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Soon after its introduction in 1987, polymerase chain reaction (PCR) has become a technique widely employed in diagnostic medical devices and forensic science with the intention of amplifying genetic information. PCR prescribes that each of its cycles must include a heating subprocess at 95 °C or more (denominated DNA denaturation and provided for allowing a claimed orderly separation of the two complementary nucleotides strands), which can produce significant damage to DNA, caused by high-speed collisions with surrounding molecules. Since such disruption should be prevented in order to reliably employ PCR, a study of the mechanics of such loss of structural integrity is herein presented, preceded by a review of the fundamental literature which has elucidated the effects of molecular agitation on DNA fragmentation. The main conclusion of this retrospective survey is that the body of examined theoretical and experimental evidence consistently and redundantly confirms scarce resilience and significant loss of structural integrity when DNA is heated at temperatures above 90 °C, even for 1 minute. Such conclusion contradicts the claimed paradigm of PCR fidelity and raises the concern that, at least for long sequences, if PCR can amplify some information, such amplified information may be unreliable for diagnostic or forensic applications, since it originates from sequences of nucleotides subjected to random fragmentation and reaggregation. Such a low-reliability scenario should be preventively considered in the various fields where DNA amplification methodologies are employed which provide for high-temperature heating under conditions equal to or similar to those prescribed by the PCR protocols reviewed in this study.
This study explores the dynamics of flexible ribbons with an added weight $G$ at the tail in uniform flow, considering key parameters like inflow Reynolds number ($Re_u$), mass ratio ($M_t$) and aspect ratio (${A{\kern-4pt}R}$). For two-dimensional ribbons, a simplified theoretical model accurately predicts equilibrium configurations and forces. Inspired by Barois & De Langre (J. Fluid Mech., vol. 735, 2013, R2), we introduce an important control parameter ($C_G$) that effectively collapses normalized forces and angle data. Vortex-induced vibration is observed, and Strouhal number ($St$) scaling laws with $C_G$ are identified. In three-dimensional scenarios, the model effectively predicts lift, but its accuracy in predicting drag is limited to situations with small $Re_u$ values. The flow along the side edges mitigates pressure differences, thereby suppressing vibration and uplift, particularly noticeable in the case of narrow ribbons. This study offers new insights into the dynamics of flexible bodies in uniform flow.
Previous studies have shown that low-frequency vortex oscillations occur around a hemisphere–cylinder body at different angles of attack, but the underlying mechanism is still unclear. In this study, we examine the origin of the vortex oscillation using numerical simulations and global linear stability analysis. The vortex oscillation is reproduced using numerical simulations, and the oscillatory modes are computed through dynamic mode decomposition (DMD). We obtain the base flow through a selective frequency damping method, which exhibits a pair of steady leeward vortices over the body. The four unstable modes are computed using a modified Arnoldi iteration. The antisymmetric mode with a Strouhal number of 0.105 is discovered to be responsible for the alternate oscillation of the vortex pair, and the mode with a Strouhal number of 0.220 corresponds to the in-phase vortex oscillation. Their frequencies have good agreement with the modes of DMD. The other two unstable modes with higher frequencies, one antisymmetric and one symmetric, are harmonic frequencies of the above two modes. The study conclusively verifies that the vortex oscillation over a hemisphere–cylinder body originates from a global flow instability.
Understanding settling motion of coral grains is important in terms of protection of coral reef systems and resotoration of the associated ecosystems. In this paper, a series of laboratory experiments was conducted to investigate the settling motion, using optical microscopy to measure shape parameters of coral grains and the particle-filtering-based object tracking to reconstruct the three-dimensional trajectory. Three characteristic descent regimes, namely, tumbling, chaotic and fluttering, are classified based on the three-dimensional trajectory, the spiral radius variation and the velocity spectrum. It is demonstrated that if one randomly picks up one coral grain, then the probabilities of occurrence of the three regimes are approximately $26\,\%$, $42\,\%$ and $32\,\%$, respectively. We have shown that first, the dimensionless settling velocity generally increases with the non-dimensional diameter and Corey shape factor and second, the drag coefficient generally decreases with the Reynolds number and Corey shape factor. Based on this, the applicability of existing models on predicting settling velocity and drag coefficient for coral grains is demonstrated further. Finally, we have proposed extended models for predicting the settling velocity. This study contributes to better understanding of settling motion and improves our predictive capacity of settling velocity for coral grains with complex geometry.
