Periodic bouncing of a plasmonic bubble in a binary liquid by competing solutal and thermal Marangoni forces

The physicochemical hydrodynamics of bubbles and droplets out of equilibrium, in particular with phase transitions, display surprisingly rich and often counterintuitive phenomena. Here we experimentally and theoretically study the nucleation and early evolution of plasmonic bubbles in a binary liquid consisting of water and ethanol. Remarkably, the submillimeter plasmonic bubble is found to be periodically attracted to and repelled from the nanoparticle-decorated substrate, with frequencies of around a few kilohertz. We identify the competition between solutal and thermal Marangoni forces as the origin of the periodic bouncing. The former arises due to the selective vaporization of ethanol at the substrate’s side of the bubble, leading to a solutal Marangoni flow toward the hot substrate, which pushes the bubble away. The latter arises due to the temperature gradient across the bubble, leading to a thermal Marangoni flow away from the substrate, which sucks the bubble toward it. We study the dependence of the frequency of the bouncing phenomenon from the control parameters of the system, namely the ethanol fraction and the laser power for the plasmonic heating. Our findings can be generalized to boiling and electrolytically or catalytically generated bubbles in multicomponent liquids.

Bubbles and bubble nucleation are ubiquitous in nature and technology, e.g., in boiling, electrolysis, and catalysis, where the phenomena connected with them have tremendous relevance for energy conversion, or in flotation, sonochemistry, cavitation, ultrasonic cleaning, and biomedical applications of ultrasound and bubbles. This also includes plasmonic bubbles, i.e., bubbles nucleating at liquid-immersed metal nanoparticles under laser irradiation, due to which an enormous amount of heat is produced because of a surface plasmon resonance (1–5). For an overview on the fundamentals of bubbles and their applications we refer to our recent review article (6). In general, in these applications the bubble nucleation does not occur in a pure liquid, but in multicomponent liquids. Because of that, various additional forces and effects come into play (7), which are not relevant in pure liquids. Examples are the Soret effect (8–10) or body forces arising due to density gradients. Once the multicomponent systems have interfaces, solutal Marangoni forces (11) become relevant. The phenomena become even richer once phase transitions occur in such systems, e.g., solidification (12, 13), evaporation (14–21), or dissolution of multicomponent droplets (22–25); or nucleation of a new phase such as in the so-called ouzo effect (26, 27); or in boiling (28), electrolysis (29, 30), or catalysis (31, 32). Similarly, also chemical reactions occurring at the interface in a multicomponent liquid lead to spectacular effects, such as swimming droplets (33, 34), phoretic self-propulsion (35–38), or pattern formation in electroconvection (39). The whole field could be summarized as physicochemical hydrodynamics, and although this is a classical subject (40), it received increasing attention in recent years due to its relevance for various applications, due to new experimental and numerical possibilities, and due to the beauty of the often surprising and counterintuitive phenomena. For recent reviews on physicochemical hydrodynamics, we refer to refs. 41 and 42.To exactly analyze the various competing forces playing a role in physicochemical hydrodynamical systems, one has to strive to have simple and clean geometries, allowing for precise measurements and a theoretical and numerical approach. For example, in refs. 43 and 44 we analyzed the competition between solutal Marangoni forces, gravity, and thermal diffusion by studying an oil droplet in a stably stratified liquid consisting of ethanol and water, imposing density and surface tension gradients on the droplet. Depending on the control parameters, the droplet was either stably levitating or jumping up and down, with a very low frequency of ∼0.02 Hz. Similar droplet and bubble oscillations originating from the competition between solutal Marangoni forces and gravity were observed in ref. 45.In this paper, we report and analyze another controlled physicochemical hydrodynamic bouncing phenomenon, even involving phase transitions, namely that of a nucleating plasmonic bubble (2, 4, 5), but now in an initially homogeneous binary liquid, for which the delay of bubble nucleation after turning on the laser depends on the composition of the binary liquid and the amount of dissolved gas (46) (next, of course, to the power of the employed laser). As in refs. 43 and 44, we will again see a bouncing behavior, but this time on a much faster timescale, corresponding to frequencies of ∼103 Hz. We will use this controlled physicochemical hydrodynamic system out of equilibrium to probe the competition between solutal and thermal Marangoni forces. That, in the presence of concentration gradients, the latter can compete with the former ones only is possible because of the very high-temperature gradients in the system of a nucleating plasmonic bubble. Under more standard conditions, such as for the evaporation of a binary droplet, the solutal Marangoni forces tend to be much stronger than the thermal ones (16).We note that plasmonic bubbles are in themselves very interesting with potential applications in biomedical diagnosis and therapy, micro- and nanomanipulation, and catalysis (1, 47–49). Also note that plasmonic bubbles directly after nucleation are pure vapor bubbles (50) originating from evaporation of the surrounding liquid, but during their expansion they are invaded by dissolved gas from the surrounding liquid (46, 51–53), which in the long term crucially determines their dynamics and lifetime.The key idea of this study here will build on the selective heating of the liquid surrounding the plasmonic bubble, namely on the side of the plasmonic nanoparticles. This leads to very strong temperature gradients across the bubble and thus to thermal Marangoni forces and at the same time to strong concentration gradients, as the evaporation of the surrounding binary liquid is selective, favoring the liquid with the lower boiling point. Thus, also solutal Marangoni forces along the bubble–liquid interface emerge. As we will see, which of these two different Marangoni forces is stronger depends on time and bubble position, leading to an oscillatory or bouncing bubble behavior.     

Emergent robustness of bacterial quorum sensing in fluid flow

Bacteria use intercellular signaling, or quorum sensing (QS), to share information and respond collectively to aspects of their surroundings. The autoinducers that carry this information are exposed to the external environment; consequently, they are affected by factors such as removal through fluid flow, a ubiquitous feature of bacterial habitats ranging from the gut and lungs to lakes and oceans. To understand how QS genetic architectures in cells promote appropriate population-level phenotypes throughout the bacterial life cycle requires knowledge of how these architectures determine the QS response in realistic spatiotemporally varying flow conditions. Here we develop and apply a general theory that identifies and quantifies the conditions required for QS activation in fluid flow by systematically linking cell- and population-level genetic and physical processes. We predict that when a subset of the population meets these conditions, cell-level positive feedback promotes a robust collective response by overcoming flow-induced autoinducer concentration gradients. By accounting for a dynamic flow in our theory, we predict that positive feedback in cells acts as a low-pass filter at the population level in oscillatory flow, allowing a population to respond only to changes in flow that occur over slow enough timescales. Our theory is readily extendable and provides a framework for assessing the functional roles of diverse QS network architectures in realistic flow conditions.

Bacteria share and respond collectively to information about their surrounding environment through the production, release, and detection of small diffusible molecules called autoinducers (AIs), in a process termed quorum sensing (QS). In QS systems, the individual bacterial expression of genes relevant to the community is promoted when AIs accumulate to a threshold concentration, typically associated with an increasing cell density (1). Population-level behaviors exhibited in QS-activated states include bioluminescence (2, 3), virulence factor production (4), modified mutation rates (5), biofilm and aggregate formation (6, 7), and biofilm dispersal (8). As AIs diffuse between cells, they are often subject to complex and fluctuating features of their environment, such as extracellular matrix components (9, 10), interference by other bacterial species (or the host organism), and external fluid flow. Recent research has started to show how such environmental factors are closely linked to the QS response, building on foundational knowledge gained from studying well-mixed laboratory cultures (11–13). However, improving our understanding of the functional role of QS systems requires understanding how these systems promote appropriate population-level phenotypes in realistic bacterial environments.Fluid flow is ubiquitous in a diverse range of bacterial habitats from rivers, lakes, and medical devices to the host teeth, gut, lungs, and nasal cavity (14). In addition to its mechanical effects on the structure of cell populations (15–19), external fluid flow has been found to have a strong influence on the transport of relevant chemicals including nutrients (8, 20), antibiotics during host treatment (21, 22), and QS AIs (23–26). Recent experimental (23–27) and numerical (28–34) studies suggest that flow-induced AI transport can affect population-level phenotypes by introducing chemical gradients within populations and, if the flow is strong enough, suppressing QS altogether. These results raise two important questions about QS genetic networks. First, how can QS networks ensure a robust population-level response in order to avoid individual cells committing to a costly multicellular phenotype in isolation, while also avoiding premature population-level QS activation in a spatiotemporally complex environment? Second, how can QS networks enable populations to sense cell density in flow environments that promote high mass transfer (35–38)?Here we answer these questions by combining simulations and a systematic asymptotic analysis of QS in a cell layer subject to an external flow; we focus on the effect of positive feedback in AI production, a common feature of QS genetic circuits (39). We begin by establishing the conditions required for the emergence of population-level QS activation in steady flow. Our results illustrate how the required conditions for activation depend on the ratio of the timescale of the external flow to the timescale of diffusion through the cell layer. If the required conditions are met in a region of the cell layer, positive feedback causes AIs to flood the population, inducing population-wide QS activation. Interestingly, by accounting for a dynamic flow in our model we find that an ability to avoid premature QS activation is built into systems with positive feedback. We predict that positive feedback acts as a low-pass filter to oscillations in the shear rate; if such oscillations occur over a time period shorter than a critical time that we calculate, the QS system is not activated, even if the required conditions for activation are met during the oscillations. Furthermore, we find that by combining multiple QS signals, a population can infer both cell density and external flow conditions. Overall, our findings suggest that positive feedback allows QS systems to act as spatiotemporally nonlocal sensors of fluid flow.     

