Regions Of High Curvature Research Articles

Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein DivIVA.

DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane.

Building a three-dimensional model of early-stage zebrafish embryo brain

We introduce a computational approach to build three-dimensional (3D) surface mesh models of the early-stage zebrafish brain primordia from time-series microscopy images. The complexity of the early-stage brain primordia and lack of recognizable landmarks pose a distinct challenge for feature segmentation and 3D modeling. Additional difficulty arises because of noise and variations in pixel intensity. We overcome these by using a hierarchical approach in which simple geometric elements, such as “beads” and “bonds,” are assigned to represent local features and their connectivity is used to smoothen the surface while retaining high-curvature regions. We apply our method to build models of two zebrafish embryo phenotypes at discrete time points between 19 and 28 h post-fertilization and collect measurements to quantify development. Our approach is fast and applicable to building models of other biological systems, as demonstrated by models from magnetic resonance images of the human fetal brain. The source code, input scripts, sample image files, and generated outputs are publicly available on GitHub.

Geodesic-HOF: 3D Reconstruction Without Cutting Corners

Single-view 3D object reconstruction is a challenging fundamental problem in machine perception, largely due to the morphological diversity of objects in the natural world. In particular, high curvature regions are not always represented accurately by methods trained with common set-based loss functions such as Chamfer Distance, resulting in reconstructions short-circuiting the surface or "cutting corners." To address this issue, we propose an approach to 3D reconstruction that embeds points on the surface of an object into a higher-dimensional space that captures both the original 3D surface as well as geodesic distances between points on the surface of the object. The precise specification of these additional "lifted" coordinates ultimately yields useful surface information without requiring excessive additional computation during either training or testing, in comparison with existing approaches. Our experiments show that taking advantage of these learned lifted coordinates yields better performance for estimating surface normals and generating surfaces than using point cloud reconstructions alone. Further, we find that this learned geodesic embedding space provides useful information for applications such as unsupervised object decomposition.

Topological defects produce kinks in biopolymer filament bundles

Bundles of stiff filaments are ubiquitous in the living world, found both in the cytoskeleton and in the extracellular medium. These bundles are typically held together by smaller cross-linking molecules. We demonstrate, analytically, numerically, and experimentally, that such bundles can be kinked, that is, have localized regions of high curvature that are long-lived metastable states. We propose three possible mechanisms of kink stabilization: a difference in trapped length of the filament segments between two cross-links, a dislocation where the endpoint of a filament occurs within the bundle, and the braiding of the filaments in the bundle. At a high concentration of cross-links, the last two effects lead to the topologically protected kinked states. Finally, we explore, numerically and analytically, the transition of the metastable kinked state to the stable straight bundle.

An a priori analysis of the structure of local subfilter-scale species surrounding flame fronts using direct numerical simulation of turbulent premixed flames

An a priori analysis of subfilter-scale (SFS) species structure important to estimate chemical reaction rates in large-eddy simulation (LES) is performed using direct numerical simulation (DNS) of a turbulent premixed flame at a turbulence Reynolds number Re0=329 and Karlovitz number Ka0=7.23 with semi-detailed finite-rate chemistry. Differences between the complete chemical reaction rates extracted from DNS and those estimated from LES-filtered variables are quantified. The spatial distributions of these differences are found to be localized in regions surrounding the flame front for representative reactions. Within these regions, variations in the localization relative to the flame, scale, and magnitude of the SFS species concentrations are quantified, and mean SFS structure is determined. SFS species structure is found in two groupings: “single-banded” structure characterized by one distinct peak and “double-banded” structure characterized by two peaks of opposite signs. Species that are produced and consumed within the flame such as CH2O and HCO are observed to have single-banded structure, and species displaying a frontal behavior such as n-C7H16 and OH are found to have double-banded structure, on average. The local SFS structure surrounding the flame is impacted by neighboring flame-flame interactions as well as by variations in flame curvature. The impacts of the flame-flame interactions are strong when the SFS species structure has “large” length scales with concentration peaks significantly displaced from the flame front. Curvature effects are shown to be strong in high curvature regions of the flame.

