Shape Fluctuations Research Articles

Two-dimensional squishy glass: yielding under oscillatory shear.

The yielding response to an imposed oscillatory shear is investigated for a model two-dimensional dense glass composed of bidisperse, deformable polymer rings, with the ring stiffness being the control parameter. In the quiescent glassy state, the more flexible rings exhibit a broader spectrum of shape fluctuations, which becomes increasingly constrained with increasing ring stiffness. Under shear, the highly packed rings yield, i.e. the thermal assembly loses rigidity, with the threshold yield strain increasing significantly with decreasing ring stiffness. Further, the rings display significant deviations in their shape compared to their unsheared counterparts. This study provides insights into the interplay between shape changes and translational rearrangements under shear, thus contributing to the understanding of yielding transition in densely packed, deformable polymer systems.

Static or dynamic pear shapes in radioactive nucleus 224Rn?

We report a comprehensive study on low-lying parity doublet states of 224Rn by mixing both quadrupole- and octupole-shaped configurations in multireference covariant density functional theory, in which broken symmetries in configurations are restored using projection techniques. The low-lying energy spectrum is reasonably reproduced when the shape fluctuations in both the quadrupole and octupole shapes are considered. Electric octupole transition strength in 224Rn is found to be B(E3;31-→01+)=43\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$B(E3; 3^-_1 \\rightarrow 0^+_1)=43$$\\end{document} W.u., comparable to that in 224Ra, whose data are 42(3) W.u.. Our results indicate that 224Rn shares similar low-energy structure with 224Ra despite the excitation energy of first 3-\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$3^-$$\\end{document} state of the former nucleus is higher than that of the latter. This study suggests 224Rn is a candidate for the search for permanent electric dipole moment.

Enhancing fruit SSC detection accuracy via a light attenuation theory-based correction method to mitigate measurement orientation variability

Nondestructive online detection and sorting for fruit quality has gradually attracted attention in the global agro-product industry. However, the detection accuracy is influenced by many factors, such as fruit orientation, fruit shape, and environmental fluctuations. This study aimed to explore the impact of measurement orientation variation on spectra and soluble solids content (SSC) detection in apples and propose a correction method to mitigate the effect. Firstly, the visible/near-infrared (Vis/NIR) spectra ranging from 550 to 950 nm were collected in four orientations. Then, calibration models were developed for each orientation separately (local models) and all orientations corporately (global models) to evaluate and compensate for the effect of orientation. After that, the novel method based on the light attenuation theory was introduced to correct the acquired raw spectra and establish corrected orientation models. Results showed that measurement orientation significantly altered spectral intensity due to variations in surface curvature and optical path, thus declining models’ predictive power and robustness. Global models proved to be less susceptible to orientation variation compared with local models. The performance of both local and global models considerably improved post-orientation correction, attributed to the decrease of spectral distribution difference, with their average Rp2 and RPD increased by 93.38 % and 8.11 %, 10.56 % and 10.57 %, respectively, while the average RMSEP decreased by 16.01 % and 10.78 %, respectively. Overall, this work provides a more cost-effective and universal approach to impair the influence of measurement orientation and improve the accuracy and reliability of fruit quality online detection.

Collective model description of parity-doublet bands in odd mass nuclei

The yrast parity doublet rotational bands in odd medium mass and heavy nuclei are described by a quadrupole–octupole axially symmetric collective model within the strong coupling assumption regarding the odd nucleon. Energy levels of the same spin and opposite parity are interpreted as symmetric and antisymmetric quantum states of the quadrupole–octupole shape fluctuation. The energy spectrum and the associated electromagnetic transitions of the parity doublet bands observed in 21 selected nuclei, are reproduced with a very good accuracy. Predictions are performed for energies of unobserved states and electromagnetic properties. The model parameters are used to establish the static or dynamic nature of the octupole correlations in the ground state and their evolution with spin. A general systematization of the octupole effects as a function of nucleon numbers is realized in conjunction with results on even–even nuclei.

