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Helices are one of the most frequently encountered symmetries in biological assemblies. Helical symmetry has been exploited in electron microscopic studies as a limited number of filament images, in principle, can provide all the information needed to do a three-dimensional reconstruction of a polymer. Over the past 25 years, three-dimensional reconstructions of helical polymers from cryo-EM images have shifted completely from Fourier–Bessel methods to single-particle approaches. The single-particle approaches have allowed people to surmount the problem that very few biological polymers are crystalline in order, and despite the flexibility and heterogeneity present in most of these polymers, reaching a resolution where accurate atomic models can be built has now become the standard. While determining the correct helical symmetry may be very simple for something like F-actin, for many other polymers, particularly those formed from small peptides, it can be much more challenging. This review discusses why symmetry determination can be problematic, and why trial-and-error methods are still the best approach. Studies of many macromolecular assemblies, such as icosahedral capsids, have usually found that not imposing symmetry leads to a great reduction in resolution while at the same time revealing possibly interesting asymmetric features. We show that for certain helical assemblies asymmetric reconstructions can sometimes lead to greatly improved resolution. Further, in the case of supercoiled flagellar filaments from bacteria and archaea, we show that the imposition of helical symmetry can not only be wrong, but is not necessary, and obscures the mechanisms whereby these filaments supercoil.
When a less-viscous solution of a reactant $A$ displaces a more-viscous solution of another reactant $B$, a fast bimolecular $A + B \rightarrow C$ reaction decreasing locally the viscosity can influence the viscous fingering (VF) instability taking place between the two miscible solutions. We show both experimentally and numerically that, for monotonic viscosity profiles, this decrease in viscosity has opposite effects on the fingering pattern depending on the injection flow rate. For high flow rates, the reaction enhances the shielding effect, creating VF patterns with a lower surface density, i.e. thinner fingers covering a smaller area. In contrast, for lower flow rates, the reaction stabilises the VF dynamics, i.e. delays the instability and gives a less-deformed displacement, reaching in some cases an almost-stable displacement. Nonlinear simulations of reactive VF show that these opposite effects at low or high flow rates can only be reproduced if the diffusivity of $A$ is larger than that of $B$, which favours a larger production of the product $C$ and, hence, a larger viscosity decrease. The analysis of one-dimensional viscosity profiles reconstructed on the basis of a one-dimensional reaction–diffusion–advection model confirms that the VF stabilisation at low Péclet number and in the presence of differential diffusion of reactants originates from an optimum reaction-driven decrease in the gradient of the monotonic viscosity profile.
In this study we consider a freely decaying, stably stratified homogeneous magnetohydrodynamic turbulent plasma with a weak vertical background magnetic field ($\boldsymbol {B}_0=B_0\hat {\boldsymbol {z}}),$ aligned with the density gradient of strength $N$ (i.e. Brunt–Väisälä frequency). Both linear theory and direct numerical simulations (DNS) are used to analyse the flow dynamics for a Boussinesq fluid with unitary magnetic and thermal Prandtl numbers. We implemented a normal mode decomposition emphasizing different types of motions depending on whether both the Froude $F_r$ and Alfvén–Mach $M$ numbers are small or only $F_r$ is small but $M$ is finite. In the former case, there is a non-propagating (NP) mode and fast modes: Alfvén waves with frequency $\omega _a$ and magnetogravity waves with frequency $\omega _{ag}$. In the latter case, there are fast gravity waves with frequency $\omega _g$ and slow modes: NP mode and slow Alfvén waves. The numerical simulations carried out are started from initial isotropic conditions with zero initial magnetic and density fluctuations, so that the initial energy of the NP mode is strictly zero, for $0< B_0/(L_iN)\leqslant 0.12$ and a weak mean magnetic field ($B_0=0.2$ or $B_0=0.4),$ where $L_i$ denotes the isotropic integral length scale. The DNS results indicate a weak turbulence regime for which $F_r$ is small and $M$ is finite. It is found that the vertical magnetic energy as well as the energy of the NP mode are drastically reduced as $N$ increases, while there is instead a forward cascade even for the magnetic field. The contribution coming from the energy of fast (gravity) waves does not exceed $50\,\%,$ while that coming from the energy of the NP mode does not exceed $10\,\%.$ Vertical motions are more affected by the effect of stratification than by the effect of the mean magnetic field, while it is the opposite for horizontal motions. We show that the spectrum of slow (Alfvén) waves and fast (gravity) waves tends to follow the power law $k_\perp ^{-3}$ for a wide range of time, $3< t<20$. At high vertical (or horizontal) wavenumbers, the main contribution to total energy comes from the energy of slow Alfvén waves. At large and intermediate horizontal (or vertical) scales, the spectra of the energy of NP mode exhibit a flat shape.