On the Nature of the Mitochondrial Permeability Transition

The mitochondrial inner membrane (IM) undergoes a dramatic permeability transition (mPT) associated with exposure to reactive oxygen species (ROS) and/or abnormally high Ca+2. The mPT is characterized by matrix swelling, loss of membrane potential and increased solute permeability. While changes are initially transient and partly reversible, repeated insult leads to irreversible loss in function associated with outer membrane (OM) rupture. While the onset of mPT is attributed to opening of a pore whose molecular identity remains undefined, much of what is known about mPT can be explained without invoking a pore. The IM has a complicated topology established by two high-curvature features: (1) catenoid-shaped junctions that connect cristae with the IM periphery, formed by proteins (MICOS, OPA1) and cardiolipin, and (2) acute folds in cristae induced and/or stabilized by dimer rows of the ATP synthase which interacts with MICOS and cardiolipin. There is considerable evidence that the ATP synthase and cardiolipin, stabilizers of IM topology, are disrupted by high Ca+2and by ROS respectively. The consequence of destabilizing regions of high IM curvature is increased mechanical stress, normally balanced by osmotic forces, which would drive water into the matrix through aquaporins. The increased membrane strain in the high-curvature regions could cause discrete, transient losses of local IM integrity, resulting in stepwise depolarization and solute influx that would mimic pore opening and closing. Predictions of mPT membrane stress models vs pore models will be compared against experimental data.

Clathrin Senses Membrane Curvature

The ability of proteins to assemble at sites of high membrane curvature is essential for various membrane remodeling processes, including clathrin-mediated endocytosis. This endocytic process is facilitated by a network of multivalent adaptor proteins that bind to the plasma membrane surface. Many of these adaptor proteins have been shown to sense regions of high membrane curvature, leading to local recruitment of the clathrin coat. Because clathrin does not bind to the membrane directly, it has remained unclear whether the clathrin coat plays an active role in sensing membrane curvature or is passively recruited by adaptor proteins.

Beyond a Critical Strain Rate, Lamin-A Dilutes and Nuclei Rupture at Sites of High Curvature

Constricted cell migration, which commonly occurs in vivo during tumor metastasis, can rupture nuclei. Associated rupture often correlates with high curvature imposed by pores, probes, or small micronuclei and with nuclear entry of chromatin-binding cGAS (cyclic-GMP-AMP synthase) from the cytoplasm. Suppression of lamin-A, a main component of the nuclear lamina, has been seen to increase rupture during constricted migration, but the dynamics of lamin-A under high curvature, and the mechanism by which lamin-A protects against rupture, remain incompletely understood. Thus, we studied the effect of curvature on lamin-A organization and nuclear rupture by passively pulling detached cells into micropipettes under controlled pressure. Additionally, using live imaging in highly elongated A549 human lung carcinoma cells, we quantified lamina dilution at pole regions of cell nuclei which underwent natural shape fluctuations. Extension of a nucleus into a micropipette caused dilution of lamin-B at the leading tip of the nucleus, proportional to aspirated length L, whereas dilution of lamin-A occurred only for L > Lcritical at the same early timepoint in aspiration. in similar experiments done with siLMNA U2OS human osteosarcoma cells transfected to express low or high levels of lamin-A-GFP (∼10-fold range), both low and high lamin-A levels required a critical strain to flow. Low levels of lamin-A showed greater lamin-A dilution and more nuclear rupture versus high levels as determined by cGAS entry and chromatin herniation. in highly elongated A549 cells, lamin-A at the high-curvature pole regions was found to be enriched relative to lamin-B, consistent with the idea that stiff elastic lamin-B responds immediately to applied stress while viscous lamin-A responds above some threshold. Lamin-A requires a critical strain rate to flow, and, importantly, nuclear rupture occurs at or above this critical dilution in lamin-A.

Clathrin senses membrane curvature

The ability of proteins to assemble at sites of high membrane curvature is essential to diverse membrane remodeling processes, including clathrin-mediated endocytosis. Multiple adaptor proteins within the clathrin pathway have been shown to sense regions of high membrane curvature, leading to local recruitment of the clathrin coat. Because clathrin triskelia do not bind to the membrane directly, it has remained unclear whether the clathrin coat plays an active role in sensing membrane curvature or is passively recruited by adaptor proteins. Using a synthetic tag to assemble clathrin directly on membrane surfaces, here we show that clathrin is a strong sensor of membrane curvature, comparable with previously studied adaptor proteins. Interestingly, this sensitivity arises from clathrin assembly rather than from the properties of unassembled triskelia, suggesting that triskelia have preferred angles of interaction, as predicted by earlier structural data. Furthermore, when clathrin is recruited by adaptors, its curvature sensitivity is amplified by 2- to 10-fold, such that the resulting protein complex is up to 100 times more likely to assemble on a highly curved surface compared with a flatter one. This exquisite sensitivity points to a synergistic relationship between the coat and its adaptor proteins, which enables clathrin to pinpoint sites of high membrane curvature, an essential step in ensuring robust membrane traffic. More broadly, these findings suggest that protein networks, rather than individual protein domains, are likely the most potent drivers of membrane curvature sensing.

