Wide Tunnel Research Articles

CryoSeek: A strategy for bioentity discovery using cryoelectron microscopy

Structural biology is experiencing a paradigm shift from targeted structural determination to structure-guided discovery of previously uncharacterized bioentities. We employed cryoelectron microscopy (cryo-EM) to analyze filtered water samples collected from the Tsinghua Lotus Pond. Here, we report the structural determination and characterization of two highly similar helical fibrils, named TLP-1a and TLP-1b, each approximately 8 nm in diameter with a 15-Å wide tunnel. These fibrils are assembled from a similar protein protomer, whose structure was conveniently automodeled in CryoNet. The protomer structure does not match any available experimental structures, but shares the same fold as many predicted structures of unknown functions. The amino-terminal β strand of protomer n + 4 inserts into a cleft in protomer n to complete an immunoglobulin (Ig)-like domain. This packing mechanism, known as donor-strand exchange (DSE), has been observed in several bacterial pilus assemblies, wherein the donor is protomer n + 1. Despite distinct shape and thickness, this reminiscence suggests that TLP-1a/b fibrils may represent uncharacterized bacterial pili. Our study demonstrates an emerging paradigm in structural biology, where high-resolution structural determination precedes and drives the identification and characterization of completely unknown objects.

Preparation, electrical properties, ab initio calculations and sodium motion in NaNi2As3O10 crystal structure

Benefiting from their structural diversity, high structural and thermal stability, and significant ionic conductivity, polyanionic framework materials are suitable for energy storage applications. This study details the synthesis and characterization of the arsenate compound NaNi2As3O10. The material was synthesized as polycrystalline powder by the citrate-nitrate combustion method and the crystal structure was determined using Rietveld analysis and confirmed by means of ab initio calculations. This phase crystallizes in the triclinic system with space group P1̅[a=6.69172 (5) Å; b=7.74930 (6) Å; c = 8.71357 (7) Å; α =108.6343 (6)°, β = 108.5190 (6)° and γ= 99.2169 (6)°]. Its crystal structure, which is isotypic to NaCo2As3O10, presents an open 3D framework that provides wide tunnels for Na+ hopping. Electrochemical Impedance Spectroscopy (EIS) and the bond valence site energy (BVSE) were used to investigate the electrical properties and the Na+ migration respectively. The overall conductivity of the sample reaches 4.58 ×10−5 S.cm−1 at 575 °C. The crystal structure enables 1D migration pathways of sodium ions within the NaNi2As3O10 network with a computed energy barrier of 1.11 eV. Compared to Na-ion conducting arsenates and other extensively studied polyanionic materials, NaNi2As3O10 presents an intermediate ionic conductivity.

Evolution, structure, and drug-metabolizing activity of mammalian prenylcysteine oxidases

Prenylcysteine oxidases (PCYOXs) metabolize prenylated cysteines produced by protein degradation. They utilize oxygen as a co-substrate to produce free cysteine, an aldehyde, and hydrogen peroxide through the unusual oxidation of a thioether bond. In this study, we explore the evolution, structure, and mechanism of the two mammalian PCYOXs. A gene duplication event in jawed vertebrates originated in these two paralogs. Both enzymes are active on farnesyl- and geranylgeranylcysteine, but inactive on molecules with shorter prenyl groups. Kinetics experiments outline a mechanism where flavin reduction and re-oxidation occur rapidly without any detectable intermediates, with the overall reaction rate limited by product release. The experimentally determined three-dimensional structure of PCYOX1 reveals long and wide tunnels leading from the surface to the flavin. They allow the isoprene substrate to curl up within the protein and position its reactive cysteine group close to the flavin. A hydrophobic patch on the surface mediates membrane association, enabling direct substrate and product exchange with the lipid bilayer. Leveraging established knowledge of flavoenzyme inhibition, we designed sub-micromolar PCYOX inhibitors. Additionally, we discovered that PCYOXs bind and slowly degrade salisirab, an anti-RAS compound. This activity suggests potential and previously unknown roles of PCYOXs in drug metabolism.

Dilated cardiomyopathy mutation in beta-cardiac myosin enhances actin activation of the power stroke and phosphate release.