Circular swimming motility and disordered hyperuniform state in an algae system

Active matter comprises individually driven units that convert locally stored energy into mechanical motion. Interactions between driven units lead to a variety of nonequilibrium collective phenomena in active matter. One of such phenomena is anomalously large density fluctuations, which have been observed in both experiments and theories. Here we show that, on the contrary, density fluctuations in active matter can also be greatly suppressed. Our experiments are carried out with marine algae (Effrenium voratum), which swim in circles at the air–liquid interfaces with two different eukaryotic flagella. Cell swimming generates fluid flow that leads to effective repulsions between cells in the far field. The long-range nature of such repulsive interactions suppresses density fluctuations and generates disordered hyperuniform states under a wide range of density conditions. Emergence of hyperuniformity and associated scaling exponent are quantitatively reproduced in a numerical model whose main ingredients are effective hydrodynamic interactions and uncorrelated random cell motion. Our results demonstrate the existence of disordered hyperuniform states in active matter and suggest the possibility of using hydrodynamic flow for self-assembly in active matter.

Active matter exists over a wide range of spatial and temporal scales (1–6) from animal groups (7, 8) to robot swarms (9–11), to cell colonies and tissues (12–16), to cytoskeletal extracts (17–20), to man-made microswimmers (21–25). Constituent particles in active matter systems are driven out of thermal equilibrium at the individual level; they interact to develop a wealth of intriguing collective phenomena, including clustering (13, 22, 24), flocking (11, 26), swarming (12, 13), spontaneous flow (14, 20), and giant density fluctuations (10, 11). Many of these observed phenomena have been successfully described by particle-based or continuum models (1–6), which highlight the important roles of both individual motility and interparticle interactions in determining system dynamics.Current active matter research focuses primarily on linearly swimming particles which have a symmetric body and self-propel along one of the symmetry axes. However, a perfect alignment between the propulsion direction and body axis is rarely found in reality. Deviation from such a perfect alignment leads to a persistent curvature in the microswimmer trajectories; examples of such circle microswimmers include anisotropic artificial micromotors (27, 28), self-propelled nematic droplets (29, 30), magnetotactic bacteria and Janus particles in rotating external fields (31, 32), Janus particle in viscoelastic medium (33), and sperm and bacteria near interfaces (34, 35). Chiral motility of circle microswimmers, as predicted by theoretical and numerical investigations, can lead to a range of interesting collective phenomena in circular microswimmers, including vortex structures (36, 37), localization in traps (38), enhanced flocking (39), and hyperuniform states (40). However, experimental verifications of these predictions are limited (32, 35), a situation mainly due to the scarcity of suitable experimental systems.Here we address this challenge by investigating marine algae Effrenium voratum (41, 42). At air–liquid interfaces, E. voratum cells swim in circles via two eukaryotic flagella: a transverse flagellum encircling the cellular anteroposterior axis and a longitudinal one running posteriorly. Over a wide range of densities, circling E. voratum cells self-organize into disordered hyperuniform states with suppressed density fluctuations at large length scales. Hyperuniformity (43, 44) has been considered as a new form of material order which leads to novel functionalities (45–49); it has been observed in many systems, including avian photoreceptor patterns (50), amorphous ices (51), amorphous silica (52), ultracold atoms (53), soft matter systems (54–61), and stochastic models (62–64). Our work demonstrates the existence of hyperuniformity in active matter and shows that hydrodynamic interactions can be used to construct hyperuniform states.     

Periscope Proteins are variable-length regulators of bacterial cell surface interactions

Changes at the cell surface enable bacteria to survive in dynamic environments, such as diverse niches of the human host. Here, we reveal “Periscope Proteins” as a widespread mechanism of bacterial surface alteration mediated through protein length variation. Tandem arrays of highly similar folded domains can form an elongated rod-like structure; thus, variation in the number of domains determines how far an N-terminal host ligand binding domain projects from the cell surface. Supported by newly available long-read genome sequencing data, we propose that this class could contain over 50 distinct proteins, including those implicated in host colonization and biofilm formation by human pathogens. In large multidomain proteins, sequence divergence between adjacent domains appears to reduce interdomain misfolding. Periscope Proteins break this “rule,” suggesting that their length variability plays an important role in regulating bacterial interactions with host surfaces, other bacteria, and the immune system.

Bacteria encounter complex and dynamic environments, including within human hosts, and have thus evolved various mechanisms that enable a rapid response for survival within, and exploitation of, new conditions. In addition to classical control by regulation of gene expression, bacteria exploit mechanisms that give rise to random variation to facilitate adaptation [e.g., phase and antigenic variation (1)]. In Gram-positive and Gram-negative human pathogens, DNA inversions (2, 3), homologous recombination (4), DNA methylation (1), and promoter sequence polymorphisms (5) govern changes in bacterial surface components, including capsular polysaccharide and protein adhesins, which can impact bacterial survival and virulence in the host (1, 6). Many of these mechanisms are very well studied and widespread across bacteria.A less well-studied mechanism is length variation in bacterial surface proteins. Variability in the number of sequence repeats in the Rib domain (7)–containing proteins on the surface of Group B streptococci has been linked to pathogenicity and immune evasion (8). The repetitive regions of the Staphylococcus aureus surface protein G (SasG) (9) and Staphylococcus epidermidis SasG homolog, Aap (10), also demonstrate sequence repeat number variability. In SasG, this variability regulates ligand binding by other bacterial proteins in vitro (11) in a process that has been proposed to enable bacterial dissemination in the host. Variations in repeat number have also been noted in the biofilm forming proteins Esp from Enterococcus faecalis (12) and, more recently, CdrA from Pseudomonas aeruiginosa (13). High DNA sequence identity in the genes that encode these proteins is likely to facilitate intragenic recombination events that would lead to repeat number variation (14) and, in turn, to protein sequence repetition. However, such sequence repetition is usually highly disfavored in large multidomain proteins (15), so its existence in these bacterial surface proteins suggests that protein length variation provides an evolutionary benefit. SasG, Aap, and Rib contain N-terminal host ligand binding domains and C-terminal wall attachment motifs; thus our recent demonstration that the repetitive regions of both SasG (16) and Rib (17) form unusual highly elongated rods suggests that host-colonization domains will be projected differing distances from the bacterial surface.Here, we show that repeat number variation in predicted bacterial surface proteins is more widespread and we characterize a third rod-like repetitive region in the Streptococcus gordonii protein (Sgo_0707) formed by tandem array of Streptococcal High Identity Repeats in Tandem (SHIRT) domains. Thus, we propose a growing class of “Periscope Proteins,” in which long, highly similar DNA repeats facilitate expression of surface protein stalks of variable length. This mechanism could enable changes in response to selection pressures and confer key advantages to the organism that include evasion of the host immune system (8) and regulation of surface interactions (11) involved in biofilm formation and host colonization.     

Cadherin cis and trans interactions are mutually cooperative

Cadherin transmembrane proteins are responsible for intercellular adhesion in all biological tissues and modulate tissue morphogenesis, cell motility, force transduction, and macromolecular transport. The protein-mediated adhesions consist of adhesive trans interactions and lateral cis interactions. Although theory suggests cooperativity between cis and trans bonds, direct experimental evidence of such cooperativity has not been demonstrated. Here, the use of superresolution microscopy, in conjunction with intermolecular single-molecule Förster resonance energy transfer, demonstrated the mutual cooperativity of cis and trans interactions. Results further demonstrate the consequent assembly of large intermembrane junctions, using a biomimetic lipid bilayer cell adhesion model. Notably, the presence of cis interactions resulted in a nearly 30-fold increase in trans-binding lifetimes between epithelial-cadherin extracellular domains. In turn, the presence of trans interactions increased the lifetime of cis bonds. Importantly, comparison of trans-binding lifetimes of small and large cadherin clusters suggests that this cooperativity is primarily due to allostery. The direct quantitative demonstration of strong mutual cooperativity between cis and trans interactions at intermembrane adhesions provides insights into the long-standing controversy of how weak cis and trans interactions act in concert to create strong macroscopic cell adhesions.

