Chemotactic separation of enzymes

A Cautionary Perspective on Hydrogel-Induced Concentration Gradient Generation for Studying Chemotaxis

The achievement of consistent and static chemical gradients is critically important in the study of diffusion and chemotaxis at the micro- and nanoscales. In this context, a number of groups have reported on hydrogel-based systems for generating concentration gradients. Here, we analyze the behavior of agarose and gelatin-based hydrogels in hybridization chambers of different heights. Our focus is on the issues that are caused by the presence of robust bulk fluid flows in such systems due to the solutes present in the hydrogel and/or the surrounding fluid. We describe the key insights derived from these experiments, offering practical guidelines for establishing gradients using hydrogel-based systems and make the community aware of different variables that can make the experiments nonreproducible and prone to misinterpretations.

The Salt-Induced Diffusiophoresis of Nonionic Micelles-Does the Salt-Induced Growth of Micelles Influence Diffusiophoresis?

Salt-induced diffusiophoresis is the migration of a colloidal particle in water due to a directional salt concentration gradient. An important example of colloidal particles is represented by micelles, generated by surfactant self-assembly in water. For non-ionic surfactants containing polyethylene glycol (PEG) groups, PEG preferential hydration at the micelle-water interface is expected to drive micelle diffusiophoresis from high to low salt concentration. However, micelles are reversible supramolecular assemblies, with salts being able to promote a significant change in micelle size. This phenomenon complicates the description of diffusiophoresis. Specifically, it is not clear to what extent the salt-induced growth of micelles affects micelle diffusiophoresis. In this paper, a multiple-equilibrium model is developed for assessing the contribution of the micelle growth and preferential hydration mechanisms to the diffusiophoresis of non-ionic micelles. The available experimental data characterizing the effect of NaCl on Triton X-100 aggregation number are combined with data on diffusiophoresis and the preferential hydration of PEG chains to show that the contribution of the micelle growth mechanism to overall diffusiophoresis is small compared to that of preferential hydration.

Current progression in application of extracellular vesicles in central nervous system diseases

Early diagnosis and pharmacological treatment of central nervous system (CNS) diseases has been a long-standing challenge for clinical research due to the presence of the blood-brain barrier. Specific proteins and RNAs in brain-derived extracellular vesicles (EVs) usually reflect the corresponding state of brain disease, and therefore, EVs can be used as diagnostic biomarkers for CNS diseases. In addition, EVs can be engineered and fused to target cells for delivery of cargo, demonstrating the great potential of EVs as a nanocarrier platform. We review the progress of EVs as markers and drug carriers in the diagnosis and treatment of neurological diseases. The main areas include visual imaging, biomarker diagnosis and drug loading therapy for different types of CNS diseases. It is hoped that increased knowledge of EVs will facilitate their clinical translation in CNS diseases.

Network Effects Lead to Self-Organization in Metabolic Cycles of Self-Repelling Catalysts

Mixtures of particles that interact through phoretic effects are known to aggregate if they belong to species that exhibit attractive self-interactions. We study self-organization in a model metabolic cycle composed of three species of catalytically active particles that are chemotactic toward the chemicals that define their connectivity network. We find that the self-organization can be controlled by the network properties, as exemplified by a case where a collapse instability is achieved by design for self-repelling species. Our findings highlight a possibility for controlling the intricate functions of metabolic networks by taking advantage of the physics of phoretic active matter.

On the utility of microfluidic systems to study protein interactions: advantages, challenges, and applications

Within the complex milieu of a cell, which comprises a large number of different biomolecules, interactions are critical for function. In this post-reductionist era of biochemical research, the 'holy grail' for studying biomolecular interactions is to be able to characterize them in native environments. While there are a limited number of in situ experimental techniques currently available, there is a continuing need to develop new methods for the analysis of biomolecular complexes that can cope with the additional complexities introduced by native-like solutions. We think approaches that use microfluidics allow researchers to access native-like environments for studying biological problems. This review begins with a brief overview of the importance of studying biomolecular interactions and currently available methods for doing so. Basic principles of diffusion and microfluidics are introduced and this is followed by a review of previous studies that have used microfluidics to measure molecular diffusion and a discussion of the advantages and challenges of this technique.

Pair dynamics of active force dipoles in an odd-viscous fluid

We discuss the lateral dynamics of two active force dipoles, which interact with each other via hydrodynamic interactions in a thin fluid layer that is active and chiral. The fluid layer is modeled as a two-dimensional (2D) compressible fluid with an odd viscosity, while the force dipole (representing an active protein or enzyme) induces a dipolar flow. Taking into account the momentum decay in the 2D fluid, we obtain analytically the mobility tensor that depends on the odd viscosity and includes nonreciprocal hydrodynamic interactions. We find that the particle pair shows spiral behavior due to the transverse flow induced by the odd viscosity. When the magnitude of the odd viscosity is large as compared with the shear viscosity, two types of oscillatory behaviors are seen. One of them can be understood as arising from closed orbits in dynamical systems, and its circular trajectories are determined by the ratio between the magnitude of the odd viscosity and the force dipole. In addition, the phase diagrams of the particle dipolar angles are obtained numerically. Our findings reveal that the nonreciprocal response leads to complex dynamics of active particles embedded in an active fluid with odd viscosity.

