Vortex Pattern Stabilization in Thin Films Resulting from Shear Thickening of Active Suspensions.

The need for structuring on micrometer scales is abundant, for example, in view of phononic applications. We here outline a novel approach based on the phenomenon of active turbulence on the mesoscale. As we demonstrate, a shear-thickening carrier fluid of active microswimmers intrinsically stabilizes regular vortex patterns of otherwise turbulent active suspensions. The fluid self-organizes into a periodically structured nonequilibrium state. Introducing additional passive particles of intermediate size leads to regular spatial organization of these objects. Our approach opens a new path toward functionalization through patterning of thin films and membranes.

Imaging of retina cellular and subcellular structures using ptychographic hard X-ray tomography.

Ptychographic hard X-ray computed tomography (PXCT) is a recent method allowing imaging with quantitative electron-density contrast. Here, we imaged, at cryogenic temperature and without sectioning, cellular and subcellular structures of a chemically fixed and stained wild-type mouse retina, including axons and synapses, with complete isotropic 3D information over tens of microns. Comparison with tomograms of degenerative retina from a mouse model of retinitis pigmentosa illustrates the potential of this method for analyzing disease processes like neurodegeneration at sub-200 nm resolution. As a non-destructive imaging method, PXCT is very suitable for correlative imaging. Within the outer plexiform layer containing the photoreceptor synapses, we identified somatic synapses. We used a small region inside the X-ray-imaged sample for further high-resolution focused ion beam/scanning electron microscope tomography. The subcellular structures of synapses obtained with the X-ray technique matched the electron microscopy data, demonstrating that PXCT is a powerful scanning method for tissue volumes of more than 60 cells and sensitive enough for identification of regions as small as 200 nm, which remain available for further structural and biochemical investigations.

Density functional approach to elastic properties of three-dimensional dipole-spring models for magnetic gels.

Magnetic gels are composite materials consisting of a polymer matrix and embedded magnetic particles. Those are mechanically coupled to each other, giving rise to the magnetostrictive effects as well as to a controllable overall elasticity responsive to external magnetic fields. Due to their inherent composite and thereby multiscale nature, a theoretical framework bridging different levels of description is indispensable for understanding the magnetomechanical properties of magnetic gels. In this study, we extend a recently developed density functional approach from two spatial dimensions to more realistic three-dimensional systems. Along these lines, we connect a mesoscopic characterization resolving the discrete structure of the magnetic particles to macroscopic continuum parameters of magnetic gels. In particular, we incorporate the long-range nature of the magnetic dipole-dipole interaction and consider the approximate incompressibility of the embedding media and relative rotations with respect to an external magnetic field breaking rotational symmetry. We then probe the shape of the model system in its reference state, confirming the dependence of magnetostrictive effects on the configuration of the magnetic particles and on the shape of the considered sample. Moreover, calculating the elastic and rotational coefficients on the basis of our mesoscopic approach, we examine how the macroscopic types of behavior are related to the mesoscopic properties. Implications for real systems of random particle configurations are also discussed.

When low-order expansions fail and all higher-order contributions matter-basic example of the mean squared displacement for Brownian motion.

Hardly any theoretically formulated realistic problem can be solved exactly. Therefore, as a standard, we resort to approximations. In this context, expansions play a major role. We are used to relying on lowest-order expansions and confining our point of view accordingly. However, one should always bear in mind that such considerations may fail at some point. Here, we address a very common example situation, namely, the motion of a Brownian particle. We know that the associated mean-squared displacement in the long term increases linearly in time. Yet, when we take the Fokker-Planck approach in combination with a low-order expansion, the direct route towards this result fails. That is, in the expansion the term linear in time vanishes. Instead, the treatment requires consideration of all higher-order contributions. Together, they restore the linear increase in time. In this way, we stress that care is always mandatory when resorting to low-order expansions, and we present in a traceable way a route to solving the considered problem.

Statistics for an object actively driven by spontaneous symmetry breaking into reversible directions.

Propulsion of otherwise passive objects is achieved by mechanisms of active driving. We concentrate on cases in which the direction of active drive is subject to spontaneous symmetry breaking. In our case, this direction will be maintained until a large enough impulse by an additional stochastic force reverses it. Examples may be provided by self-propelled droplets, gliding bacteria stochastically reversing their propulsion direction, or nonpolar vibrated hoppers. The magnitude of active forcing is regarded as constant, and we include the effect of inertial contributions. Interestingly, this situation can formally be mapped to stochastic motion under (dry, solid) Coulomb friction, however, with a negative friction parameter. Diffusion coefficients are calculated by formal mapping to the situation of a quantum-mechanical harmonic oscillator exposed to an additional repulsive delta-potential. Results comprise a ditched or double-peaked velocity distribution and spatial statistics showing outward propagating maxima when starting from initially concentrated arrangements.