Cadherin adhesion proteins are essential for the hierarchical organization of all multicellular organisms, and their dysfunction is associated with several pathologies (1–8). For example, deficiencies in cadherin-mediated adhesion are correlated with the onset and metastasis of multiple cancers and tissue diseases (6–8). Cadherin-mediated adhesion involves the formation of adherens junctions (9, 10), which entail interactions between cadherin extracellular domains in cis and trans configurations, where cis interactions occur between proteins on the same cell membrane, and trans interactions occur between proteins on opposing membranes (11–26). Theory suggests that these cis and trans bonds form cooperatively (11–26). For example, cis interactions are believed to enhance molecular ordering (15) and may increase intercellular adhesion through cluster avidity (16, 27, 28), with potential applications related to angiogenesis and therefore cancer therapies (29–31). Early studies suggested that cis interactions enhanced the cadherin adhesive function (16). However, observations of lateral cis interactions between cadherin extracellular domains have been elusive because of their low affinity and the challenges of studying membrane-bound proteins (32–34). Observations of cis interactions in crystal structures and the disruption of cadherin organization within junctions by putative cis mutants suggested that they operate in tandem with trans interactions (15, 35). One hypothesis was that initial trans binding enhances the cis-binding affinity, leading to lateral clustering, junction nucleation, and growth (36). Such trans → cis cooperativity was predicted theoretically but not verified experimentally (37).Recent single-molecule (SM) studies successfully demonstrated that cis interactions induced clustering between cadherin extracellular domains on a supported lipid bilayer (SLB) (38, 39). The latter result suggested that conformational constraints associated with membrane immobilization increased the cis-binding affinity sufficiently to induce clustering, even in the absence of trans interactions. This observation raised the possibility of the reciprocal cooperativity (i.e., cis → trans), in which initial cis binding may enhance adhesion. Although the probability (but not the strength) of trans binding was found to increase for cadherin dimer constructs, relative to the monomer (34), the connection to cis interactions, if any, remains unclear. Demonstrating cis/trans cooperativity would require demonstrating that the presence of cis interactions alters the strength of trans bonds quantitatively and vice versa.In this study, we systematically identified and quantified cis/trans cooperativity, using dynamic SM Förster resonance energy transfer (FRET). These measurements determine whether cis interactions increase trans-binding lifetimes and, conversely, whether trans interactions increase cis-binding lifetimes. They further elucidated the putative role of cis/trans cooperativity in the formation and growth of cadherin junctions between opposing membranes. We find that cis and trans interactions are strongly and mutually cooperative. Most importantly, results show that cis interactions dramatically increase trans-binding lifetimes by more than an order of magnitude, and these cooperative interactions are shown to facilitate the assembly of large junctions. A detailed analysis of trans-binding kinetics as a function of cluster size provide insight into the molecular mechanism of the elevated trans lifetimes. The results presented suggest that specific cis interactions allosterically activate trans-binding interactions.     

Rapidly deployable and morphable 3D mesostructures with applications in multimodal biomedical devices

Structures that significantly and rapidly change their shapes and sizes upon external stimuli have widespread applications in a diversity of areas. The ability to miniaturize these deployable and morphable structures is essential for applications in fields that require high-spatial resolution or minimal invasiveness, such as biomechanics sensing, surgery, and biopsy. Despite intensive studies on the actuation mechanisms and material/structure strategies, it remains challenging to realize deployable and morphable structures in high-performance inorganic materials at small scales (e.g., several millimeters, comparable to the feature size of many biological tissues). The difficulty in integrating actuation materials increases as the size scales down, and many types of actuation forces become too small compared to the structure rigidity at millimeter scales. Here, we present schemes of electromagnetic actuation and design strategies to overcome this challenge, by exploiting the mechanics-guided three-dimensional (3D) assembly to enable integration of current-carrying metallic or magnetic films into millimeter-scale structures that generate controlled Lorentz forces or magnetic forces under an external magnetic field. Tailored designs guided by quantitative modeling and developed scaling laws allow formation of low-rigidity 3D architectures that deform significantly, reversibly, and rapidly by remotely controlled electromagnetic actuation. Reconfigurable mesostructures with multiple stable states can be also achieved, in which distinct 3D configurations are maintained after removal of the magnetic field. Demonstration of a functional device that combines the deep and shallow sensing for simultaneous measurements of thermal conductivities in bilayer films suggests the promising potential of the proposed strategy toward multimodal sensing of biomedical signals.

Deployable and morphable structures capable of changing their sizes and shapes significantly are essential in engineering (e.g., aerocrafts) and daily life (e.g., tents, umbrellas, and folding fans) (1, 2). Miniaturizing such structures to be comparable to the small scale in natural and/or human-engineered living systems such as arteries (1∼10 mm) (3), early-stage lesions (4), and organoids (∼1 mm) (5), and in minimally invasive surgeries (4) could broaden their applications in biomedical, healthcare, and electronic devices (6, 7). Recent advances in manufacture, fabrication, and assembly techniques enable the use of materials that respond to irradiation (8–12), magnetic field (13–21), electric field (22–27), electromagnetic field (28, 29), heat (17, 30–36), chemicals (37, 38), and pressures (39, 40) to remotely actuate large structural deformations (41–47). For example, the three-dimensional (3D) printing technique of programmed ferromagnetic domains developed by Kim et al. (13) realized the fast transformation between complex 3D configurations using magnetic field. By programming the magnetic configurations of nanomagnets, the micromachines developed by Cui et al. (19) could be transformed among multiple configurations. Mao et al. (28) presented soft electromagnetic actuators driven by Lorentz forces to fold two-dimensional (2D) precursors into various 3D shapes in spatially varying magnetic field. The silicon-lithium alloying reaction was exploited by Xia et al. (38) to drive the transformation of silicon-coated microlattices whose deformed shapes could be locked via plastic deformations.Despite the significant progress, most of the existing strategies are demonstrated only at relatively large sizes (>1 cm), while the ability to scale the deployable and morphable structures down to small sizes, such as millimeter and submillimeter scales, is crucial for many applications, such as the minimally invasive surgery and the sensing of early-stage lesion. With the reduction of the structural size, the integration of actuation components with 3D structures becomes more challenging, and many types of actuation forces, especially those (e.g., Lorentz forces and magnetic forces) that can be controlled remotely, decrease significantly compared to the structural rigidity. Therefore, the strategies that work effectively at relatively large sizes (>1 cm) may not be applicable at millimeter and submillimeter scales. In particular, the following two aspects are worthy of further exploration. On one hand, while a few different strategies have been developed to lock the deformed shape after removing the external stimuli, such as those based on plastic deformations (38, 48), shape-memory effects (49–52), and multistable structures (53–61), none is without limitations. For example, plastic deformations could reduce the durability of 3D architectures, and the prolonged period of phase transition in the shape-memory effect limits the speed of the reconfiguration (49–51). For specially engineered 2D patterns, the mechanics-guided, deterministic 3D assembly through the use of diverse release paths of biaxial prestrain allowed the transformation of assembled structures among multiple stable states (53–55), but applying a mechanical force to the underlying elastomeric substrate in situ is difficult. Incorporating dielectric elastomers that deform under an applied electric field as the assembly platform allows the formation of reconfigurable 3D mesostructures but requires high voltages and patterned electrodes (62, 63). Other strategies including the bistable Kresling patterns in response to the distributed magnetic actuation (15) were demonstrated at relatively large scales (>1 cm). A rapid, robust, and reversible shape reconfiguration at a small scale requires an actuation source that can be easily controlled, as well as a tailored design of low-rigidity structures. On the other hand, many deployable and morphable structures adopted intrinsically soft materials, such as elastomers (modulus ≤ 10 MPa) (64), which limits their applications in microelectronics and biomedical devices. This is because the inorganic functional materials (e.g., metals, silicons, and piezoelectric ceramics) often have large moduli (≥50 GPa) and may not be directly incorporated into those soft structures, due to the incompatibility of the fabrication technique and the increased structural rigidity. Three-dimensional structures made of intrinsically hard functional materials have been previously reported by our group (65–68), but active, large deformations are not accessible, due to the large rigidity and/or the lack of actuation components.Here, based on the mechanics-guided, deterministic 3D assembly (69–82), we introduce schemes of electromagnetic actuation and strategic structural designs to overcome the above limitations. The 3D assembly technique enables the integration of actuation components such as current-carrying metals (66) and magnetic materials (71) into small-scale 3D architectures to generate driving forces with portable magnets, as well as functional components ranging from silicons (67, 68), commercial chips (83–86), to piezoelectric ceramics/polymers (65, 87, 88). The design of low-rigidity structures guided by the finite element analysis (FEA) allows access to large deformations driven by those forces that are otherwise too small for conventional structures (89) at small sizes (e.g., <5 mm). The proposed strategies enable the assembly of millimeter-scale structures of various geometric configurations with submillimeter-scale feature sizes (e.g., ribbon width), ranging from 3D serpentines, kirigami patterns, to pop-up books that can switch rapidly and reversibly among multiple stables states. In particular, combined computational and experimental studies allow the formation of millimeter-scale deployable structures that can rapidly change their sizes by approximately one order of amplitude, which are unachievable previously. Furthermore, we demonstrate a functional device for detection of the thermal conductivities of a bilayer material, which can be actively switched between the deep and shallow sensing modes.     