Laminar flow-based microfluidic systems for molecular interaction analysis-Part 1: Chip development, system operation and measurement setup

The recent advent of laminar flow-based microfluidic systems for molecular interaction analysis has enabled transformative new profiling of proteins in regards to their structure, disordering, complex formation and interactions in general. Based on the diffusive transport of molecules perpendicular to the direction of laminar flow in a microfluidic channel, systems of this type promise continuous-flow, high-throughput screening of complex, multi-molecule interactions, while remaining tolerant to heterogeneous mixtures. Using common microfluidic device processing, the technology provides unique opportunities, as well as device design and experimental challenges, for integrative sample handling approaches that can investigate biomolecular interaction events in complex samples with readily available laboratory equipment. In this first chapter of a two-part series, we introduce system design and experimental setup requirements for a typical laminar flow-based microfluidic system for molecular interaction analysis in the form of what we call the 'LaMInA system' (Laminar flow-based Molecular Interaction Analysis system). We provide microfluidic device development advice on choice of device material, device design, including impact of channel geometry on the signal acquisition, and on design limitations and possible post-fabrication treatments to redress these. Finally. we cover aspects of fluidic actuation, such as selecting, measuring and controlling the flow rate appropriately, and provide a guide to possible fluorescent labels for proteins, as well as options for the fluorescence detection hardware, all in the context of assisting the reader in developing their own laminar flow-based experimental setup for biomolecular interaction analysis.

Controlled propulsion of micro/nanomotors: operational mechanisms, motion manipulation and potential biomedical applications

Inspired by natural mobile microorganisms, researchers have developed micro/nanomotors (MNMs) that can autonomously move by transducing different kinds of energies into kinetic energy. The rapid development of MNMs has created tremendous opportunities for biomedical fields including diagnostics, therapeutics, and theranostics. Although the great progress has been made in MNM research, at a fundamental level, the accepted propulsion mechanisms are still a controversial matter. In practical applications such as precision nanomedicine, the precise control of the motion, including the speed and directionality, of MNMs is also important, which makes advanced motion manipulation desirable. Very recently, diverse MNMs with different propulsion strategies, morphologies, sizes, porosities and chemical structures have been fabricated and applied for various uses. Herein, we thoroughly summarize the physical principles behind propulsion strategies, as well as the recent advances in motion manipulation methods and relevant biomedical applications of these MNMs. The current challenges in MNM research are also discussed. We hope this review can provide a bird's eye overview of the MNM research and inspire researchers to create novel and more powerful MNMs.

Diffusiophoresis of a Nonionic Micelle in Salt Gradients; Roles of Preferential Hydration and Salt-Induced Surfactant Aggregation

Diffusiophoresis is the migration of a colloidal particle in water driven by concentration gradients of cosolutes such as salts. We have experimentally characterized the diffusiophoresis of tyloxapol micelles in the presence of MgSO₄, a strong salting-out agent. Specifically, we determined the multicomponent-diffusion coefficients using Rayleigh interferometry, cloud points, and dynamic-light-scattering diffusion coefficients on the ternary tyloxapol-MgSO₄-water system at 25 °C. Our experimental results show that micelle diffusiophoresis occurs from a high to a low salt concentration (positive diffusiophoresis). Moreover, our data were used to characterize the effect of salt concentration on micelle size and salt osmotic diffusion, which occurs from a high to a low surfactant concentration. Although micelle diffusiophoresis can be attributed to the preferential hydration of the polyethylene glycol surface groups, salting-out salts also promote an increase in the size of micellar aggregates, ultimately leading to phase separation at high salt concentration. This complicates diffusiophoresis description, as it is not clear how salt-induced surfactant aggregation contributes to micelle diffusiophoresis. We, therefore, developed a two-state aggregation model that successfully describes the observed effect of salt concentration on the size of tyloxapol micelles, in the case of MgSO₄ and the previously reported case of Na₂SO₄. Our model was then used to theoretically evaluate the contribution of salt-induced aggregation to diffusiophoresis. Our analysis indicates that salt-induced aggregation promotes micelle diffusiophoresis from a low to a high salt concentration (negative diffusiophoresis). However, we also determined that this mechanism marginally contributes to overall diffusiophoresis, implying that preferential hydration is the main mechanism causing micelle diffusiophoresis. Our results suggest that sulfate salts may be exploited to induce the diffusiophoresis of PEG-functionalized particles such as micelles, with potential applications to microfluidics, enhanced oil recovery, and controlled-release technologies.

Engineered Exosomes with Independent Module/Cascading Function for Therapy of Parkinson's Disease by Multistep Targeting and Multistage Intervention Method

Current exosome engineering methods usually lead to the damage of exosome morphology and membrane, which cannot meet the complex needs of disease treatment. Herein, the concept of an "independent module/cascading function" is proposed to construct an engineered exosome nanotherapy platform including an independent artificial module and a natural module. The artificial module with movement/chemotaxis function is first synthesized, and then it is controllably combined with the natural exosome module with "one by one" mode through a "differentiated" modification method. The whole process can not only maintain the activity of the natural exosome module, but also endows it with motion ability, so as to realize the purpose of "cascading function" in the process of disease treatment. The above engineered exosomes are used in the treatment of Parkinson's disease (PD). Moreover, the multistep targeting strategy of "disease microenvironment-damaged cells-diseased mitochondria" and the multistage intervention concept of "inhibiting deterioration and promoting repair" are proposed, so as to break through the bottleneck of the existing treatment of PD.

Active matter dynamics in confined microfluidic environments

The field of active matter is a nascent area of research in soft condensed matter physics, which is drawing on the expertise of researchers from diverse disciplines. Small scale active particles-both inorganic and biological-display non-trivial emergent dynamics and interactions that could help us understand complex biological processes and phenomena. Recently, using microfluidic technologies, several research groups have performed important experimental and theoretical studies to understand the behavior of self-propelled particles and molecular active matter within confined environments-to glean a fundamental understanding of the cellular processes occurring under ultra-low Reynolds number conditions. In this chapter, we would like to review applications of microfluidics in active matter research, highlighting a few important theoretical and experimental investigations. We will conclude the discussion with a note on the future of this field mentioning a few open questions that are at the forefront of our minds.

