Institute for Atomic and Molecular Physics

Arbuscular mycorrhizal (AM) fungi are ancient plant mutualists that are ubiquitous across terrestrial ecosystems. These fungi are unique among most eukaryotes because they form multinucleate, open-pipe mycelial networks, where nutrients, organelles, and chemical signals move bidirectionally across a continuous cyto-plasm. AM fungi play a crucial role in ecosystem functioning by supporting plant growth, mediating ecosystem diversity, and contributing to carbon cycling. It is estimated that plant communities allocate ∼3.93 Gt CO 2 e to AM fungi every year, much of which is stored as lipids inside the fungal network. Despite their ecological significance, the cellular biology of AM fungi remains underexplored. Here, we synthesise the current knowledge on AM fungal cellular structure and organisation. We examine AM fungal development at different biological levels-the hypha and its content, hyphal networks and AM fungal spores-and explore key cellular dynamics. This includes cell wall composition, cytoplasmic contents, nuclear and lipid organisation and dynamics, network architecture, and connectivity. We highlight how their unique cellular arrangement enables complex cytoplasmic flow and nutrient exchange processes across their open-pipe mycelial networks. We discuss how both established and novel techniques, including microscopy, culturing, and high-throughput image analysis, are helping to resolve previously unknown aspects of AM fungal biology. By comparing these insights with established knowledge in other, well-studied filamentous fungi, we identify critical knowledge gaps and propose questions for future research to further our understanding of fundamental AM fungal cell biology and its contributions to ecosystem health.

End-stage heart failure is a deadly disease. Current total artificial hearts (TAHs) carry high mortality and morbidity and offer low quality of life. To overcome current biocompatibility issues, we propose the concept of a soft robotic, hybrid (pumping power comes from soft robotics, innerlining from the patient’s own cells) TAH. The device features a pneumatically driven actuator (septum) between two ventricles and is coated with supramolecular polymeric materials to promote anti-thrombotic and tissue engineering properties. In vitro, the Hybrid Heart pumps 5.7 L/min and mimics the native heart’s adaptive function. Proof-of-concept studies in rats and an acute goat model demonstrate the Hybrid Heart’s potential for clinical use and improved biocompatibility. This paper presents the first proof-of-concept of a soft, biocompatible TAH by providing a platform using soft robotics and tissue engineering to create new horizons in heart failure and transplantation medicine.

Motivation Cells are dynamic, continually responding to intra- and extracellular signals. Measuring the response to these signals in individual cells is challenging. Signal transduction is fast, but reporters for downstream gene expression are slow: fluorescent proteins must be expressed and mature. An alternative is to fluorescently tag and monitor the intracellular locations of transcription factors and other effectors. These proteins enter or exit the nucleus in minutes, after upstream signalling modifies their phosphorylation state. Although such approaches are increasingly popular, there is no consensus on how to quantify nuclear localization. Results Using budding yeast, we developed a convolutional neural network that determines nuclear localization from fluorescence and, optionally, bright-field images. Focusing on changing extracellular glucose, we generated ground-truth data using strains with a transcription factor and a nuclear protein tagged with fluorescent markers. We showed that the neural network–based approach outperformed seven published methods, particularly when predicting single-cell time series, which are key to determining how cells respond. Collectively, our results are conclusive—using machine learning to automatically determine the appropriate image processing consistently outperforms ad hoc approaches. Adopting such methods promises to both improve the accuracy and, with transfer learning, the consistency of single-cell analyses. Availability and implementation We performed our analysis in Python; code is available at https://git.ecdf.ed.ac.uk/v1jhurba/neunet-nucloc.git.

