Bubble Core Research Articles

Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase

RNA polymerases (RNAPs) carry out the first step in the central dogma of molecular biology by transcribing DNA into RNA. Despite their importance, much about how RNAPs work remains unclear, in part because the small (3.4 Angstrom) and fast (~40 ms/nt) steps during transcription were difficult to resolve. Here, we used high-resolution nanopore tweezers to observe the motion of single Escherichia coli RNAP molecules as it transcribes DNA ~1,000 times improved temporal resolution, resolving single-nucleotide and fractional-nucleotide steps of individual RNAPs at saturating nucleoside triphosphate concentrations. We analyzed RNAP during processive transcription elongation and sequence-dependent pausing at the yrbL elemental pause sequence. Each time RNAP encounters the yrbL elemental pause sequence, it rapidly interconverts between five translocational states, residing predominantly in a half-translocated state. The kinetics and force-dependence of this half-translocated state indicate it is a functional intermediate between pre- and post-translocated states. Using structural and kinetics data, we show that, in the half-translocated and post-translocated states, sequence-specific protein-DNA interaction occurs between RNAP and a guanine base at the downstream end of the transcription bubble (core recognition element). Kinetic data show that this interaction stabilizes the half-translocated and post-translocated states relative to the pre-translocated state. We develop a kinetic model for RNAP at the yrbL pause and discuss this in the context of key structural features.

Bioinspired Confined Assembly of Cellulosic Cholesteric Liquid Crystal Bubbles.

Construction of biomimetic models for structural color evolution not only gives new photonic phenomena but also provide cues for biological morphogenesis. Here, a novel confined self-assembly method is proposed for the generation of hydroxypropyl cellulose (HPC)-based cholesteric liquid crystals (CLCs) microbubbles. The assembly process relies on the combination of droplet microfluidics, solvent extraction, and a volume confined environment. The as-prepared HPC structural color microbubbles have a transparent shell, an orderly arranged cholesteric liquid crystal (CLC)middle layer, and an innermost bubble core. The size of the microbubble, shell thickness, and the color of the CLC layer can be adjusted by altering the microfluidic parameters. Intriguingly, benefited from the compartmentalization effect provided by droplet microfluidics, microbubbles with multiple cores of different color combinations are generated under precise control. The self-assembled CLCs microbubbles have bright structural color, suspending ability, and good temperature-sensitive characteristics, making them ideal underwater sensors. The present confined assembly approach will shed light on creating novel photonic structures and the HPC microbubble will find widespread applications in multifunctional sensing, optical display, and other related fields are believed.

TEM investigation of helium bubble evolution in tungsten and ZrC-strengthened tungsten at 800 and 1000°C under 40keV He+ irradiation

Helium-induced defect nucleation and accumulation in polycrystalline W and W0.5 wt%ZrC (W0.5ZrC) were studied in-situ using the transmission electron microscopy (TEM) combined with 40 keV He+ irradiation at 800 and 1000°С at the maximum damage level of 1 dpa. Radiation-induced dislocation loops were not observed in the current study. W0.5ZrC was found to be less susceptible to irradiation damage in terms of helium bubble formation and growth, especially at lower temperature (800 °C) when vacancies were less mobile. The ZrC particles present in the W matrix pin the forming helium bubbles via interaction between C atom and neighbouring W atom at vacancies. This reduces the capability of helium to trap a vacancy which is required to form the bubble core and, as a consequence, delays, the bubble nucleation.At 1000 °C, significant bubble growth occurred in both materials and all the present bubbles transitioned from spherical to faceted shape, whereas at 800 °C, the faceted helium bubble population was dominated in W.

Suspended bubble microcapsule delivery systems from droplet microfluidic technology for the local treatment of gastric cancer

Microcapsules are promising drug carriers for disease treatment. Specifically, for drug delivery in the stomach, a key point is to enable retention of the carriers regardless of gastric emptying and peristalsis. Here, we designed novel drug-loaded bubble microcapsules, which were prepared by microfluidic technology and used for oral drug delivery. The bubble microcapsules were composed of a PLGA shell and a bubble core, which was derived from osmotic-triggered cavitation. The PLGA shell ensured efficient drug encapsulation and sustained release; the bubble core enabled retention of the microcapsules in the stomach and thus facilitated long-term treatment. Based on this, we confirmed anti-tumor effects of drug-loaded bubble microcapsules in vivo and in vitro. The drug-loaded bubble microcapsules significantly inhibited the growth and metastasis of tumors. These results suggest that the suspended bubble microcapsules can be used as an ideal drug release platform for cancer therapy. It is foreseeable that the suspension bubble microcapsules prepared by this method would have broader application prospects as oral delivery vehicles for the treatment of gastrointestinal diseases.