Characterization of the strain-rate–dependent mechanical response of single cell–cell junctions

Cell–cell adhesions are often subjected to mechanical strains of different rates and magnitudes in normal tissue function. However, the rate-dependent mechanical behavior of individual cell–cell adhesions has not been fully characterized due to the lack of proper experimental techniques and therefore remains elusive. This is particularly true under large strain conditions, which may potentially lead to cell–cell adhesion dissociation and ultimately tissue fracture. In this study, we designed and fabricated a single-cell adhesion micro tensile tester (SCAµTT) using two-photon polymerization and performed displacement-controlled tensile tests of individual pairs of adherent epithelial cells with a mature cell–cell adhesion. Straining the cytoskeleton–cell adhesion complex system reveals a passive shear-thinning viscoelastic behavior and a rate-dependent active stress-relaxation mechanism mediated by cytoskeleton growth. Under low strain rates, stress relaxation mediated by the cytoskeleton can effectively relax junctional stress buildup and prevent adhesion bond rupture. Cadherin bond dissociation also exhibits rate-dependent strengthening, in which increased strain rate results in elevated stress levels at which cadherin bonds fail. This bond dissociation becomes a synchronized catastrophic event that leads to junction fracture at high strain rates. Even at high strain rates, a single cell–cell junction displays a remarkable tensile strength to sustain a strain as much as 200% before complete junction rupture. Collectively, the platform and the biophysical understandings in this study are expected to build a foundation for the mechanistic investigation of the adaptive viscoelasticity of the cell–cell junction.

Adhesive organelles between neighboring epithelial cells form an integrated network as the foundation of complex tissues (1). As part of normal physiology, this integrated network is constantly exposed to mechanical stress and strain, which is essential to normal cellular activities, such as proliferation (2–4), migration (5, 6), differentiation (7), and gene regulation (7, 8) associated with a diverse set of functions in tissue morphogenesis (9–11) and wound healing (9). A host of developmental defects or clinical pathologies in the form of compromised cell–cell associations will arise when cells fail to withstand external mechanical stress due to genetic mutations or pathological perturbations (12, 13). Indeed, since the mechanical stresses are mainly sustained by the intercellular junctions, which may represent the weakest link and limit the stress tolerance within the cytoskeleton network of a cell sheet, mutations or disease-induced changes in junction molecules and components in adherens junctions and desmosomes lead to cell layer fracture and tissue fragility, which exacerbate the pathological conditions (14–17). This clinical relevance gives rise to the importance of understanding biophysical transformations of the cell–cell adhesion interface when cells are subjected to mechanical loads.As part of their normal functions, cells often experience strains of tens to a few hundred percent at strain rates of 10⁻⁴ to 1 s⁻¹ (18–21). For instance, embryonic epithelia are subjected to strain rates in the range of 10⁻⁴ to 10⁻³ s⁻¹ during normal embryogenesis (22). Strain rates higher than 0.1 s⁻¹ are often experienced by adult epithelia during various normal physiological functions (21, 23, 24), such as breathing motions in the lung (1 to 10 s⁻¹) (25), cardiac pulses in the heart (1 to 6.5 s⁻¹) (20), peristaltic movements in the gut (0.4 to 1.5 s⁻¹), and normal stretching of the skin (0.1 to 5 s⁻¹). Cells have different mechanisms to dissipate the internal stress produced by external strain to avoid fracture, often via cytoskeleton remodeling and cell–cell adhesion enhancement (26, 27). These coping mechanisms may have different characteristic timescales. Cytoskeleton remodeling can dissipate mechanical stress promptly due to its viscoelastic nature and the actomyosin-mediated cell contractility (17, 28–32). Adhesion enhancement at the cell–cell contact is more complex in terms of timescale. Load-induced cell–cell adhesion strengthening has been shown via the increase in the number of adhesion complexes (33–35) or by the clustering of adhesion complexes (36–39), which occurs on a timescale ranging from a few minutes up to a few hours after cells experience an initial load (28). External load on the cell–cell contact also results in a prolonged cell–cell adhesion dissociation time (40, 41), suggesting cadherin bonds may transition to catch bonds under certain loading conditions (42, 43), which can occur within seconds (44). With the increase in cellular tension, failure to dissipate the stress within the cell layer at a rate faster than the accumulation rate will inevitably lead to the fracture of the cell layer (45). Indeed, epithelial fracture often aggravates the pathological outcomes in several diseases, such as acute lung injuries (46), skin disorders (47), and development defects (48). It is generally accepted that stress accumulation in the cytoskeleton network (49, 50) and potentially in the cytoplasm is strain-rate–dependent (51). However, to date, there is a lack of understanding about the rate-dependent behavior of cell–cell adhesions, particularly about which of the stress-relaxation mechanisms are at play across the spectrum of strain rates. In addition, it remains unclear how the stress relaxation interplays with adhesion enhancement under large strains, especially at high strain rates which may lead to fracture, that is, a complete separation of mature cell–cell adhesions under a tensile load (45, 52, 53). Yet, currently, there is a lack of quantitative technology that enables the investigation of these mechanobiological processes in a precisely controlled manner. This is especially true at high strain rates.To delineate this mechanical behavior, the cleanest characterization method is to directly measure stress dynamics at a single mature cell–cell adhesion interface. Specifically, just as a monolayer cell sheet is a reduction from three-dimensional (3D) tissue, a single cell–cell adhesion interface, as a reduction from a monolayer system, represents the smallest unit to study the rheological behavior of cellular junctions. The mechanistic understanding uncovered with this single unit will inform cellular adaptations to a more complex stress microenvironment in vivo and in vitro, in healthy and diseased conditions. To this end, we developed a single-cell adhesion micro tensile tester (SCAµTT) platform based on nanofabricated polymeric structures using two-photon polymerization (TPP). This platform allows in situ investigation of stress–strain characteristics of a mature cell–cell junction through defined strains and strain rates. With SCAµTT, we reveal some interesting biophysical phenomena at the single cell–cell junction that were previously not possible to observe using existing techniques. We show that cytoskeleton growth can effectively relax intercellular stress between an adherent cell pair in a strain-rate–dependent manner. Along with cadherin-clustering–induced bond strengthening, it prevents failure to occur at low strain rates. At high strain rates, insufficient relaxation leads to stress accumulation, which results in cell–cell junction rupture. We show that a remarkably large strain can be sustained before junction rupture (>200%), even at a strain rate as high as 0.5 s⁻¹. Collectively, the rate-dependent mechanical characterization of the cell–cell junction builds the foundation for an improved mechanistic understanding of junction adaptation to an external load and potentially the spatiotemporal coordination of participating molecules at the cell–cell junction.     

Patterns of bacterial motility in microfluidics-confining environments

Understanding the motility behavior of bacteria in confining microenvironments, in which they search for available physical space and move in response to stimuli, is important for environmental, food industry, and biomedical applications. We studied the motility of five bacterial species with various sizes and flagellar architectures (Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic environments presenting various levels of confinement and geometrical complexity, in the absence of external flow and concentration gradients. When the confinement is moderate, such as in quasi-open spaces with only one limiting wall, and in wide channels, the motility behavior of bacteria with complex flagellar architectures approximately follows the hydrodynamics-based predictions developed for simple monotrichous bacteria. Specifically, V. natriegens and V. fischeri moved parallel to the wall and P. putida and E. coli presented a stable movement parallel to the wall but with incidental wall escape events, while M. marinus exhibited frequent flipping between wall accumulator and wall escaper regimes. Conversely, in tighter confining environments, the motility is governed by the steric interactions between bacteria and the surrounding walls. In mesoscale regions, where the impacts of hydrodynamics and steric interactions overlap, these mechanisms can either push bacteria in the same directions in linear channels, leading to smooth bacterial movement, or they could be oppositional (e.g., in mesoscale-sized meandered channels), leading to chaotic movement and subsequent bacterial trapping. The study provides a methodological template for the design of microfluidic devices for single-cell genomic screening, bacterial entrapment for diagnostics, or biocomputation.