Inherited mutations in human beta-cardiac myosin (M2β) can lead to severe forms of heart failure. The E525K mutation in M2β is associated with dilated cardiomyopathy (DCM) and was found to stabilize the interacting heads motif (IHM) and autoinhibited super-relaxed (SRX) state in dimeric heavy meromyosin. However, in monomeric M2β subfragment 1 (S1) we found that E525K enhances (threefold) the maximum steady-state actin-activated ATPase activity (k cat) and decreases (eightfold) the actin concentration at which ATPase is one-half maximal (K ATPase). We also found a twofold to fourfold increase in the actin-activated power stroke and phosphate release rate constants at 30 μM actin, which overall enhanced the duty ratio threefold. Loaded motility assays revealed that the enhanced intrinsic motor activity translates to increased ensemble force in M2β S1. Glutamate 525, located near the actin binding region in the so-called activation loop, is highly conserved and predicted to form a salt bridge with another conserved residue (lysine 484) in the relay helix. Enhanced sampling molecular dynamics simulations predict that the charge reversal mutation disrupts the E525-K484 salt bridge, inducing conformations with a more flexible relay helix and a wide phosphate release tunnel. Our results highlight a highly conserved allosteric pathway associated with actin activation of the power stroke and phosphate release and suggest an important feature of the autoinhibited IHM is to prevent this region of myosin from interacting with actin. The ability of the E525K mutation to stabilize the IHM likely overrides the enhanced intrinsic motor properties, which may be key to triggering DCM pathogenesis.

Unveiling the influence of temperature and interface traps on the performance of source-all-around vertical TFET

This study investigates the electrical performance of a line-tunneling based source-all-around vertical Tunnel Field-Effect Transistor (SAA-VTFET) under diverse temperature and trap charge conditions. The proposed device achieves remarkable performance improvements across DC and AC parameters by employing strategically engineered III-V semiconductors and a wide source-channel tunneling heterojunction. Key metrics like on-state current (ION = 6.35 × 10−5 A/μm), off-state current (IOFF = 3.17 × 10−17 A/μm), threshold voltage (VT = ⁓0.18V), subthreshold swing (SSavg = ⁓7 mV/dec), transconductance (gm = 0.16 mS), cut-off frequency (fc = ⁓0.42 THz), gain bandwidth product (GBP), delay (τ), and various capacitances are thoroughly analyzed. Sentaurus TCAD 3D simulations employed in this study demonstrate the promising future of SAA-VTFETs in low-power and high-speed electronics.

Donut-shaped Corneal Allogeneic Intrastromal Segment as an Alternative to Deep Anterior Lamellar Keratoplasty in Advanced Keratoconus.

The aim of this study was to describe a new technique of selective corneal stromal transplantation for keratoconus treatment, donut-shaped CAIRS (corneal allogeneic intrastromal ring segment). A donut-shaped corneal graft is obtained using a double-bladed trephine. Descemet membrane, endothelium, and epithelium are all removed from the graft. Only stromal tissue is transplanted. A wide 360-degree intrastromal tunnel is created using the femtosecond laser, with a 30-degree angulation. The diameter is from 5.4 mm to 8 mm optical zone. After dehydration, the corneal graft is inserted into the tunnel. We report the clinical and tomographic outcomes after the procedure in 3 patients. The mean follow-up time after donut-shaped CAIRS was 6.01 ± 1.02 months. In case 1, best spectacle-corrected visual acuity improved from 20/150 to 20/40. In case 2, it improved from 20/400 to 20/40, and in case 3 from 20/200 to 20/40. The mean preoperative K was 57.3 ± 4.5 D and reduced to 44.2 ± 2.5 D after donut-shaped CAIRS. The mean spherical equivalent decreased from -9.8 ± 3.2 preoperatively to -3.2 ± 2.2 postoperatively. No intraoperative or postoperative complications were observed. Anterior segment OCT showed a mid-stroma implant, fusiform in shape, equidistant from the epithelium and endothelium. Donut-shaped CAIRS is a variation of the traditional CAIRS technique and showed to be an alternative option for keratoconus treatment, especially in moderate to advanced cases with a central clear cornea without scars. The technique is minimally invasive, and the visual axis remains untouched.