A simple theory for molecular chemotaxis driven by specific binding interactions

Recent experiments have suggested that enzymes and other small molecules chemotax toward their substrates. However, the physical forces driving this chemotaxis are currently debated. In this work, we consider a simple thermodynamic theory for molecular chemotaxis that is based on the McMillan-Mayer theory of dilute solutions and Schellman's theory for macromolecular binding. Even in the absence of direct interactions, the chemical binding equilibrium introduces a coupling term into the relevant free energy, which then reduces the chemical potential of both enzymes and their substrates. Assuming a local thermodynamic equilibrium, this binding contribution to the chemical potential generates an effective thermodynamic force that promotes chemotaxis by driving each solute toward its binding partner. Our numerical simulations demonstrate that, although small, this thermodynamic force is qualitatively consistent with several experimental studies. Thus, our study may provide additional insight into the role of the thermodynamic binding free energy for molecular chemotaxis.

Relative Diffusivities of Bound and Unbound Protein Can Control Chemotactic Directionality

Enzyme-based systems have been shown to undergo chemotactic motion in response to their substrate gradient. This phenomenon has been exploited to direct the motion of enzymes and enzyme-attached particles to specific locations in space. Here, we propose a new kinetic model to analyze the directional movement of an ensemble of protein molecules in response to a gradient of the ligand. We also formulate a separate model to probe the motion of enzyme molecules in response to a gradient of the substrate under catalytic conditions. The only input for the new enzymatic model is the Michaelis-Menten constant which is the relevant measurable constant for enzymatic reactions. We show how our model differs from previously proposed models in a significant manner. For both binding and catalytic reactions, a net movement up the ligand/substrate gradient is predicted when the diffusivity of the ligand/substrate-bound protein is lower than that of the unbound protein (positive chemotaxis). Conversely, movement down the ligand/substrate gradient is expected when the diffusivity of the ligand/substrate-bound protein is higher than that of the unbound protein (negative chemotaxis). However, there is no net movement of protein/enzyme when the diffusivities of the bound and free species are equal. The work underscores the critical importance of measuring the diffusivity of the bound protein and comparing it with that of the free protein.

Apoptotic Tumor DNA Activated Nanomotor Chemotaxis

Inspired by the tactic organisms in Nature that can self-direct their movement following environmental stimulus gradient, we proposed a DNase functionalized Janus nanoparticle (JNP) nanomotor system for the first time, which can be powered by ultralow nM to μM levels of DNA. The system exhibited interesting chemotactic behavior toward a DNA richer area, which is physiologically related with many diseases including tumors. In the presence of the subtle DNA gradient generated by apoptotic tumor cells, the cargo loaded nanomotors were able to sense the DNA signal released by the cells and demonstrate directional motion toward tumor cells. For our system, the subtle DNA gradient by a small amount (10 μL) of tumor cells is sufficient to induce the chemotaxis behavior of self-navigating and self-targeting ability of our nanomotor system, which promises to shed new light for tumor diagnosis and therapy.

Non-equilibrium phase separation in mixtures of catalytically active particles: size dispersity and screening effects

Biomolecular condensates in cells are often rich in catalytically active enzymes. This is particularly true in the case of the large enzymatic complexes known as metabolons, which contain different enzymes that participate in the same catalytic pathway. One possible explanation for this self-organization is the combination of the catalytic activity of the enzymes and a chemotactic response to gradients of their substrate, which leads to a substrate-mediated effective interaction between enzymes. These interactions constitute a purely non-equilibrium effect and show exotic features such as non-reciprocity. Here, we analytically study a model describing the phase separation of a mixture of such catalytically active particles. We show that a Michaelis-Menten-like dependence of the particles' activities manifests itself as a screening of the interactions, and that a mixture of two differently sized active species can exhibit phase separation with transient oscillations. We also derive a rich stability phase diagram for a mixture of two species with both concentration-dependent activity and size dispersity. This work highlights the variety of possible phase separation behaviours in mixtures of chemically active particles, which provides an alternative pathway to the passive interactions more commonly associated with phase separation in cells. Our results highlight non-equilibrium organizing principles that can be important for biologically relevant liquid-liquid phase separation.

Single-particle diffusional fingerprinting: A machine-learning framework for quantitative analysis of heterogeneous diffusion

Single-particle tracking (SPT) analysis of individual biomolecules is an indispensable tool for extracting quantitative information from dynamic biological processes, but often requires some a priori knowledge of the system. Here we present “single-particle diffusional fingerprinting,” a more general approach for extraction of diffusional patterns in SPT independently of the biological system. This method extracts a set of descriptive features for each SPT trajectory, which are ranked upon classification to yield mechanistic insights for the species under comparison. We demonstrate its capacity to yield a dictionary of diffusional traits across multiple systems (e.g., lipases hydrolyzing fat, transcription factors diffusing in cells, and nanoparticles in mucus), supporting its use on multiple biological phenomena (e.g., drug delivery, receptor dynamics, and virology).