We present spectroscopic properties of 22 Ly$\alpha$ emitters (LAEs) at $z = 5.5 - 6.6$ with Ly$\alpha$ luminosity $\mathrm{log}( L_{\mathrm{Ly}\alpha} \, [\mathrm{erg} \, \mathrm{s}^{-1}]) = 42.4 - 43.5 $, obtained using VLT/MUSE as part of the Middle Ages Galaxy Properties with Integral Field Spectroscopy (MAGPI) survey. Additionally, we incorporate broad-band photometric data from the Subaru Hyper Suprime-Cam (HSC) Wide layer for 17 LAEs in our sample. The HSC-y band magnitudes show that our LAEs are UV-bright, with rest-frame absolute UV magnitudes $ -19.74 \leq \mathrm{M}_{\mathrm{UV}} \leq -23.27$. We find that the Ly$\alpha$ line width increases with Ly$\alpha$ luminosity, and this trend becomes more prominent at $z \gt 6$ where Ly$\alpha$ lines become significantly broadened ($\gtrsim+260 \, \mathrm{km}\, \mathrm{s}^{-1}$) at luminosities $\mathrm{log}( L_{\mathrm{Ly}\alpha} \, [\mathrm{erg} \, \mathrm{s}^{-1}]) \gt 43 $. This broadening is consistent with previous studies, suggesting that these sources are located inside larger ionised bubbles. We observe a slightly elevated ionising photon production efficiency estimated for LAEs at $z \gt 6$, which indicates that younger galaxies could be producing more ionising photons per UV luminosity. A tentative anti-correlation between ionising photon production efficiency and Ly$\alpha$ rest-frame equivalent width is noticed, which could indicate a time delay between production and escape of ionising photon primarily due to supernovae activity. Furthermore, we find a positive correlation between radius of ionised regions and Ly$\alpha$ line width, which again suggests that large ionised bubbles are created around these LAEs, which are allowing them to self-shield from the scattering effects of the intergalactic medium (IGM). We also detect two very closely separated LAEs at $z = 6.046$ (projected spatial distance between the cores is 15.92 kpc). This is the LAE pair with the smallest separation ever discovered in the reionisation epoch. The size of their respective bubbles suggests that they likely sit inside a common large ionised region. Such a closely separated LAE pair increases the size of ionised bubble, potentially allowing a boosted transmission of Ly$\alpha$ through neutral IGM and also supports an accelerated reionisation scenario.
The motion of small non-spherical particles is often studied using the unsteady Stokes equations. Zhang & Stone (J. Fluid Mech., vol. 367, 1998, pp. 329–358) reported an asymptotic treatment for nearly spherical particles, to first order in particle non-sphericity, i.e. $O(\epsilon )$, where $\epsilon$ quantifies the shape deviation from a sphere. Importantly, key physical phenomena are absent at $O(\epsilon )$, including (1) coupling between the torque experienced by the particle and its linear translation, (2) coupling between the force the particle experiences and its rotation and (3) the effect of non-sphericity on the orientation averages of these forces and torques. We present an explicit asymptotic theory to second order in particle non-sphericity, i.e. $O(\epsilon ^2)$, for the force and torque acting on a particle in a general unsteady Stokes flow. The derived analytical formulae apply to particles of arbitrary shape, providing the leading-order asymptotic theory for the three above-mentioned phenomena. The theory is demonstrated for several example nearly spherical particles including a spheroid, a ‘pear-shaped’ particle and a simple model for a SARS-CoV-2 virion. This includes formulae for force and torque as a function of particle orientation and their corresponding orientation averages. Our study reveals that the orientation-averaged forces and torques experienced by a nearly spherical particle cannot be generally represented by a perfect sphere. The reported formulae are validated using finite-amplitude three-dimensional direct numerical simulations of the Navier–Stokes equations. A Mathematica notebook is also provided, facilitating implementation of the theory for particle shapes of the user's choosing.