Saturated flow film boiling on a sphere has been numerically studied in this work for both vertical and horizontal flow configurations. The simulations were performed using a numerical methodology developed by the authors for boiling flows on three-dimensional unstructured meshes. For interface capturing, the coupled level set and volume of fluid method is used. The interface evolution, vapour wake dynamics and heat transfer have been thoroughly investigated by varying the saturated liquid flow velocity, sphere diameter and wall superheat. The relative importance of both the buoyancy and the inertial forces is described in terms of the Froude number $(Fr)$. The vapour bubble evolves periodically at low $Fr$ values, while a stable vapour column develops at high $Fr$ values. The interface evolution pattern obtained in the present work is in good agreement with the results of experimental studies available in the literature. For all the values of $Fr$, a stable vapour column develops for a large-diameter sphere and releases vapour bubbles of varying sizes. Furthermore, for a large-diameter sphere, surface capillary waves are observed at the interface, similar to the observations of some of the experimental studies available in the literature. The flow in the liquid and vapour wakes appears to be strongly coupled. The heat transfer in the present work is estimated using the spatially and temporally averaged Nusselt numbers. Finally, an fast Fourier transform analysis of the space-averaged Nusselt number reveals a strong interaction among the different forces.
We investigate the phenomena of crater formation and gas release caused by projectile impact on underwater beds, which occurs in many natural, geophysical and industrial applications. The bed in our experiment is constructed of hydrophobic particles, which trap a substantial amount of air in the pores of the bed. In contrast to dry beds, the air–water interface in a submerged bed generates a granular skin that provides rigidity to the medium by producing skin over the bulk. The projectile's energy is used to reorganize the grains, which causes the skin to crack, allowing the trapped air to escape. The morphology of the craters as a function of impact energy in submerged beds exhibits different scaling laws than what is known for dry beds. This phenomenon is attributed to the contact line motion on the hydrophobic fractal-like surface of submerged grains. The volume of the gas released is a function of multiple factors, chiefly the velocity of the projectile, depth of the bed and depth of the water column.
Small finite-size particles suspended in fluid flow through an enclosed curved duct can focus to points or periodic orbits in the two-dimensional duct cross-section. This particle focusing is due to a balance between inertial lift forces arising from axial flow and drag forces arising from cross-sectional vortices. The inertial particle focusing phenomenon has been exploited in various industrial and medical applications to passively separate particles by size using purely hydrodynamic effects. A fixed size particle in a circular duct with a uniform rectangular cross-section can have a variety of particle attractors, such as stable nodes/spirals or limit cycles, depending on the radius of curvature of the duct. Bifurcations occur at different radii of curvature, such as pitchfork, saddle-node and saddle-node infinite period (SNIPER), which result in variations in the location, number and nature of these particle attractors. By using a quasi-steady approximation, we extend the theoretical model of Harding et al. (J. Fluid Mech., vol. 875, 2019, pp. 1–43) developed for the particle dynamics in circular ducts to spiral duct geometries with slowly varying curvature, and numerically explore the particle dynamics within. Bifurcations of particle attractors with respect to radius of curvature can be traversed within spiral ducts and give rise to a rich nonlinear particle dynamics and various types of tipping phenomena, such as bifurcation-induced tipping (B-tipping), rate-induced tipping (R-tipping) and a combination of both, which we explore in detail. We discuss implications of these unsteady dynamical behaviours for particle separation and propose novel mechanisms to separate particles by size in a non-equilibrium manner.