Single-particle tracking (SPT) is a key tool for quantitative analysis of dynamic biological processes and has provided unprecedented insights into a wide range of systems such as receptor localization, enzyme propulsion, bacteria motility, and drug nanocarrier delivery. The inherently complex diffusion in such biological systems can vary drastically both in time and across systems, consequently imposing considerable analytical challenges, and currently requires an a priori knowledge of the system. Here we introduce a method for SPT data analysis, processing, and classification, which we term “diffusional fingerprinting.” This method allows for dissecting the features that underlie diffusional behavior and establishing molecular identity, regardless of the underlying diffusion type. The method operates by isolating 17 descriptive features for each observed motion trajectory and generating a diffusional map of all features for each type of particle. Precise classification of the diffusing particle identity is then obtained by training a simple logistic regression model. A linear discriminant analysis generates a feature ranking that outputs the main differences among diffusional features, providing key mechanistic insights. Fingerprinting operates by both training on and predicting experimental data, without the need for pretraining on simulated data. We found this approach to work across a wide range of simulated and experimentally diverse systems, such as tracked lipases on fat substrates, transcription factors diffusing in cells, and nanoparticles diffusing in mucus. This flexibility ultimately supports diffusional fingerprinting’s utility as a universal paradigm for SPT diffusional analysis and prediction.

Surface adhesion of viruses and bacteria: Defend only and/or vibrationally extinguish also?! A perspective

Coronaviruses COVID-19, SARS-CoV and NL63 use spikes in their corona to bind to angiotensin converting enzyme 2 (ACE2) sites on cytoskeletal membranes of host cells to deliver their viral payload. While groups such as disulfides in ACE2's zinc metallopeptidase, and also in COVID-19's spikes, facilitate such binding, it is worth exploring how similar complementary sites on materials such as polymers, metals, ceramics, fabrics, and biomaterials promote binding of viruses and bacteria and how they could be further engineered to prevent bioactivity, or to act as agents to collect viral payloads in filters or similar devices. In that vein, this article offers a perspective on novel tools and approaches for chemically and topologically modifying most utilitarian surfaces via defensive topological vibrational engineering to either prevent such adhesion or to enhance adhesion and elicit vibrational characteristics/'musical signatures' from the surfaces so that the structure of the binding sites of viruses and bacteria is permanently altered and/or their cellular machinery is permanently disabled by targeted chemical transformations.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1557/s43580-021-00079-0.

Micro-Bio-Chemo-Mechanical-Systems: Micromotors, Microfluidics, and Nanozymes for Biomedical Applications

Wireless nano-/micromotors powered by chemical reactions and/or external fields generate motive forces, perform tasks, and significantly extend short-range dynamic responses of passive biomedical microcarriers. However, before micromotors can be translated into clinical use, several major problems, including the biocompatibility of materials, the toxicity of chemical fuels, and deep tissue imaging methods, must be solved. Nanomaterials with enzyme-like characteristics (e.g., catalase, oxidase, peroxidase, superoxide dismutase), that is, nanozymes, can significantly expand the scope of micromotors' chemical fuels. A convergence of nanozymes, micromotors, and microfluidics can lead to a paradigm shift in the fabrication of multifunctional micromotors in reasonable quantities, encapsulation of desired subsystems, and engineering of FDA-approved core-shell structures with tuneable biological, physical, chemical, and mechanical properties. Microfluidic methods are used to prepare stable bubbles/microbubbles and capsules integrating ultrasound, optoacoustic, fluorescent, and magnetic resonance imaging modalities. The aim here is to discuss an interdisciplinary approach of three independent emerging topics: micromotors, nanozymes, and microfluidics to creatively: 1) embrace new ideas, 2) think across boundaries, and 3) solve problems whose solutions are beyond the scope of a single discipline toward the development of micro-bio-chemo-mechanical-systems for diverse bioapplications.

Chemically-powered swimming and diffusion in the microscopic world

The past decade has seen intriguing reports and heated debates concerning the chemically-driven enhanced motion of objects ranging from small molecules to millimetre-size synthetic robots. These objects, in solutions in which chemical reactions were occurring, were observed to diffuse (spread non-directionally) or swim (move directionally) at rates exceeding those expected from Brownian motion alone. The debates have focused on whether observed enhancement is an experimental artefact or a real phenomenon. If the latter were true, then we would also need to explain how the chemical energy is converted into mechanical work. In this Perspective, we summarize and discuss recent observations and theories of active diffusion and swimming. Notably, the chemomechanical coupling and magnitude of diffusion enhancement are strongly size-dependent and should vanish as the size of the swimmers approaches the molecular scale. We evaluate the reliability of common techniques to measure diffusion coefficients and finish by considering the potential applications and chemical to mechanical energy conversion efficiencies of typical nanoswimmers and microswimmers.

Fundamentals and applications of enzyme powered micro/nano-motors

Micro/nanomotors (MNMs) are miniaturized machines that can convert many kinds of energy into mechanical motion. Over the past decades, a variety of driving mechanisms have been developed, which have greatly extended the application scenarios of MNMs. Enzymes exist in natural organisms which can convert chemical energy into mechanical force. It is an innovative attempt to utilize enzymes as biocatalyst providing driving force for MNMs. The fuels for enzymatic reactions are biofriendly as compared to traditional counterparts, which makes enzyme-powered micro/nanomotors (EMNMs) of great value in biomedical field for their nature of biocompatibility. Until now, EMNMs with various shapes can be propelled by catalase, urease and many others. Also, they can be endowed with multiple functionalities to accomplish on-demand tasks. Herein, combined with the development process of EMNMs, we are committed to present a comprehensive understanding of EMNMs, including their types, propelling principles, and potential applications. In this review, we will introduce single enzyme that can be used as motor, enzyme powered molecule motors and other micro/nano-architectures. The fundamental mechanism of energy conversion process of EMNMs and crucial factors that affect their movement behavior will be discussed. The current progress of proof-of-concept applications of EMNMs will also be elaborated in detail. At last, we will summarize and prospect the opportunities and challenges that EMNMs will face in their future development.

