Substrate Topology Research Articles

A proteolytic AAA+ machine poised to unfold protein substrates

AAA+ proteolytic machines unfold proteins before degrading them. Here, we present cryoEM structures of ClpXP-substrate complexes that reveal a postulated but heretofore unseen intermediate in substrate unfolding/degradation. A ClpX hexamer draws natively folded substrates tightly against its axial channel via interactions with a fused C-terminal degron tail and ClpX-RKH loops that flexibly conform to the globular substrate. The specific ClpX-substrate contacts observed vary depending on the substrate degron and affinity tags, helping to explain ClpXP’s ability to unfold/degrade a wide array of different cellular substrates. Some ClpX contacts with native substrates are enabled by upward movement of the seam subunit in the AAA+ spiral, a motion coupled to a rearrangement of contacts between the ClpX unfoldase and ClpP peptidase. Our structures additionally highlight ClpX’s ability to translocate a diverse array of substrate topologies, including the co-translocation of two polypeptide chains.

The Standardized Spectroscopic Mixture Model

The standardized spectral mixture model combines the specificity of a physically based representation of a spectrally mixed pixel with the generality and portability of a spectral index. Earlier studies have used spectrally and geographically diverse collections of broadband and spectroscopic imagery to show that the reflectance of the majority of ice-free landscapes on Earth can be represented as linear mixtures of rock and soil substrates (S), photosynthetic vegetation (V) and dark targets (D) composed of shadow and spectrally absorptive/transmissive materials. However, both broadband and spectroscopic studies of the topology of spectral mixing spaces raise questions about the completeness and generality of the Substrate, Vegetation, Dark (SVD) model for imaging spectrometer data. This study uses a spectrally diverse collection of 40 granules from the EMIT imaging spectrometer to verify the generality and stability of the spectroscopic SVD model and characterize the SVD topology and plane of substrates to assess linearity of spectral mixing. New endmembers for soil and non-photosynthetic vegetation (NPV; N) allow the planar SVD model to be extended to a tetrahedral SVDN model to better accommodate the 3D topology of the mixing space. The SVDN model achieves smaller misfit than the SVD, but does so at the expense of implausible fractions beyond [0, 1]. However, a refined spectroscopic SVD model still achieves small (<0.03) RMS misfit, negligible sensitivity to endmember variability and strongly linear scaling over more than an order of magnitude range of spatial resolution.

Myotube formation on micropatterns guiding by centripetal cellular motility and crowding

The physical microenvironment, including substrate rigidity and topology, impacts myoblast differentiation and myotube maturation. However, the interplay effect and physical mechanism of mechanical stimuli on myotube formation is poorly understood. In this study, we utilized elastic substrates, microcontact patterning technique, and particle image velocimetry to investigate the effect of substrate rigidity and topological constraints on myoblast behaviors. Our findings suggested the interplay of substrate stiffness and cellular confinement improved the myotube formation by inducing centripetal cellular motility. These results shed light on the impact of the topological substrate on myoblast differentiation and emphasize the critical role of asymmetrical cell motility during this process, which is highly correlated with cell movement and crowding. Our research provides insights into the intricate interplay between substrate properties, cell motility, and myotube formation during myogenesis. Understanding these mechanisms could trigger tissue engineering strategies and therapies to enhance muscle regeneration and function.

Shp2 contributes to the regulation of nuclear shape and cellular viscoelasticity in response to substrate spatial cues

Cell polarization can be guided by substrate topology through space constraints and adhesion induction, which are part of cellular mechanosensing pathways. Here, we demonstrated that protein tyrosine phosphatase Shp2 plays a crucial role in mediating the response of cells to substrate spatial cues. When compared to cells spreading on surfaces coated uniformly with fibronectin (FN), cells attached to 10 μm-width FN-strip micropattern (MP), which provides spatial cues for uniaxial spreading, exhibited elongated focal adhesions (FAs) and aligned stress fibers in the direction of the MP. As a result of uniaxial cell spreading, nuclei became elongated, dependent on ROCK-mediated actomyosin contractility. Additionally, intracellular viscoelasticity also increased. Shp2-deficient cells did not display elongated FAs mediated by MP, well-aligned stress fibers, or changes in nuclear shape and intracellular viscoelasticity. Overall, our data suggest that Shp2 is involved in regulating FAs and the actin cytoskeleton to modulate nuclear shape and intracellular physical properties in response to substrate spatial cues.