Polarization lidar observations of diurnal and seasonal variations in the atmospheric mixing layer above a tropical rural place gadanki, India

This study presents the daily and seasonal variation of the atmospheric mixing layer height (MLH) over Gadanki, India (13.45°N, 79.18°E), a tropical rural location based on polarization lidar observations. The observations spanned the years 2009–2014, encompassing 303 instances, and coinciding with radiosonde and surface weather station measurements. The MLH was determined through the analysis of aerosol profiles and confirmed with the MLH values derived from radiosonde data. The lidar depolarization ratio was employed to characterize aerosol shape. This study aims to establish a connection between aerosol backscatter and its shape through lidar observations, considering diurnal and seasonal variations, while also identifying the influencing factors. This study illustrates four distinct case studies conducted during different seasons to depict aerosol behavior in both convectively active and non-active periods. These case studies unveil the influence of aerosol shape on water intake and subsequent residual layer and cloud formation. The observed fluctuations in MLH and aerosol shape suggest a dynamic relationship between local meteorology and long-range aerosol transport.

Active particles confined in deformable droplets

Active particles under soft confinement such as droplets or vesicles present intriguing phenomena, as collective motion emerges alongside the deformation of the environment. A model is employed to systematically investigate droplet morphology and particle distribution in relation to activity and concentration,revealing that active particles have the capacity to induce enhanced shape fluctuations in the droplet interface with respect to the thermal fluctuations, aligning with recent experimental observations. A rich phase behaviour can be identified with two different mechanism of droplet breakage.

Interannual fluctuations in precipitation shape the trajectory of ecosystem respiration along a grazing exclusion chronosequence in a typical steppe in Inner Mongolia

Grazing exclusion (GE), as an effective strategy for revitalizing degraded grasslands, possesses the potential to increase ecosystem respiration (Re) and significantly influence the capacity of grassland soils to sequester carbon. However, our current grasp of Re dynamics in response to varying durations of GE, particularly in the context of precipitation fluctuations, remains incomplete. To fill this knowledge gap, we conducted a monitoring of Re over a 40-year GE chronosequence within Inner Mongolia temperate typical steppe across two distinct hydrologically years. Overall, Re exhibited a gradual saturation curve and an increasing trend with the duration of GE in the wet year of 2021 and the normal precipitation year of 2022, respectively. The variance primarily stemmed from relatively higher microbial biomass carbon observed in the short-term GE during 2022 in contrast to 2021. Moreover, the impacts of GE on the sensitivities of Re to moisture and temperature were intricately tied to precipitation patterns. increasing significantly with prolonged GE duration in 2022 but not in 2021. Our study highlights the intricate interplay between GE duration, precipitation variability, and Re dynamics. This deeper understanding enhances our ability to predict and manage carbon cycling within typical steppe in Inner Mongolia, offering invaluable insights for effective restoration strategies and climate change mitigation.

Self-Adaptive Turbulence Eddy Simulation of Supersonic Combustor Considering Thermal Radiation

The newly developed self-adaptive turbulence eddy simulation (SATES) method coupled with three turbulent combustion models, i.e., the finite-rate model, eddy-dissipation model, and steady laminar flamelet model, is used to numerically study the non-premixed supersonic hydrogen combustion in a DLR (German Aerospace Center) model scramjet combustor with a wedge flame holder. The study investigates the interactions of the shock waves and the flowfields as well as the flame structures. The SATES-based combustion simulation results demonstrate satisfactory agreement with the available experimental data. The study also explores the effect of fuel injection temperature on the combustion process and reveals that an increase in hydrogen temperature improves combustion efficiency. Additionally, thermal radiation effects are considered with the discrete ordinates method/weighted-sum-of-gray-gases method. The results indicate that thermal radiation heat transfer reduces the flame temperature and significantly affects the flame shape and temperature fluctuations. Also, radiation heat flux is an important factor and should be included in supersonic combustion simulations. The study demonstrates the potential of the SATES method for complex supersonic combustion and also provides a reference for thermal radiation in supersonic combustion.

