promise for building more complex nonbiological networks, to ultimately arrive at signal transduction in organic materials.

Modulation of spatiotemporal dynamics in the bromate–sulfite–ferrocyanide reaction system by visible light

We have carried out the first systematic study of the effects of visible light on the homogenous dynamics in the bromate–sulfite–ferrocyanide (BSF) reaction. Under flow conditions, the reaction system displayed photoinduction and photoinhibition behavior, and the oscillatory period decreased with the increase of light intensity, which is due to the fact that light irradiation mainly enhanced the negative process and affected the positive feedback. The light effect on positive and negative feedback is studied by analyzing the period length of pH increasing and decreasing in detail. With the increase of light intensity, the period length of pH increasing decreases monotonically, while the period length of pH decreasing changes nonmonotonically. These results suggest that light could be used as a powerful tool to control homogenous dynamics. Results obtained from numerical simulations are in good agreement with experimental data.

The BSF reaction system displayed photoinduction and photoinhibition behavior under flow conditions. The oscillatory period decreased as the light irradiation mainly enhanced the negative process and affected the positive feedback.

Reversible Photoswitchable Inhibitors Generate Ultrasensitivity in Out-of-Equilibrium Enzymatic Reactions

Ultrasensitivity is a ubiquitous emergent property of biochemical reaction networks. The design and construction of synthetic reaction networks exhibiting ultrasensitivity has been challenging, but would greatly expand the potential properties of life-like materials. Herein, we exploit a general and modular strategy to reversibly regulate the activity of enzymes using light and show how ultrasensitivity arises in simple out-of-equilibrium enzymatic systems upon incorporation of reversible photoswitchable inhibitors (PIs). Utilizing a chromophore/warhead strategy, PIs of the protease α-chymotrypsin were synthesized, which led to the discovery of inhibitors with large differences in inhibition constants (K_i) for the different photoisomers. A microfluidic flow setup was used to study enzymatic reactions under out-of-equilibrium conditions by continuous addition and removal of reagents. Upon irradiation of the continuously stirred tank reactor with different light pulse sequences, i.e., varying the pulse duration or frequency of UV and blue light irradiation, reversible switching between photoisomers resulted in ultrasensitive responses in enzymatic activity as well as frequency filtering of input signals. This general and modular strategy enables reversible and tunable control over the kinetic rates of individual enzyme-catalyzed reactions and makes a programmable linkage of enzymes to a wide range of network topologies feasible.

Information processing using an integrated DNA reaction network

Living organisms use interconnected chemical reaction networks (CRNs) to exchange information with the surrounding environment and respond to diverse external stimuli. Inspired by nature, numerous artificial CRNs with a complex information processing function have been recently introduced, with DNA as one of the most attractive engineering materials. Although much progress has been made in DNA-based CRNs in terms of controllable reaction dynamics and molecular computation, the effective integration of signal translation with information processing in a single CRN remains to be difficult. In this work, we introduced a stimuli-responsive DNA reaction network capable of integrated information translation and processing in a stepwise manner. This network is designed to integrate sensing, translation, and decision-making operations by independent modules, in which various logic units capable of performing different functions were realized, including information identification (YES and OR gates), integration (AND and AND-AND gates), integration-filtration (AND-AND-NOT gate), comparison (Comparator), and map-to-map analysis (Feynman gate). Benefitting from the modular and programmable design, continuous and parallel processing operations are also possible. With the innovative functions, we show that the DNA network is a highly useful addition to the current DNA-based CRNs by offering a bottom-up strategy to design devices capable of cascaded information processing with high efficiency.

Progress in Photobiomodulation for Bone Fractures: A Narrative Review

Objective: The aim of this article is to examine current concepts and the future direction of implementing photobiomodulation (PBM) for fracture treatment. Background data: The effectiveness of PBM for bone regeneration has been demonstrated throughout in vitro studies and animal models. Yet, insufficient clinical trials have been reported on treating fractures with PBM. Materials and methods: A narrative review was composed on the basis of a literary search. Inclusion criteria consisted of studies between 2000 and 2019 using animal or human fracture models. Exclusion criteria consisted of studies that did not pertain to complete fractures or used other forms of intervention. Results: Ten animal studies on rats and rabbits and four clinical trials were found on using PBM for complete fractures. Conclusions: Based on positive outcomes in animal trials, parameter optimization of PBM for human fractures still requires extensive research on factors such as dosage, wavelength, penetration depth, treatment frequency, and the use of pulsed waves.

