Transient Structures Research Articles

Air–water properties of unsteady breaking bores part 1: Novel Eulerian and Lagrangian velocity measurements using intrusive and non-intrusive techniques

Transient motion, turbulence and bubble dynamics make any velocity quantification extremely difficult in unsteady gas–liquid flows. In the present study, novel Eulerian and Lagrangian techniques of velocimetry were developed, using both intrusive and non-intrusive measurements. The selected unsteady gas–liquid flow was a breaking bore, featured with a transient motion, air entrainment and coherent structures. Intrusively, Eulerian probe measurements resulted to the development of a single bubble event detection (SBED) technique in unsteady air–water flows. Non-intrusively, the motion of air–water pattern was detected using a novel particle tracking velocimetry (PTV). Both velocities obtained using SBED and PTV techniques were validated against the established optical flow (OF) results, achieving consistent velocity data among the three techniques. The filtering criteria of the SBED and PTV techniques were discussed, showing the best options in the breaking bore. It is concluded that the most robust velocity measurements in gas–liquid flow are achieved with consistent velocity data between the SBED, PTV and OF techniques.

Sequential changes in cellular properties accompanying amniote somite formation.

Somites are transient structures derived from the pre-somitic mesoderm (PSM), involving mesenchyme-to-epithelial transition (MET) where the cells change their shape and polarize. Using Scanning electron microscopy (SEM), immunocytochemistry and confocal microscopy, we study the progression of these events along the tail-to-head axis of the embryo, which mirrors the progression of somitogenesis (younger cells located more caudally). SEM revealed that PSM epithelialization is a gradual process, which begins much earlier than previously thought, starting with the dorsalmost cells, then the medial ones, and then, simultaneously, the ventral and lateral cells, before a somite fully separates from the PSM. The core (internal) cells of the PSM and somites never epithelialize, which suggests that the core cells could be 'trapped' within the somitocoele after cells at the surfaces of the PSM undergo MET. Three-dimensional imaging of the distribution of the cell polarity markers PKCζ, PAR3, ZO1, the Golgi marker GM130 and the apical marker N-cadherin reveal that the pattern of polarization is distinctive for each marker and for each surface of the PSM, but the order of these events is not the same as the progression of cell elongation. These observations challenge some assumptions underlying existing models of somite formation.

Markers of senescence are often associated with neuronal differentiation in the developing sensory systems.

It has been shown that senescent cells accumulate in transient structures of the embryo that normally degenerate during tissue development. A collection of biomarkers is generally accepted to define senescence in embryonic tissues. The histochemical detection of β-galactosidase activity at pH 6.0 (β-gal-pH6) is the most widely used assay for cellular senescence. Immunohistochemical detection of common mediators of senescence which block cell cycle progression, including p16, p21, p63, p15 or p27, has also been used to characterize senescent cells in the embryo. However, the reliability of this techniques has been discussed in recent publications because non-senescent cells are also labelled during development. Indeed, increased levels of senescent markers promote differentiation over apoptosis in developing neurons, suggesting that machinery used for the establishment of cellular senescence is also involved in neuronal maturation. Notably, it has recently been argued that a comparable state of cellular senescence might be adopted by terminally differentiated neurons. The developing sensory systems provide excellent models for studying if canonical markers of senescence are associated with terminal neuronal differentiation.

Priming self-assembly pathways by stacking block copolymers

Block copolymers spontaneously self-assemble into well-defined nanoscale morphologies. Yet equilibrium assembly gives rise to a limited set of structures. Non-equilibrium strategies can, in principle, expand diversity by exploiting self-assembly’s responsive nature. In this vein, we developed a pathway priming strategy combining control of thin film initial configurations and ordering history. We sequentially coat distinct materials to form prescribed initial states, and use thermal annealing to evolve these manifestly non-equilibrium states through the assembly landscape, traversing normally inaccessible transient structures. We explore the enormous associated hyperspace, spanning processing (annealing temperature and time), material (composition and molecular weight), and layering (thickness and order) dimensions. We demonstrate a library of exotic non-native morphologies, including vertically-oriented perforated lamellae, aqueduct structures (vertical lamellar walls with substrate-pinned perforations), parapets (crenellated lamellae), and networks of crisscrossing lamellae. This enhanced structural control can be used to modify functional properties, including accessing regimes that surpass their equilibrium analogs.