Overexpansion-dominated coronal mass ejection formation and induced radio bursts

Aims. Coronal mass ejections (CMEs) are the most fascinating explosions in the Solar System. Their formation is still not fully understood, however. Methods. We investigated a well-observed CME on 2021 May 7 that showed a typical three-component structure and was continuously observed from 0 to 3 R⊙ by a combination of SDO/AIA (0–1.3 R⊙), PROBA2/SWAP (0–1.7 R⊙), and MLSO/K-Cor (1.05–3 R⊙). Furthermore, we compared the morphological discrepancy between the CME white-light bright core and the extreme-UV (EUV) blob. We finally explored the origin of various radio bursts that are closely related to the interaction of the CME overexpansion with a nearby streamer. Results. An interesting finding is that the height increases of the CME leading front and of the bright core are dominated by the overexpansion during the CME formation. The aspect ratios of the CME bubble and bright core, quantifying the overexpansion, are found to decrease as the SO/STIX 4–10 keV and GOES 1–8 Å soft X-ray flux of the associated flare increases near the peaks. This indicates that the flare reconnection plays an important role in the first overexpansion. The CME bubble even undergoes a second overexpansion, although it is relatively weak, which is closely related to the compression with a nearby streamer and likely arises from an ideal magnetohydrodynamics process. Moreover, the CME EUV blob is found to be relatively lower and wider than the CME white-light bright core, which may correspond to the bottom part of the growing CME flux rope. The interaction between the CME and the streamer leads to two type II radio bursts, one that is drifting normally and another that is stationary, which are speculated to be induced by two different sources of the CME-driven shock front. The bidirectional electrons shown in series of C-shaped type III bursts suggest that the interchange reconnection is also involved during the interaction of the CME and streamer.

Impact of bubble size on turbulent statistics in bubble plumes in unstratified quiescent water

We report an experimental investigation of turbulence in bubble plumes released in unstratified quiescent water. The focus is to study the detailed turbulent statistics and the budget terms in the equations of turbulent kinetic energy (TKE), particularly about their distributions in the radial direction of bubble plumes compared to those in the single-phase momentum jets and buoyant plumes. Two types of diffusers were used to generate plumes consisting of different bubble sizes and population at the same source gas discharge. The bubble plumes have different growth behaviors under different combination of sizes and population: the plumes with many small bubbles show decreasing centerline velocities along the vertical direction; the plumes with larger but fewer bubbles have a tighter bubble core, a smaller spreading ratio, and almost constant centerline velocities. The ratio of turbulence-to-mean in momentum flux is strongly affected by bubble sizes and population, demonstrated in the profiles of normalized turbulent velocity correlations using mean flow parameterizations. Velocity fluctuations show a strong vertical-to-horizontal anisotropy in bubble plumes compared to those in single-phase jets and plumes. Strong vertical fluctuating velocity component contributes a significant role in re-shaping the radial profiles of turbulent stresses and transport terms when the bubble plume is composed of larger but fewer bubbles. Local balance cannot be established in the equation of TKE traditionally used for single-phase flows. A bubble-related source term in the governing equation is needed to close the budget. An empirical equation using drag force and bubble slip velocity is validated for the TKE closure. We provide a diagram of TKE budget to illustrate the pathway of TKE terms in the radial direction, with the magnitude of each term influenced by bubble characteristics.

Ultrafast Growth and Locomotion of Dandelion-Like Microswarms with Tubular Micromotors.