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Clear classification and description of different enzyme-powered micro/nanomotors (EMNMs).

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Discussion of the fundamental mechanism of energy conversion process of EMNMs and their movement influence factors.

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Introduction of the current progress of proof-of-concept applications of EMNMs.

Self-Propelled Micro/Nanomotors for On-Demand Biomedical Cargo Transportation

Micro/nanomotors (MNMs) are miniaturized machines that can perform assigned tasks at the micro/nanoscale. Over the past decade, significant progress has been made in the design, preparation, and applications of MNMs that are powered by converting different sources of energy into mechanical force, to realize active movement and fulfill on-demand tasks. MNMs can be navigated to desired locations with precise controllability based on different guidance mechanisms. A considerable research effort has gone into demonstrating that MNMs possess the potential of biomedical cargo loading, transportation, and targeted release to achieve therapeutic functions. Herein, the recent advances of self-propelled MNMs for on-demand biomedical cargo transportation, including their self-propulsion mechanisms, guidance strategies, as well as proof-of-concept studies for biological applications are presented. In addition, some of the major challenges and possible opportunities of MNMs are identified for future biomedical applications in the hope that it may inspire future research.

Separation of nanoparticles via surfing on chemical wavefronts

The separation of micro and nanoscale colloids is a necessary step in most biological microassay techniques, and is a common practice in microchemical processing. Chemical waves are frequently encountered in biochemical systems driven far from equilibrium. Here, we put forward a strategy for separating small suspending colloids by means of their surfing on substrate chemical wavefronts. The colloids with catalytic activities sensitive to the substrates are activated to show self-propulsion and consequently exhibit a chemotactic response to the traveling wavefronts, which results in their spontaneous separation from the multicomponent complex mixture via self-diffusiophoresis. The dynamics of the process is analyzed through a particle-based simulation. In addition, it is found that separation can be carried out according to particle size. The mechanisms underpinning the chemical and physical separation processes are discussed, and the dependencies on the reaction rate constant and particle size are presented. The results may prove relevant for further experimental and theoretical studies of separation in complex active environments.

Cooperatively enhanced reactivity and "stabilitaxis" of dissociating oligomeric proteins

Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein complexes assembled from a few proteins. By studying the generic spatial transport properties of such proteins, we investigate here whether their ability to reversibly associate and dissociate may confer on them a functional advantage with respect to nondissociating proteins. In uniform environments with position-independent association-dissociation, we find that enhanced diffusion in the monomeric state coupled to reassociation into the functional oligomeric form leads to enhanced reactivity with localized targets. In nonuniform environments with position-dependent association-dissociation, caused by, for example, spatial gradients of an inhibiting chemical, we find that dissociating proteins generically tend to accumulate in regions where they are most stable, a process that we term "stabilitaxis."

The 2020 motile active matter roadmap

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of 'active matter' in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines. The 2020 motile active matter roadmap of Journal of Physics: Condensed Matter addresses the current state of the art of the field and provides guidance for both students as well as established scientists in their efforts to advance this fascinating area.

Amplification of Salt-Induced Protein Diffusiophoresis by Varying Salt from Potassium to Sodium to Magnesium Chloride in Water

Salt-induced diffusiophoresis is the migration of a macromolecule or a colloidal particle induced by a concentration gradient of salt in water. Here, the effect of salt type on salt-induced diffusiophoresis of the protein lysozyme at pH 4.5 and 25 °C was examined as a function of salt concentration for three chloride salts: NaCl, KCl, and MgCl₂. Diffusiophoresis coefficients were calculated from experimental ternary diffusion coefficients on lysozyme-salt-water mixtures. In all cases, diffusiophoresis of this positively charged protein occurs from high to low salt concentration. An appropriate mass transfer process was theoretically examined to show that concentration gradients of MgCl₂ produce significant lysozyme diffusiophoresis. This is attributed to the relatively low mobility of Mg²⁺ ions compared to that of Cl^- ions at low salt concentration and a strong thermodynamic nonideality of this salt at high salt concentration. These findings indicate that MgCl₂ concentration gradients could be exploited for protein manipulation in solution (e.g., using microfluidic technologies) with applications to protein adsorption and purification. The dependence of lysozyme diffusiophoresis on salt type was theoretically examined and linked to protein charge. The effect of salts on hydrogen-ion titration curves was experimentally characterized to understand the role of salt type on protein charge. Our results indicate that binding of Mg²⁺ ions to lysozyme further enhances protein diffusiophoresis.

Mechanobiology of dynamic enzyme systems

This Perspective paper advances a hypothesis of mechanosensation by endothelial cells in which the cell is a dynamic crowded system, driven by continuous enzyme activity, that can be shifted from one non-equilibrium state to another by external force. The nature of the shift will depend on the direction, rate of change, and magnitude of the force. Whether force induces a pathophysiological or physiological change in cell biology will be determined by whether the dynamics of a cellular system can accommodate the dynamics and magnitude of the force application. The complex interplay of non-static cytoskeletal structures governs internal cellular rheology, dynamic spatial reorganization, and chemical kinetics of proteins such as integrins, and a flaccid membrane that is dynamically supported; each may constitute the necessary dynamic properties able to sense external fluid shear stress and reorganize in two and three dimensions. The resulting reorganization of enzyme systems in the cell membrane and cytoplasm may drive the cell to a new physiological state. This review focuses on endothelial cell mechanotransduction of shear stress, but may lead to new avenues of investigation of mechanobiology in general requiring new tools for interrogation of mechanobiological systems, tools that will enable the synthesis of large amounts of spatial and temporal data at the molecular, cellular, and system levels.