Triaging of α-helical proteins to the mitochondrial outer membrane by distinct chaperone machinery based on substrate topology

Mitochondrial outer membrane ⍺-helical proteins play critical roles in mitochondrial-cytoplasmic communication, but the rules governing the targeting and insertion of these biophysically diverse proteins remain unknown. Here, we first defined the complement of required mammalian biogenesis machinery through genome-wide CRISPRi screens using topologically distinct membrane proteins. Systematic analysis of nine identified factors across 21 diverse ⍺-helical substrates reveals that these components are organized into distinct targeting pathways that act on substrates based on their topology. NAC is required for the efficient targeting of polytopic proteins, whereas signal-anchored proteins require TTC1, a cytosolic chaperone that physically engages substrates. Biochemical and mutational studies reveal that TTC1 employs a conserved TPR domain and a hydrophobic groove in its C-terminal domain to support substrate solubilization and insertion into mitochondria. Thus, the targeting of diverse mitochondrial membrane proteins is achieved through topological triaging in the cytosol using principles with similarities to ER membrane protein biogenesis systems.

A Modular Turn-On Strategy to Profile E2-Specific Ubiquitination Events in Living Cells.

A cascade of three enzymes, E1-E2-E3, is responsible for transferring ubiquitin to target proteins, which controls many different aspects of cellular signaling. The role of the E2 has been largely overlooked, despite influencing substrate identity, chain multiplicity, and topology. Here we report a method-targeted charging of ubiquitin to E2 (tCUbE)-that can track a tagged ubiquitin through its entire enzymatic cascade in living mammalian cells. We use this approach to reveal new targets whose ubiquitination depends on UbcH5a E2 activity. We demonstrate that tCUbE can be broadly applied to multiple E2s and in different human cell lines. tCUbE is uniquely suited to examine E2-E3-substrate cascades of interest and/or piece together previously unidentified cascades, thereby illuminating entire branches of the UPS and providing critical insight that will be useful for identifying new therapeutic targets in the UPS.

Effect of substrate heterogeneity and topology on epithelial tissue growth dynamics.

Tissue growth kinetics and interface dynamics depend on the properties of the tissueenvironment and cell-cell interactions. In cellular environments, substrate heterogeneity and geometry arise from a variety factors, such as the structure of the extracellular matrix and nutrient concentration. We used the CellSim3D model, a kinetic cell division simulator, to investigate the growth kinetics and interface roughness dynamics of epithelial tissue growth on heterogeneous substrates with varying topologies. The results show that the presence of quenched disorder has a clear effect on the colony morphology and the roughness scaling of the interface in the moving interface regime. In a medium with quenched disorder, the tissue interface has a smaller interface roughness exponent, α, and a larger growth exponent, β. The scaling exponents also depend on the topology of the substrate and cannot be categorized by well-known universality classes.

Unusual effects of a nanoporous gold substrate on cell adhesion and differentiation because of independent multi-branch signaling of focal adhesions

A variety of cell behaviors, such as cell adhesion, motility, and fate, can be controlled by substrate characteristics such as surface topology and chemistry. In particular, the surface topology of substrates strongly affects cell behaviors, and the topological spacing is a critical factor in inducing cell responses. Various works have demonstrated that cell adhesion was enhanced with decreasing topological spacing although differentiation progressed slowly. However, there are exceptions, and thus, correlations between topological spacing and cell responses are still debated. We show that a nanoporous gold substrate affected cell adhesion while it neither affected osteogenic nor adipogenic differentiation. In addition, the cell adhesion was reduced with decreasing pore size. These do not agree with previous findings. A focal adhesion (FA) is an aggregate of modules comprising specific proteins such as FA kinase, talin, and vinculin. Therefore, it is suggested that because various extracellular signals can be independently branched off from the FA modules, the unusual effects of nanoporous gold substrates are related to the multi-branching of FAs.Graphical

Thermocapillary oscillations in liquid thin films: Interplay of substrate topography and thermal wave

Liquid flows over patterned and/or contoured substrates is utilized in many practical applications e.g., lubrication flow in MEMS (micro-electromechanical systems) /NEMS (nano-electromechanical systems) devices, cell sorting operations in biology, etc. The topological gradients in such geometries induce thermal gradients, which in turn generates Marangoni hydrodynamics. Here, we theoretically showcase the interplay of substrate topology, imposed wavy temperature stimulus, and chemically patterned wall slip to generate thermo-capillarity in thin liquid films. We obtain analytical solutions for the thermal and the hydrodynamic fields for low Marangoni Ma and Reynolds Re number thermocapillary effect. Vorticity is observed to generate and transport at the liquid-gas interface, and further transported to the bulk film by vertical diffusion and convection. We also study further to understand the significance of different geometric and physical parameters on the Marangoni thermo-fluid-dynamics. Interplay of constructive and destructive interference between the wave forms of the substrate topology and imposed periodic thermal stimulus may yield maximum interfacial temperature gradients and strong thermo-capillarity. It is also observed that the lower values of system Biot number Bi enables better diffusion of heat from the patterned substrate to obtain stable thermo-capillarity. Further, the presence of optimal slip patterning allows for stronger and tuned circulations in the liquid film.