Dynamic assembly and cooperation represent future frontiers for next generations of advanced micro/nano robots, but the required local interaction and communication cannot be directly translated from macroscale robots through the minimization because of tremendous technological challenges. Here, an ultrafast growth and locomotion methodology is presented for dandelion-like microswarms assembled from catalytic tubular micromotors. With ultrasound oscillation of self-generated bubbles, such microswarms could overcome the tremendous and chaotic drag force from extensive and disordered bubble generation in single units. Tubular MnO2 micromotor individuals headed by self-generated oxygen bubbles are ultrasonically driven to swim rapidly in surfactant-free H2 O2 solutions. A large bubble core fused from multiple microbubbles is excited to oscillate and the resultant local intensified acoustic field attracts the individual micromotors to school around it, leading to a simultaneous growth of dandelion-like microswarms. The bubble-carried micromotor groups driven by ultrasound could swarm at a zigzag pattern with an average speed of up to 50 mm s-1 , which is validated in low H2 O2 concentrations. Additionally, such superfast locomotion could be ultrasonically modulated on demand. The ultrafast microswarm growth and locomotion strategy offers a new paradigm for constructing distinct dynamic assemblies and rapid transmission of artificial microrobots, paving the way to a myriad of promising applications.

Temperature insensitive fiber Fabry-Perot/Mach-Zehnder hybrid interferometer based on photonic crystal fiber for transverse load and refractive index measurement

An in-line Fabry-Perot/Mach-Zehnder hybrid interferometer based on photonic crystal fiber (PCF) for transverse load and refractive index measurement is proposed and experimentally demonstrated. The interferometer is fabricated by fusion splicing a section PCF between hollow core silica tube air bubble and hollow core silica tube (HCST). The hollow core silica tube air bubble is both a beam splitter for the Mach-Zehnder interferometer (MZI) and a Fabry-Perot interferometer (FPI) component, that is, there are both MZI and FPI functions on one sensor. Thanks to the structure of this special hollow core silica tube air bubble, transverse load measurement can be achieved. Meanwhile, this sensor also can measure refractive index and temperature. Experimental results show that the transverse load and refractive index sensitivities are 1.5277 nm/N and 99.2907 nm/RIU, respectively. In addition, the temperature sensitivity (−13.7 pm/°C) is relatively low. This sensor has outstanding advantages of high sensitivity, design flexibility, easy fabrication and compact size, which make it attractive in the field of multiparameter sensing applications.

Manias and Mimesis: Applying René Girard’s Mimetic Theory to Financial Bubbles

While next-generation models in quantitative finance have illuminated the origins of market bubbles and crashes by incorporating herding and imitation behavior, the underlying cause of imitation in financial markets remains elusive. Given that imitation is at the core of bubbles, we need a deeper understanding of the phenomenon. In this paper, we apply Rene Girard’s mimetic theory in a series of case studies of historical speculative manias, from the 1840s railway mania to the ICO boom and collapse, and even to present-day mimesis-driven market distortions.

Molecular simulation on viscous effects for microscale combustion in reactive shock-bubble interaction

Molecular simulations of reacting shock-bubble interaction were performed to study viscous effects on the supersonic premixed combustion, using the Direct Simulation Monte Carlo (DSMC) method. Different bubble diameters that are comparable to the thickness of the normal shock wave (Mach=2) were taken into account. The evolution of bubble morphology indicates that viscous effects (diffusion and dissipation) leads to the disappearance of some typical phenomena, including the shock focusing, positive viscosity deposition and wake-like cross-section. Meanwhile, the viscous dissipation is mainly responsible for the enstrophy degeneration, which is enhanced by reducing the bubble scale and heat release in combustion. The observed combustion process, which is prominent near the bubble core, is more evident with a larger bubble diameter and unlikely to occur with the smallest bubble diameter. The corresponding reason is that the strong viscous diffusion reduces the collision events between fuel and oxygen molecules. In addition, a time-scale analysis was conducted to illustrate the viscous diffusion in the hydrodynamic and chemical reaction time-scales with different bubble diameters. As a consequence, a changing dimensionless Damkohler number was presented to understand the dominant diffusion effect in microscale supersonic premixed combustion.