Topological imaging of turbulent premixed, prevaporized liquid fuel jet flames using CH (C-X) band PLIF

New imaging capabilities for topology in prevaporized, liquid-fuel flames are presented with the application of CH-radical planar laser-induced fluorescence (PLIF) using the C2Σ+-X2Π (v′=0, v″=0) band. Imaging of turbulent flame structure for ethanol, n-heptane, n-dodecane, and kerosene (JP-8) fuels has been conducted in jet flames using a piloted McKenna burner with a central jet tube. This work presents the first application of CH PLIF for the study of full flame structure and curvature effects with prevaporized liquid fuels, particularly n-dodecane and kerosene. Liquid fuel structure is also compared to results with methane and ethylene. Results show that good signal-to-noise ratio (SNR) is achieved for all fuels, and the method is feasible in the presence of a dilute droplet field, despite the resonant nature of the technique. Reaction-zone structures clearly depict evidence of nonequidiffusive (Le ≠ 1) effects: strong variation in CH fluorescence is observed in regions of high curvature. Simultaneous excitation of the OH radical is also possible with prevaporized liquid fuels, for combined imaging of the reaction and heat-release zones. In kerosene flames, with aromatic species, fuel fluorescence may also be simultaneously captured, in addition to that from CH and OH, providing information on vapor localization.

Surface Curvature Effects on Film Cooling Performance for Shaped Holes on a Model Turbine Blade

Abstract Surface curvature has been shown to have significant effects on the film cooling performance of round holes, but the literature include few studies of its effects on shaped holes despite their prevalence in gas turbines. Experiments were performed using two rows of holes placed on the suction side of a scaled-up turbine blade in a low Mach number linear cascade wind tunnel with low freestream turbulence. The rows were placed in regions of high and low convex surface curvature. Geometries and flow conditions for the rows were matched to those from previous flat plate studies. Comparison of the adiabatic effectiveness results from the high curvature and flat plate rows revealed the same trends as those in the literature using round holes, with increased performance for the high curvature row at lower blowing ratios and the opposite at higher ones. The low curvature row had similar performance to the flat plate row at lower blowing ratios, suggesting the mild convex curvature had little beneficial effect. At higher blowing ratios, the low curvature row had inferior performance, which was attributed to the local freestream adverse pressure gradient that generated additional turbulence, promoting jet-to-mainstream mixing and decreasing performance.

Assessing the impact of multicomponent diffusion in direct numerical simulations of premixed, high-Karlovitz, turbulent flames

Implementing multicomponent diffusion models in numerical combustion studies is computationally expensive; to reduce cost, numerical simulations commonly use mixture-averaged diffusion treatments or simpler models. However, the accuracy and appropriateness of mixture-averaged diffusion has not been verified for three-dimensional, turbulent, premixed flames. In this study we evaluated the role of multicomponent mass diffusion in premixed, three-dimensional high Karlovitz-number hydrogen, n-heptane, and toluene flames, representing a range of fuel Lewis numbers. We also studied a premixed, unstable two-dimensional hydrogen flame due to the importance of diffusion effects in such cases. Our comparison of diffusion flux vectors revealed differences of 10–20% on average between the mixture-averaged and multicomponent diffusion models, and greater than 40% in regions of high flame curvature. Overall, however, the mixture-averaged model produces small differences in diffusion flux compared with global turbulent flame statistics. To evaluate the impact of these differences between the two models, we compared normalized turbulent flame speeds and conditional means of species mass fraction and source term. We found differences of 5–20% in the mean normalized turbulent flame speeds, which seem to correspond to differences of 5–10% in the peak fuel source terms. Our results motivate further study into whether the mixture-averaged diffusion model is always appropriate for DNS of premixed turbulent flames.