Structural color from solid-state polymerization-induced phase separation.

Structural colors are produced by wavelength-dependent scattering of light from nanostructures. While living organisms often exploit phase separation to directly assemble structurally colored materials from macromolecules, synthetic structural colors are typically produced in a two-step process involving the sequential synthesis and assembly of building blocks. Phase separation is attractive for its simplicity, but applications are limited due to a lack of robust methods for its control. A central challenge is to arrest phase separation at the desired length scale. Here, we show that solid-state polymerization-induced phase separation can produce stable structures at optical length scales. In this process, a polymeric solid is swollen and softened with a second monomer. During its polymerization, the two polymers become immiscible and phase separate. As free monomer is depleted, the host matrix resolidifies and arrests coarsening. The resulting polymeric composites have a blue or white appearance. We compare these biomimetic nanostructures to those in structurally-colored feather barbs, and demonstrate the flexibility of this approach by producing structural color in filaments and large sheets.

Nanostructure surveys of macroscopic specimens by small-angle scattering tensor tomography.

The mechanical properties of many materials are based on the macroscopic arrangement and orientation of their nanostructure. This nanostructure can be ordered over a range of length scales. In biology, the principle of hierarchical ordering is often used to maximize functionality, such as strength and robustness of the material, while minimizing weight and energy cost. Methods for nanoscale imaging provide direct visual access to the ultrastructure (nanoscale structure that is too small to be imaged using light microscopy), but the field of view is limited and does not easily allow a full correlative study of changes in the ultrastructure over a macroscopic sample. Other methods of probing ultrastructure ordering, such as small-angle scattering of X-rays or neutrons, can be applied to macroscopic samples; however, these scattering methods remain constrained to two-dimensional specimens or to isotropically oriented ultrastructures. These constraints limit the use of these methods for studying nanostructures with more complex orientation patterns, which are abundant in nature and materials science. Here, we introduce an imaging method that combines small-angle scattering with tensor tomography to probe nanoscale structures in three-dimensional macroscopic samples in a non-destructive way. We demonstrate the method by measuring the main orientation and the degree of orientation of nanoscale mineralized collagen fibrils in a human trabecula bone sample with a spatial resolution of 25 micrometres. Symmetries within the sample, such as the cylindrical symmetry commonly observed for mineralized collagen fibrils in bone, allow for tractable sampling requirements and numerical efficiency. Small-angle scattering tensor tomography is applicable to both biological and materials science specimens, and may be useful for understanding and characterizing smart or bio-inspired materials. Moreover, because the method is non-destructive, it is appropriate for in situ measurements and allows, for example, the role of ultrastructure in the mechanical response of a biological tissue or manufactured material to be studied.

The inner workings of the hydrazine synthase multiprotein complex.

Anaerobic ammonium oxidation (anammox) has a major role in the Earth's nitrogen cycle and is used in energy-efficient wastewater treatment. This bacterial process combines nitrite and ammonium to form dinitrogen (N2) gas, and has been estimated to synthesize up to 50% of the dinitrogen gas emitted into our atmosphere from the oceans. Strikingly, the anammox process relies on the highly unusual, extremely reactive intermediate hydrazine, a compound also used as a rocket fuel because of its high reducing power. So far, the enzymatic mechanism by which hydrazine is synthesized is unknown. Here we report the 2.7 Å resolution crystal structure, as well as biophysical and spectroscopic studies, of a hydrazine synthase multiprotein complex isolated from the anammox organism Kuenenia stuttgartiensis. The structure shows an elongated dimer of heterotrimers, each of which has two unique c-type haem-containing active sites, as well as an interaction point for a redox partner. Furthermore, a system of tunnels connects these active sites. The crystal structure implies a two-step mechanism for hydrazine synthesis: a three-electron reduction of nitric oxide to hydroxylamine at the active site of the γ-subunit and its subsequent condensation with ammonia, yielding hydrazine in the active centre of the α-subunit. Our results provide the first, to our knowledge, detailed structural insight into the mechanism of biological hydrazine synthesis, which is of major significance for our understanding of the conversion of nitrogenous compounds in nature.

Stimuli-responsive twist actuators made from soft elastic composite materials-linking mesoscopic and macroscopic descriptions.