Synthesis and characterization of some Cr-Zr and Cr-Zr-O nanostructures

The co-depositions of Cr-Zr and those of Cr-Zr-O coatings of 500 nm thick were made using magnetron sputtering in continuous mode, in a circular enclosure with a volume of 0.05 m3 evacuated prior to the deposition process under 10-6 mbar vacuum conditions. Silicon and Carbon substrates measuring 12x15mm were used for deposition. The topology of all of the CrZr and CrZrO2 coatings deposited on silicon and carbon substrates have been investigated by Scanning Electron Microscopy (SEM) at three magnifications: 1000x, 5000x and 10.000x. For all of the coatings deposited on Silicon substrates, at all three magnifications, was observed very smooth surfaces with only small topological elements. In some samples, few droplets of around 100nm can be observed. The appearance of particulates is caused by the arching events that occur at target surface during the deposition proces and are more pronounced during reactive sputtering. The coatings deposited on the Carbon substrate show more morphological features as these substrates have a lower grade surface polish finish as to sliced Silicon wafers; the deposited film tends to follow the substrate topology and cracks can be seen on the surface. Were investigated the mechanical properties of the samples of Cr+Zr, respectively Cr+Zr+O2 using The Bruker Hysitron TI 980 TriboIndenter which allows to extrapolate mechanical properties such Young’ s Modulus (YM) and Hardness (H). The experimental results obtained through nanoindentation studies, show: In the absence of oxygen during deposition ( Zr-Cr structures), the Young’s Modulus and Hardness are influenced by the concentration ratio of the two components Cr and Zr, i.e., there is the practical possibility of adjusting the two parameters YM and H by correspondingly changing the concentrations of the components of the structure . In the case of the Cr+Zr+O2 structures, for sample where the concentration of Chromium is maximum and the concentration of Zirconium is minimum, the presence of Oxygen causes a decrease for YM and respectively a decrease for H (in this case Cr-O bonds are predominant). In the case of sample in which the concentration of Zirconium is maximum and the concentration of Chromium is minimum, in the presence of Oxygen (now the bonds Zr-O being predominant), an increase for YM and an increase for H are observed. The crystalline structure was investigated using X-Ray Diffraction (XRD) method, using a setup composed of a diffractometer equipped with a Cu-Kα X-ray sourse, with a specific wavelength of 0.154nm, in a Bragg-Bretano type geometry. In the case of the Cr-Zr sample, diffractograms show that only the peaks corresponding to the Si substrate are visible, highlighting the amorphous character of the structure. Also, the measurements reveal the amorfous character of the Cr-Zr-O sample. In order to highlight the effect of the element Cr together with Zr and O, the diffractogram of the ZrO2 sample and diffractogram of Cr-Zr-O sample are examinated for comparison. Considering the application of these materials in dentistry, the 2 wide amorphous strips in the case of ZrO2 sample and amorfous character found in the case of Cr-Zr-O sample, could correspond to the adhesive used to attach the veneer to the tooth of such structures. From this perspective, it can be stated that the presence of the Cr element in the Cr-Zr-O structure widens the possibility of its use as an adhesive to attach the veneer to the tooth.

3D substrate complexity analysis using cardiac MRI predicts ICD therapy in post-infarct ventricular tachycardia