Finding shortcuts through collective tunnel excavations in a subterranean termite

Abstract Facilitating efficient resource transfer requires building an optimized transportation network which balances cost minimization with benefit maximization. For animals which forage for food located remotely, optimizing their transportation networks is critically related to survival. This process often involves finding and using the shortest route to save time and energy. Subterranean termites forage for wood resources by excavating underground foraging networks for search and transport. Because termites have no prior knowledge of food location during the food searching phase, establishment of a short tunnel between the nest and feeding site is difficult at the beginning of foraging. Thus, finding a short route should logically follow initial food discovery. However, it remains elusive as to how subterranean termites find the shortest route for food transportation. We simulated different scenarios using Coptotermes formosanus by providing different shapes and distances of pre-formed tunnels (straight, detour, and detour + twisting arenas) to food, where food items were located at a fixed distance from the arena entrance. Termites in the straight arena continuously used the pre-formed tunnel, showing negligible branching efforts. However, termites in the detour and detour + twisting arenas followed the pre-formed tunnel only for the initial few hours before excavating many branching tunnels. This branching activity ultimately resulted in termites finding shorter commuting routes than the pre-formed tunnels. In addition, the shortest established routes were widened over time. This study demonstrated that C. formosanus could actively alter tunnel networks to minimize the cost in food transportation by using short and wide tunnels.

Exploring Factors Affecting Crash Injury Severity with Consideration of Secondary Collisions in Freeway Tunnels

Although there have been several studies conducted exploring the factors affecting injury severity in tunnel crashes, most studies have focused on identifying factors that directly influence injury severity. In particular, variables related to crash characteristics and tunnel characteristics affect the injury severity, but the inconvenient driving environment in a tunnel space, characterized by narrow space and dark lighting, can affect crash characteristics such as secondary collisions, which in turn can affect the injury severity. Moreover, studies on secondary collisions in freeway tunnels are very limited. The objective of this study was to explore factors affecting injury severity with the consideration of secondary collisions in freeway tunnel crashes. To account for complex relationships between multiple exogenous variables and endogenous variables by considering the direct and indirect relationships between them, this study used a structural equation modeling with tunnel crash data obtained from Korean freeway tunnels from 2013 to 2017. Moreover, based on high-definition closed-circuit televisions installed every 250 m to monitor incidents in Korean freeway tunnels, this study utilized unique crash characteristics such as secondary collisions. As a result, we found that tunnel characteristics indirectly affected injury severity through crash characteristics. In addition, one variable regarding crashes involving drivers younger than 40 years old was associated with decreased injury severity. By contrast, ten variables exhibited a higher likelihood of severe injuries: crashes by male drivers, crashes by trucks, crashes in March, crashes under sunny weather conditions, crashes on dry surface conditions, crashes in interior zones, crashes in wider tunnels, crashes in longer tunnels, rear-end collisions, and secondary collisions with other vehicles.

In Vitro Investigation of the Fixation Performance of a Bioabsorbable Magnesium ACL Interference Screw Compared to a Conventional Interference Screw.

An anterior cruciate ligament (ACL) reconstruction is a common treatment for patients with ACL rupture that aims to regain pre-injury knee stability and kinematics. During the ACL reconstruction, one method to fix the graft is the use of an interference screw (IS). The IS should provide initial stability and secure the graft during the healing period. In recent years, magnesium has emerged as an alternative material to permanent metal and polymer ISs. In addition, differences in designs, such as the shape of the IS, can influence the fixation performance of the IS. Therefore, in this biomechanical experiment, two different screw designs with two ligament materials were compared in an insertion and a pull-out test at a rate of 1 mm/s. The screw designs were a conventional polymer screw and a magnesium screw. Porcine tendon and nylon rope were used as ligament materials. All tests were performed in polyurethane foam blocks with 15 PCF density (Synbone AG, Switzerland). As a result, both screw designs required an insertion torque of less than 3 Nm. There was a significant difference between the porcine and nylon rope in pull-out tests for each screw design. The magnesium screw had the highest pull-out force at 412.14 ± 50.00 N for porcine tendon and 707.38 ± 21.81 N for nylon rope. There were no significant differences in tunnel widening (narrow-wide ratio) between each ligament material. The magnesium screw showed the lowest narrow-wide tunnel ratio, implying a better ability to compress the graft to the tunnel. In conclusion, a more optimized magnesium IS design resulted in better graft fixation and an improved ACL reconstruction outcome.