Very recently, the construction of twist actuators from magnetorheological gels and elastomers has been suggested. These materials consist of magnetizable colloidal particles embedded in a soft elastic polymeric environment. The twist actuation is enabled by a net chirality of the internal particle arrangement. Upon magnetization by a homogeneous external magnetic field, the systems feature an overall torsional deformation around the magnetization direction. Starting from a discrete minimal mesoscopic model setup, we work toward a macroscopic characterization. The two scales are linked by identifying expressions for the macroscopic system parameters as functions of the mesoscopic model parameters. In this way, the observed behavior of a macroscopic system can, in principle, be mapped to and illustratively be understood from an appropriate mesoscopic picture. Our results apply equally well to corresponding soft electrorheological gels and elastomers.

A nitric oxide-binding heterodimeric cytochrome c complex from the anammox bacterium Kuenenia stuttgartiensis binds to hydrazine synthase.

Anaerobic ammonium oxidation (anammox) is a microbial process responsible for significant nitrogen loss from the oceans and other ecosystems. The redox reactions at the heart of anammox are catalyzed by large multiheme enzyme complexes that rely on small cytochrome c proteins for electron shuttling. Among the most highly abundant of these cytochromes is a unique heterodimeric complex composed of class I and class II c-type cytochromes called NaxLS, which has distinctive biochemical and spectroscopic properties. Here, we present the 1.7 Å resolution crystal structure of this complex from the anammox organism Kuenenia stuttgartiensis (KsNaxLS). The structure reveals that the heme irons in each subunit exhibit a rare His/Cys ligation, which, as we show by substitution, causes the observed unusual spectral properties. Unlike its individual subunits, the KsNaxLS complex binds nitric oxide (NO) only at the distal heme side, forming 6cNO adducts. This is likely due to steric immobilization of the proximal heme-binding motifs upon complex formation, a finding that may be of functional relevance, because NO is an intermediate in the central anammox metabolism. Pulldown experiments with K. stuttgartiensis cell-free extract showed that the KsNaxLS complex binds specifically to one of the central anammox enzyme complexes, hydrazine synthase, which uses NO as one of its substrates. It is therefore possible that the KsNaxLS complex plays a role in binding the volatile NO to retain it in the cell for transfer to hydrazine synthase. Alternatively, we propose that KsNaxLS may shuttle electrons to this enzyme complex.

Dynamical Crystallites of Active Chiral Particles.

One of the intrinsic characteristics of far-from-equilibrium systems is the nonrelaxational nature of the system dynamics, which leads to novel properties that cannot be understood and described by conventional pathways based on thermodynamic potentials. Of particular interest are the formation and evolution of ordered patterns composed of active particles that exhibit collective behavior. Here we examine such a type of nonpotential active system, focusing on effects of coupling and competition between chiral particle self-propulsion and self-spinning. It leads to the transition between three bulk dynamical regimes dominated by collective translative motion, spinning-induced structural arrest, and dynamical frustration. In addition, a persistently dynamical state of self-rotating crystallites is identified as a result of a localized-delocalized transition induced by the crystal-melt interface. The mechanism for the breaking of localized bulk states can also be utilized to achieve self-shearing or self-flow of active crystalline layers.

Towards an analytical description of active microswimmers in clean and in surfactant-covered drops.

Geometric confinements are frequently encountered in the biological world and strongly affect the stability, topology, and transport properties of active suspensions in viscous flow. Based on a far-field analytical model, the low-Reynolds-number locomotion of a self-propelled microswimmer moving inside a clean viscous drop or a drop covered with a homogeneously distributed surfactant, is theoretically examined. The interfacial viscous stresses induced by the surfactant are described by the well-established Boussinesq-Scriven constitutive rheological model. Moreover, the active agent is represented by a force dipole and the resulting fluid-mediated hydrodynamic couplings between the swimmer and the confining drop are investigated. We find that the presence of the surfactant significantly alters the dynamics of the encapsulated swimmer by enhancing its reorientation. Exact solutions for the velocity images for the Stokeslet and dipolar flow singularities inside the drop are introduced and expressed in terms of infinite series of harmonic components. Our results offer useful insights into guiding principles for the control of confined active matter systems and support the objective of utilizing synthetic microswimmers to drive drops for targeted drug delivery applications.

Signal amplification and transduction in phytochrome photosensors.

Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light-sensing kinases that control diverse cellular functions in plants, bacteria and fungi. Bacterial phytochromes consist of a photosensory core and a carboxy-terminal regulatory domain. Structures of photosensory cores are reported in the resting state and conformational responses to light activation have been proposed in the vicinity of the chromophore. However, the structure of the signalling state and the mechanism of downstream signal relay through the photosensory core remain elusive. Here we report crystal and solution structures of the resting and activated states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans. The structures show an open and closed form of the dimeric protein for the activated and resting states, respectively. This nanometre-scale rearrangement is controlled by refolding of an evolutionarily conserved 'tongue', which is in contact with the chromophore. The findings reveal an unusual mechanism in which atomic-scale conformational changes around the chromophore are first amplified into an ångstrom-scale distance change in the tongue, and further grow into a nanometre-scale conformational signal. The structural mechanism is a blueprint for understanding how phytochromes connect to the cellular signalling network.