Abstract Funding Acknowledgements Type of funding sources: Foundation. Main funding source(s): EACVI, Netherlands Heart Institute. Background Implantable cardiac defibrillator (ICD) implantation can protect against sudden cardiac death (SCD) after a myocardial infarction. However, relatively few patients with an ICD experience a life-threatening arrhythmic event. Imaging studies have proposed metrics based on 2D analysis of late gadolinium enhancement (LGE) characteristics to predict post-infarct malignant arrhythmias and improve SCD risk assessment. However, given the intrinsic 3D nature of the electrical pathways through the infarcted regions, 3D reconstructions of the scar substrate from LGE imaging may be required to fully characterize the pro-arrhythmic nature of the scar substrate. Aim To evaluate the accuracy of LGE based 3D metrics such as conduction corridors (regions of borderzone (BZ) surrounded by scar core) and 3D interface surfaces (boundaries between scar and myocardium) towards predicting ICD therapy. Methods ADAS LV and custom-made software was used to generate 3D patient-specific ventricular models in a prospective cohort of post-infarct patients (n=40) having undergone LGE imaging pre-ICD implantation. The extent of variation in scar-characteristics was evaluated in ADAS by quantifying the BZ, scar core, the number and weight of conduction corridors i.e. BZ surrounded by scar core. Custom-written scripts were used to calculate metrics describing the 3D topology of the scar substrate, specifically the interface area between myocardium and total enhancement (BZ+core), and the interface between BZ and core. These metrics were compared with ICD therapy during follow-up. Results Total corridors were comparable between both groups (6.53 ± 7.9 vs. 4.6 ± 4, p = .38). Corridor weight demonstrated a trend towards higher mass in the event group (2.7 ± 2.1g vs. 1.6 ± 1.4g, p = .06). Patients with an event (n=17) had higher myocardium-total enhancement interface (103.8±35.1cm2 vs. 77.4±33.7cm2, p = .021) and BZ-core interface (76±27.5cm2 vs. 55.2±27.6cm2, p = .024). Cox-regression demonstrated a significant independent association of myocardium-total enhancement interface with an event (HR 2.79; 1.44–5.44, p < .01). Kaplan-Meier analysis (Figure 1) showed a significantly higher event rate in patients with an interface area between myocardium-total enhancement of more than 72cm2 and BZ-core more than 42.3cm2. Conclusion These results demonstrate that patients with appropriate device therapy had larger myocardium-total enhancement and BZ-core surface interface areas. Conceptually, the BZ-core interface could be considered to be related to the reentrant circuit path-length whilst the myocardium-total enhancement interface reflects the surfaces most-likely to initiate unidirectional block, both of which can be consider pro-arrhythmic substrates. These findings emphasize the importance of visualizing and thereby characterizing substrate as a 3D entity instead of the currently applied 2D approach to facilitate early identification of high-risk patients.

3D substrate complexity analysis using cardiac MRI predicts ICD therapy in post-infarct ventricular tachycardia

Abstract Funding Acknowledgements Type of funding sources: Public Institution(s). Main funding source(s): EACVI Research Grant Academy Van Leersum grant of the Academy Medical Sciences Fund (Royal Netherlands Academy of Arts & Sciences). Background Implantable cardiac defibrillator (ICD) implantation can protect against sudden cardiac death (SCD) after a myocardial infarction. However, relatively few patients with an ICD experience a life-threatening arrhythmic event. Imaging studies have proposed metrics based on 2D analysis of late gadolinium enhancement (LGE) characteristics to predict post-infarct malignant arrhythmias and improve SCD risk assessment. However, given the intrinsic 3D nature of the electrical pathways through the infarcted regions, 3D reconstructions of the scar substrate from LGE imaging may be required to fully characterize the pro-arrhythmic nature of the scar substrate. Aim To evaluate the accuracy of LGE based 3D metrics such as conduction corridors (regions of borderzone (BZ) surrounded by scar core) and 3D interface surfaces (boundaries between scar and myocardium) towards predicting ICD therapy. Methods ADAS LV and custom-made software was used to generate 3D patient-specific ventricular models in a prospective cohort of post-infarct patients (n=40) having undergone LGE imaging pre-ICD implantation. The extent of variation in scar-characteristics was evaluated in ADAS by quantifying the BZ, scar core, the number and weight of conduction corridors i.e. BZ surrounded by scar core. Custom-written scripts were used to calculate metrics describing the 3D topology of the scar substrate, specifically the interface area between myocardium and total enhancement (BZ+core), and the interface between BZ and core. These metrics were compared with ICD therapy during follow-up. Results Total corridors were comparable between both groups (6.53 ± 7.9 vs. 4.6 ± 4, p = .38). Corridor weight demonstrated a trend towards higher mass in the event group (2.7 ± 2.1g vs. 1.6 ± 1.4g, p = .06). Patients with an event (n=17) had higher myocardium-total enhancement interface (103.8±35.1cm2 vs. 77.4±33.7cm2, p=.021) and BZ-core interface (76±27.5cm2 vs. 55.2±27.6cm2, p=.024). Cox-regression demonstrated a significant independent association of myocardium-total enhancement interface with an event (HR 2.79; 1.44-5.44, p < .01). Kaplan-Meier analysis showed a significantly higher event rate in patients with an interface area between myocardium-total enhancement of more than 72cm2 (Figure 1A) and BZ-core more than 42.3cm2 (Figure 1B). Conclusion These results demonstrate that patients with appropriate device therapy had larger myocardium-total enhancement and BZ-core surface interface areas. Conceptually, the BZ-core interface could be considered to be related to the reentrant circuit path-length whilst the myocardium-total enhancement interface reflects the surfaces most-likely to initiate unidirectional block, both of which can be consider pro-arrhythmic substrates. These findings emphasize the importance of visualizing and thereby characterizing substrate as a 3D entity instead of the currently applied 2D approach to facilitate early identification of high-risk patients.