Analytical Model of InP QWs for Efficiency Improvement in GaInP/Si Dual Junction Solar Cell

Quantum wells (QWs) are proven to enhance the short circuit current and voltage preservation measures help in efficiency enhancement with little degradation of open circuit voltage . Herein, an integrated GaInP/Si dual junction solar cell is proposed by incorporating the QWs in the top cell and carrier‐selective passivated contact at the bottom cell of the design. The QW increases the photon absorption of sub‐bandgap energies, buffer layer reduces the misfits between the lattice mismatched layers, and passivation mechanism improves the overall efficiency. Increasing the number of QWs increases the depletion width of QW region. This reduces the carrier lifetime () and increases the recombinations in the QW region. It results in the reduction in passivation quality and, therefore, reduces the open circuit voltage (). QW strain balancing and measures to reduce the threading dislocations has been considered. Also, the wide bandgap GaInP tunnel junction along with highly doped GaAs tunnel junction has been analyzed to observe the parasitic effect. The GaInP/Si‐integrated model achieves efficiency of 33.39% when the QWs are incorporated in the top cell. The effect of wide bandgap tunnel junction is also evaluated using GaInP tunnel junction.

Modelling soil stability in wide tunnels using FELA and multivariate adaptive regression splines analysis

Modelling soil stability in wide tunnels using FELA and multivariate adaptive regression splines analysis

Platypnea-Orthodeoxia Syndrome in the Setting of Patent Foramen Ovale Without Pulmonary Hypertension or Major Lung Disease.

BackgroundPatent foramen ovale (PFO)‐associated platypnea‐orthodeoxia syndrome is characterized by dyspnea and hypoxemia when upright. The pathogenesis is thought to involve an increase in right atrial pressure or change in degree of right to left shunting with upright posture.Methods and ResultsWe sought to characterize patients with platypnea‐orthodeoxia syndrome related to PFO without pulmonary hypertension. We retrospectively reviewed databases at 3 tertiary referral hospitals in New South Wales, Australia from 2000 to 2019. Fourteen patients with a mean age of 69±14 years had a PFO with wide tunnel separation. Mean New York Heart Association Classification was II (±0.9) and 7 inpatients had been confined to bed (from postural symptoms). Baseline oxygen saturations supine were 93%±5% and 84%±6% upright. Two patients had a minor congenital heart defect and 4 had mild parenchymal lung disease with preserved lung function. The mean aortic root diameter was 37±6 mm and distance between aortic root and posterior atrial wall was 16±2 mm. Platypnea‐orthodeoxia syndrome was preceded by surgery in 5 patients and 1 patient had mild pneumonia. Successful closure of the PFO using an Amplatzer device was performed in 11 of 14 patients. Post‐closure, all patients had New York Heart Association Classification I (improvement 1.6±0.9, P<0.003) and semi‐recumbent oxygen saturations increased by 13%±8% (P<0.001, n=10).ConclusionsPlatypnea‐orthodeoxia syndrome is a debilitating condition, curable by PFO closure. Anatomical distortion of the atrial septum related to a dilated aortic root or shortening of the distance between the aortic root and posterior atrial wall may contribute to the syndrome.

Upper-Bound face stability analysis of rectangular shield-driven tunnels in undrained clays

The face stability of rectangular shield-driven tunnels in undrained clays where the undrained shear strength increases linearly with depth is investigated numerically and analytically in this paper. In the framework of the kinematic approach of limit analysis, two new failure mechanisms based on the translational movement of rigid blocks and continuous deformation of soil mass are proposed for collapse and blowout cases. The analytical solutions of the failure mechanisms were compared with those of finite element simulations and the existing approaches in the literature to evaluate their validity and productivity. The critical support pressures obtained from the analytical models are relatively consistent with the results of the numerical simulations for square and wide rectangular tunnels. Simple design formulas were provided for analytical models to compute the limit support pressure for practical use. Finally, parametric studies were performed to explore the impact of different geometrical and geotechnical parameters pertaining to the stability of the tunnel face.