Numerical investigation of unsteady shedding behaviors of a reentrant jet supercavity

To investigate the unsteady shedding characteristics of a reentrant jet supercavity with a low Froude number, a high-fidelity numerical model based on the inhomogeneous multiphase model is developed to predict the complex supercavitation flow that occurs during supercavity development. The developed solver is validated quantitatively against experimental results in terms of supercavity geometry and closure mode. This study focuses on the initial generation and development process of a reentrant jet supercavity, revealing three distinct stages: foam cavity, transparent supercavity with rapid growth in dimensions, and fully developed supercavity exhibiting significant deformation. Owing to reverse flow of the gas–water mixture, interfacial instabilities arise from the unsteady cavity shedding, leading to fluctuations in supercavity shape. The types of large-scale cavity shedding observed in this work—wing-like and cloud-like—are caused by the concave deformation resulting from the reentrant jet. As the gas entrainment coefficient increases, the unsteady characteristics of pressure oscillation weaken, and the instance of wing-like cavities decreases. When the gas entrainment coefficient reaches a critical value, the twin-vortex closure mode occurs, resulting in a more stable flow behavior. In sum, we propose a theoretical model that elucidates the strength of the reentrant jet and reveals its unsteady shedding behavior during supercavity development.

Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus

ABSTRACT Abnormal cell nuclear shapes are hallmarks of diseases, including progeria, muscular dystrophy, and many cancers. Experiments have shown that disruption of heterochromatin and increases in euchromatin lead to nuclear deformations, such as blebs and ruptures. However, the physical mechanisms through which chromatin governs nuclear shape are poorly understood. To investigate how heterochromatin and euchromatin might govern nuclear morphology, we studied chromatin microphase separation in a composite coarse-grained polymer and elastic shell simulation model. By varying chromatin density, heterochromatin composition, and heterochromatin-lamina interactions, we show how the chromatin phase organization may perturb nuclear shape. Increasing chromatin density stabilizes the lamina against large fluctuations. However, increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations by a “wetting”-like interaction. In contrast, fluctuations are insensitive to heterochromatin’s internal structure. Our simulations suggest that peripheral heterochromatin accumulation could perturb nuclear morphology, while nuclear shape stabilization likely occurs through mechanisms other than chromatin microphase organization.

Splines for Fast-Contracting Polyhedral Control Nets

Rapid reduction in the number of quad-strips, to accommodate narrower surface passages or reduced shape fluctuation, leads to configurations that challenge existing spline surface constructions. A new spline surface construction for fast contracting polyhedral control-nets delivers good shape. A nestedly refinable construction of piecewise degree (2,4) is compared with a uniform degree (3,3) spline construction.

Red blood cell flickering activity locally controlled by holographic optical tweezers

Red blood cells possess a singular mechanobiology, enabling efficient navigation through capillaries smaller than their own size. Their plasma membrane exhibits non-equilibrium shape fluctuation, often reported as enhanced flickering activity. Such active membrane motion is propelled by motor proteins that mediate interactions between the spectrin skeleton and the lipid bilayer. However, modulating the flickering in living red blood cells without permanently altering their mechanical properties represents a significant challenge. In this study, we developed holographic optical tweezers to generate a force field distributed along the equatorial membrane contour of individual red blood cells. In free-standing red blood cells, we observed heterogeneous flickering activity, attributed to localized membrane kickers. By employing holographic optical forces, these active kickers can be selectively halted under minimal invasion. Our findings shed light on the dynamics of membrane flickering and established a manipulation tool that could open new avenues for investigating mechanotransduction processes in living cells.