Study on the transient evolution law of internal flow field and dynamic stress of reactor coolant pump under rotor seizure accident

When the reactor coolant pump (RCP) operates under rated conditions, the rotor is suddenly forced to stop rotating in a very short time because of the great resistance moment. This nuclear accident is called rotor seizure accident and is the most extreme nuclear accident in a nuclear power plant. After the rotor seizure accident, the coolant flow rate of the primary circuit system drops sharply, the core temperature rises, and the fuel rod is forced in a danger of deviating from the bubble core boiling (DNB). In this paper, the AP1000 reactor coolant pump is taken as the research object, and the transient transition process under the rotor seizure condition are studied. Firstly, the simulation calculation of bidirectional fluid-structure coupling was verified by experiments. Then on the basis of considering the bidirectional fluid-solid coupling, the numerical simulation method is applied to study the flow law inside the reactor coolant pump and the deformation and stress distribution of the blade under the rotor seizure condition. The results show: the rotor seizure accident condition is a transient transition from a normal pump condition to a reverse turbine condition; when the rotor seizure accident occurs, the high specific pressure energy zone in the pump is gradually transferred from the volute to the inlet section; due to the direct impact of the liquid flow, the impeller is a concentrated area of high stress; high pivot dynamic stress was generated easily at the juncture between the inlet and outlet edges and the front and back cover plates of the impeller, which would transfer with the evolution of the rotor seizure accident.

High-speed observations of Acoustic Cluster Therapy “activation” and “therapy”

Acoustic Cluster Therapy (ACTTM) is a novel and versatile drug delivery platform, based on electrostatically bound clusters of negatively charged contrast agent microbubbles (SonazoidTM, GE Healthcare) and positively charged oil microdroplets, for co-administration with drug to the vasculature. Preliminary in-vitro high-speed observations at up to 10 million frames per second of both “activation” (exposure of clusters to 2.19 MHz focused ultrasound, at mechanical index, MI ≈ 0.15) and “therapy” (exposure of the resulting vapour bubbles, to 675 kHz with MI ranging from 0.1 to 0.4) will be presented. At low MI, the therapy exposure induces quasi-linear oscillations of the vapour bubble, with higher MIs inducing high-order surface wave activity. In the latter case, the amplitude of the non-spherical oscillations increase during the exposure until involutions neck, generating intra-bubble droplets that traverse the bubble core at speeds of up to several m/s. Possible mechanisms for activation and therapy will be discussed, based on the observations. [This research was supported by ERC Starting Grant TheraCav, 336189, and Glasgow Knowledge Exchange project DefACT.]

Observation of high-temperature bubbles in an ECR plasma

Creation and annihilation of high-temperature bubbles have been observed in an electron cyclotron resonance plasma. The electron temperature in the bubble core is three times higher than that in the ambient region, and the size perpendicular to the magnetic field is much smaller than the plasma diameter. Formation of a bubble accompanies large negative spikes in the floating potential of a Langmuir probe, and the spatiotemporal behavior of the bubble has been visualized with a high-impedance wire grid detector. It is found that the bubble is in a prolate spheroidal shape with the axis along the magnetic field and occurs randomly in time and independently in space.

Pinning and hysteresis in the field dependent diameter evolution of skyrmions in Pt/Co/Ir superlattice stacks

We have imaged Néel skyrmion bubbles in perpendicularly magnetised polycrystalline multilayers patterned into 1 µm diameter dots, using scanning transmission x-ray microscopy. The skyrmion bubbles can be nucleated by the application of an external magnetic field and are stable at zero field with a diameter of 260 nm. Applying an out of plane field that opposes the magnetisation of the skyrmion bubble core moment applies pressure to the bubble and gradually compresses it to a diameter of approximately 100 nm. On removing the field the skyrmion bubble returns to its original diameter via a hysteretic pathway where most of the expansion occurs in a single abrupt step. This contradicts analytical models of homogeneous materials in which the skyrmion compression and expansion are reversible. Micromagnetic simulations incorporating disorder can explain this behaviour using an effective thickness modulation between 10 nm grains.

Critical heat flux prediction model for low quality flow boiling of water in vertical circular tube

Based on the viewpoint of bubble crowding in near-wall bubble layer, a critical heat flux (CHF) prediction model was developed for low quality flow boiling of water in uniformly heated vertical circular tube under high pressure and low flow rate conditions. In this model, a CHF formula was derived from the conservation equations of mass, momentum and energy, where the transverse mass transport between the near-wall bubble layer and core is assumed to be limited. Taking account of the convective shear effect caused by the frictional drag on the wall-attached bubbles, the limiting transverse interchange of mass flux crossing the bubble layer–core interface was determined from the momentum balance equations. A new formula of bubble departure diameter considering the effect of buoyancy was put forward and used to solve the model with numerous other empirical correlations (e.g. bubble departure point, turbulence velocity profile, void fraction and so on). The model shows good agreements with the experimental data of uniformly heated circular tube. Based on this, the effects of flow variables such as pressure, mass flux and inlet subcooling on CHF prediction results were also discussed.