High-fidelity fluid structure interaction simulations of turbulent-like aneurysm flows reveals high-frequency narrowband wall vibrations: A stimulus of mechanobiological relevance?

Recent high-fidelity/resolution computational fluid dynamics simulations of intracranial aneurysm hemodynamics have revealed turbulent-like flows. We hypothesized that the associated high-frequency pressure fluctuations could promote aneurysm wall vibrations. We performed fully coupled high-fidelity transient fluid structure interaction simulations between the blood flow and compliant aneurysm sac wall taking 5,000 time steps per second using a 3D patient-specific model previously shown to harbour turbulent-like flow. Our results show that the flow velocity contained fluctuations with a smooth and continuously decaying energy up to ∼160Hz, and fluctuating pressures with characteristic frequency peaks at approximately 30, 130 and 210Hz. There was a strong two-way coupling between the pressure and the wall deformation, for which the frequency spectrum showed similar characteristics, but with a narrow band peak at ∼120Hz with large regional differences in amplitude up to 80μm. The physics of the flow is broadly consistent with clinical reports of turbulent-like flows, while the physics of the wall is consistent with reports of spectral peaks in aneurysm patients. As many aneurysms are known to harbour turbulent-like flows, wall vibrations could be a widespread phenomenon. Finally, since aneurysms are vascular pathologies by definition and many/most aneurysms do not have endothelial cells but still display a focal remodeling, we hypothesize that vibrations and stresses within the wall itself might play a role in the mechanobiological processes of vessel wall pathology.

Vertical Motions in Orographic Cloud Systems over the Payette River Basin. Part II: Fixed and Transient Updrafts and Their Relationship to Forcing

Abstract Updrafts in wintertime cloud systems over mountainous regions can be described as fixed, mechanically driven by the terrain under a given ambient wind and stability profile (i.e., vertically propagating gravity waves tied to flow over topography), and transient, associated primarily with vertical wind shear and conditional instability within passing weather systems. This analysis quantifies the magnitude of fixed and transient updraft structures over the Payette River basin sampled during the Seeded and Natural Orographic Wintertime Clouds: The Idaho Experiment (SNOWIE). Vertical motions were retrieved from Wyoming Cloud Radar measurements of radial velocity using the algorithm presented in Part I. Transient circulations were removed, and fixed orographic circulations were quantified by averaging vertical circulations along repeated cross sections over the same terrain during the campaign. Fixed orographic vertical circulations had magnitudes of 0.3–0.5 m s−1. These fixed vertical circulations were composed of a background circulation in which transient circulations were embedded. Transient vertical circulations are shown to be associated with transient wave motions, cloud-top generating cells, convection, and turbulence. Representative transient vertical circulations are illustrated, and data from rawinsondes over the Payette River basin are used to infer the relationship of the vertical circulations to shear and instability. Maximum updrafts are shown to exceed 5 m s−1 within Kelvin–Helmholtz waves, 4 m s−1 associated with transient gravity waves, 3 m s−1 in generating cells, 6 m s−1 in elevated convection, 4 m s−1 in surface-based deep convection, 5 m s−1 in boundary layer turbulence, and 9 m s−1 in shear-induced turbulence.

Delicate superconductivity in nodal-line NaAlGe single crystal

Nodal-line superconductor NaAlSi with a transition temperature () of 7 K has attracted considerable attention in recent years, whereas its Ge counterpart, NaAlGe, does not superconduct down to the lowest temperature regardless of their similar atomic and electrical structures. To tackle this enigma, we resort to the growth of NaAlGe single crystal and characterize its ground state. Interestingly, when hole doped by oxidation or extracting Na, single-crystalline NaAlGe transforms from a semimetal/semiconductor to a superconductor ( 3.3 K) with zero resistivity and a diamagnetic shielding fraction over 100, but without a thermodynamic response in heat capacity. Continuous x-ray diffraction reveals a transient new structure with a larger c axis, which is suggested to have arisen from the minor loss of Na and to be responsible for the emergence of the delicate superconductivity. Our findings place NaAlGe on an equal footing with NaAlSi and provide an alternative for studying the intriguing relationship between superconductivity and nodal-line topology.