Abstract 3008: Aortic Arch Endovascular Stent Grafts With Zone 0 Proximal Landing Zones For Geometrically Complex Aortas

Objectives: Fluctuation in total curvature (δK) significantly outperforms all other available measurements of shape in predicting clinical outcomes after thoracic endovascular aortic repair (TEVAR). We aim to identify if the Nexus® Aortic Arch Stent Graft System is a suitable and safe treatment modality for aortas with high δK. Methods: Twenty-five patients that underwent transcatheter aortic arch repair using the Nexus stent graft were included. 3D aortic models were segmented from the CTA image data using Simpleware ScanIP. The aorta segmentations were then smoothed and the outer surface isolated. A triangular mesh from the outer surface was generated in Python, and the mesh was divided into a number of partitions. δK was calculated by the sum of per partition total curvatures and the fluctuation in total curvature across the entire manifold surface. Failed TEVAR was defined by a) any device-related mortality or b) unplanned or device-related secondary surgical intervention 30 days from index TEVAR. This data was plotted into a pre-defined (δK,L –1 )-feature space with pre-established machine learning-derived boundary conditions. Results: Within a (δK,L –1 )-feature space defined by patients with aortic stent grafts with zone 2 or 3 proximal landing zones, our group used predictive modeling to classify patients into three zones (normal, successful TEVAR, and unsuccessful TEVAR) with 92.8% mean accuracy. Within this pre-defined boundary zone of unsuccessful TEVAR, 72.2% (13/18) of patients with the Nexus stent graft with zone 0 proximal landing zone underwent a successful TEVAR without need for re-intervention. Conclusions: Transcatheter aortic arch repair with a single branch, two-stent graft system with a zone 0 proximal landing zone can offer patients with a high degree of aortic shape fluctuation a greater chance at successful TEVAR than traditional aortic stent grafts with zone 2 or 3 landing zones.

Glycerophospholipid polyunsaturation modulates resveratrol action on biomimetic membranes

The phytoalexin resveratrol has received increasing attention for its potential to prevent oxidative damages in human organism. To shed further light on molecular mechanisms of its interaction with lipid membranes we study resveratrol influence on the organisation and mechanical properties of biomimetic lipid systems composed of synthetic phosphatidylcholines with mixed aliphatic chains and different degree of unsaturation at sn-2 position (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, POPC, and 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine, PDPC). High-sensitivity isothermal titration calorimetric measurements reveal stronger spontaneous resveratrol association to polyunsaturated phosphatidylcholine bilayers compared to the monounsaturated ones resulting from hydrophobic interactions, conformational changes of the interacting species and desolvation of molecular surfaces. The latter is supported by the results from Laurdan spectroscopy of large unilamellar vesicles providing data on hydration at the glycerol backbones of glycerophospholipides. Higher degree of lipid order is reported for POPC membranes compared to PDPC. While resveratrol mostly enhances the hydration of PDPC membranes, increasing POPC dehydration is reported upon treatment with the polyphenol. Dehydration of the polyunsaturated lipid bilayers is measured only at the highest phytoalexin content studied (resveratrol/lipid 0.5 mol/mol) and is less pronounced than the effect reported for POPC membranes. The polyphenol effect on membrane mechanics is probed by thermal shape fluctuation analysis of quasispherical giant unilamellar vesicles. Markedly different trend of the bending elasticity with increasing resveratrol concentration is reported for the two types of phospholipid bilayers studied. POPC membranes become more rigid in the presence of resveratrol, whereas PDPC-containing bilayers exhibit softening at lower concentrations of the polyphenol followed by a slight growth without bilayer stiffening even at the highest resveratrol content explored. The new data on the structural organization and membrane properties of resveratrol-treated phosphatidylcholine membranes may underpin the development of future liposomal applications of the polyphenol in medicinal chemistry.