Many motile bacteria live in confining microenvironments (e.g., animal or plant tissue, soil, waste, granulated, and porous materials) and consequently are important to many applications like health [infectious diseases (1, 2), pharmaceuticals (3), and nutrition (4)], agriculture [veterinary (5) and crops (6)], environmental science [photosynthesis (7), biodegradation (8), and bioremediation (9)], and industrial activities [mining (10) and biofouling (11)]. Bacterial motility is essential in the search for available physical space as well as for enabling bacterial taxis in response to external stimuli, such as temperature (12), chemical gradients (13, 14), mechanical cues (15), or magnetic fields (16).To thrive in environments with diverse geometrical and physical characteristics, from open spaces to constraining environments, motile bacteria have evolved a multitude of propelling mechanisms (17), with flagellum-driven being the most common (18, 19). Flagellum-based machinery features various numbers of flagella (20) and designs: monotrichous, lophotrichous, amphitrichous, or peritrichous. The mechanics of this machinery, coupled with cell morphology (21) (e.g., coccus, rod-like, or curved) translates into several motility modes (e.g., turn angle, run-and-tumble, or run-and-flick) (22), and various motility behaviors (e.g., swimming, tumbling, and swarming) (17, 23). Environmental factors (24, 25) (e.g., chemical composition, viscosity, temperature, pH, and the chemistry and the roughness of adjacent surfaces) also influence bacterial motility.“Pure” bacterial motility, unbiased by chemotaxis or fluid flow, was reported near simple flat surfaces (26, 27) and in channels (28–30). Simulations of model bacteria in analogous conditions were also undertaken (31–37), but owing to the complexity of bacterial mechanics (38), modeling from first principles did not provide sufficient understanding to accurately predict movement patterns of different species in complex, confined environments. Consequently, studies of the effects of bacterial geometry in confined geometries were limited to models of simple, monotrichous bacteria with an assumed rigid flagellum (32, 39).Microfluidic devices (40, 41) are commonly used for the manipulation of individual or small populations of cells in micrometer-sized channels for medical diagnostics (42), drug screening (43), cell separation (44, 45), detection and sorting (46), and single-cell genomics (47). While microfluidic structures are used for the study of the motility of mammalian cells (48, 49), and microorganisms [e.g., fungi (50, 51), algae (52), or bacteria (29, 53–56)], these studies typically focus on a single species.To make progress toward a more general understanding of the motility of individual bacterial cells in confining microenvironments, as well as to assess the extent to which the behavior of bacteria with complex architectures can be assimilated with that of the more predictable monotrichous bacteria, the present work investigated the movement of five species (i.e., Vibrio natriegens, Magnetococcus marinus, Pseudomonas putida, Vibrio fischeri, and Escherichia coli) in microfluidic geometries with various levels of confinement and geometrical complexity.     

Identifying hydrophobic protein patches to inform protein interaction interfaces

Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.

Protein–protein interactions play a crucial role in numerous biological processes, ranging from signal transduction and immune response to protein aggregation and phase behavior (1–3). Consequently, being able to understand, predict, and modulate protein interactions has important implications for understanding cellular processes and mitigating the progression of disease (4, 5). A necessary first step toward this ambitious goal is uncovering the interfaces through which proteins interact (6–8). In principle, identifying hydrophobic protein regions, which interact weakly with water, should be a promising strategy for uncovering protein interaction interfaces (9, 10). Indeed, the release of weakly interacting hydration waters from hydrophobic regions can drive protein interactions, as well as other aqueous assemblies (11–13). However, even when the structure of a protein is available at atomistic resolution, it is challenging to identify its hydrophobic patches because they are not uniformly nonpolar, but display variations in polarity and charge at the nanoscale. Moreover, the emergent hydrophobicity of a protein patch stems from the collective response of protein hydration waters to the nanoscale chemical and topographical patterns displayed by the patch (14–20) and cannot be captured by simply counting the number of nonpolar groups in the patch, or even through more involved additive approaches, such as hydropathy scales or surface-area models (21–28).To address this challenge, we build upon seminal theoretical advances and molecular simulation studies, which have shown that near a hydrophobic surface, it is easier to disrupt surface–water interactions and form interfacial cavities (29–34). To uncover protein regions that have the weakest interactions with water, here, we employ specialized molecular simulations, wherein protein–water interactions are disrupted by systematically displacing water molecules from the protein hydration shell (35–37). By identifying the protein patches that nucleate cavities most readily in our simulations, we are then able to uncover the most hydrophobic protein regions. Interestingly, we find that both hydrophobic and hydrophilic protein patches are highly heterogeneous and contain comparable numbers of nonpolar and polar atoms. Our results thus highlight the nontrivial relationship between the chemical composition of protein patches and their emergent hydrophobicity (24–26), and further emphasize the importance of accounting for the collective solvent response in characterizing protein hydrophobicity (16). We then interrogate whether the most hydrophobic protein patches, which nucleate cavities readily, are also likely to mediate protein interactions. Across five proteins that participate in either homodimer or heterodimer formation, we find that roughly 60 to 70% of interfacial contacts and only about 10 to 20% of noncontacts nucleate cavities. Our work thus provides a versatile computational framework for characterizing hydrophobicity and uncovering interaction interfaces of not just proteins, but also of other complex amphiphilic solutes, such as cavitands, dendrimers, and patchy nanoparticles (38–41).     

Fouling-resistant zwitterionic polymers for complete prevention of postoperative adhesion

Postoperative adhesions are most common issues for almost any types of abdominal and pelvic surgery, leading to adverse consequences. Pharmacological treatments and physical barrier devices are two main approaches to address postoperative adhesions but can only alleviate or reduce adhesions to some extent. There is an urgent need for a reliable approach to completely prevent postoperative adhesions and to significantly improve the clinical outcomes, which, however, is unmet with current technologies. Here we report that by applying a viscous, cream-like yet injectable zwitterionic polymer solution to the traumatized surface, postoperative adhesion was completely and reliably prevented in three clinically relevant but increasingly challenging models in rats. The success rate of full prevention is over 93% among 42 animals tested, which is a major leap in antiadhesion performance. Clinically used Interceed film can hardly prevent the adhesion in any of these models. Unlike current antiadhesion materials serving solely as physical barriers, the “nonfouling” zwitterionic polymer functioned as a protective layer for antiadhesion applications with the inherent benefit of resisting protein/cell adhesions. The nonfouling nature of the polymer prevented the absorption of fibronectins and fibroblasts, which contribute to the initial and late-stage development of the adhesion, respectively. This is the key working mechanism that differentiated our “complete prevention” approach from current underperforming antiadhesion materials. This work implies a safe, effective, and convenient way to fully prevent postoperative adhesions suffered by current surgical patients.