Enhanced Diffusion and Chemotaxis of Enzymes

Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, lead to a novel view of enzymes as active matter. Enzyme chemotaxis and EED may be important in biology and could have practical applications in biotechnology and nanotechnology. They are also of considerable biophysical interest; indeed, their physical mechanisms are still quite uncertain. This review provides an analytic summary of experimental studies of these phenomena and of the mechanisms that have been proposed to explain them and offers a perspective on future directions for the field.

Enzyme catalysis powered micro/nanomotors for biomedical applications

This review provides insights on enzyme powered motors using fuels present in biological environments for biomedical applications.

Positive and negative chemotaxis of enzyme-coated liposome motors

The ability of cells or cell components to move in response to chemical signals is critical for the survival of living systems. This motion arises from harnessing free energy from enzymatic catalysis. Artificial model protocells derived from phospholipids and other amphiphiles have been made and their enzymatic-driven motion has been observed. However, control of directionality based on chemical cues (chemotaxis) has been difficult to achieve. Here we show both positive or negative chemotaxis of liposomal protocells. The protocells move autonomously by interacting with concentration gradients of either substrates or products in enzyme catalysis, or Hofmeister salts. We hypothesize that the propulsion mechanism is based on the interplay between enzyme-catalysis-induced positive chemotaxis and solute-phospholipid-based negative chemotaxis. Controlling the extent and direction of chemotaxis holds considerable potential for designing cell mimics and delivery vehicles that can reconfigure their motion in response to environmental conditions.

Dynamic Transport Control of Colloidal Particles by Repeatable Active Switching of Solute Gradients

Diffusiophoresis (DP) is described as typically being divided into chemiphoresis (CP) and electrophoresis (EP), and the related theory is well-established. However, not only the individual effect of CP and EP but also the size dependency on the resulting DP of colloidal particles has not yet been comprehensively demonstrated in an experimental manner. In this paper, we present a dynamic transport control mechanism for colloidal particles by developing a micro-/nanofluidic DP platform (MNDP). We demonstrate that the MNDP can generate transient and/or steady-state concentration gradients, making it possible to control the direction and rate of transport of colloidal particles through the individual manipulation of CP and EP by simply and rapidly switching solutions. In addition, the MNDP allows the size-dependent separation as well as fractionation of submicron particles through the individual manipulation of CP and EP, thus empirically validating the classic theoretical model for DP under the influence of electrical double layer (EDL) thickness. Furthermore, we provide theoretical analysis and simulation results that will enable the development of a versatile separation and/or fractionation technique for various colloidal particles, including biosamples, according to their size or electrical feature.

Motility of Enzyme-Powered Vesicles

Autonomous nanovehicles powered by energy derived from chemical catalysis have potential applications as active delivery agents. For in vivo applications, it is necessary that the engine and its fuel, as well as the chassis itself, be biocompatible. Enzyme molecules have been shown to display enhanced motility through substrate turnover and are attractive candidates as engines; phospholipid vesicles are biocompatible and can serve as cargo containers. Herein, we describe the autonomous movement of vesicles with membrane-bound enzymes in the presence of the substrate. We find that the motility of the vesicles increases with increasing enzymatic turnover rate. The enhanced diffusion of these enzyme-powered systems was further substantiated in real time by tracking the motion of the vesicles using optical microscopy. The membrane-bound protocells that move by transducing chemical energy into mechanical motion serve as models for motile living cells and are key to the elucidation of the fundamental mechanisms governing active membrane dynamics and cellular movement.

Chemical and hydrodynamic alignment of an enzyme

Motivated by the implications of the complex and dynamic modular geometry of an enzyme on its motion, we investigate the effect of combining long-range internal and external hydrodynamic interactions due to thermal fluctuations with short-range surface interactions. An asymmetric dumbbell consisting of two unequal subunits, in a nonuniform suspension of a solute with which it interacts via hydrodynamic interactions as well as non-contact surface interactions, is shown to have two alignment mechanisms due to the two types of interactions. In addition to alignment, the chemical gradient results in a drift velocity that is modified by hydrodynamic interactions between the constituents of the enzyme.

Artificial Chemotaxis of Self-Phoretic Active Colloids: Collective Behavior

Microorganisms use chemotaxis, regulated by internal complex chemical pathways, to swim along chemical gradients to find better living conditions. Artificial microswimmers can mimic such a strategy by a pure physical process called diffusiophoresis, where they drift and orient along the gradient in a chemical density field. Similarly, for other forms of taxis in nature such as photo- or thermotaxis the phoretic counterpart exists. In this Account, we concentrate on the chemotaxis of self-phoretic active colloids. They are driven by self-electro- and diffusiophoresis at the particle surface and thereby acquire a swimming speed. During this process, they also produce nonuniform chemical fields in their surroundings through which they interact with other colloids by translational and rotational diffusiophoresis. In combination with active motion, this gives rise to effective phoretic attraction and repulsion and thereby to diverse emergent collective behavior. A particular appealing example is dynamic clustering in dilute suspensions first reported by a group from Lyon. A subtle balance of attraction and repulsion causes very dynamic clusters, which form and resolve again. This is in stark contrast to the relatively static clusters of motility-induced phase separation at larger densities. To treat chemotaxis in active colloids confined to a plane, we formulate two Langevin equations for position and orientation, which include translational and rotational diffusiophoretic drift velocities. The colloids are chemical sinks and develop their long-range chemical profiles instantaneously. For dense packings, we include screening of the chemical fields. We present a state diagram in the two diffusiophoretic parameters governing translational, as well as rotational, drift and, thereby, explore the full range of phoretic attraction and repulsion. The identified states range from a gaslike phase over dynamic clustering states 1 and 2, which we distinguish through their cluster size distributions, to different types of collapsed states. The latter include a full chemotactic collapse for translational phoretic attraction. Turning it into an effective repulsion, with increasing strength first the collapsed cluster starts to fluctuate at the rim, then oscillates, and ultimately becomes a static collapsed cloud. We also present a state diagram without screening. Finally, we summarize how the famous Keller-Segel model derives from our Langevin equations through a multipole expansion of the full one-particle distribution function in position and orientation. The Keller-Segel model gives a continuum equation for treating chemotaxis of microorganisms on the level of their spatial density. Our theory is extensible to mixtures of active and passive particles and allows to include a dipolar correction to the chemical field resulting from the dipolar symmetry of Janus colloids.