Viewpoint: Homeostasis as Inspiration-Toward Interactive Materials

Homeostatic systems combine an ability to maintain integrity over time with an incredible capacity for interactive behavior. Fundamental to such systems are building blocks of "mini-homeostasis": feedback loops in which one component responds to a stimulus and another opposes the response, pushing the module to restore its original configuration. Particularly when they cross time and length scales, perturbation of these loops by external changes can generate diverse and complex phenomena. Here, it is proposed that by recognizing and implementing mini-homeostatic modules-often composed of very different physical and chemical processes-into synthetic materials, numerous interactive behaviors can be obtained, opening avenues for designing multifunctional materials. How a variety of controlled, nontrivial material responses can be evoked from even simple versions of such synthetic feedback modules is illustrated. Moreover, random events causing seemingly random responses give insights into how one can further explore, understand and control the full interaction space. Ultimately, material fabrication and exploration of interactivity become inseparable in the rational design of such materials. Homeostasis provides a lens through which one can learn how to combine and perturb coupled processes across time and length scales to conjure up exciting behaviors for new materials that are both robust and interactive.

Therapeutic Efficacy of Home-Use Photobiomodulation Devices: A Systematic Literature Review

Objective: Perform systematic literature review on photobiomodulation (PBM) devices used at home for nonesthetic applications. Background: Home-use PBM devices have been marketed for cosmetic and therapeutic purposes. This is the first systematic literature review for nonesthetic applications. Methods: A systematic literature search was conducted for PBM devices self-applied at home at least thrice a week. Two independent reviewers screened the articles and extracted the data. Treatment dosage appropriateness was compared to the World Association for Laser Therapy (WALT) recommendations. The efficacy was evaluated according to the relevant primary end-point for the specific indication. Results: Eleven studies were suitable. Devices were applied for a range of indications, including pain, cognitive dysfunction, wound healing, diabetic macular edema, and postprocedural side effects, and were mostly based on near-infrared, pulsed light-emitting diodes with dosages within WALT recommendations. Regarding efficacy, studies reported mostly positive results. Conclusions: Home-use PBM devices appear to mediate effective, safe treatments in a variety of conditions that require frequent applications. Conclusive evaluation of their efficacy requires additional, randomized controlled studies.

Structural organization of biocatalytic systems: the next dimension of synthetic metabolism

In natural metabolic networks, more than 2000 different biochemical reactions are operated and spatially and temporally co-ordinated in a reaction volume of <1 µm³. A similar level of control and precision has not been achieved in chemical synthesis, so far. Recently, synthetic biology succeeded in reconstructing complex synthetic in vitro metabolic networks (SIVMNs) from individual proteins in a defined fashion bottom-up. In this review, we will highlight some examples of SIVMNs and discuss how the further advancement of SIVMNs will require the structural organization of these networks and their reactions to (i) minimize deleterious side reactions, (ii) efficiently energize these networks from renewable energies, and (iii) achieve high productivity. The structural organization of synthetic metabolic networks will be a key step to create novel catalytic systems of the future and advance ongoing efforts of creating cell-like systems and artificial cells.

On the importance of reaction networks for synthetic living systems

The goal of creating a synthetic cell necessitates the development of reaction networks which will underlie all of its behaviours. Recent developments in in vitro systems, based upon both DNA and enzymes, have created networks capable of a range of behaviours e.g. information processing, adaptation and diffusive signalling. These networks are based upon reaction motifs that when combined together produce more complex behaviour. We highlight why it is inevitable that networks, based on enzymes or enzyme-like catalysts, will be required for the construction of a synthetic cell. We outline several of the challenges, including (a) timing, (b) regulation and (c) energy distribution, that must be overcome in order to transition from the simple networks we have today to much more complex networks capable of a variety of behaviours and which could find application one day within a synthetic cell.

Compositional Persistence in a Multicyclic Network of Synthetic Replicators

The emergence of collections of simple chemical entities that create self-sustaining reaction networks, embedding replication and catalysis, is cited as a potential mechanism for the appearance on the early Earth of systems that satisfy minimal definitions of life. In this work, a functional reaction network that creates and maintains a set of privileged replicator structures through auto- and cross-catalyzed reaction cycles is created from the pairwise combinations of four reagents. We show that the addition of individual preformed templates to this network, representing instructions to synthesize a specific replicator, induces changes in the output composition of the system that represent a network-level response. Further, we establish through sets of serial transfer experiments that the catalytic connections that exist between the four replicators in this network and the system-level behavior thereby encoded impose limits on the compositional variability that can be induced by repeated exposure to instructional inputs, in the form of preformed templates, to the system. The origin of this persistence is traced through kinetic simulations to the properties and inter-relationships between the critical ternary complexes formed by the auto- and crosscatalytic templates. These results demonstrate that in an environment where there is no continuous selection pressure the network connectivity, described by the catalytic relationships and system-level interactions between the replicators, is persistent, thereby limiting the ability of this network to adapt and evolve.