Converting stroked primitives to filled primitives

Vector graphics formats offer support for both filled and stroked primitives. Filled primitives paint all points in the region bounded by a set of outlines. Stroked primitives paint all points covered by a line drawn over the outlines. Editors allow users to convert stroked primitives to the outlines of equivalent filled primitives for further editing. Likewise, renderers typically convert stroked primitives to equivalent filled primitives prior to rendering. This conversion problem is deceivingly difficult to solve. Surprisingly, it has received little to no attention in the literature. Existing implementations output too many segments, do not satisfy accuracy requirements, or fail under a variety of conditions, often spectacularly. In this paper, we present a solution to the stroke-to-fill conversion problem that addresses these issues. One of our key insights is to take into account the evolutes of input outlines, in addition to their offsets, in regions of high curvature. Furthermore, our approach strives to maintain continuity between the input and the set of painted points. Our implementation is available in open source.

3D confocal microscope imaging of macromolecule uptake in the intact brachiocephalic artery

Background and aimsElevated uptake of plasma macromolecules by the arterial wall is an early event in atherogenesis. Existing optical techniques for detecting macromolecular tracers in the wall have poor depth penetration and hence require en face imaging of flattened arterial segments. Imaging uptake in undistorted curved and branched vessels would be useful in understanding disease development. MethodsDepth penetration was increased by applying optical clearing techniques. The rat aorto-brachiocephalic junction was imaged intact by confocal microscopy after it had been exposed to circulating rhodamine-labelled albumin in vivo, fixed in situ, excised and then cleared with benzyl alcohol/benzyl benzoate. Tracer uptake was mapped onto a 3D surface mesh of the arterial geometry. ResultsTracer fluorescence was detectable throughout the wall closest to the objective lens and, despite a vessel diameter of c. 1 mm, in the wall on the other side of the artery, across the lumen. By tile scanning, tracer concentrations were mapped in the aorta, the brachiocephalic artery and their junction without opening or flattening either vessel. Optical clearing was also shown to be compatible with immunofluorescent staining and imaging of experimental atherosclerosis. ConclusionsThe technique obviates the need for labour-intensive sample preparation associated with standard en face imaging. More importantly, it preserves arterial geometry, facilitating co-localisation of uptake maps with maps of biomechanical factors, which typically exist on 3D surface meshes. It will permit the correlation of haemodynamic wall shear stress with macromolecule permeability more accurately in regions of high curvature or branching, such as in the coronary arteries.

Low Temperature Li Plating and Corrosion Safety Hazard in Li-Ion Batteries

The Li(Ni0.5Mn0.3Co0.2)/LixC6 (NMC532/graphite) Li-ion battery chemistry has proven to be reliable in electric vehicle battery applications due to its high capacity, good energy density, and high cyclability.1 Under normal operating conditions (at slightly above room temperature), the long-term battery stability and response to charge/discharge is very well understood. However, there are other possible applications for Li-ion batteries where they would be forced to operate under extreme cold such as high elevation/cold climate electric vehicles, satallites, electric aircraft, unmanned underwater vehicles. At these ultra-low temperatures, the degradation mechanisms are less understood and less predictable by current modeling approaches.What is known is that destructive events2 like thermal runaway can occur even at very low temperatures (-30oC, which is a rated temperature for Li-ion batteries). They are caused by Li plating events where stratified mossy-like Li0 deposition occurs around highly stressed regions (e.g. edges, regions of high curvature) while deposition is more uniform around the electrode center. Morphological studies by SEM reveal considerable fusing (i.e. indistinguishable boundaries or complete collapse of particle-particle interfaces) of graphite particles, which leads to drasitic morphological changes to the graphite electrode structure. Moreover, severe gassing and displacement of anode material can lead to significant warping of the electrode material. Low temperature volumetric expansion and contraction can cause warping of the electrode in ripple-type formation. In addition, XPS and Raman spectroscopy revealed formation of lithium carbides from the corrosion of LixC6-Li0 on the peak of the ripple-type pattern and absent at the trough. The reasoning for this anisotropic distribution of Li is attributed to the preference for electron transfer at regions of high stress (e.g. edges, peaks, and regions of high curvature).In this study, a non-thermal runaway overpressurization of the cell was found to occur after a 50Ah NMC532/graphite cell was cycled at room temperature after repetitive low temperature experiments. In addition, a parallel cell was stored at room temperature (i.e. no movement, no current, no temperature) for 2 weeks before it spontaneously went into catastrophic thermal runaway. The presentation will provide a thorough study of the 50 Ah large format NMC532 /graphite cells3 and will elucidate low temperature degradation processes that occur, leading to thermal runaway.

Geometrically Structured Microtumors in 3D Hydrogel Matrices.