Selective formation of multicomponent structures via the self-assembly of numerous building blocks is ubiquitous in biological systems but challenging to emulate synthetically. More components introduce additional possibilities for kinetic intermediates with trap-state ability, hampering access to desired products. In covalent chemistry, templates, reagents and catalysts are applied to create alternative pathways for desired product formation. Analogously, we enlist exo-templating to mould the formation of large, multicomponent supramolecular structures. Specifically, a charged ring docks at 1,5-dioxynaphthalene stations within exo-functionalized building blocks to promote formation of cuboctahedral Pd12L24 nanospheres via exoskeletal templating. With the exo-templating ring present, nanosphere formation occurs via small Pdx–Ly oligomers, while in the absence of the ring a Pdx–Ly polymer resting state rapidly evolves, from which nanosphere formation occurs slowly. We demonstrate a form of kinetic templating—via intermediate destabilization—resembling properties observed in catalysis. Importantly, unlike typically employed endo-templates, we demonstrate that exo-templating is particularly suited for larger, complex, self-assembled structures.

Chaperones are essential to the co-translational folding of most proteins. However, the principles of co-translational chaperone interaction throughout the proteome are poorly understood, as current methods are restricted to few substrates and cannot capture nascent protein folding or chaperone binding sites, precluding a comprehensive understanding of productive and erroneous protein biosynthesis. Here, by integrating genome-wide selective ribosome profiling, single-molecule tools, and computational predictions using AlphaFold we show that the binding of the main E. coli chaperones involved in co-translational folding, Trigger Factor (TF) and DnaK correlates with “unsatisfied residues” exposed on nascent partial folds – residues that have begun to form tertiary structure but cannot yet form all native contacts due to ongoing translation. This general principle allows us to predict their co-translational binding across the proteome based on sequence only, which we verify experimentally. The results show that TF and DnaK stably bind partially folded rather than unfolded conformers. They also indicate a synergistic action of TF guiding intra-domain folding and DnaK preventing premature inter-domain contacts, and reveal robustness in the larger chaperone network (TF, DnaK, GroEL). Given the complexity of translation, folding, and chaperone functions, our predictions based on general chaperone binding rules indicate an unexpected underlying simplicity.

Animals achieve robust locomotion by offloading regulation from the brain to physical couplings within the body. In contrast, locomotion in artificial systems often depends on centralized processors. Here, we introduce a rapid and autonomous locomotion strategy with synchronized gaits emerging through physical interactions between self-oscillating limbs and the environment, without control signals. Each limb is a single soft tube that only requires a constant flow of air to perform cyclic stepping motions at frequencies reaching 300 hertz. Physical synchronization of several of these self-oscillating limbs enables locomotion speeds that are orders of magnitude faster than those of comparable state-of-the-art robots. Through body-environment dynamics, these seemingly simple devices exhibit autonomy, including obstacle avoidance, amphibious gait transitions, and phototaxis.

Despite its various potential uses, untethered pneumatics have little practical use due to the speed, power, and controllability limitations of power systems, and system-design restrictions (dead volume contained in pneumatic circuits and hardware needed to handle high actuator pressures). In this work, we present a compact monopropellant engine that localizes pressure generation to actuators. Our approach minimizes dead volume by eliminating pneumatic circuitry and allows high-pressure actuation from a low-pressure fuel source. We introduce the architecture, present a hardware implementation, and prove our pressure-amplification working principle experimentally. We also experimentally demonstrate fast response time (<30 ms), high-pressure capability (>100 kPa), high flow rate capacity (140 SLM/kg), and the ability to control the rate of gas output and volume of produced gas. Finally, we interface the engine with two distinct soft actuators to demonstrate its plug-and-play ease of use, operating at both high speeds and high pressures, and estimating a promising power output range (~5-25 W/kg). With this design, we hope to move closer towards self-contained pneumatic muscles that interface with low-pressure embodied energy storage, which may increase the viability of pneumatic actuation for untethered robotic applications.