Depinning of liquid droplets on substrates by flow of a surrounding immiscible fluid is central to applications such as cross-flow microemulsification, oil recovery and waste cleanup. Surface roughness, either natural or engineered, can cause droplet pinning, so it is of both fundamental and practical interest to determine the flow strength of the surrounding fluid required for droplet depinning on rough substrates. Here, we develop a lubrication-theory-based model for droplet depinning on a substrate with topographical defects by flow of a surrounding immiscible fluid. The droplet and surrounding fluid are in a rectangular channel, a pressure gradient is imposed to drive flow and the defects are modelled as Gaussian-shaped bumps. Using a precursor-film/disjoining-pressure approach to capture contact-line motion, a nonlinear evolution equation is derived describing the droplet thickness as a function of distance along the channel and time. Numerical solutions of the evolution equation are used to investigate how the critical pressure gradient for droplet depinning depends on the viscosity ratio, surface wettability and droplet volume. Simple analytical models are able to account for many of the features observed in the numerical simulations. The influence of defect height is also investigated, and it is found that, when the maximum defect slope is larger than the receding contact angle of the droplet, smaller residual droplets are left behind at the defect after the original droplet depins and slides away. The model presented here yields considerably more information than commonly used models based on simple force balances, and provides a framework that can readily be extended to study more complicated situations involving chemical heterogeneity and three-dimensional effects.
Wall temperature has a significant effect on shock wave/turbulent boundary layer interactions (STBLIs) and has become a non-negligible factor in the design process of hypersonic vehicles. In this paper, direct numerical simulations are conducted to investigate the wall temperature effects on STBLIs over a 34° compression ramp at Mach number 6. Three values of the wall-to-recovery-temperature ratio (0.50, 0.75 and 1.0) are considered in the simulations. The results show that the size of the separation bubble declines significantly as the wall temperature decreases. This is because the momentum profile of the boundary layer becomes fuller with wall cooling, which means the near-wall fluid has a greater momentum to suppress flow separation. An equation based on the free-interaction theory is proposed to predict the distributions of the wall pressure upstream of the corner at different wall temperatures. The prediction results are generally consistent with the simulation results (Reynolds number Reτ ranges from 160 to 675). In addition, the low-frequency unsteadiness is studied through the weighted power spectral density of the wall pressure and the correlation between the upstream and downstream. The results indicate that the low-frequency motion of the separation shock is mainly driven by the downstream mechanism and that wall cooling can significantly suppress the low-frequency unsteadiness, including the strength and streamwise range of the low-frequency motions.
This study proposes a novel super-resolution (or SR) framework for generating high-resolution turbulent boundary layer (TBL) flow from low-resolution inputs. The framework combines a super-resolution generative adversarial neural network (SRGAN) with down-sampling modules (DMs), integrating the residual of the continuity equation into the loss function. The DMs selectively filter out components with excessive energy dissipation in low-resolution fields prior to the super-resolution process. The framework iteratively applies the SRGAN and DM procedure to fully capture the energy cascade of multi-scale flow structures, collectively termed the SRGAN-based energy cascade reconstruction framework (EC-SRGAN). Despite being trained solely on turbulent channel flow data (via ‘zero-shot transfer’), EC-SRGAN exhibits remarkable generalization in predicting TBL small-scale velocity fields, accurately reproducing wavenumber spectra compared to direct numerical simulation (DNS) results. Furthermore, a super-resolution core is trained at a specific super-resolution ratio. By leveraging this pretrained super-resolution core, EC-SRGAN efficiently reconstructs TBL fields at multiple super-resolution ratios from various levels of low-resolution inputs, showcasing strong flexibility. By learning turbulent scale invariance, EC-SRGAN demonstrates robustness across different TBL datasets. These results underscore the potential of EC-SRGAN for generating and predicting wall turbulence with high flexibility, offering promising applications in addressing diverse TBL-related challenges.