We investigate the effect of three-dimensionality on the synchronisation characteristics of the wake behind an oscillating circular cylinder at ${\textit {Re}} = 300$. Cylinder oscillations in rotation, transverse translation and streamwise translation are considered. We utilise phase-reduction analysis, which quantifies the phase-sensitivity function of periodic flows, to examine the synchronisation properties. Here, we present an ensemble-based framework for phase-reduction analysis to handle three-dimensional wakes that are not perfectly time-periodic. Based on the phase-sensitivity functions, synchronisability to three types of cylinder oscillations is evaluated. In spite of similar trends, we find that phase-sensitivity functions involving three-dimensional wakes are lower in magnitude compared with those of two-dimensional wakes, which leads to narrower conditions for synchronisation to weak cylinder oscillations. We unveil that the difference between the phase-sensitivity functions of two- and three-dimensional flows is strongly correlated to the amplitude variation of the three-dimensional flow by the cylinder motions. This finding reveals that the cylinder motion modifies the three-dimensionality of the wake as well as the phase of vortex shedding, which leads to reduced phase modulation. The synchronisation conditions of three-dimensional wakes, predicted by phase-reduction analysis, agree with the identification by parametric studies using direct numerical simulations for forced oscillations with small amplitudes. This study presents the potential capability of phase-reduction to study synchronisation characteristics of complex flows.
To aid in prediction of turbulent boundary layer flows over rough surfaces, a new model is proposed to estimate hydrodynamic roughness based solely on geometric surface information. The model is based on a fluid-mechanics motivated geometric parameter called the wind-shade factor. Sheltering is included using a rapid algorithm adapted from the landscape shadow literature, while local pressure drag is estimated using a piecewise potential flow approximation. Similarly to evaluating traditional surface parameters such as skewness or average slope magnitude, the wind-shade factor is purely geometric and can be evaluated efficiently from knowing the surface elevation map and the mean flow direction. The wind-shade roughness model is applied to over 100 different surfaces available in a public roughness database and some others, and the predicted sandgrain-roughness heights are compared with measured values. Effects of various model ingredients are analysed, and transitionally rough surfaces are treated by adding a term representing the viscous stress component.
We establish a theoretical framework for predicting friction and heat transfer coefficients in variable-property forced air convection. Drawing from concepts in high-speed wall turbulence, which also involves significant temperature, viscosity and density variations, we utilize the mean momentum balance and mean thermal balance equations to develop integral transformations that account for the impact of variable fluid properties. These transformations are then applied inversely to predict the friction and heat transfer coefficients, leveraging the universality of passive scalars transport theory. Our proposed approach is validated using a comprehensive dataset from direct numerical simulations (DNS), covering both heating and cooling conditions up to a friction Reynolds number $\textit {Re}_\tau \approx 3200$. The predicted friction and heat transfer coefficients closely match the DNS data with accuracy margin 1–2 %, representing a significant improvement over the current state of the art.
Understanding the linear growth of disturbances due to external forcing is crucial for flow stability analysis, flow control, and uncertainty quantification. These applications typically require a large number of forward simulations of the forced linearized dynamics, often in a brute-force fashion. When dealing with simple steady-state or periodic base flows, there exist powerful and cost-effective solution operator techniques. Once these solution operators are constructed, they can be used to determine the response to various forcings with negligible computational cost. However, these methods do not apply to problems with arbitrarily time-dependent base flows. This paper develops and investigates reduced-order modelling with time-dependent bases to build low-rank solution operators for forced linearized dynamics with arbitrarily time-dependent base flows. In particular, we use forced optimally time-dependent decomposition (f-OTD), which extracts the time-dependent correlated structures of the flow response to various excitations. Several demonstrations are included to illustrate the utility of the f-OTD low-rank approximation for performing global transient stability analysis. Additionally, we demonstrate the application of f-OTD in computing the post-transient response of linearized Navier–Stokes equations to a large number of impulses, which has applications in flow control.