Exploring the Piezoelectric Properties of Bismuth Ferrite Thin Films Using Piezoelectric Force Microscopy: A Case Study.

Over recent decades, the scientific community has managed to make great progress in the theoretical investigation and practical characterization of bismuth ferrite thin films. However, there is still much work to be completed in the field of magnetic property analysis. Under a normal operational temperature, the ferroelectric properties of bismuth ferrite could overcome the magnetic properties due to the robustness of ferroelectric alignment. Therefore, investigation of the ferroelectric domain structure is crucial for functionality of any potential devices. This paper reports deposition and analyzation of bismuth ferrite thin films by Piezoresponse Force Microscopy (PFM) and XPS methods, aiming to provide a characterization of deposited thin films. In this paper, thin films of 100 nm thick bismuth ferrite material were prepared by pulsed laser deposition on multilayer substrates Pt/Ti(TiO2)/Si. Our main purpose for the PFM investigation in this paper is to determine which magnetic pattern will be observed on Pt/Ti/Si and Pt/TiO2/Si multilayer substrates under certain deposition parameters by utilizing the PLD method and using samples of a deposited thickness of 100 nm. It was also important to determine how strong the measured piezoelectric response will be, considering parameters mentioned previously. By establishing a clear understanding of how prepared thin films react on various biases, we have provided a foundation for future research involving the formation of piezoelectric grains, thickness-dependent domain wall formations, and the effect of the substrate topology on the magnetic properties of bismuth ferrite films.

Asymmetric catalysis by flavin-dependent halogenases.

In nature, flavin-dependent halogenases (FDHs) catalyze site-selective chlorination and bromination of aromatic natural products. This ability has led to extensive efforts to engineer FDHs for selective chlorination, bromination, and iodination of electron rich aromatic compounds. On the other hand, FDHs are unique among halogenases and haloperoxidases that exhibit catalyst-controlled site selectivity in that no examples of enantioselective FDH catalysis in natural product biosynthesis have been characterized. Over the past several years, our group has established that FDHs can catalyze enantioselective reactions involving desymmetrization, atroposelective halogenation, and halocyclization. Achieving high activity and selectivity for these reactions has required extensive mutagenesis and mitigation of problems resulting from hypohalous acid generated during FDH catalysis. The single-component flavin reductase/FDH AetF is unique among the wild type enzyme we have studied in that it provides high activity and selectivity toward several asymmetric transformations. These results highlight the ability of FDH active sites to tolerate different substrate topologies and suggest that they could be useful for a broad range of oxidative halogenations.

Cross-Domain Service Function Chain Routing: Multiagent Reinforcement Learning Approaches

The service function chain (SFC) routing has been increasingly associated with multi-domain networks. However, several multi-domain SFC routing issues, linked to cross-domain interactions and emphasized by the heterogeneity of substrate topologies and administrative authorities, present a challenge. We propose the Cooperative Multi-agent Reinforcement Learning (CMRL) based algorithm for multi-domain SFC routing problem. Simulations on the real-world network topology demonstrate that our proposal can provide more than two and four times reduction in terms of the run time and network resource cost, respectively.

Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT

The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. Cryo-EM resolves four near-atomic-resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Intrinsically disordered CCT C termini within the chamber promote subsequent folding of tubulin's core and middle domains and GTP-binding. Thus, TRiC's chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates.