On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome.

Phytochromes are photoreceptors in plants, fungi, and various microorganisms and cycle between metastable red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Their light responses are thought to follow a conserved structural mechanism that is triggered by isomerization of the chromophore. Downstream structural changes involve refolding of the so-called tongue extension of the phytochrome-specific GAF-related (PHY) domain of the photoreceptor. The tongue is connected to the chromophore by conserved DIP and PRXSF motifs and a conserved tyrosine, but the role of these residues in signal transduction is not clear. Here, we examine the tongue interactions and their interplay with the chromophore by substituting the conserved tyrosine (Tyr263) in the phytochrome from the extremophile bacterium Deinococcus radiodurans with phenylalanine. Using optical and FTIR spectroscopy, X-ray solution scattering, and crystallography of chromophore-binding domain (CBD) and CBD-PHY fragments, we show that the absence of the Tyr263 hydroxyl destabilizes the ß-sheet conformation of the tongue. This allowed the phytochrome to adopt an α-helical tongue conformation regardless of the chromophore state, hence distorting the activity state of the protein. Our crystal structures further revealed that water interactions are missing in the Y263F mutant, correlating with a decrease of the photoconversion yield and underpinning the functional role of Tyr263 in phytochrome conformational changes. We propose a model in which isomerization of the chromophore, refolding of the tongue, and globular conformational changes are represented as weakly coupled equilibria. The results also suggest that the phytochromes have several redundant signaling routes.

Incubation Effect of Pre-Irradiation on Bubble Formation and Ablation in Laser Ablation in Liquids.

Pulsed laser ablation in liquids (PLAL) is a multi-scale process, which is widely studied either in batch ablation with prolonged target irradiation as well as mechanistic investigations, in a defined (single-shot) process. However, fundamental studies on defined pulse series are rare. We have investigated the effect of a developing rough morphology of the target surface on the PLAL process with nanosecond pulses and, partially, picosecond pulses. At low fluence the cavitation bubble growth as well as the ablation yield depend on the irradiation history of the target. The bubble size increases with repeated irradiation on one spot for the first 2-30 pulses as well as with the applied dose. This is discussed within the framework of incubation effects. Incubation is found to be important, resulting in a bubble volume increase by a factor of six or more between pristine and corrugated targets. The target surface, changing from smooth to corrugated, induces a more efficient localization of laser energy at the solid-liquid interface. This is accompanied by a suppressed reflectivity and more efficient coupling of energy into the laser-induced plasma. Thus, the cavitation bubble size increases as well as ablation being enhanced. At high fluence, such incubation is masked by the rapid development of surface damage within the first shots, which eventually would lead to a reduction of bubble sizes.

Creeping motion of a solid particle inside a spherical elastic cavity: II. Asymmetric motion.

An analytical method is proposed for computing the low-Reynolds-number hydrodynamic mobility function of a small colloidal particle asymmetrically moving inside a large spherical elastic cavity, the membrane of which is endowed with resistance toward shear and bending. In conjunction with the results obtained in the first part (A. Daddi-Moussa-Ider, H. Löwen, S. Gekle, Eur. Phys. J. E 41, 104 (2018)), in which the axisymmetric motion normal to the surface of an elastic cavity is investigated, the general motion for an arbitrary force direction can now be addressed. The elastohydrodynamic problem is formulated and solved using the classic method of images through expressing the hydrodynamic flow fields as a multipole expansion involving higher-order derivatives of the free-space Green's function. In the quasi-steady limit, we demonstrate that the particle self-mobility function of a particle moving tangent to the surface of the cavity is larger than that predicted inside a rigid stationary cavity of equal size. This difference is justified by the fact that a stationary rigid cavity introduces additional hindrance to the translational motion of the encapsulated particle, resulting in a reduction of its hydrodynamic mobility. Furthermore, the motion of the cavity is investigated, revealing that the translational pair (composite) mobility, which linearly couples the velocity of the elastic cavity to the force exerted on the solid particle, is solely determined by membrane shear properties. Our analytical predictions are favorably compared with fully-resolved computer simulations based on a completed-double-layer boundary integral method.

Reconstructing state mixtures from diffraction measurements.