Postoperative peritoneal adhesions are frequent complications for almost any types of abdominal and pelvic surgery and are found in up to 93% of the patients (1, 2). Postoperative adhesions are severe issues leading to many adverse consequences including chronic pain, female infertility, intestinal obstruction, and even death (3, 4). This significantly increases the suffering and economic burden to the patients (5–7). To address the adhesion-related complications, further surgical interventions (e.g., adhesiolysis) are always indispensable in clinical practice (8, 9). Nevertheless, the established tissue adhesions from previous surgery can result in difficult surgical procedures and longer operation times during the reoperation (10). In addition, patients may suffer a high risk of recurrent adhesion following the surgical lysis of preexisting adhesions (11–14).Pharmacological treatments and physical barrier-based devices are two main approaches having been evaluated to prevent or reduce the formation of postoperative adhesions (4, 5, 15–18). Local or systemic administration of antiinflammatory drugs and anticoagulants, including aspirin, dexamethasone, and heparin, have been tested for postoperative adhesion prevention, but the rapid clearance of drugs in the abdominal cavity greatly limits their therapeutic effects (19, 20). So far none of the drug treatments was able to completely prevent adhesion in clinics.The physical barrier-based systems used to prevent postoperative adhesions include solid sheets, polymer solutions, and hydrogels. The most widely used and Food and Drug Administration (FDA)–approved products in the United States are solid antiadhesion films, Interceed (oxidized regenerated cellulose; Johnson & Johnson) and Seprafilm (sodium hyaluronate-carboxymethyl cellulose; Genzyme). Nevertheless, all these film products can hardly be placed to cover the entire injured tissues with irregular shapes (20, 21). Furthermore, Interceed requires meticulous hemostasis during the application (22), which is impractical during a surgery. Seprafilm can easily adhere to any moist surface, including the surgeon’s gloves, during the placement, causing inconvenience, reposition issues, and even failure (23). Infusing polymer solutions such as liters of Adept (icodextrin 4% solution) were found to overcome the disadvantages of film products to some extent, but their applications are in general very limited due to the short dwelling time in the abdominal cavity (24, 25). Adept obtained FDA approval for a marginal reduction of adhesion in patients undergoing gynecological laparoscopic adhesiolysis (26). Injectable hydrogels are easy to handle, can completely cover the injured site, and have been tested for preventing or alleviating postoperative adhesions (27–30). Few of them have proven to be consistently effective in the subsequent clinical trials, and to the best of our knowledge none of them has been approved by the FDA for antiadhesion applications in the United States.Overall, it remained a major challenge to develop a safe, effective, and convenient approach to fully prevent postoperative adhesions given a number of barrier systems developed for postoperative adhesion prevention (27–31). From a clinical perspective, a complete prevention of postoperative adhesions is highly needed to significantly improve patient outcomes such as reoperation rates, chronic abdominal pain, or infertility (32).The mechanism for adhesion development has been debatable (1, 32–35), but in general it is believed to be triggered by a mass of serosanguinous exudates on the traumatized surface within a few hours after surgery. The exudate contains platelets and extracellular matrices and activated coagulation cascade and fibrin deposition at the wound surface—a natural wound-healing process. The fibrin matrix serves as a weak, temporal adhesive and a tissue–tissue adherence can quickly form resulting from a physical contact. The matrix is next invaded by inflammatory cells which further recruit other cells, in particular fibroblasts, enriched by day 4 after the surgery. The gradually clusterized and aligned fibroblasts together with the collagen secretion replace the temporal fibrin matrix and form a mature and permanent adhesion by the first week.Zwitterionic polymers are known for ultralow fouling property in resisting protein and cell adhesion (36, 37). Zwitterionic carboxybetaine polymers, in particular, have structures similar to glycine betaine that is present in human tissue and daily diet (28). They are generally considered biocompatible and nontoxic and have been safely applied in several in vitro and in vivo conditions, showing no observable cytotoxicity (38, 39), no stimulation of an immune response against the polymer (40), and no inflammatory signs or foreign body reaction to the polymer implant (38, 41, 42). Inspired by the protein and cell adhesion process prevailing during the adhesion development, we hypothesized that a full prevention of postoperative adhesions can be accomplished by applying a protective layer of “nonfouling” zwitterionic polymers on the traumatized surface, which can prevent the adhesion of protein containing exudate and fibroblasts that contributes to the initial and late-stage development of the adhesion, respectively. It should be noted that current antiadhesion materials mainly served as a physical barrier but without the “nonfouling” characteristics and typically resulted in limited antiadhesion performance.Here we prepared a viscous, gelatinous yet injectable zwitterionic poly(carboxybetaine acrylamide) (PCBAA) solution and first evaluated its efficacy in resisting protein adsorption and fibroblasts adhesion in vivo. We demonstrated that fibronectin adsorption (a key extracellular matrix protein in the exudate) can be fully prevented on the zwitterionic polymer-protected injured surface of the rat abdominal wall wound in vivo within 24 h of surgery. In addition, applying PCBAA on the traumatized surface could remarkably reduce fibroblast invasion and adhesion on the abdominal wall wound in vivo by day 4 after surgery. With these promising results, we further evaluated the in vivo antiadhesion efficacy of the prepared zwitterionic polymers, employing three different but increasingly challenging adhesion models (Fig. 1A). The results showed that zwitterionic PCBAA polymer can completely and reliably prevent postoperative adhesion in all three models (abdominal wall defect–cecum abrasion adhesion model: 12 out of 12 animals; repeated-injury adhesion model: 11 out of 12, except 1 developed the lowest level of adhesion [score 1] surrounding sutured area; 70% hepatectomy adhesion model: 18 out of 18 in the diaphragm and hepatic hilum, 16 out of 18 on the cut surface, except 2 developed the lowest level of adhesion [score 1]), whereas Interceed film (most popular in the United States) can only slightly reduce but cannot fully prevent adhesion in all these models.Open in a separate windowFig. 1.(A) The injectable cream-like zwitterionic PCBAA and its antiadhesion efficacy evaluation in rat sidewall defect–cecum abrasion adhesion model, repeated-injury recurrent adhesion model, and 70% hepatectomy-induced adhesion model, respectively. (B) GPC spectrum of the prepared PCBAA. (C) Steady-shear rheology of PCBAA solutions at 25 °C showing a shear-thinning behavior. (D) In vitro dissolution studies of PCBAA solutions with different concentrations. Data presented as mean ± SD (n = 3).The zwitterionic PCBAA we report here is able to completely prevent postoperative adhesion as illustrated in these three models and is expected to efficiently resolve adhesion issues in clinical operative scenarios. The antiadhesion working mechanism of PCBAA has also been elucidated through in vivo studies—we found reduced fibronectin adhesion was associated with reduced fibroblast cell adhesion and high performance in preventing adhesion in the three animal models; similar mechanistic exploration, however, has rarely been conducted on current antiadhesion materials.     

Surface plasmon mediates the visible light–responsive lithium–oxygen battery with Au nanoparticles on defective carbon nitride

Aprotic lithium-oxygen (Li-O₂) batteries have gained extensive interest in the past decade, but are plagued by slow reaction kinetics and induced large-voltage hysteresis. Herein, we use a plasmonic heterojunction of Au nanoparticle (NP)–decorated C₃N₄ with nitrogen vacancies (Au/N_V-C₃N₄) as a bifunctional catalyst to promote oxygen cathode reactions of the visible light–responsive Li-O₂ battery. The nitrogen vacancies on N_V-C₃N₄ can adsorb and activate O₂ molecules, which are subsequently converted to Li₂O₂ as the discharge product by photogenerated hot electrons from plasmonic Au NPs. While charging, the holes on Au NPs drive the reverse decomposition of Li₂O₂ with a reduced applied voltage. The discharge voltage of the Li-O₂ battery with Au/N_V-C₃N₄ is significantly raised to 3.16 V under illumination, exceeding its equilibrium voltage, and the decreased charge voltage of 3.26 V has good rate capability and cycle stability. This is ascribed to the plasmonic hot electrons on Au NPs pumped from the conduction bands of N_V-C₃N₄ and the prolonged carrier life span of Au/N_V-C₃N₄. This work highlights the vital role of plasmonic enhancement and sheds light on the design of semiconductors for visible light–mediated Li-O₂ batteries and beyond.

The aprotic lithium-oxygen (Li-O₂) battery promises ultrahigh theoretical energy density (∼3,600 Wh·kg⁻¹) and is operated with oxygen reduction to generate the product of Li₂O₂ and its reverse oxidation (2Li⁺ + O₂ + 2e⁻ ↔ Li₂O₂, E⁰ = 2.96 V) (1–5). The sluggish oxygen cathode reactions, including the oxygen evolution reaction (OER) and the oxygen reduction reaction (ORR), lead to a high discharge/charge overvoltage (∼1.0 V) during cycles and low round-trip efficiency (6–9). Since the pioneering work on the photoinvolved Li-O₂ battery using TiO₂ (10) or C₃N₄ (11) under ultraviolet (UV)-light irradiation, reduction of the charge/discharge overvoltage via a photomediated strategy has been extensively studied and is anticipated to solve the kinetic issues of the Li-O₂ battery (12–18). However, the light absorption of most semiconductors used is confined in the region of UV light, accounting for only ca. 4% of the solar spectrum (14–16). Expanding the light harvesting from UV to visible light is the long-term goal and challenge of photocatalysis (17–20). Simultaneously, high carrier recombination consumes the majority of photoelectrons and holes before catalyzing the targeted reactions, resulting in a mismatch between the carrier lifetime and kinetics of ORR or OER (19–21). This necessitates a structural design of semiconducting materials for visible-light harvesting to accelerate the cathode reactions in Li-O₂ batteries.Localized surface plasmon resonance (LSPR), which refers to the collective oscillation of conduction band (CB) electrons in metal nanocrystals under resonant excitation, has recently gained much attention (22–25). The decay of excited LSPR can produce hot electrons and holes, which initiate various chemical reactions (22, 23). Intriguingly, when plasmonic metal (e.g., Au, Ag) nanoparticles (NPs) come into contact with a semiconductor such as MoS₂, TiO₂, etc., an interfacial Schottky barrier forms; this barrier functions as a filter to force the energetic electrons or holes to migrate across the interface while inhibiting their reverse movement, thereby leading to effective electron–hole separation and suppressed charge–carrier recombination (26–30). LSPR systems generally are composed of plasmonic metal and semiconductors and exhibit the benefits of a low electron–hole recombination rate, enhanced light harvesting, and tailored response wavelengths from the visible to the near-infrared region (22). Recently, Au/CdSe (31) and Au/Ni(OH)₂ (32) heterojunctions have been attempted for a photocatalytic hydrogen evolution reaction and OER with the aid of hot electrons and holes under visible light. Coupling the plasmonic metal with suitable semiconductors for broadened light harvesting and a plasmon-enhanced effect is highly desirable for both ORR and OER in the Li-O₂ battery.Herein, we report defective C₃N₄ (Au/N_V-C₃N₄) decorated with plasmonic Au NPs as a bifunctional heterojunction catalyst that promotes cathode reactions of the Li-O₂ battery under visible light. The N_V on N_V-C₃N₄ is prone to adsorb and activate O₂, and the plasmon-excited electrons on Au migrate to the CB of N_V-C₃N₄ and relax to the N_V-induced defect band (DB) for O₂ reduction to LiO₂; then it undergoes electron reduction to Li₂O₂. Reversely, the Li₂O₂ is removed by the holes on the Au NPs driven by the applied voltage. The discharge voltage is raised to 3.16 V, and the charge voltage is lowered to 3.26 V at 0.05 mA·cm⁻² with a good rate capability and cycle stability. This investigation integrates a plasmonic heterojunction into the aprotic Li-O₂ battery and illustrates photoenergy conversion and storage under visible light.     