Revisiting the Photon/Cell Interaction Mechanism in Low-Level Light Therapy

Objective: Several reports claim that the enzyme cytochrome c oxidase (CCO) is the primary absorber for red-to-near-infrared (R-NIR) light in cells and causal for mitochondrial adenosine triphosphate (ATP) upregulation, and that pulsed R-NIR light has frequent therapeutic effects, which are superior to those of the continuous wave (CW) mode used in low-level light therapy (LLLT). Background data: Convincing evidence that the absorption of R-NIR photons by CCO is involved in mitochondrial ATP upregulations as well as a coherent explanation for the superiority of the pulsed irradiation mode is presently lacking in the literature. Methods: A comprehensive literature search and rigorous analysis of the data published on the idea that CCO is the primary absorber for R-NIR light, and of the claim that the effectivity of the pulsed irradiation mode can be derived from the absorption of R-NIR photons by CCO, reveal a number of severe inconsistencies. Results: A systematical analysis covering both the theory that CCO is the primary acceptor for R-NIR light and of its use to interpret differences between the biological effect of pulsed light and CW casts doubt on the general validity of the CCO-based hypothesis. Instead, we are offered a simple and conflict-free model accounting for both ATP upregulation and superiority of the pulsed mode in LLLT, which is in agreement with the results of recent laboratory experiments. Conclusions: CCO is not the primary acceptor for R-NIR light.

Progress in synthesizing protocells

IMPACT STATEMENT

Advances in the understanding of the biophysics of membranes, the nonenzymatic and enzymatic polymerization of RNA, and in the design of complex chemical reaction networks have led to a new, integrated way of viewing the shared chemistry needed to sustain life. Although a protocell capable of Darwinian evolution has yet to be built, the seemingly disparate pieces are beginning to fit together. At the very least, better cellular mimics are on the horizon that will likely teach us much about the physicochemical underpinnings of cellular life.

Delayed feedback control of active particles: a controlled journey towards the destination

We explore theoretically the navigation of an active particle based on delayed feedback control. The delayed feedback enters in our expression for the particle orientation which, for an active particle, determines (up to noise) the direction of motion in the next time step. Here we estimate the orientation by comparing the delayed position of the particle with the actual one. This method does not require any real-time monitoring of the particle orientation and may thus be relevant also for controlling sub-micron sized particles, where the imaging process is not easily feasible. We apply the delayed feedback strategy to two experimentally relevant situations, namely, optical trapping and photon nudging. To investigate the performance of our strategy, we calculate the mean arrival time analytically (exploiting a small-delay approximation) and by simulations.

Therapeutic Efficacy of Home-Use Photobiomodulation Devices: A Systematic Literature Review

OBJECTIVE

Perform systematic literature review on photobiomodulation (PBM) devices used at home for nonesthetic applications.

BACKGROUND

Home-use PBM devices have been marketed for cosmetic and therapeutic purposes. This is the first systematic literature review for nonesthetic applications.

METHODS

A systematic literature search was conducted for PBM devices self-applied at home at least thrice a week. Two independent reviewers screened the articles and extracted the data. Treatment dosage appropriateness was compared to the World Association for Laser Therapy (WALT) recommendations. The efficacy was evaluated according to the relevant primary end-point for the specific indication.

RESULTS

Eleven studies were suitable. Devices were applied for a range of indications, including pain, cognitive dysfunction, wound healing, diabetic macular edema, and postprocedural side effects, and were mostly based on near-infrared, pulsed light-emitting diodes with dosages within WALT recommendations. Regarding efficacy, studies reported mostly positive results.

CONCLUSIONS

Home-use PBM devices appear to mediate effective, safe treatments in a variety of conditions that require frequent applications. Conclusive evaluation of their efficacy requires additional, randomized controlled studies.

The hallmarks of living systems: towards creating artificial cells

Despite the astonishing diversity and complexity of living systems, they all share five common hallmarks: compartmentalization, growth and division, information processing, energy transduction and adaptability. In this review, we give not only examples of how cells satisfy these requirements for life and the ways in which it is possible to emulate these characteristics in engineered platforms, but also the gaps that remain to be bridged. The bottom-up synthesis of life-like systems continues to be driven forward by the advent of new technologies, by the discovery of biological phenomena through their transplantation to experimentally simpler constructs and by providing insights into one of the oldest questions posed by mankind, the origin of life on Earth.