Resonant standing waves excited on the water surface in a deep narrow rectangular cavity by a fully immersed cylinder harmonically oscillating in the vertical direction are studied theoretically and experimentally. The effect of the finite wavemaker size is considered in the framework of the potential two-dimensional flow theory. Nonlinearities and weak dissipation at solid surfaces are accounted for. The spatio-temporal structure of the waves in the presence of detuning between the forcing and the natural frequency of the system is analysed. The variation of the surface shape in space and time studied in experiments supports the assumption of two-dimensional flow. The finite size of the wavemaker causes a downshift of the effective resonant frequency of the cavity; this effect is enhanced by the nonlinearity. For small amplitude waves, the surface elevation evolution in time is decomposed into the sum of the time-periodic function, corresponding to the forcing frequency, and its second harmonic; the shape of the wavenumber spectra of these components depends on the forcing frequency. For larger wave amplitudes, additional peaks in the frequency spectrum appear. The theoretical predictions are compared with the experimental results.
We investigated the stability of the bottom boundary layer (BBL) beneath periodic internal solitary waves (ISWs) of depression over a flat bottom through two-dimensional direct numerical simulations. We explored the convective versus absolute/global nature of the BBL instability in response to changes in Reynolds number, and the sensitivity of the instability to seeding noise in the front of the ISW – spanning laboratory to geophysical scales. The BBL was laminar at $Re_{ISW}=90$ and convectively unstable at $Re_{ISW}=300$. At laboratory-scale $Re_{ISW}=300$, the convective wave packet was periodically amplified by each successive ISW, until vortex shedding occurred. The associated noise-amplification behaviour potentially explains the discrepancies of the critical $Re_{ISW}$ between the lock–release laboratory experiments and our Dubreil–Jacotin–Long-initialized numerical simulations as the result of the difference in background noise. Instability energy decreased under the front shoulder of the ISW, analogous to flow relaminarization under a favourable pressure gradient. At geophysical-scale $Re_{ISW}=900$, the BBL was initially convectively unstable, and then the instability tracked with the ISW, appearing phenomenologically similar to a global instability. The simulated initial convective instability at both $Re_{ISW}=300$ and $Re_{ISW}=900$ is in agreement with local linear stability analysis which predicts that the instability group speed is always lower than the ISW celerity. Increased free stream perturbations in front of the ISW and larger $Re_{ISW}$ shift the location of vortex shedding (and enhanced bed shear stress) beneath the wave, closer to the ISW trough, thereby potentially changing the location of maximum sediment resuspension, in agreement with field observations at higher $Re_{ISW}$.
The efficacy of steady large-amplitude blowing/suction on instability and transition control for a hypersonic flat plate boundary layer with Mach number 5.86 is investigated systematically. The influence of the blowing/suction flux and amplitude on instability is examined through direct numerical simulation and resolvent analysis. When a relatively small flux is used, the two-dimensional instability critical frequency that distinguishes the promotion/suppression mode effect closely aligns with the synchronisation frequency. For the oblique wave, as the spanwise wavenumber increases, the suppression effects would become weaker and the mode suppression bandwidth diminishes/increases in general in the blowing/suction control. Increasing the blowing/suction flux can effectively broaden the frequency bandwidth of disturbance suppression. The influence of amplitude on disturbance suppression is weak in a scenario of constant flux. To gain a deeper insight into disturbance suppression mechanism, momentum potential theory (MPT) and kinetic energy budget analysis are further employed in analysing disturbance evolution with and without control. When the disturbance is suppressed, the blowing induces the transport of certain acoustic components along the compression wave out of the boundary layer, whereas the suction does not. The velocity fluctuations are derived from the momentum fluctuations of the MPT. Compared with the momentum fluctuations, the evolutions indicated by each component's velocity fluctuations greatly facilitate the investigations of the acoustic nature of the second mode. The rapid variation of disturbance amplitude near the blowing is caused by the oscillations of the acoustic component and phase speed differences between vortical and thermal components. Kinetic energy budget analysis is performed to address the non-parallel effect of the boundary layer introduced by blowing/suction, which tends to suppress disturbances near the blowing. Moreover, viscous effects leading to energy dissipation are identified to be stronger in regions where the boundary layer is rapidly thickening. Finally, it is demonstrated that a flat plate boundary layer transition triggered by a random disturbance can be delayed by a blowing/suction combination control. The resolvent analysis further demonstrates that disturbances with frequencies that dominate the early transition stage are dampened in the controlled base flow.