The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA

Self versus non-self discrimination is a key element of innate and adaptive immunity across life. In bacteria, CRISPR-Cas and restriction-modification systems recognize non-self nucleic acids through their sequence and their methylation state, respectively. Here, we show that the Wadjet defense system recognizes DNA topology to protect its host against plasmid transformation. By combining cryoelectron microscopy with cross-linking mass spectrometry, we show that Wadjet forms a complex similar to the bacterial condensin complex MukBEF, with a novel nuclease subunit similar to a type II DNA topoisomerase. Wadjet specifically cleaves closed-circular DNA in a reaction requiring ATP hydrolysis by the structural maintenance of chromosome (SMC) ATPase subunit JetC, suggesting that the complex could use DNA loop extrusion to sense its substrate's topology, then specifically activate the nuclease subunit JetD to cleave plasmid DNA. Overall, our data reveal how bacteria have co-opted a DNA maintenance machine to specifically recognize and destroy foreign DNAs through topology sensing.

Fabrication of Concave Microwells and Their Applications in Micro-Tissue Engineering: A Review.

At present, there is an increasing need to mimic the in vivo micro-environment in the culture of cells and tissues in micro-tissue engineering. Concave microwells are becoming increasingly popular since they can provide a micro-environment that is closer to the in vivo environment compared to traditional microwells, which can facilitate the culture of cells and tissues. Here, we will summarize the fabrication methods of concave microwells, as well as their applications in micro-tissue engineering. The fabrication methods of concave microwells include traditional methods, such as lithography and etching, thermal reflow of photoresist, laser ablation, precision-computerized numerical control (CNC) milling, and emerging technologies, such as surface tension methods, the deformation of soft membranes, 3D printing, the molding of microbeads, air bubbles, and frozen droplets. The fabrication of concave microwells is transferring from professional microfabrication labs to common biochemical labs to facilitate their applications and provide convenience for users. Concave microwells have mostly been used in organ-on-a-chip models, including the formation and culture of 3D cell aggregates (spheroids, organoids, and embryoids). Researchers have also used microwells to study the influence of substrate topology on cellular behaviors. We will briefly review their applications in different aspects of micro-tissue engineering and discuss the further applications of concave microwells. We believe that building multiorgan-on-a-chip by 3D cell aggregates of different cell lines will be a popular application of concave microwells, while integrating physiologically relevant molecular analyses with the 3D culture platform will be another popular application in the near future. Furthermore, 3D cell aggregates from these biosystems will find more applications in drug screening and xenogeneic implantation.

Shear-induced motion of a bead on regular substrates at small particle Reynolds numbers

We study experimentally the impact of substrate topology on shear-flow-induced motion of a single bead at low particle Reynolds numbers. The substrates are regular quadratic and triangular arrangements of fixed spherical particles. Their topology is varied by using different spacings between the spheres. Here, we show that it has a strong impact not only on the critical Shields number for incipient bead motion but also on its motion above threshold. We focus on Shields numbers where the bead velocity is smaller than the settling velocity. For the different substrates, the data on the average bead velocity collapse on a master curve, showing the impact of the critical Shields number on the bead motion. To describe the bead motion, we develop a model for creeping flows based on expressions by Goldman, Cox and Brenner for the flow-induced forces and torques on a moving bead near a plane. Our model considers rolling and sliding motion. The bead detaches from the substrate on the downhill side at larger substrate spacing or higher Shields numbers, and flies through the interstices of the substrate until hitting the neighbouring substrate spheres. While sliding has only a minor effect on the average bead velocity, detachment has a strong impact. At large substrate spacings, it leads to a bistability, usually associated with inertial flows, even for adhesionless particles under creeping-flow conditions. The model shows good agreement with the experimental results.

Reconfigurable Acoustic Absorber Comprising Flexible Tubular Resonators for Broadband Sound Absorption

Typical acoustic metamaterial absorbers rely on relatively rigid materials for acoustic resonances, which, however, poses a challenge in reshaping and reconfiguring them. Here, we demonstrate soft reconfigurable acoustic absorbers, which are realized by the use of flexible tubular resonators. Owing to the structural compliance, the tube absorbers promote intriguing acoustic-structure coupling and exhibit hybrid resonances of acoustic and structural modes, which are characterized by Rabi splitting in the strong-coupling regime and Fano-like resonance in the weak-coupling regime. Also, the soft walls of the flexible resonators induce decreased resonance frequencies for low-frequency absorption by reducing the effective sound speed inside the tube. Moreover, we find that these hybrid resonances are critically influenced by the structural loss of the flexible resonators. While elucidating the role of the material rigidity and structural loss in acoustic resonances, this work allows us to design versatile broadband absorbers that can be reconfigured depending on the topology of a target substrate.