We study single bubble deformation statistics in an homogeneous and isotropic turbulent flow by means of direct numerical simulations. We consider bubbles at low Weber number ($We <3$) that have not been broken. We show that we can reproduce bubble deformations with a linear dynamics for each spherical harmonic mode. Inferring the coefficients of the linear model from the DNS data, we find that the natural frequency corresponds to the Rayleigh frequency, derived in a quiescent flow. However, the effective damping increases by a factor 7 compared with the quiescent case, at Taylor Reynolds number $\textit {Re}_\lambda = 55$. Looking at the flow structure around the bubble, we argue that the enhanced damping originates from a thick boundary layer surrounding the bubble. We demonstrate that the effective forcing, originating from the turbulent flow forcing on the bubble surface, is independent of bubble deformability. Therefore, the interface deformations are only one-way coupled to the flow. From this model we conclude that bubbles break rather from turbulent fluctuations than from a resonant mechanism. Eventually, we investigate the pressure modes’ statistics in the absence of bubbles and compare them with the effective forcing statistics. We show that both fields share the same probability distribution function, characterized by exponential tails, and a characteristic time scale corresponding to the eddy turnover time at the mode scale.
Floating fluid-filled membrane breakwater (FFMB) is a temporary structure that can attenuate waves in the deep sea. In this paper the hydrodynamic performance of the FFMB is analysed by using the eigenfunction expansion boundary element method (EEBEM) and physical model experiments. A general motion equation is derived that considers both the dynamic tension and curvature of the membrane. Moreover, an integral expression for the dynamic tension is provided. On this basis, a linear model for solving wave–membrane interaction is established through the EEBEM. Newly designed physical experiments are performed to verify the model and elucidate the nonlinear characteristics of the FFMB. Following verification of the model, this paper investigates the effects of various structural parameters of the FFMB on the wave transmission coefficient, reflection coefficient, horizontal wave force, vertical wave force and dynamic tension. Furthermore, the interrelationship between the structural resonant response and the hydrodynamic performance is elucidated, and the optimal density and filling ratio of the FFMB for engineering applications are proposed. The results demonstrate that the numerical and experimental results are in good agreement, indicating that the model and the motion equation are both practical and highly accurate. By optimizing the structural parameters, the FFMB is capable of effectively attenuating waves within a specific frequency band, while minimizing the wave force.
Neutral and singly ionised states of the magnesium (Mg) are the origin of several spectral lines that are useful for solar diagnostic purposes. An important element in modelling such solar lines is collisional data of the Mg with different perturbers abundant in the Sun, specially with neutral hydrogen. This work aims at providing complete depolarisation and polarisation and population transfer data for Mg II due to collisions with hydrogen atoms. For this purpose, a general formalism is employed to calculate the needed rates of MgII due to collisions with hydrogen atoms. The resulting collisional rates are then employed to investigate the impact of collisions on the polarisation of 25 Mg II lines relevant to solar applications by solving the governing statistical equilibrium equations within multi-level and multi-term atomic models. We find that the polarisation of some Mg II lines starts to be sensitive to collisions for hydrogen density $n_H \!\gtrsim\!$ 10$^{14}$ cm$^{-3}$.
Liquid plug formation in thin channels due to the Plateau–Rayleigh instability of a liquid film is observed in a variety of fields. In this paper, complementarity between theoretical solutions and direct numerical simulations (DNS) based on a front-tracking algorithm is explored to evaluate the importance of inertia for the case of a cylindrical capillary. A linear stability analysis is first performed and DNS results are then used to investigate the spatial distributions of inertial, convective and viscous terms of the Navier–Stokes equation. The existence of both viscous and inertial regimes is evidenced with a threshold given by the film thickness. The presence of the core fluid slows down the instability. In the viscous regime, predictions of the lubrication theory are verified. An example of liquid water as the outer fluid film and water vapour as the inner core fluid is simulated with application to the fuel cells.