We consider the long-time propagation of a Boussinesq inertia–buoyancy (large-Reynolds- number) gravity current released from a lock over a downslope of angle $\gamma$, affected by entrainment and drag. We show that the shallow-water (depth-averaged) equations with a Benjamin-type front-jump condition admit a similarity solution $x_N(t) = K t^{2/3}$ while $h, \phi, u$ change like $t$ to the power of $2/3, -4/3, -1/3$, respectively; here $x_N, h, \phi, u$ and $t$ are the position of the nose (distance from backwall), thickness, concentration of dense fluid, velocity and time, respectively, and K is a constant. Assuming that $\gamma$ and the coefficients of entrainment and drag are constant, we derive an analytical exact solution for the similarity profiles and show that $K \propto (\tan \gamma )^{1/3}$; the driving of the slope is balanced by entrainment and/or drag. The predicted $t^{2/3}$ propagation is in agreement with previously published experimental data but a conclusive quantitative assessment of the present theory cannot be performed due to various uncertainties (discussed in the paper) that must be resolved by future work.
In the present study, we perform direct numerical simulations of compressible turbulent boundary layers at free stream Mach numbers $2\unicode{x2013}6$ laden with dilute phase of spherical particles to investigate the Mach number effects on particle transport and dynamics. Most of the phenomena observed and well-recognized for inertia particles in incompressible wall-bounded turbulent flows – such as near-wall preferential accumulation and clustering beneath low-speed streaks, flatter mean velocity profiles, and trend variation of the particle velocity fluctuations – are identified in the compressible turbulent boundary layer as well. However, we find that the compressibility effects are significant for large inertia particles. As the Mach number increases, the near-wall accumulation and the small-scale clustering are alleviated, which is probably caused by the variations of the fluid density and viscosity that are crucial to particle dynamics. This can be affected by the fact that the forces acting on the particles with viscous Stokes number greater than 500 are modulated by the comparatively high particle Mach numbers in the near-wall region. This is also the reason for the abatement of the streamwise particle velocity fluctuation intensities with the Mach numbers.
Cryogenic carbon capture (CCC) is an innovative technology to desublimate $\text {CO}_2$ out of industrial flue gases. A comprehensive understanding of $\text {CO}_2$ desublimation and sublimation is essential for widespread application of CCC, which is highly challenging due to the complex physics behind. In this work, a lattice Boltzmann (LB) model is proposed to study $\text {CO}_2$ desublimation and sublimation for different operating conditions, including the bed temperature (subcooling degree $\Delta T_s$), gas feed rate (Péclet number $Pe $) and bed porosity ($\psi$). The $\text {CO}_2$ desublimation and sublimation properties are reproduced. Interactions between convective $\text {CO}_2$ supply and desublimation/sublimation intensity are analysed. In the single-grain case, $Pe $ is suggested to exceed a critical value $Pe _c$ at each $\Delta T_s$ to avoid the convection-limited regime. Beyond $Pe _c$, the $\text {CO}_2$ capture rate ($v_c$) grows monotonically with $\Delta T_s$, indicating a desublimation-limited regime. In the packed bed case, multiple grains render the convective $\text {CO}_2$ supply insufficient and make CCC operate under the convection-limited mechanism. Besides, in small-$\Delta T_s$ and high-$Pe $ tests, $\text {CO}_2$ desublimation becomes insufficient compared with convective $\text {CO}_2$ supply, thus introducing the desublimation-limited regime with severe $\text {CO}_2$ capture capacity loss ($\eta _d$). Moreover, large $\psi$ enhances gas mobility while decreasing cold grain volume. A moderate porosity $\psi _c$ is recommended for improving the $\text {CO}_2$ capture performance. By analysing $v_c$ and $\eta _d$, regime diagrams are proposed in $\Delta T_s$–$Pe $ space to show distributions of convection-limited and desublimation-limited regimes, thus suggesting optimal conditions for efficient $\text {CO}_2$ capture. This work develops a viable LB model to examine CCC under extensive operating conditions, contributing to facilitating its application.