Theoretical and experimental analysis of the critical velocity of interface instability in gas jet forming

Gas jet forming can be used for creating optical reflectors, but under certain conditions, the surface shape fluctuation of the gas-liquid interface, that is, interface instability, may occur during the forming process. This study investigated the mechanism of interface instability in gas jet forming by combining the Kelvin-Helmholtz instability and the gas jet flow velocity distribution law. Theoretical analysis revealed that when the nozzle height is fixed, interface instability occurs when the gas flow rate reaches a certain value, which increases with the distance between the nozzle and the liquid surface. In order to verify the results of the theoretical analysis, experiments were carried out within the range of nozzle height from 0 to 42 mm, based on the formulas of the transition section between the potential core region and the self-similarity region in the gas jet. Within this range, the critical velocity of interface instability was found to be the minimum, 9.946 m/s, when the nozzle height was 0 mm, and the maximum, 15.562 m/s, when the nozzle height was 42 mm. The results of the theoretical analysis and experiments were used to establish a predictive model for the critical condition of interface instability, with a mean prediction deviation of 0.119 m/s. This model can provide a basis for selecting parameters for gas jet forming.

Red Blood Cell Adenylate Energetics Is Related to Endothelial and Microvascular Function in Long COVID.

Adenine nucleotides play a critical role in maintaining essential functions of red blood cells (RBCs), including energy metabolism, redox status, shape fluctuations and RBC-dependent endothelial and microvascular functions. Recently, it has been shown that infection with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) might lead to morphological and metabolic alterations in erythrocytes in both mild and severe cases of coronavirus disease (COVID-19). However, little is known about the effects of COVID-19 on the nucleotide energetics of RBCs nor about the potential contribution of nucleotide metabolism to the long COVID syndrome. This study aimed to analyze the levels of adenine nucleotides in RBCs isolated from patients 12 weeks after mild SARS-CoV-2 infection who suffered from long COVID symptoms and to relate them with the endothelial and microvascular function parameters as well as the rate of peripheral tissue oxygen supply. Although the absolute quantities of adenine nucleotides in RBCs were rather slightly changed in long COVID individuals, many parameters related to the endothelial and microcirculatory function showed significant correlations with RBC adenosine triphosphate (ATP) and total adenine nucleotide (TAN) concentration. A particularly strong relationship was observed between ATP in RBCs and the serum ratio of arginine to asymmetric dimethylarginine-an indicator of endothelial function. Consistently, a positive correlation was also observed between the ATP/ADP ratio and diminished reactive hyperemic response in long COVID patients, assessed by the flow-mediated skin fluorescence (FMSF) technique, which reflected decreased vascular nitric oxide bioavailability. In addition, we have shown that patients after COVID-19 have significantly impaired ischemic response parameters (IR max and IR index), examined by FMSF, which revealed diminished residual bioavailability of oxygen in epidermal keratinocytes after brachial artery occlusion. These ischemic response parameters revealed a strong positive correlation with the RBC ATP/ADP ratio, confirming a key role of RBC bioenergetics in peripheral tissue oxygen supply. Taken together, the outcomes of this study indicate that dysregulation of metabolic processes in erythrocytes with the co-occurring endothelial and microvascular dysfunction is associated with diminished intracellular oxygen delivery, which may partly explain long COVID-specific symptoms such as physical impairment and fatigue.

Interaction of KLAKLAK-NH2 and Analogs with Biomimetic Membrane Models.

Specifically designed peptide mimetics offer higher selectivity regarding their toxicity to mammalian cells. In addition to the α-helix conformation, the specific activity is related to the peptide's ability to penetrate the cell membrane. The alterations in lipid membrane properties were addressed in the presence of the peptide KLAKLAK-NH2 and analogs containing β-alanine, strengthening the antibacterial activity and/or naphtalimide with proven anticancer properties. The molecular interactions of the peptide mimetics with POPC bilayers were studied using FTIR-ATR spectroscopy. The thermal shape fluctuation analysis of quasispherical unilamellar vesicles was applied to probe the membrane bending elasticity. The impedance characteristics of bilayer lipid membranes were measured using fast Fourier-transform electrochemical impedance spectroscopy. A lateral peptide association with the membrane is reported for β-alanine-containing peptides. The most pronounced membrane softening is found for the NphtG-KLβAKLβAK-NH2 analog containing both active groups that corroborate with the indications for 1,8-naphthalimide penetration in the lipid hydrophobic area obtained from the FTIR-ATR spectra analysis. The β-alanine substitution induces strong membrane-rigidifying properties even at very low concentrations of both β-alanine-containing peptides. The reported results are expected to advance the progress in tailoring the pharmacokinetic properties of antimicrobial peptides with strengthened stability towards enzymatic degradation. The investigation of the nonspecific interactions of peptides with model lipid membranes is featured as a useful tool to assess the antitumor and antimicrobial potential of new peptide mimetics.