Enhanced Diffusion and Chemotaxis at the Nanoscale

Enzymes have been recently proposed to have mechanical activity associated with their chemical activity. In a number of recent studies, it has been reported that enzymes undergo enhanced diffusion in the presence of their corresponding substrate when this substrate is uniformly distributed in solution. Moreover, if the concentration of the substrate is nonuniform, enzymes and other small molecules have been reported to show chemotaxis (biased stochastic movement in the direction of the substrate gradient), typically toward higher concentrations of this substrate, with a few exceptions. The underlying physical mechanisms responsible for enhanced diffusion and chemotaxis at the nanoscale, however, are still not well understood. Understanding these processes is important both for fundamental biological research, for example, in the context of spatial organization of enzymes in metabolic pathways (metabolon formation), as well as for engineering applications, such as in the design of new vehicles for targeted drug delivery. In this Account, we will review the available experimental observations of both enhanced diffusion and chemotaxis, and we will discuss critically the different theories that have been proposed to explain the two. We first focus on enhanced diffusion, beginning with an overview of the experimental results. We then discuss the two main types of mechanisms that have been proposed, namely, active mechanisms relying on the catalytic step of the enzymatic reaction and equilibrium mechanisms, which consider the reversible binding and unbinding of the substrate to the enzyme. We put particular emphasis on an equilibrium model recently introduced by us, which describes how the diffusion of dumbbell-like modular enzymes can be enhanced in the presence of substrate thanks to a binding-induced reduction of the internal fluctuations of the enzyme. We then turn to chemotaxis, beginning with an overview of the experimental evidence for the chemotaxis of enzymes and small molecules, followed by a description of a number of shortcomings and pitfalls in the thermodynamic and phenomenological models for chemotaxis introduced in those and other works in the literature. We then discuss a microscopic model for chemotaxis including both noncontact interactions and specific binding between enzyme and substrate recently developed by us, which overcomes many of these shortcomings and is consistent with the experimental observations of chemotaxis. Finally, we show that the results of this model may be used to engineer chemically active macromolecules that are directed in space via patterning of the concentrations of their substrates.

Powering Motion with Enzymes

Enzymes are ubiquitous in living systems. Apart from traditional motor proteins, the function of enzymes was assumed to be confined to the promotion of biochemical reactions. Recent work shows that free swimming enzymes, when catalyzing reactions, generate enough mechanical force to cause their own movement, typically observed as substrate-concentration-dependent enhanced diffusion. Preliminary indication is that the impulsive force generated per turnover is comparable to the force produced by motor proteins and is within the range to activate biological adhesion molecules responsible for mechanosensation by cells, making force generation by enzymatic catalysis a novel mechanobiology-relevant event. Furthermore, when exposed to a gradient in substrate concentration, enzymes move up the gradient: an example of chemotaxis at the molecular level. The driving force for molecular chemotaxis appears to be the lowering of chemical potential due to thermodynamically favorable enzyme-substrate interactions and we suggest that chemotaxis promotes enzymatic catalysis by directing the motion of the catalyst and substrates toward each other. Enzymes that are part of a reaction cascade have been shown to assemble through sequential chemotaxis; each enzyme follows its own specific substrate gradient, which in turn is produced by the preceding enzymatic reaction. Thus, sequential chemotaxis in catalytic cascades allows time-dependent, self-assembly of specific catalyst particles. This is an example of how information can arise from chemical gradients, and it is tempting to suggest that similar mechanisms underlie the organization of living systems. On a practical level, chemotaxis can be used to separate out active catalysts from their less active or inactive counterparts in the presence of their respective substrates and should, therefore, find wide applicability. When attached to bigger particles, enzyme ensembles act as "engines", imparting motility to the particles and moving them directionally in a substrate gradient. The impulsive force generated by enzyme catalysis can also be transmitted to the surrounding fluid and molecular and colloidal tracers, resulting in convective fluid pumping and enhanced tracer diffusion. Enzyme-powered pumps that transport fluid directionally can be fabricated by anchoring enzymes onto a solid support and supplying the substrate. Thus, enzyme pumps constitute a novel platform that combines sensing and microfluidic pumping into a single self-powered microdevice. Taken in its entirety, force generation by active enzymes has potential applications ranging from nanomachinery, nanoscale assembly, cargo transport, drug delivery, micro- and nanofluidics, and chemical/biochemical sensing. We also hypothesize that, in vivo, enzymes may be responsible for the stochastic motion of the cytoplasm, the organization of metabolons and signaling complexes, and the convective transport of fluid in cells. A detailed understanding of how enzymes convert chemical energy to directional mechanical force can lead us to the basic principles of fabrication, development, and monitoring of biological and biomimetic molecular machines.