Progress in imaging and metrology depends on exquisite control over and comprehensive characterization of wave fields. As reflected in its name, coherent diffractive imaging relies on high coherence when reconstructing highly resolved images from diffraction intensities alone without the need for image-forming lenses. Fully coherent light can be described adequately by a single pure state. Yet partial coherence and imperfect detection often need to be accounted for, requiring statistical optics or the superposition of states. Furthermore, the dynamics of samples are increasingly the very objectives of experiments. Here we provide a general analytic approach to the characterization of diffractive imaging systems that can be described as low-rank mixed states. We use experimental data and simulations to show how the reconstruction technique compensates for and characterizes various sources of decoherence quantitatively. Based on ptychography, the procedure is closely related to quantum state tomography and is equally applicable to high-resolution microscopy, wave sensing and fluctuation measurements. As a result, some of the most stringent experimental conditions in ptychography can be relaxed, and susceptibility to imaging artefacts is reduced. Furthermore, the method yields high-resolution images of mixed states within the sample, which may include quantum mixtures or fast stationary stochastic processes such as vibrations, switching or steady flows.

Magnetostriction in magnetic gels and elastomers as a function of the internal structure and particle distribution.

Magnetic gels and elastomers are promising candidates to construct reversibly excitable soft actuators, triggered from outside by magnetic fields. These magnetic fields induce or alter the magnetic interactions between discrete rigid particles embedded in a soft elastic polymeric matrix, leading to overall deformations. It is a major challenge in theory to correctly predict from the discrete particle configuration the type of deformation resulting for a finite-sized system. Considering an elastic sphere, we here present such an approach. The method is in principle exact, at least within the framework of linear elasticity theory and for large enough interparticle distances. Different particle arrangements are considered. We find, for instance, that regular simple cubic configurations show elongation of the sphere along the magnetization if oriented along a face or space diagonal of the cubic unit cell. Contrariwise, with the magnetization along the edge of the cubic unit cell, they contract. The opposite is true in this geometry for body- and face-centered configurations. Remarkably, for the latter configurations but the magnetization along a face or space diagonal of the unit cell, contraction was observed to revert to expansion with decreasing Poisson ratio of the elastic material. Randomized configurations were considered as well. They show a tendency of elongating the sphere along the magnetization, which is more pronounced for compressible systems. Our results can be tested against actual experiments for spherical samples. Moreover, our approach shall support the search of optimal particle distributions for a maximized effect of actuation.

Membrane penetration and trapping of an active particle.

The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the particles can pass through cell membranes via passive endocytosis or by active penetration to reach a target cellular compartment or organelle. In this manuscript, we develop a simple model to describe the interaction of a self-driven spherical particle (moving through an effective constant active force) with a minimal membrane system, allowing for both penetration and trapping. We numerically calculate the state diagram of this system, the membrane shape, and its dynamics. In this context, we show that the active particle may either get trapped near the membrane or penetrate through it, where the membrane can either be permanently destroyed or recover its initial shape by self-healing. Additionally, we systematically derive a continuum description allowing us to accurately predict most of our results analytically. This analytical theory helps in identifying the generic aspects of our model, suggesting that most of its ingredients should apply to a broad range of membranes, from simple model systems composed of magnetic microparticles to lipid bilayers. Our results might be useful to predict the mechanical properties of synthetic minimal membranes.

The role of ions in the self-healing behavior of soft particle suspensions.

Impurities in crystals generally cause point defects and can even suppress crystallization. This general rule, however, does not apply to colloidal crystals formed by soft microgel particles [Iyer ASJ, Lyon LA (2009) Angew Chem Int Ed 48:4562-4566], as, in this case, the larger particles are able to shrink and join the crystal formed by a majority of smaller particles. Using small-angle X-ray scattering, we find the limit in large-particle concentration for this spontaneous deswelling to persist. We rationalize our data in the context of those counterions that are bound to the microgel particles as a result of the electrostatic attraction exerted by the fixed charges residing on the particle periphery. These bound counterions do not contribute to the suspension osmotic pressure in dilute conditions, as they can be seen as internal degrees of freedom associated with each microgel particle. In contrast, at sufficiently high particle concentrations, the counterion cloud of each particle overlaps with that of its neighbors, allowing these ions to freely explore the space outside the particles. We confirm this scenario by directly measuring the osmotic pressure of the suspension. Because these counterions are then no longer bound, they create an osmotic pressure difference between the inside and outside of the microgels, which, if larger than the microgel bulk modulus, can cause deswelling, explaining why large, soft microgel particles feel the squeeze when suspended with a majority of smaller particles. We perform small-angle neutron scattering measurements to further confirm this remarkable behavior.