Binary-FRET reveals transient excited-state structure associated with activity-dependent CaMKII - NR2B binding and adaptation

Synaptic functions are mediated and modulated by a coordinated choreography of protein conformational changes and interactions in response to intracellular calcium dynamics. Time-lapse Förster resonance energy transfer can be used to study the dynamics of both conformational changes and protein-protein interactions simultaneously under physiological conditions if two resonance energy transfer reactions can be multiplexed. Binary-FRET is a technique developed to independently monitor the dynamics of calcium-calmodulin dependent protein kinase-II catalytic-domain pair separation in the holoenzyme, and its role in establishing activity-dependent holoenzyme affinity for the NR2B binding fragment of the N-methyl-D-aspartate receptor. Here we show that a transient excited-state intermediate exists where paired catalytic-domains in the holoenzyme first separate prior to subsequent NR2B association. Additionally, at non-saturating free calcium concentrations, our multiplexed approach reveals that the holoenzyme exhibits a biochemical form of plasticity, calcium dependent adaptation of T-site ligand binding affinity.

Two-dimensional simulation of cool and double flame formation induced by the laser ignition under shock-tube conditions

The laser ignition-induced spherical cool and double flame’s initiation, propagation, and transition are studied using a two-dimensional simulation with a detailed mechanism using n-heptane/O2/Ar/He mixture. The current study’s primary goal is to reveal how the radicals and flow field produced by the laser ignition lead to cool, hot, or double flame formation and to determine the flame propagation modes. It is found that after the laser spark, the over-driven shock wave results in vortex pairs, which significantly distorts the temperature field and the spatial distribution of the radicals. A torus-like hot flame is ignited at the ignition kernel center instantaneously. The results show that the laser-ignited hot flame can transit to a cool or double flame depending on the laser pulse energy. On the one hand, the hot flame extinguishes under a small laser ignition energy condition, at which the radicals at the hot flame front are transported by the vortex pair and lead to a cool flame formation. On the other hand, when the laser spark energy is large, a transient premixed double flame structure is observed. The double flame can be localized, and the appearance location is primarily affected by the spatial distribution of laser-induced radicals. The cool flame can coexist with a trailing hot flame for milliseconds, dramatically accelerating the hot flame propagation and fundamentally impacting the flame speed interpolation. Computational singularity perturbation (CSP) analysis identifies key reactions that belong to typical low-temperature chemistry in the double flame zone. A comparative simulation case with an initial temperature above the low-temperature chemistry regime confirms that no double flame structure can be formed under high-temperature conditions. The present study provides essential insight and guidance for the flame speed measurement using laser ignition under engine-relevant conditions.

Probing Transient Riboswitch Structures via Single Molecule Accessibility Analysis.

Riboswitches are a class of RNA motifs in the untranslated regions of bacterial messenger RNAs (mRNAs) that can adopt different conformations to regulate gene expression. The binding of specific small molecule or ion ligands, or other RNAs, influences the conformation the riboswitch adopts. Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) offers an approach for probing this structural isomerization, or conformational switching, at the level of single mRNA molecules. SiM-KARTS utilizes fluorescently labeled, short, sequence-complementary DNA or RNA oligonucleotide probes that transiently access a specific RNA conformation over another. Binding and dissociation to a surface-immobilized target RNA of arbitrary length are monitored by Total Internal Reflection Fluorescence Microscopy (TIRFM) and quantitatively analyzed, via spike train and burst detection, to elucidate the rate constants of isomerization, revealing mechanistic insights into riboswitching.

Kölliker's organ-supporting cells and cochlear auditory development.