A Theory of Enzyme Chemotaxis: From Experiments to Modeling

Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with an increasing substrate concentration. In addition, enzymes perform directional motion toward regions with a high substrate concentration, termed as chemotaxis. While a variety of enzymes has been shown to undergo chemotaxis, there remains a lack of quantitative understanding of the phenomenon. Here, we derive a general expression for the active movement of an enzyme in a concentration gradient of its substrate. The proposed model takes into account both the substrate-binding and catalytic turnover step, as well as the enhanced diffusion of the enzyme. We have experimentally measured the chemotaxis of a fast and a slow enzyme: urease under catalytic conditions and hexokinase for both full catalysis and for simple noncatalytic substrate binding. There is good agreement between the proposed model and the experiments. The model is general, has no adjustable parameters, and only requires three experimentally defined constants to quantify chemotaxis: enzyme-substrate binding affinity ( K_d), Michaelis-Menten constant ( K_M), and level of diffusion enhancement in the associated substrate (α).

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.

Light-Driven Micro/Nanomotor for Promising Biomedical Tools: Principle, Challenge, and Prospect

A micro/nanomotor (MNM), as miniaturized machinery, can potentially bridge the application gap between the traditional macroscale motor and the molecular motor to manipulate materials at the cellular scale. The fascinating biomedical potential application for these tiny robots has been long envisioned by science fiction, such as "Fantastic Voyage", where complicated surgery can be performed at single cell precision without any surgical incision. However, to enter the highly conservative biomedical and healthcare industry in practice, the MNM must provide unique advantages over existing technology without introducing additional health risk, which has not been fully materialized. As an emerging approach, light-driven micro/nanomotors (LMNMs) have demonstrated several unique advantages over other MNMs, which will be addressed in this Account. As a control signal, light promises additional degrees of freedom to manipulate MNMs by modulating the light intensity, frequency, polarization, and propagation direction with spatial and temporal precision, which enables excellent controllability and programmability of LMNMs. Additionally, the fruitful knowledge and catalysts from the well-studied photocatalysis can be readily transferred to LMNMs for photoelectrochemical reactions, which provides a rich materials inventory for the development of advanced LMNM systems. A model LMNM in general can be regarded as a miniaturized solar cell combined with electrokinetic propulsion parts, where electric current is provided by the photovoltaic effect and then converted to propulsion thrust through a variety of electrokinetic mechanisms. It can be envisioned that the electric current may be further regulated with the onboard electronic circuit for advanced logic-controlled nanorobots. Finally, because incident photons instead of active chemicals provide the energy for LMNM propulsion, the highly active but toxic chemical fuels can be avoided, which suggested their better biocompatibility. It is essential to emphasize that all of these promises rely on the in-depth understanding of the photoelectrochemical reaction as well as the physics of electrokinetic phenomena, which requires further investigations. As a persistent endeavor, the biomedical application is the most attractive but challenging target for MNMs. Currently, most of the MNMs are demonstrated with in vitro conditions largely deviating from the biological environment, and nontrivial in vivo studies and cytotoxicity experiments are rarely reported. As merits of MNMs, the efficiency, biocompatibility, ion tolerance, and controllability critically determine the future success of MNMs. In this Account, existing and prospective solutions in these aspects are systemically discussed for light-propelled MNMs. We believe that, with a better understanding of the fundamental photoelectrochemical and electrokinetic processes, the development of motor design strategies, and improved fabrication methods, the promised practical biomedical application, such as early disease diagnosis, interventional therapy, targeted therapy, and microsurgery, could be realized in the near future.

Active Brownian Filamentous Polymers under Shear Flow

The conformational and rheological properties of active filaments/polymers exposed to shear flow are studied analytically. Using the continuous Gaussian semiflexible polymer model extended by the activity, we derive analytical expressions for the dependence of the deformation, orientation, relaxation times, and viscosity on the persistence length, shear rate, and activity. The model yields a Weissenberg-number dependent shear-induced deformation, alignment, and shear thinning behavior, similarly to the passive counterpart. Thereby, the model shows an intimate coupling between activity and shear flow. As a consequence, activity enhances the shear-induced polymer deformation for flexible polymers. For semiflexible polymers/filaments, a nonmonotonic deformation is obtained because of the activity-induced shrinkage at moderate and swelling at large activities. Independent of stiffness, activity-induced swelling facilitates and enhances alignment and shear thinning compared to a passive polymer. In the asymptotic limit of large activities, a polymer length- and stiffness-independent behavior is obtained, with universal shear-rate dependencies for the conformations, dynamics, and rheology.

Phoresis and Enhanced Diffusion Compete in Enzyme Chemotaxis

Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for chemotaxis that is valid for enzymes and other small molecules. Our theory includes both nonspecific interactions between enzyme and substrate as well as complex formation through specific binding between the enzyme and the substrate. We find that two distinct mechanisms contribute to enzyme chemotaxis: a diffusiophoretic mechanism due to the nonspecific interactions and a new type of mechanism due to binding-induced changes in the diffusion coefficient of the enzyme. The latter chemotactic mechanism points toward lower substrate concentration if the substrate enhances enzyme diffusion and toward higher substrate concentration if the substrate inhibits enzyme diffusion. For a typical enzyme, attractive phoresis and binding-induced enhanced diffusion will compete against each other. We find that phoresis dominates above a critical substrate concentration, whereas binding-induced enhanced diffusion dominates for low substrate concentration. Our results resolve an apparent contradiction regarding the direction of urease chemotaxis observed in experiments and, in general, clarify the relation between the enhanced diffusion and the chemotaxis of enzymes. Finally, we show that the competition between the two distinct chemotactic mechanisms may be used to engineer nanomachines that move toward or away from regions with a specific substrate concentration.