Exopsychology is a sub-discipline of psychology concerned with how humans contemplateextraterrestrials as well as forming hypothesis about how these beings may think, feel and behave. While researching the former is undoubtedly a subject for empirical science, aspects of the latter remain uncertain. Given the contemporary scientific insight, it may still be possible to identify a set of cornerstones and eventually create a space of possible configurations of the extraterrestrial mind. Here, we identify three basic compatibility requirements: first, any form of life must navigate internal and external (environmental) demands and thus actively ensure the compatibility of its current state with the same demands. Second, any advanced cognitive development and the emergence of remotely detectable technosignatures require not only the relevant capabilities for manipulation but also compatibility with a permissive environment. Lastly, requirements also concern the compatibility of extraterrestrial thinking and behaviour with our search method. In its most basic understanding, search for extraterrestrial intelligence (SETI) searches for something done by somebody. However, the meaning of this simple formula and the psychological theory behind it is underdeveloped. Hence, psychological aid is needed to assist SETI in its effort to reveal whether galactic information indicates the presence of a mere object or activity of an identified subject with whom humans may establish contact. The fact that people believe in and search for extraterrestrials emphasizes that psychology should pay attention to this domain of phenomena. Hence, different imaginations of the extraterrestrial, ranging from benign to cruel, from superior to equally developed, are briefly discussed regarding their emergence and function as coping and motivating mechanisms for the uncertain search.
We propose a novel approach for non-Newtonian viscoelastic steady flows based on a decomposition of the rate-of-deformation tensor which here, in a simplified version, leads to an anisotropic generalised Newtonian fluid-like model with separated treatment of kinematics pertaining to shear and extensional flows. Care is taken to assure that the approach is objective and does not introduce spurious effects due to dependence on a specific reference frame. This is done by separating the rate-of-deformation tensor into shear and elongational components, with the local scalar shear and elongation rates being the second invariant of each tensor separately, and by modifying the method used to separate the rate-of-deformation tensor so that it becomes independent of superimposed rigid rotations, thus satisfying the principle of material indifference. We assess the model with two test cases: planar contraction flow, often employed to evaluate numerical methods or constitutive equations and for which experimentally observed corner vortex enhancement and pressure drop increase are seldom found in numerical simulations; and flow past confined or unconfined cylinders, for which experiments indicate a drag increase due to elasticity and most predictions give a drag decrease. With our anisotropic model, incorporating additional elongational-flow-related terms, large vortices and accentuated pressure drop coefficients can be predicted for the contraction problem and enhanced drag coefficient for the cylinder problems. This is the first work where problems of non-Newtonian fluid mechanics are solved numerically with separation of strain rate into shear and elongational components.
We report a high-power ultra-narrow fiber-coupled diode laser using a Faraday anomalous dispersion optical filter (FADOF) as an external cavity element. An external cavity suitable for both the fiber-coupled package and FADOF configuration has been proposed. Using a 87Rb-based FADOF as the frequency-selective element, we realized a 103 W continuous laser output with a uniform circular beam. The center wavelength was precisely locked at the D2 line of the Rb resonance, and the bandwidth was narrowed from 1.8 nm (free-running, full width at half maximum (FWHM)) to 0.013 nm (6.9 GHz, FWHM). The side mode suppression ratio reached 31 dB. Such diode lasers with precise wavelength and high spectral brightness have critical applications in many fields, such as high-energy gas laser pumping, spin-exchange optical pumping, Raman spectroscopy and nonlinear optics.
Graph theory, a branch of mathematics that focuses on the study of graphs (networks of nodes and edges), provides a robust framework for analysing the structural and functional properties of biomolecules. By leveraging molecular dynamics (MD) simulations, atoms or groups of atoms can be represented as nodes, while their dynamic interactions are depicted as edges. This network-based approach facilitates the characterization of properties such as connectivity, centrality, and modularity, which are essential for understanding the behaviour of molecular systems. This review details the application and development of graph theory-based models in studying biomolecular systems. We introduce key concepts in graph theory and demonstrate their practical applications, illustrating how innovative graph theory approaches can be employed to design biomolecular systems with enhanced functionality. Specifically, we explore the integration of graph theoretical methods with MD simulations to gain deeper insights into complex biological phenomena, such as allosteric regulation, conformational dynamics, and catalytic functions. Ultimately, graph theory has proven to be a powerful tool in the field of molecular dynamics, offering valuable insights into the structural properties, dynamics, and interactions of molecular systems. This review establishes a foundation for using graph theory in molecular design and engineering, highlighting its potential to transform the field and drive advancements in the understanding and manipulation of biomolecular systems.