The Kölliker’s organ is a transient cellular cluster structure in the development of the mammalian cochlea. It gradually degenerates from embryonic columnar cells to cuboidal cells in the internal sulcus at postnatal day 12 (P12)–P14, with the cochlea maturing when the degeneration of supporting cells in the Kölliker’s organ is complete, which is distinct from humans because it disappears at birth already. The supporting cells in the Kölliker’s organ play a key role during this critical period of auditory development. Spontaneous release of ATP induces an increase in intracellular Ca2+ levels in inner hair cells in a paracrine form via intercellular gap junction protein hemichannels. The Ca2+ further induces the release of the neurotransmitter glutamate from the synaptic vesicles of the inner hair cells, which subsequently excite afferent nerve fibers. In this way, the supporting cells in the Kölliker’s organ transmit temporal and spatial information relevant to cochlear development to the hair cells, promoting fine-tuned connections at the synapses in the auditory pathway, thus facilitating cochlear maturation and auditory acquisition. The Kölliker’s organ plays a crucial role in such a scenario. In this article, we review the morphological changes, biological functions, degeneration, possible trans-differentiation of cochlear hair cells, and potential molecular mechanisms of supporting cells in the Kölliker’s organ during the auditory development in mammals, as well as future research perspectives.

Study of the transient flow structures generated by a pulsed nanosecond plasma actuator on a delta wing

The transient flow structures produced by a pulsed nanosecond plasma actuator and the mechanism by which they are generated are investigated experimentally and through simulations for the case of flow control on a non-slender delta wing. Phase-averaged particle image velocimetry reveals a phenomenon in which, after each discharge pulse, two sub-vortices are generated in sequence and move along the shear layer regardless of the angle of attack, and this is confirmed by hot-wire anemometry. However, at high actuation frequencies (F+ = fc/U∞ ≥ 6.435), this phenomenon of double sub-vortices is not observed, and only one sub-vortex is generated per period. The results of pressure measurements indicate that each sub-vortex gives rise to a distinct pressure fluctuation on the wing surface. Numerical simulations reveal a number of residual heats resulting from plasma thermal effects in the shear layer, each of which turns out to induce a corresponding sub-vortex. At low actuation frequencies (F+ ≤ 4.29), there is a division of the initial residual heat into two independent residual heats and, hence, double sub-vortices per period, whereas at high actuation frequencies (F+ ≥ 6.435), residual heats from two consecutive periods merge into one, resulting in just one sub-vortex per period, which provides an explanation for the experimentally observed flow behavior.

Fibroblast-derived Hgf controls recruitment and expansion of muscle during morphogenesis of the mammalian diaphragm.

The diaphragm is a domed muscle between the thorax and abdomen essential for breathing in mammals. Diaphragm development requires the coordinated development of muscle, connective tissue, and nerve, which are derived from different embryonic sources. Defects in diaphragm development cause the common and often lethal birth defect, congenital diaphragmatic hernias (CDH). HGF/MET signaling is required for diaphragm muscularization, but the source of HGF and the specific functions of this pathway in muscle progenitors and effects on phrenic nerve have not been explicitly tested. Using conditional mutagenesis in mice and pharmacological inhibition of MET, we demonstrate that the pleuroperitoneal folds (PPFs), transient embryonic structures that give rise to the connective tissue in the diaphragm, are the source of HGF critical for diaphragm muscularization. PPF-derived HGF is directly required for recruitment of MET+ muscle progenitors to the diaphragm and indirectly (via its effect on muscle development) required for phrenic nerve primary branching. In addition, HGF is continuously required for maintenance and motility of the pool of progenitors to enable full muscularization. Localization of HGF at the diaphragm's leading edges directs dorsal and ventral expansion of muscle and regulates its overall size and shape. Surprisingly, large muscleless regions in HGF and Met mutants do not lead to hernias. While these regions are likely more susceptible to CDH, muscle loss is not sufficient to cause CDH.

The insufficiency of Dlx5 for ventral patterning in post-migratory neural crest cells reveals a loss of plasticity in early jaw-forming tissue