317 Gb/in2 Recording Areal Density on Strontium Ferrite Tape

The recording performance of a new prototype magnetic tape based on perpendicularly oriented strontium ferrite particles is investigated using a 29 nm wide tunneling magnetoresistive reader. At a linear density of 702 kbpi, a post-detection byte-error rate (BER) of 2.8e−2 is demonstrated based on measured recording data and a software read channel. The read channel uses a 64-state implementation of an extended version of a data-dependent noise-predictive maximum-likelihood detection scheme that tracks the first- and second-order statistics of the data-dependent noise. At the demonstrated post-detection BER, a post-error-correction-coding BER of less than 1e−20 can be achieved using an iterative decoding architecture. To facilitate aggressive track-density scaling, we made multiple advances in the area of track following. First, we developed a new timing-based servo pattern and implemented a novel quad channel averaging scheme. Second, we developed a new field programmable gate array prototyping platform to enable the implementation of quad channel averaging. Third, we enhanced our low disturbance tape transport with a pair of 20 mm diameter air bearing tape guides and a prototype track-following actuator. Fourth, we developed a novel low friction tape head and, finally, we designed a set of tape speed optimized track-following controllers using the model-based $H_{\infty }$ design framework. Combining these technologies, we achieved a position error signal (PES) characterized by a standard deviation ≤ 3.18 nm over a tape speed range of 1.2–4.1 m/s. This magnitude of PES in combination with a 29 nm wide reader enables reliable recording at a track width of 56.2 nm corresponding to a track density of 451.9 ktpi, for an equivalent areal density of 317.3 Gb/in2.

An In0.53Ga0.47As/In0.52Al0.48As/In0.53Ga0.47As double hetero-junction junctionless TFET

In this paper, an In0.53Ga0.47As/In0.52Al0.48As/In0.53Ga0.47As double hetero-junction junctionless tunnel field-effect transistor (JL-TFET) is proposed, whose N+-channel is formed through the two-dimensional electron gas (2DEG) generated by the hetero-junction without directly implementing physical doping. It can not only effectively suppress the random dopant fluctuation in traditional JL-TFET, but also solve the problem that the electron tunneling is hindered by the wide tunneling barrier at the tunneling junction in conventional dopingless TFET. The existence of 2DEG at the source/channel junction for the proposed JL-TFET can decrease the lateral tunneling distance and enlarge the energy range for tunneling, thereby promoting the device performance. Investigations on effects of the thickness of channel layer (T c), the N-type doping concentration (N+D) in doping layer, and the gate dielectric on JL-TFET demonstrate that the optimal device characteristics can be obtained when T c = 2 nm, N+D = 1 × 1019 cm−3, and the high-K dielectric is adopted.

Development of Ji Micromechanics Model for Electrical Conductivity of Carbon Nanotubes-reinforced Samples

In this paper, Ji model for tensile modulus of nanocomposites is expanded to forecast the conductivity of polymer nanocomposites including carbon nanotubes (CNT) summarized as PCNT. The advanced model undertakes the volume fraction of networked CNT and the inherent resistances of tunneling and interphase sections. CNT loading, CNT size and interphase depth suggest the proportion of networked CNT. In addition, the tunneling confrontation is correlated to tunneling width, tunneling distance and polymer tunneling resistivity. The advanced model is used to express the parameters’ roles in the conductivity. Furthermore, the predictions of advanced model are linked to the experimental results of some examples. The proper impressions of all factors on the conductivity as well as the fine agreements among experimental data and calculations justify the advanced model. The radius and length of CNT mainly handle the conductivity, but CNT conduction is useless. Also, a dense interphase causes desirable conductivity, but the interphase conduction cannot govern the conductivity. Moreover, wide tunnels, deprived polymer tunneling resistivity and minuscule tunneling distance enhance the conductivity.

Development and simplification of a micromechanic model for conductivity of carbon nanotubes-reinforced nanocomposites

In the current paper, Hui-Shia model for composite’s modulus is simplified and advanced to evaluate the electrical conductivity of carbon nanotubes (CNT)-reinforced nanocomposites (PCNT) by CNT aspect ratio, CNT network part, interphase district and tunnels between adjacent CNT. CNT loading, CNT magnitude and interphase depth suggest the proportion of networked CNT. In addition, CNT and tunneling intrinsic resistances express the entire conductivity of included components in nanocomposites. The reasonable roles of all factors in the conductivity and the proper matching between trial data and predictions approve the established model. Both dense interphase and long CNT improve the conductivity; however, reedy interphase or short CNT induces an insulated sample. The polymer tunneling resistivity negatively affects the conductivity, while CNT conductivity is an unsuccessful term. Furthermore, both short and wide tunnels desirably control the nanocomposite’s conductivity.