Improved bounds on entropy production in living systems

Living systems maintain or increase local order by working against the second law of thermodynamics. Thermodynamic consistency is restored as they consume free energy, thereby increasing the net entropy of their environment. Recently introduced estimators for the entropy production rate have provided major insights into the efficiency of important cellular processes. In experiments, however, many degrees of freedom typically remain hidden to the observer, and, in these cases, existing methods are not optimal. Here, by reformulating the problem within an optimization framework, we are able to infer improved bounds on the rate of entropy production from partial measurements of biological systems. Our approach yields provably optimal estimates given certain measurable transition statistics. In contrast to prevailing methods, the improved estimator reveals nonzero entropy production rates even when nonequilibrium processes appear time symmetric and therefore may pretend to obey detailed balance. We demonstrate the broad applicability of this framework by providing improved bounds on the energy consumption rates in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells.

Thermodynamic laws place fundamental limits on the efficiency and fitness of living systems (1, 2). To maintain cellular order and perform essential biological functions such as sensing (3–6), signaling (7), replication (8, 9) or locomotion (10), organisms consume energy and dissipate heat. In doing so, they increase the entropy of their environment (2), in agreement with the second law of thermodynamics (11). Obtaining reliable estimates for the energy consumption and entropy production in living matter holds the key to understanding the physical boundaries (12–14) that constrain the range of theoretically and practically possible biological processes (3). Recent experimental (6, 15, 16) and theoretical (17–20) advances in the imaging and modeling of cellular and subcellular dynamics have provided groundbreaking insights into the thermodynamic efficiency of molecular motors (14, 21), biochemical signaling (16, 22, 23) and reaction (24) networks, and replication (9) and adaption (25) phenomena. Despite such major progress, however, it is also known that the currently available entropy production estimators (26, 27) can fail under experimentally relevant conditions, especially when only a small set of observables is experimentally accessible or nonequilibrium transport currents (28–30) vanish.To help overcome these limitations, we introduce here a generic optimization framework that can produce significantly improved bounds on the entropy production in living systems. We will prove that these bounds are optimal given certain measurable statistics. From a practical perspective, our method requires observations of only a few coarse-grained state variables of an otherwise hidden Markovian network. We demonstrate the practical usefulness by determining improved entropy production bounds for bacterial flagella motors (10, 31), growing microtubules (32, 33), and calcium oscillations (7, 34) in human embryonic kidney cells.Generally, entropy production rates can be estimated from the time series of stochastic observables (35). Thermal equilibrium systems obey the principle of detailed balance, which means that every forward trajectory is as likely to be observed as its time reversed counterpart, neutralizing the arrow of time (36). By contrast, living organisms operate far from equilibrium, which means that the balance between forward and reversed trajectories is broken and net fluxes may arise (1, 37–39). When all microscopic details of a nonequilibrium system are known, one can measure the rate of entropy production by comparing the likelihoods of forward and reversed trajectories in sufficiently large data samples (35, 36). However, in most if not all biophysical experiments, many degrees of freedom remain hidden to the observer, demanding methods (28, 40, 41) that do not require complete knowledge of the system. A powerful alternative is provided by thermodynamic uncertainty relations (TURs), which use the mean and variance of steady-state currents to bound entropy production rates (18, 19, 26, 42–48). Although highly useful when currents can be measured (44–47), or when the system can be externally manipulated (40, 49), these methods give, by construction, trivial zero bounds for current-free nonequilibrium systems, such as driven one-dimensional (1D) nonperiodic oscillators. In the absence of currents, potential asymmetries in the forward and reverse trajectories can still be exploited to bound the entropy production rate (29, 30, 50), but to our knowledge no existing method is capable of producing nonzero bounds when forward and reverse trajectories are statistically identical. Moreover, even though previous bounds can become tight in some cases (51), optimal entropy production estimators for nonequilibrium systems are in general unknown.To obtain bounds that are provably optimal under reasonable conditions on the available data, we reformulate the problem here within an optimization framework. Formally, we consider any steady-state Markovian dynamics for which only coarse-grained variables are observable, where these observables may appear non-Markovian. We then search over all possible underlying Markovian systems to identify the one which minimizes the entropy production rate while obeying the observed statistics. More specifically, our algorithmic implementation leverages information about successive transitions, allowing us to discover nonzero bounds on entropy production even when the coarse-grained statistics appear time symmetric. We demonstrate this for both synthetic test data and experimental data (52) for flagella motors. Subsequently, we consider the entropy production of microtubules (33), which slowly grow before rapidly shrinking in steady state, to show how refined coarse graining in space and time leads to improved bounds. The final application to calcium oscillations in human embryonic kidney cells (34) illustrates how external stimulation with drugs can increase entropy production.     

A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases

Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus–disease associations are found.

The human virome is the sum total of all viruses that are intimately associated with people. This includes viruses that directly infect human cells (1, 2) but mostly consists of viruses infecting resident bacteria (i.e., phages) (3). While the large majority of microbiome studies have focused on the bacteriome, revealing numerous important functions for bacteria in human physiology (4), information about the human virome has lagged. However, a number of recent studies have begun making inroads into characterizing the virome (5–13).Just as human-tropic viruses can have dramatic effects on people, phages are able to dramatically alter bacterial physiology and regulate host population size. A variety of evolutionary dynamics can be at play in the phage/bacterium arena, including Red Queen (11), arms-race (14), and piggyback-the-winner (15) relationships, to name just a few. In the gut, many phages enter a lysogenic or latent state and are retained as integrated or episomal prophages within the host bacterium (16). In some instances, the prophage can buttress host fitness (at least temporarily) rather than destroy the host cell. To this effect, prophages often encode genes that can dramatically alter the phenotype of the bacteria, such as toxins (17), virulence factors (18), antibiotic resistance genes (19), photosystem components (20), other auxiliary metabolic genes (21), and CRISPR-Cas systems (22), along with countless genes of unknown function. Experimental evidence has shown that bacteria infected with particular phages (i.e., “virocells”) are physiologically distinct from cognate bacteria that lack those particular phages (21).There have been a few documented cases in which phages have been shown to be mechanistically involved in human health and disease, sometimes through direct interactions with human cells. This includes roles in increased bacterial virulence (17), response to cancer immunotherapy (23), clearance of bacterial infection (24), and resistance to antibiotics (25). Furthermore, phage therapy, the targeted killing of specific bacteria using live phage particles, has shown increasing promise for treatment of antibiotic-resistant bacterial infections (26). Considering the progress already made, phages represent attractive targets of and tools for microbiome restructuring in the interest of improving health outcomes.In addition, several studies have conducted massively parallel sequencing on virus-enriched samples of human stool, finding differential abundance of some phages in disease conditions (6, 27–29). A major issue encountered by these studies is that there is not yet a comprehensive database of annotated virus genome sequences, and de novo prediction of virus sequences from metagenomic assemblies remains a daunting challenge (3). Further, though some tools are able to predict virus-derived sequences with high specificity (30, 31), these tools have not been applied to human metagenomes at a large scale [with a possible exception (13)], and, regrettably, most uncovered virus genomes do not end up in central repositories. One study suggests that only 31% of the assembled sequence data in virion-enriched virome surveys could be identified as recognizably viral (32). On the other hand, another study of 12 individuals was able to recruit over 80% of reads from virus-enriched samples to putative virus contigs (11). Still, most of the potential viral contigs from this study were unclassifiable sequences, and a large majority of contigs appeared to represent subgenomic fragments under 10 kb.The current study sought to overcome the traditional challenges of sparse viral databases and poor detection of highly divergent viral sequences by using Cenote-Taker 2, a new virus discovery and annotation tool (33). The pipeline was applied to sequencing data from nearly 6,000 human metagenome samples. Strict criteria identified over 180,000 viral contigs representing 45,033 specific taxa. In most cases, 70 to 99% of reads from virus-enriched stool datasets could be back-aligned to the Cenote-Taker 2–compiled Human Virome Database. Furthermore, the curated database allowed read-alignment–based abundance profiling of the virome in human metagenomic datasets, enabling the reanalysis of a panel of existing case-control studies. The reanalysis revealed previously undetected associations between chronic diseases and the abundance of 2,265 specific virus taxa.     