The articulated jaws of vertebrates arise from the first pharyngeal arch, the most rostral of several transient ventral structures in pharyngeal stage embryos. Migratory cranial neural crest cells from the caudal midbrain and rostral hindbrain populate the first arch as ectomesenchyme and supply the progenitors of skeletal and soft tissues that form the upper (maxillary) and lower (mandibular) jaws. Dlx genes encode key transcriptional regulators that profoundly influence jaw development through their actions in first pharyngeal arch patterning. The broadly conserved nested expression of Dlx paralogues in vertebrate embryos points to a retained ancestral role in patterning first arch tissue. Loss-of-function experiments consistently highlight the necessity of Dlx gene function for jaw morphogenesis. Specifically, the combined effects of Dlx5 and Dlx6 are required to specify ventral/mandibular fate and forced expression of Dlx5 in migrating neural crest cells results in the ectopic upregulation of ventral markers in the maxillary arch. Here, we ask whether Dlx5 is also sufficient to respecify post-migratory ectomesenchyme in the maxillary branch as mandibular. Unexpectedly, we show that Dlx5 is not sufficient to activate mandibular marker genes in the maxillary branch of PA1, highlighting a loss of plasticity in post-migratory first arch ectomesenchyme.

Dynamics and structure of detonations in stratified product-gas diluted mixtures

The dynamics and structure of detonations in stratified, product-gas diluted mixtures are examined using high resolution two-dimensional simulations with detailed chemistry. A stoichiometric methane/oxygen/nitrogen mixture with a product-gas dilution level similar to that found in rotating detonation engines is considered. A parametric analysis of the stratification size is performed. For stratification sizes larger than the induction length lind, the traditional detonation cell structure is lost and triple-points are absent. For stratification sizes an order of magnitude larger than lind, large regions of unburned, cold gases are found far behind the detonation front, and are subsequently consumed through an isobaric combustion process initiated by scalar mixing. This mechanism results in a deficit of energy provided to the detonation and to a significant reduction in the overall detonation velocity. A one-dimensional model using ZND theory is constructed to gain insights on the transient detonation structure. This model predicts a slower detonation velocity through the cold gases, which is supported by the results from the simulations with large stratification sizes. In these cases, the detonation structure is well predicted by the model in the regions that undergo ignition by shock compression, i.e., for intermediate and high levels of product-gas dilution. In the absence of triple-points, the detonation structure and dynamics can be locally considered as quasi-one-dimensional. The model and simulation results have a larger discrepancy for small stratification sizes, implying that phenomena other than adiabatic shock compression, involving heat and/or mass transfer, might play a role to ignite the reactants.

Cell cycle expression of FLJ25439, a cytokinesis-associated protein, is mediated by D-box recognition and APC/C-Cdc20 regulated degradation

The midbody is a transient structure forming out of the central spindle at late telophase. Both the midbody and central spindle have important functions ensuring completion of cytokinesis and defects in this process may lead to genetic diseases, including cancer. Thus, understanding the mechanisms that control cytokinesis during mitosis can reveal the key components taking part in some of the processes that promote accurate cell division. Our previous study showed that overexpression of FLJ25439 causes cytokinesis defect with midbody arrest and induces tetraploids with prolonged cell growth/cell cycle progression (Pan et al., 2015). Here, we extend our investigation with regard to the expression profile/regulation and cellular localization/function of FLJ25439 during mitosis/cytokinesis. Using a monoclonal antibody 2A4 we found that FLJ25439 expression is cell cycle-dependent and subjected to APC/C complex regulation. Furthermore, it is a novel substrate for the APC/C-Cdc20 complex and its degradation is proteasome-dependent through D-box recognition during mitotic exit. Immunofluorescence microscopy showed it is distributed at the central spindle and midbody, two structures considered important for completion of cell division, in telophase and cytokinesis, respectively, during cell cycle progression. Depletion of FLJ25439 expression revealed defects in chromosome alignment/segregation and delayed mitosis/cytokinesis progression. We thus conclude that FLJ25439 is a hitherto undiscovered factor involved in cytokinesis regulation.

Simulation and Experimental Verification of Dynamic Characteristics on Gas Foil Thrust Bearings Based on Multi-Physics Three-Dimensional Computer Aided Engineering Methods