During cancer progression, a growing tumor encounters variation in the surrounding microenvironment leading to a diverse landscape at the tumor-matrix interface. Topological cues at the interface are believed to influence invasive characteristics; however, most laboratory models involve tumor spheroids that develop a uniform geometry within a homogenous hydrogel. In this communication, a method for templating hydrogels in well-defined 3D architectures is reported. Using melanoma as a model cancer, fabrication of geometrically structured model tumors in a myriad of shapes and sizes is demonstrated. These microtumors can be encapsulated in virtually any polymeric matrix, with demonstrations using poly(ethylene glycol) and gelatin-based hydrogels. Light sheet imaging reveals uniform viability throughout with regions of high curvature at the periphery influencing cellular heterogeneity. These hydrogel encapsulated microtumors can be harvested and implanted in animal models, providing a unique xenograft system where relationships between geometry, progression, and invasion may be systematically studied.

A Comparison of Layered Tetrahedral and Cartesian meshing in Additive Manufacturing Simulation

Abstract In additive manufacturing simulation most of the time the overall aim is to compensate residual stress induced deformations of a printed part. For this goal a high result accuracy is needed. In order to achieve this, simulation engineers have to take numerous decisions. This article provides assistance in the determination of a reasonable meshing type using a complex to mesh test sample that is close to the real geometry of round metallic fatigue test samples. The traditional Cartesian meshing strategy with and without the use of a projection factor is compared with layered tetrahedral meshing, which is newly introduced to additive manufacturing simulation. Additionally the displacement results are set side by side with a scan of an additive manufactured part. The study shows that layered tetrahedral meshing can achieve more accurate results with coarser mesh sizes, especially in regions of high curvature.

PDE-Based Multidimensional Extrapolation of Scalar Fields over Interfaces with Kinks and High Curvatures

We present a PDE-based approach for the multidimensional extrapolation of smooth scalar quantities across interfaces with kinks and regions of high curvature. Unlike the commonly used method of [T. Aslam, J. Comput. Phys., 193 (2004), pp. 349--355], in which normal derivatives are extrapolated, the proposed approach is based on the extrapolation and weighting of Cartesian derivatives. As a result, second- and third-order accurate extensions in the $L^\infty$ norm are obtained with linear and quadratic extrapolations, respectively, even in the presence of sharp geometric features. The accuracy of the method is demonstrated on a number of examples in two and three spatial dimensions and compared to the approach of [T. Aslam, J. Comput. Phys., 193 (2004), pp. 349--355]. The importance of accurate extrapolation near sharp geometric features is highlighted on an example of solving the diffusion equation on evolving domains.

Two-Lane Path Planning of Autonomous Vehicles in 2.5D Environments

We present a two-lane path planning of autonomous vehicles in two-and-a-half-dimensional (2.5D) environments. Our method builds on collision-free two-dimensional (2D) path-planning techniques from our previous work, and extends these techniques to 2.5D by mapping a 2D path in the parameter space onto a terrain graph surface, as a curve on the surface in the object space. Based on this path on the terrain surface, we propose a novel method of designing cross slopes in high curvature regions of the path, such that vehicles need not slow down in these regions. Furthermore, we apply time-optimal control techniques developed in robotics to compute the minimal-time speed control along the specified path. Examples are provided to demonstrate the effectiveness of the proposed algorithm.

Target Image Mask Correction Based on Skeleton Divergence

Traditional approaches to modeling and processing discrete pixels are mainly based on image features or model optimization. These methods often result in excessive shrinkage or expansion of the restored pixel region, inhibiting accurate recovery of the target pixel region shape. This paper proposes a simultaneous source and mask-images optimization model based on skeleton divergence that overcomes these problems. In the proposed model, first, the edge of the entire discrete pixel region is extracted through bilateral filtering. Then, edge information and Delaunay triangulation are used to optimize the entire discrete pixel region. The skeleton is optimized with the skeleton as the local optimization center and the source and mask images are simultaneously optimized through edge guidance. The technique for order of preference by similarity to ideal solution (TOPSIS) and point-cloud regularization verification are subsequently employed to provide the optimal merging strategy and reduce cumulative error. In the regularization verification stage, the model is iteratively simplified via incremental and hierarchical clustering, so that point-cloud sampling is concentrated in the high-curvature region. The results of experiments conducted using the moving-target region in the RGB-depth (RGB-D) data (Technical University of Munich, Germany) indicate that the proposed algorithm is more accurate and suitable for image processing than existing high-performance algorithms.