Real-time measurements of aminoglycoside effects on protein synthesis in live cells

The spread of antibiotic resistance is turning many of the currently used antibiotics less effective against common infections. To address this public health challenge, it is critical to enhance our understanding of the mechanisms of action of these compounds. Aminoglycoside drugs bind the bacterial ribosome, and decades of results from in vitro biochemical and structural approaches suggest that these drugs disrupt protein synthesis by inhibiting the ribosome’s translocation on the messenger RNA, as well as by inducing miscoding errors. So far, however, we have sparse information about the dynamic effects of these compounds on protein synthesis inside the cell. In the present study, we measured the effect of the aminoglycosides apramycin, gentamicin, and paromomycin on ongoing protein synthesis directly in live Escherichia coli cells by tracking the binding of dye-labeled transfer RNAs to ribosomes. Our results suggest that the drugs slow down translation elongation two- to fourfold in general, and the number of elongation cycles per initiation event seems to decrease to the same extent. Hence, our results imply that none of the drugs used in this study cause severe inhibition of translocation.

Antibiotic resistance has become one of the biggest public health challenges of the 21st century. What used to be easily treatable diseases are becoming deadly as a consequence of commonly used antibiotics increasingly turning ineffective. To aid the development of new strategies to address this challenge, it is necessary to improve our understanding of the mechanism of action of these antibacterial compounds. Many antibiotics currently in use target the bacterial ribosome with high specificity (1). These compounds affect different stages of protein synthesis, depending on their binding sites in the bacterial ribosome or their binding to protein factors involved in protein synthesis.Aminoglycosides are a class of natural and semisynthetic chemical compounds of broad-spectrum therapeutic relevance (2, 3) categorized as critically important by the World Health Organization (4). Aminoglycosides are presently used against multidrug-resistant bacterial infections (5, 6) and, more recently, considered as potential treatments for genetic diseases such as cystic fibrosis and Duchenne muscular dystrophy (3, 7, 8). The clinical relevance of aminoglycosides is only shadowed by side effects such as nephrotoxicity and irreversible ototoxicity (5, 6). A subclass of these molecules has a conserved aminocyclitol, a 2-deoxystreptamine, with linked amino sugar groups at different positions. Structural studies showed that these molecules bind at the major groove of the 16S ribosomal RNA (rRNA) in the A-site in close contact with the decoding center of the bacterial 30S ribosomal subunit (9–12). At the decoding center, the adenines A1492 and A1493 take part in monitoring the correct codon–anticodon interaction (13). Aminoglycoside molecules bound to this site have been suggested to interact with A1492/1493 and restrict their mobility (12, 14), which in turn interferes with the selection of cognate transfer RNA (tRNA) (9, 11, 15–18) as well as with the translocation step (11, 16, 19–22).A secondary binding site for 4,5- and 4,6-substituted aminoglycosides has been identified at H69 in the 50S ribosomal subunit, in close contact with A- and P-site tRNAs (23). Based on crystal structures (23) and in vitro kinetics assays (24), it has been suggested that drugs bound to this secondary binding site affect ribosome recycling and also intersubunit rotation—potentially also affecting translocation.The synergistic effect of aminoglycosides binding to multiple sites in the bacterial ribosome contributes to the misreading of codons and defective translocation, which eventually leads to cell death. The mechanism of action of various aminoglycosides on the ribosome has been characterized using diverse structure biology methods (as reviewed in ref. 25), classical in vitro functional biochemical assays (15, 20, 26), and, more recently, in vitro single-molecule approaches (11, 21, 27). Even though the mechanistic steps are described in detail by these complementary in vitro techniques, the reported effects of these drugs on the kinetics of protein synthesis are significantly different. For example, whereas single-molecule Förster resonance energy transfer (FRET) studies report a four- to sixfold inhibition of messenger RNA (mRNA) movement during translocation (21), stopped-flow experiments report a 160-fold inhibition (20). Recent advances in live-cell single-molecule tracking methods have now opened up the possibility to measure the drug’s effects on protein synthesis kinetics directly in live cells (28, 29).In the present study, we measured the effect of three structurally different aminoglycosides, apramycin, gentamicin, and paromomycin, on the kinetics of translation elongation at a single-ribosome level in live Escherichia coli cells. By tracking single dye-labeled tRNAs and analyzing the diffusion trajectories using a Hidden Markov Model-based (HMM) approach, we measured dwell-times of elongator [Cy5]tRNA^Phe and initiator [Cy5]tRNA^fMet on the ribosome, which suggest an overall slower, but ongoing, protein synthesis in intact cells exposed to the aminoglycosides.     

Primate phageomes are structured by superhost phylogeny and environment

Humans harbor diverse communities of microorganisms, the majority of which are bacteria in the gastrointestinal tract. These gut bacterial communities in turn host diverse bacteriophage (hereafter phage) communities that have a major impact on their structure, function, and, ultimately, human health. However, the evolutionary and ecological origins of these human-associated phage communities are poorly understood. To address this question, we examined fecal phageomes of 23 wild nonhuman primate taxa, including multiple representatives of all the major primate radiations. We find relatives of the majority of human-associated phages in wild primates. Primate taxa have distinct phageome compositions that exhibit a clear phylosymbiotic signal, and phage–superhost codivergence is often detected for individual phages. Within species, neighboring social groups harbor compositionally and evolutionarily distinct phageomes, which are structured by superhost social behavior. Captive nonhuman primate phageome composition is intermediate between that of their wild counterparts and humans. Phage phylogenies reveal replacement of wild great ape–associated phages with human-associated ones in captivity and, surprisingly, show no signal for the persistence of wild-associated phages in captivity. Together, our results suggest that potentially labile primate-phage associations have persisted across millions of years of evolution. Across primates, these phylosymbiotic and sometimes codiverging phage communities are shaped by transmission between groupmates through grooming and are dramatically modified when primates are moved into captivity.

Mammals harbor diverse communities of microorganisms, the majority of which are bacteria in the gastrointestinal tract. Gut bacterial communities in turn host diverse phage communities that influence their structure, function, colonization patterns, and ultimately superhost health [the superhost is the host for bacteria that in turn host the phages (1)]. For example, enriched phage communities in human intestinal mucus can act as an acquired immune system by limiting mucosal bacterial populations (2), while dysbiotic gut phageomes are associated with health conditions such as type II diabetes (3), colitis (4), and stunting (5). Transplantation of healthy viral filtrates restored health in Clostridioides difficile patients (6), while in vitro studies suggest phages from stunted children shape bacterial populations differently from those of healthy children (5), supporting a direct link between phageome composition and disease. However, despite their importance in gut microbial ecosystems, the ecological and evolutionary processes that gave rise to these communities remain poorly resolved. Recent work on the widespread crAssphage suggests it might demonstrate long-term associations with its superhosts (7), similar to patterns described for many bacteria (8, 9).Primates host distinct bacterial communities, such that more phylogenetically related host taxa have more similar gut microbial composition (8, 10). The structure of these communities thus recapitulates the host phylogeny [i.e., phylosymbiosis (8, 10)], potentially reflecting widespread cospeciation of bacteria and hosts or phylogenetic conservation of the environments that shape bacterial communities (8, 9). Such long-term host–bacterial associations would imply restricted transmission of bacterial lineages within—rather than between—host lineages (8). This pattern of transmission may be facilitated by the tendency for primates to live in organized societies (11), creating opportunities for bacterial transmission to conspecifics (12, 13). When removed from their natural social and ecological environments and placed in captivity, primates quickly develop humanized bacterial microbiomes (14, 15). This apparent plasticity makes the long-term associations of primates with particular bacterial lineages all the more striking (8, 9).Here, we investigate whether these key findings about primate-associated gut bacterial communities can be generalized to phages. We explore drivers of phage community composition and individual phage lineage evolution in primate superhosts across multiple scales and environments, with a particular emphasis on the potential role of social transmission. We then examine the phageomes of captive primates to understand the flexibility of phage communities in response to the environment and the potential of phage transmission between superhosts. Lastly, we explore whether temperate versus virulent phage lifestyles influence the observed patterns in phage community composition and/or individual phage lineage evolution.