Determining a reliable method to detect life on another planet is an essential first step in the pursuit of discovering extraterrestrial life. Polyhydroxyalkanoates (PHAs), bioplastic polymers created by microorganisms, are strong candidates for defining the presence of extraterrestrial life due to their water insolubility, strong ultraviolet resistance, high melting points and high crystallinity, amongst other qualities. PHAs are abundant on Earth, and their chemical properties can easily be distinguished from non-biological matter. Their widespread distribution and conferred resistance to astrobiologically relevant extreme environments render PHAs highly favourable candidates for astrobiological detection. Integrating detection of PHA biosignatures into current and future life-detection instruments would be useful for the planetary search for life. PHAs are analysed and characterized in laboratories by gas chromatography-mass spectrometry, infrared spectroscopy, Raman spectroscopy and immunoassay analysis in addition to other methods. We outline a path forward to integrate PHA detection in astrobiology missions to aid the search for extraterrestrial life.
We investigate the concentration fluctuations of passive scalar plumes emitted from small, localised (point-like) steady sources in a neutrally stratified turbulent boundary layer over a rough wall. The study utilises high-resolution large-eddy simulations for sources of varying sizes and heights. The numerical results, which show good agreement with wind-tunnel studies, are used to estimate statistical indicators of the concentration field, including spectra and moments up to the fourth order. These allow us to elucidate the mechanisms responsible for the production, transport and dissipation of concentration fluctuations, with a focus on the very near field, where the skewness is found to have negative values – an aspect not previously highlighted. The gamma probability density function is confirmed to be a robust model for the one-point concentration at sufficiently large distances from the source. However, for ground-level releases in a well-defined area around the plume centreline, the Gaussian distribution is found to be a better statistical model. As recently demonstrated by laboratory results, for elevated releases, the peak and shape of the pre-multiplied scalar spectra are confirmed to be independent of the crosswind location for a given downwind distance. Using a stochastic model and theoretical arguments, we demonstrate that this is due to the concentration spectra being directly shaped by the transverse and vertical velocity components governing the meandering of the plume. Finally, we investigate the intermittency factor, i.e. the probability of non-zero concentration, and analyse its variability depending on the thresholds adopted for its definition.
The molecular mechanism of olfaction, namely, how we smell with limited olfactory receptors to recognize exceedingly diverse and large numbers of scents remains unknown despite the recent advances in chemistry, chemical, structural, and molecular biology. Olfactory receptors are notoriously difficult to study because they are fully embedded in the cell membrane. After decades of efforts and significant funding, there are only three olfactory receptor structures known. To understand olfaction, we carried out the structural bioinformatic study of six human olfactory receptors including OR51E1, OR51E2, OR52cs, OR1A1, OR1A2, TAAR9, and their AlphaFold3 predicted water-soluble QTY variants with odorants. We applied the QTY code to replace leucine (L) with glutamine (Q), isoleucine (I) and valine (V) with threonine (T), and phenylalanine (F) with tyrosine (Y) only in the transmembrane helices. Therefore, these QTY variants become water-soluble. We also present the superimposed structures of native olfactory receptors and their water-soluble QTY variants. The superimposed structures show remarkable similarity with RMSDs between 0.441 and 1.275 Å despite significant changes to the protein sequence of the transmembrane domains (43.03%–50.31%). We also show the differences in hydrophobicity surfaces between the native olfactory receptors and their QTY variants. Furthermore, we also used AlphaFold3 and molecular dynamics to study the odorant octanoate with OR1A2 and spermidine with TAAR9. Our bioinformatics studies provide insight into the differences between the hydrophobic helices and hydrophilic helices, and will likely further stimulate designs of water-soluble integral transmembrane proteins and other aggregated proteins.