This paper presents a method to simulate the dynamic operating characteristics of a gas foil thrust bearing based on linear elastic support and constant ambient temperature to mimic the transient structure–fluid interactions. In the physical model, the top and bump foils are simply represented by an infinite number of Hookean springs attached to a solid wall with a small amount of deformation, whereas the gas film in the bearing is under quasi-steady lubrication flow conditions with hydrodynamic pressure distributed on the little-deformed top foil. A three-dimensional multi-physics model in a cylindrical coordinate system is established via a commercial computer-aided engineering software package to predict the nominal dynamic characteristics of the gas foil thrust bearing. To verify the multi-physics model, an experimental bench was built in-house to measure the thrust force on the support of the bearing. With the pertinent bearing parameters being entered into the package, the simulations agree well with the experimental thrust forces. As a further step, a simulation model of a clamped-rotor gas foil thrust bearing design was thoroughly investigated under nominal operating conditions, resulting in predictions of underdamped oscillations in rotor motions. The phenomenon could be described using a linear mass–spring–damper model that is dependent on the gas film thickness. The stiffness and damping coefficients could serve as a base reference for rotor dynamics analysis. This concludes the potential development of a digital twin for gas foil thrust bearing systems.

Dynamic Stability of Copper Single-Atom Catalysts under Working Conditions.

The long-term stability of single-atom catalysts is a major factor affecting their large-scale commercial application. How to evaluate the dynamic stability of single-atom catalysts under working conditions is still lacking. Here, taking a single copper atom embedded in N-doped graphene as an example, the "constant-potential hybrid-solvation dynamic model" is used to evaluate the reversible transformation between copper single atoms and clusters under realistic reaction conditions. It is revealed that the adsorption of H is a vital driving force for the leaching of the Cu single atom from the catalyst surface. The more negative the electrode potential, the stronger the adsorption of H. As a result, the competitive hydrogen evolution reaction is inhibited, and Cu-N bonds are weakened, resulting in some Cu atoms being tethered on the catalyst surface and some being dissolved in the aqueous solution. The collision of the Cu atoms in the two states forms a transient Cu cluster structure as a true catalytic active site to promote CO2 reduction to ethanol. As the applied potential is released or switched to a positive value, hydroxyl radicals (OH•) play a dominant role in the oxidation process of the Cu cluster, and then Cu returns to the initial atomic dispersion state by redeposition, completing the reconstruction cycle of the copper catalyst. Our work provides a fundamental understanding of the dynamic stability of Cu single-atom catalysts under working conditions at the atomic level and calls for a reassessment of the stability of currently reported single-atom catalysts considering realistic reaction conditions.

Transient RNA structures cause aberrant influenza virus replication and innate immune activation.

During infection, the influenza A virus RNA polymerase produces both full-length and aberrant RNA molecules, such as defective viral genomes (DVGs) and mini viral RNAs (mvRNAs). Subsequent innate immune activation involves the binding of host pathogen receptor retinoic acid–inducible gene I (RIG-I) to viral RNAs. However, it is not clear what factors determine which influenza A virus RNAs are RIG-I agonists. Here, we provide evidence that RNA structures, called template loops (t-loops), stall the viral RNA polymerase and contribute to innate immune activation by mvRNAs during influenza A virus infection. Impairment of replication by t-loops depends on the formation of an RNA duplex near the template entry and exit channels of the RNA polymerase, and this effect is enhanced by mutation of the template exit path from the RNA polymerase active site. Overall, these findings are suggestive of a mechanism involving polymerase stalling that links aberrant viral replication to the activation of the innate immune response.

Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins.

Recent advances in residue-level coarse-grained (CG) computational models have enabled molecular-level insights into biological condensates of intrinsically disordered proteins (IDPs), shedding light on the sequence determinants of their phase separation. The existing CG models that treat protein chains as flexible molecules connected via harmonic bonds cannot populate common secondary-structure elements. Here, we present a CG dihedral angle potential between four neighboring beads centered at Cα atoms to faithfully capture the transient helical structures of IDPs. In order to parameterize and validate our new model, we propose Cα-based helix assignment rules based on dihedral angles that succeed in reproducing the atomistic helicity results of a polyalanine peptide and folded proteins. We then introduce sequence-dependent dihedral angle potential parameters (εd) and use experimentally available helical propensities of naturally occurring 20 amino acids to find their optimal values. The single-chain helical propensities from the CG simulations for commonly studied prion-like IDPs are in excellent agreement with the NMR-based α-helix fraction, demonstrating that the new HPS-SS model can accurately produce structural features of IDPs. Furthermore, this model can be easily implemented for large-scale assembly simulations due to its simplicity.