A special support design for a large-span tunnel crossing an active fault (T9 Tunnel, Ankara–Sivas High-Speed Railway Project, Turkey)

Throughout construction process of a tunnel in an active tectonic region, it may be impossible to avoid active faults. Active faults create two adverse effects on the tunnels which are sudden fault displacement and weak ground conditions in fault zone. If a tunnel crossed by an active fault, the tunnel might be damaged by sudden movement of the fault. However, the main goal is to localize this damage without complete loss of tunnel. In this study, a special design developed for a wide span tunnel cut by an active fault is presented and the performance of the design is verified by numerical analyses. T9 tunnel was constructed within the scope of Ankara–Sivas High-Speed Train Project, Turkey, and the special design at the intersection of T9 tunnel with the Akdagmadeni active fault is the main subject of this study. T9 tunnel predominantly passes through agglomerate, basalt, marble and gneiss units and the tunnel route crosses the Akdagmadeni fault at around Km: 327 + 915. At this location, major deformations occurred in the tunnel and the tunnel excavation had to stop for a certain period. After the re-design phase, a special tunnel support system for this location were developed and proposed design was analyzed with numerical analyses. In addition, the possible displacement of the Akdagmadeni fault was estimated and the inner lining was re-designed considering the seismic parameters (i.e. peak ground acceleration and maximum displacement during a large earthquake). Consequently, in the present study, the effects of active fault crossing on the tunnel were explained and a special inner lining design was proposed to localize the possible damages, which are originated from the sudden displacement of the active fault.

First-principles study of the structural and electrochemical properties of NaxTi2O4 (0 ≤x≤ 1) with tunnel structure for anode applications in alkali-ion batteries.

Due to their low cost and easy synthesis method, several kinds of sodium titanates have been explored as anode materials for sodium ion batteries (SIBs). However, some of them have not yet been considered as electrode materials for SIBs, and here we have carried out a first-principles study on NaxTi2O4 compounds with two different tunnel structures, denoted as single and double phases, to demonstrate their structural and electrochemical properties upon Na or Li insertion. Our calculation results reveal that these compounds exhibit structural stability during sodiation/desodiation and a moderate electrode voltage of ∼0.82 V vs. Na+/Na with a specific capacity of ∼150 mA h g-1. In particular, the activation energy of Na+ ion migration in the double phase is estimated to be as low as 0.28 eV, which is the lowest value among the SIB electrodes developed so far, and this can be attributed to the wide tunnel structure. In addition, we verify their potentiality for use as anode materials in lithium ion batteries (LIBs) by exploring their properties upon Li insertion. Since these compounds are predicted to be promising anode materials for SIBs or LIBs by our calculations, we believe that our findings will promote further experimental studies.

Investigation of Sine Groove Waveguide Slow Wave Structure for Terahertz Traveling Wave Tube

A novel sine groove waveguide slow wave structure (SGW-SWS), originated from the sine waveguide (SW), is proposed for a wideband terahertz (THz) traveling wave tube (TWT). SGW-SWS not only has high interaction impedance in a relatively wide frequency band, but also has a wide beam tunnel. In addition, it can be fabricated using the Nano-Computer Numerical Control (CNC) milling techniques. The high-frequency simulation results show that, under the same dispersion, the passband of SGW-SWS is 23 GHz wider than that of SW-SWS, and the average interaction impedance of SGW-SWS is higher than that of SW-SWS in the whole passband. And the transverse dimension of beam tunnel is independent of the dispersion characteristics of SGW-SWS, so the beam current can be further increased by enlarging the size of beam tunnel. Moreover, the particle-in-cell (PIC) simulation results reveal that the saturated power and electronic efficiency of SGW-TWT in the frequency range of 201–260 GHz are more than 84.9 W and 2.72%, respectively, when the operating voltage is 20.8 kV and the beam current is 150 mA.