The classical Helmholtz–Smoluchowski (HS) model of electroosmosis holds for homogeneously charged interfaces in contact with a fluid layer bearing an equal and opposite net charge. However, inhomogeneities in the surface charge and topography are inevitable, either as practical materials and fabrication artefacts, or at times as deliberately introduced modulations for flow control. In an effort to arrive at an analytically tractable theoretical framework for addressing the underlying electro-mechanical coupling, here, we generalize the traditional HS theory to an extent where both the surface charge and topographies may bear arbitrary and independent periodic forms. Using a spectral-asymptotic approach, we further arrive at closed-form expressions for describing the resulting electroosmotic pumping for topographic features with small characteristic amplitude to pattern period ratio, as relevant for most practical scenarios. We subsequently execute full-scale numerical simulations without any restrictions on the surface charge and topography variations to assess the efficacy of the theoretical framework. The corresponding test beds include distinctive signature patterns – for example, a square-wave surface charge distribution on trapezoidal pit topographies. Our results reveal that the charge–topography interplay induces an anisotropic flow drift, deviating from the classical HS paradigm. This, in turn, provides new quantitative insights into highly selective electroosmotic flow control via judicious design of the charge and topographical patterns, resulting in controllable accentuation, attenuation, nullification, deflection and even complete reversal of the flow. Our analysis further establishes a provision of estimating the zeta potentials of naturally ‘contaminated’ surfaces, as well as explaining the electrophoresis of large inhomogeneous particles; a paradigm that remained to be explored thus far.
The prototypical diffuse-interface model for incompressible fluid mixtures is the Navier–Stokes Cahn–Hilliard (Allen–Cahn) model. Despite its foundation in continuum mixture theory, it is not fully compatible with this theory due to the diffusive flux approximation. This paper introduces a class of thermodynamically consistent diffuse-interface incompressible fluid mixture models that is fully compatible with the continuum theory of mixtures. The proposed models can be formulated in either constituent or mixture quantities, enabling a direct comparison with the Navier–Stokes Cahn–Hilliard (Allen–Cahn) model with non-matching densities. This comparison reveals the key modelling simplifications employed in the latter.
As a promising machine learning method for active flow control (AFC), deep reinforcement learning (DRL) has been successfully applied in various scenarios, such as the drag reduction for stationary cylinders under both laminar and weakly turbulent conditions. However, current applications of DRL in AFC still suffer from drawbacks including excessive sensor usage, unclear search paths and insufficient robustness tests. In this study, we aim to tackle these issues by applying DRL-guided self-rotation to suppress the vortex-induced vibration (VIV) of a circular cylinder under the lock-in condition. With a state space consisting only of the acceleration, velocity and displacement of the cylinder, the DRL agent learns an effective control strategy that successfully suppresses the VIV amplitude by $99.6\,\%$. Through systematic comparisons between different combinations of sensory-motor cues as well as sensitivity analysis, we identify three distinct stages of the search path related to the flow physics, in which the DRL agent adjusts the amplitude, frequency and phase lag of the actions. Under the deterministic control, only a little forcing is required to maintain the control performance, and the VIV frequency is only slightly affected, showing that the present control strategy is distinct from those utilizing the lock-on effect. Through dynamic mode decomposition analysis, we observe that the growth rates of the dominant modes in the controlled case all become negative, indicating that DRL remarkably enhances the system stability. Furthermore, tests involving various Reynolds numbers and upstream perturbations confirm that the learned control strategy is robust. Finally, the present study shows that DRL is capable of controlling VIV with a very small number of sensors, making it effective, efficient, interpretable and robust. We anticipate that DRL could provide a general framework for AFC and a deeper understanding of the underlying physics.
This study investigates the potential use of an active device to efficiently absorb water waves propagating in a channel. The active device comprises a dipole source consisting of two sources in quasi-opposition of phase. We explore the feasibility of this approach to achieve perfect absorption of guided waves through interference phenomena. To accomplish this, we establish the law governing the waves emitted by the dipole source to optimize the absorption of specific incident waves. The validity of this law is demonstrated through numerical simulations and laboratory experiments, encompassing both the harmonic and transient regimes of the experimental set-up.