Photonic Crystal Microbubbles as Suspension Barcodes.

A novel suspension array was developed that uses photonic crystal (PhC) microbubbles as barcode particles. The PhC microbubbles have an outer transparent polymeric shell, a middle PhC shell, and an inner bubble core, and they were achieved by extraction-derived self-assembly of colloidal nanoparticles in semipermeable solid microcapsules. The encoded elements of the microbubbles originated from their PhC structure with a coated shell, which not only improved the stability of the codes but also provided a flexible surface for bioassays. By using multicompartmental microcapsule templates, PhC microbubbles with substantial coding levels and controllable movement could also be achieved. In addition, as the size of the encapsulated bubbles could be tailored, the overall density of the PhC microbubbles could be adjusted to match the density of a detection solution and to remain in suspension. These remarkable properties make the PhC microbubbles excellent barcode particles.

SELF-SIMILARITY OF VERTICAL BUBBLY JETS

An integral model for vertical bubbly jets with nearly monodisperse bubble sizes is presented. The model is based on the Gaussian type self-similarity of mean liquid velocity, bubble velocity and void fraction, as well as on functional relationships for initial liquid jet velocity and radius, bubble diameter and relative velocity. Adjusting the model to experimental data available in the literature for a wide range of densimetric Froude numbers provide constant values for the entrainment coefficient, momentum amplification factor, and spreading ratio of the bubble core for different flow conditions. Consistency and sensitivity of key model parameters are also verified. Overall, the deviations between model predictions and axial/radial profiles of mean liquid velocity, bubble velocity and void fraction are lower than about 20%, which suggests that bubbly jets tend to behave as self-preserving shear flows, similarly to single-phase jets and plumes. Furthermore, model simulations indicate a behavior similar to those of single-phase buoyant jets and slurry jets, but some differences with respect to confined bubbly jets are highlighted. This article provides not only a contribution to the problem of self-similarity in two-phase jets, but also a comprehensive model that can be used for analysis of artificial aeration/mixing systems involving bubbly jets.

Molecular dynamics study of helium bubble pressure in tungsten

Molecular dynamics simulations were performed to calculate the stress field in a tungsten matrix containing a nano-scale helium bubble. A helium bubble in tungsten is found to consist of a core and an interface of finite thickness of approximately 0.6nm. The core contains only helium atoms that are uniformly distributed. The interface is composed of both helium and tungsten atoms. In the periphery region of the helium bubble, the stress filed is found to follow the stress formula based on the elasticity theory of solid. The pressure difference between both sides of the interface can be well described by the Young–Laplace equation for the core size of a helium bubble as small as 0.48nm. A comparison was performed between the pressure in the helium bubble core and the pressure in pure helium. For a core size larger than 0.3nm, the pressure in the core of a helium bubble is in good agreement with the pressure in pure helium of the same helium density. These results provide guidance to larger scale simulation methods, such as in kinetic Monte Carlo methods and rate theory.

Modified Bubble Core Fields and Bubble Shape in Laser Driven Plasma

Bubble core fields as well bubble shape modification due to the nondepleted electrons inside the bubble is investigated theoretically. It is found that the slope of transverse fields are reduced significantly, however, the slope of longitudinal electric field, which plays a key role on electrons acceleration in bubble, changes little. Moreover a modified longitudinal compressed bubble shape leads to a shorter dephasing distance which makes the electrons acceleration energy reduced to some extent. As a comparison we perform particle-in-cell simulations whose results are consistent with that of our theoretical consideration.

Plasma core at the center of a sonoluminescing bubble

Considering high temperature and pressure during single bubble sonoluminescence collapse, a hot plasma core is generated at the center of the bubble. In this paper a statistical mechanics approach is used to calculate the core pressure and temperature. A hydrochemical model alongside a plasma core is used to study the bubble dynamics in two host liquids of water and sulfuric acid 85 wt % containing Ar atoms. Calculation shows that the extreme pressure and temperature in the plasma core are mainly due to the interaction of the ionized Ar atoms and electrons, which is one step forward to sonofusion. The thermal bremsstrahlung mechanism of radiation is used to analyze the emitted optical energy per flash of the bubble core.