Localized optical field enhancement enables strong light-matter interactions necessary for efficient manipulation and sensing of light. Specifically, tunable broadband energy localization in nanoscale hotspots offers many applications in nanophotonics and quantum optics. We experimentally demonstrate a mechanism for the local enhancement of electromagnetic fields based on strong suppression of backscattering. This is achieved at a designed termination of a topologically nontrivial waveguide that nearly preserves the valley degree of freedom. The symmetry origin of the valley degree of freedom prevents edge states to undergo intervalley scattering at waveguide discontinuities that obey the symmetry of the crystal. Using near-field microscopy, we reveal that this leads to strong confinement of light at the termination of a topological photonic waveguide, even without breaking reciprocity. We emphasize the importance of symmetry conservation by comparing different waveguide termination geometries, confirming that the origin of suppressed backscattering lies with the near conservation of the valley degree of freedom, and show the broad bandwidth of the effect.

Mechanical snapping instabilities are leveraged by natural systems, metamaterials, and devices for rapid sensing, actuation, and shape changes, as well as to absorb impact. In all current forms of snapping, shapes deform in the same direction as the exerted forces, even though there is no physical law that dictates this. Here, we realize countersnapping mechanical structures that respond in the opposite way. In contrast to regular snapping, countersnapping manifests itself in a sudden shortening transition under increasing tension or a sudden increase in tensile force under increasing extension. We design these structures by combining basic flexible building blocks that leverage geometric nonlinearities. We demonstrate experimentally that countersnapping can be employed to obtain new exotic properties, such as unidirectional stick–slip motion, switchable stiffness that does not otherwise affect the state of the system, and passive resonance avoidance. Moreover, we demonstrate that combining multiple countersnapping elements allows sequential stiffness switching for elements coupled in parallel, or instantaneous collective switching for elements in series. By expanding the repertoire of realizable elastic instabilities, our work opens routes to principles for mechanical sensing, computation, and actuation.

Current organic light-emitting diode (OLED) technology uses light-emitting molecules in a molecular host. We report green circularly polarized luminescence (CPL) in a chirally ordered supramolecular assembly, with 24% dissymmetry in a triazatruxene (TAT) system. We found that TAT assembled into helices with a pitch of six molecules, associating angular momentum to the valence and conduction bands and obtaining the observed CPL. Cosublimation of TAT as the “guest” in a structurally mismatched “host” enabled fabrication of thin films in which chiral crystallization was achieved in situ by thermally triggered nanophase segregation of dopant and host while preserving film integrity. The OLEDs showed external quantum efficiencies of up to 16% and electroluminescence dissymmetries ≥10%. Vacuum deposition of chiral superstructures opens new opportunities to explore chiral-driven optical and transport phenomena.

Nanoribbons, nanometre-wide strips of a two-dimensional material, are a unique system in condensed matter. They combine the exotic electronic structures of low-dimensional materials with an enhanced number of exposed edges, where phenomena including ultralong spin coherence times1,2, quantum confinement³ and topologically protected states4,5 can emerge. An exciting prospect for this material concept is the potential for both a tunable semiconducting electronic structure and magnetism along the nanoribbon edge, a key property for spin-based electronics such as (low-energy) non-volatile transistors⁶. Here we report the magnetic and semiconducting properties of phosphorene nanoribbons (PNRs). We demonstrate that at room temperature, films of PNRs show macroscopic magnetic properties arising from their edge, with internal fields of roughly 240 to 850 mT. In solution, a giant magnetic anisotropy enables the alignment of PNRs at sub-1-T fields. By leveraging this alignment effect, we discover that on photoexcitation, energy is rapidly funnelled to a state that is localized to the magnetic edge and coupled to a symmetry-forbidden edge phonon mode. Our results establish PNRs as a fascinating system for studying the interplay between magnetism and semiconducting ground states at room temperature and provide a stepping-stone towards using low-dimensional nanomaterials in quantum electronics.