Bottom-up approach to explore alpha-amylase assisted membrane remodelling

Soluble alpha-amylases play an important role in the catabolism of polysaccharides. In this work, we show that the malt α -amylase can interact with the lipid membrane and further alter its mechanical properties. Vesicle fluctuation spectroscopy is used for quantitative measurement of the membrane bending rigidity of phosphatidylcholines lipid vesicles from the shape fluctuation based on the whole contour of Giant Unilamellar Vesicles (GUVs). The bending rigidity of the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine lipid vesicles in water increases significantly with the presence of 0.14 micromolar alpha-amylase (AA) in the exterior solution. It appears that the enzyme present in the external solution interacts with the outer layer of the bilayer membrane, leading to an asymmetry of the solution on either side of the bilayer membrane and altering its elasticity. At AA concentration of 1.5 micromolars and above, changes in the morphology of the GUV membrane are observed. The interaction between AA in the external solution and the external leaflet causes the bilayer membrane to curve spontaneously, leading to the formation of outbuds, giving a positive spontaneous curvature of C0 ≤ 0.05 μm−1 at ≈ 1 mg / ml of the AA concentration. We validate and characterize its concentration-dependent role in stabilizing the membrane curvature. Our findings indicate that the involvement of the enzyme, depending on the concentration, can have a considerable effect on the mechanical characteristics of the membrane.

Heterogeneous nucleation in the random field Ising model.

We investigate the nucleation dynamics of the three-dimensional random field Ising model under an external field. We use umbrella sampling to compute the free-energy cost of a critical nucleus and use forward flux sampling for the direct estimation of nucleation rates. For moderate to strong disorder, our results indicate that the size of the nucleating cluster is not a good reaction coordinate, contrary to the pure Ising model. We rectify this problem by introducing a coordinate that also accounts for the location of the nucleus. Using the free energy barrier to predict the nucleation rate, we find reasonable agreement, although deviations become stronger as disorder increases. We attribute this effect to cluster shape fluctuations. We also discuss finite-size effects on the nucleation rate.

Physical limits to membrane curvature sensing by a single protein.

Membrane curvature sensing is essential for a diverse range of biological processes. Recent experiments have revealed that a single nanometer-sized septin protein has different binding rates to membrane-coated glass beads of 1-µm and 3-µm diameters, even though the septin is orders of magnitude smaller than the beads. This sensing ability is especially surprising since curvature-sensing proteins must deal with persistent thermal fluctuations of the membrane, leading to discrepancies between the bead's curvature and the local membrane curvature sensed instantaneously by a protein. Using continuum models of fluctuating membranes, we investigate whether it is feasible for a protein acting as a perfect observer of the membrane to sense micron-scale curvature either by measuring local membrane curvature or by using bilayer lipid densities as a proxy. To do this, we develop algorithms to simulate lipid density and membrane shape fluctuations. We derive physical limits to the sensing efficacy of a protein in terms of protein size, membrane thickness, membrane bending modulus, membrane-substrate adhesion strength, and bead size. To explain the experimental protein-bead association rates, we develop two classes of predictive models: (i) for proteins that maximally associate to a preferred curvature and (ii) for proteins with enhanced association rates above a threshold curvature. We find that the experimentally observed sensing efficacy is close to the theoretical sensing limits imposed on a septin-sized protein. Protein-membrane association rates may depend on the curvature of the bead, but the strength of this dependence is limited by the fluctuations in membrane height and density.