Background In cardiovascular engineering, the recent introduction of soft robotic technologies sheds new light on the future of implantable cardiac devices, enabling the replication of complex bioinspired architectures and motions. To support human heart function, assistive devices and total artificial hearts have been developed. However, the system's functionality, hemocompatibility, and overall implantability are still open challenges. Methods Here, the design of a soft robotic artificial cardiac wall is presented: the action of a bioinspired myocardium of pneumatic McKibben actuators in a double helix is coupled with an engineered passive and deformable endocardial layer made of silicone. The correlation between the helix angle of the actuators and the ejection fraction of the artificial cardiac wall was preliminarily studied with a simplified analytical model. A FEM model was introduced to represent the complex deformation of the endocardial layer during the actuation of the cardiac wall. Results Experimental tests report an ejection fraction of 68%, i.e., 77.2 ± 0.4 mL against 90 mmHg, satisfying the minimum physiological requirements and, therefore, proving the concept's functionality. Conclusions The conceived device paves the way for a new generation of innovative approaches where engineered bioinspiration might be the key to future artificial cardiac pumps that could support or even substitute the human failing heart.

For nearly 450 million years, mycorrhizal fungi have constructed networks to collect and trade nutrient resources with plant roots1,2. Owing to their dependence on host-derived carbon, these fungi face conflicting trade-offs in building networks that balance construction costs against geographical coverage and long-distance resource transport to and from roots³. How they navigate these design challenges is unclear⁴. Here, to monitor the construction of living trade networks, we built a custom-designed robot for high-throughput time-lapse imaging that could track over 500,000 fungal nodes simultaneously. We then measured around 100,000 cytoplasmic flow trajectories inside the networks. We found that mycorrhizal fungi build networks as self-regulating travelling waves—pulses of growing tips pull an expanding wave of nutrient-absorbing mycelium, the density of which is self-regulated by fusion. This design offers a solution to conflicting trade demands because relatively small carbon investments fuel fungal range expansions beyond nutrient-depletion zones, fostering exploration for plant partners and nutrients. Over time, networks maintained highly constant transport efficiencies back to roots, while simultaneously adding loops that shorten paths to potential new trade partners. Fungi further enhance transport flux by both widening hyphal tubes and driving faster flows along ‘trunk routes’ of the network⁵. Our findings provide evidence that symbiotic fungi control network-level structure and flows to meet trade demands, and illuminate the design principles of a symbiotic supply-chain network shaped by millions of years of natural selection.

Crystallization is a powerful method to isolate enantiopure molecules from racemates if enantiomers self-sort into separate enantiopure crystals. Unfortunately, this behavior is unpredictable and rare (5–10%), as both enantiomers predominantly crystallize together to form racemic crystals, hindering any such chiral sorting. These unfavorable statistics might be overcome using nonequilibrium conditions. Therefore, we systematically characterize energy differences (ΔGΦ) between racemic and enantiopure crystal phases for libraries of target molecules (phenylglycine, praziquantel) with different chemical modifications. Surprisingly, these libraries reveal wide but similar continuous distributions of ΔGΦ, wherein similar chemical modifications group together. This grouping allows a directed evolution strategy to discover racemic crystals with low ΔGΦ for isolating desired enantiomers by crystallization under nonequilibrium conditions. Comparison with over a hundred previously reported compounds suggests that as many as half of all chiral molecules may kinetically form enantiopure crystals (∼50%). These insights open new previously unconsidered possibilities for isolating enantiopure molecules.

Cell populations must adjust their phenotypic composition to adapt to changing environments. One adaptation strategy is to maintain distinct phenotypic subsets within the population and to modulate their relative abundances via gene regulation. Another strategy involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. We found that the migrating populations became enriched with high-performing swimming phenotypes in each environment, allowing the populations to adapt without requiring mutations or gene regulation. This adaptation is dynamic and rapid, reversing in a few doubling times when migration ceases. By measuring the chemoreceptor abundance distributions during migration toward different attractants, we demonstrated that adaptation acts on multiple chemotaxis-related traits simultaneously. These measurements are consistent with a general mechanism in which adaptation results from a balance between cell growth generating diversity and collective migration eliminating underperforming phenotypes. Thus, collective migration enables cell populations with continuous, multidimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions.