Groove Tracking Research Articles

Structural basis for TBP displacement from TATA box DNA by the Swi2/Snf2 ATPase Mot1.

The Swi2/Snf2 family transcription regulator Modifier of Transcription 1 (Mot1) uses adenosine triphosphate (ATP) to dissociate and reallocate the TATA box-binding protein (TBP) from and between promoters. To reveal how Mot1 removes TBP from TATA box DNA, we determined cryogenic electron microscopy structures that capture different states of the remodeling reaction. The resulting molecular video reveals how Mot1 dissociates TBP in a process that, intriguingly, does not require DNA groove tracking. Instead, the motor grips DNA in the presence of ATP and swings back after ATP hydrolysis, moving TBP to a thermodynamically less stable position on DNA. Dislodged TBP is trapped by a chaperone element that blocks TBP's DNA binding site. Our results show how Swi2/Snf2 proteins can remodel protein-DNA complexes through DNA bending without processive DNA tracking and reveal mechanistic similarities to RNA gripping DEAD box helicases and RIG-I-like immune sensors.

Converging-guiding-track design enables 100% growth deployment rate of ultrathin monocrystalline silicon nanowire channels

A low temperature catalytic growth of orderly ultrathin silicon nanowires (SiNWs) is desirable for the construction of monolithic 3D stacked electronics but usually suffers a large diameter fluctuation and a low growth deployment rate (GDR). In this work, the ultra-confined growth dynamics of in-plane solid–liquid–solid SiNWs within narrow groove tracks has been systematically investigated, and a converging-guiding-track strategy is proposed and testified to accomplish 100% GDR of ultra-dense and uniform SiNW array, with diameter and spacing of only Dnw = 22.5±3.5 nm and 25 nm, respectively. Despite a low temperature growth at 350 °C, the SiNWs are found to be all monocrystalline and Si⟨100⟩ oriented, while prototype Schottky barrier tunneling field effect transistors built on the SiNW channels demonstrate a high Ion/off ratio and subthreshold swing of >105 and 197 mV dec−1. This new strategy complements a long-missing key capability of catalytic growth approach to serve a reliable integration technology of ultrafine high quality 1D c-Si channels, without the need of preexisting wafer substrate, for a wide range of 3D electronics, neuromorphic, and logic-in-memory functionalities.

Self-propelled continuous transport of nanoparticles on a wedge-shaped groove track.

Controlling the directional motion of nanoparticles on the surface is particularly important for human life, but achieving continuous transport is a time-consuming and demanding task. Here, a spontaneous movement of nanoflakes on a wedge-shaped groove track is demonstrated by using all-atom molecular dynamics (MD) simulations. Moreover, an optimized track, where one end of the substrate is cut into an angle, is introduced to induce a sustained directional movement. It is shown that the wedge-shaped interface results in a driving force for the nanoflakes to move from the diverging to the converging end, and the angular substrate provides an auxiliary driving force at the junction to maintain continuous transport. A force analysis is carried out in detail to reveal the driving mechanism. Moreover, the sustained transport is sensitive to the surface energy and structural characteristics of the track: the nanoflakes are more likely to move continuously on the track with lower surface energy and a smaller substrate and groove opening angle. The present findings are useful for designing nanodevices to control the movement of nanoparticles.

Conformational Change of Transcription Factors from Search to Specific Binding: A lac Repressor Case Study.

In a process known as facilitated diffusion, DNA-binding proteins find their target sites by combining three-dimensional diffusion and one-dimensional scanning of the DNA. Following the trade-off between speed and stability, agile exploration of DNA requires loose binding, whereas, at the DNA target site, the searching protein needs to establish tight interactions with the DNA. To enable both efficient search and stable binding, DNA-binding proteins and DNA often switch conformations upon recognition. Here, we study the one-dimensional diffusion and DNA binding of the dimeric lac repressor (LacI), which was reported to adopt two different conformations when binding different conformations of DNA. Using coarse-grained molecular dynamic simulations, we studied the diffusion and the sequence-specific binding of these conformations of LacI, as well as their truncated or monomeric variants, with two DNA conformations: straight and bent. The simulations were compared to experimental observables. This study supports that linear diffusion along DNA combines tight rotation-coupled groove tracking and rotation-decoupled hopping, where the protein briefly dissociates and reassociates just a few base pairs away. Tight groove tracking is crucial for target-site recognition, while hopping speeds up the overall search process. We investigated the diffusion of different LacI conformations on DNA and show how the flexibility of LacI's hinge regions ensures agility on DNA as well as faithful groove tracking. If the hinge regions instead form α-helices at the protein-DNA interface, tight groove tracking is not possible. On the contrary, the helical hinge region is essential for tight binding to bent, specific DNA, for the formation of the specific complex. Based on our study of different encounter complexes, we argue that the conformational change in LacI and DNA bending are somewhat coupled. Our findings underline the importance of two distinct protein conformations for facilitated diffusion and specific binding, respectively.

A Study of Ball Rolling Noise Radiation from a Ball Screw

Aiming to clarify the mechanism of vibration and noise radiation induced by ball rolling in a ball screw two simple models of the ball screw are established and theorecally and experimentally examined. Equations on the behaviour of rolling ball between crossing two straight grooves and contact forces acting them are formulated and solved. Experiments with an apparatus with straight groove plates reveal that proposed model can predict rolling behavior and contact forces with an adequate accuracy, considering crossed axis angle, groove velocity, preload and surface roughness of groove tracks. Then, a circular plates model consisting of multiple balls and relatively rotating two thick circular plates with circular track groove is proposed and analyzed to predict vibration and noise radiation of the rotating plate due to moving excitation given with surface roughness of groove and ball contact stiffness. Since the frequency characteristics of the estimated vibration and noise agree well with those measured with another experimental apparatus, the mechanism of ball rolling induced noise is thus clarified.

Analysis and Prediction of Trough Track Superelevation Based on Big Data

The detection of the safety status of urban rail transit is an important part of ensuring the operation of the rail. Using the data detected by the rail to analyze and predict the quality of the rail is very important for the research of rail inspection. Based on the existing research, this paper uses big data to analyze the collected superelevation data, and builds a trough-track superelevation big data prediction model based on the combination of the stochastic oscillation sequence gray model and ALO-Elman network to analyze the historical superelevation data and mine information about superelevation trends. In this paper, the average value of superelevation data of the equal-spaced groove track in a certain interval is collected for verification. The experimental results show that the method can reasonably predict the change trend of the ultra-elevation. The change trend is basically in line with the original data change trend, and the deviation is controlled to be small within range.

Gender differences in femoral trochlea morphology.

This study aimed to analyze the morphology of the anterior femoral condyle using a quantitative three-dimensional reconstruction method. The morphological data were compared between genders. Computed tomography scans of femurs were taken from 90 healthy subjects and then reconstructed in 3D modeling software. Coaxial cutting planes were created at 10° increments to measure the lateral and medial anterior condylar heights (LACH and MACH, respectively), lateral and medial trochlear groove widths (LTW and MTW, respectively), and for trochlear groove tracking. The absolute values and normalized data were compared between male and female subjects. The sulcus angle and deepest point of the trochlear groove at each cross-section were also analyzed to determine the differences in the depth of the trochlear groove. The absolute dimensions of LACH, MACH, LTW, and MTW were significantly smaller in the female subjects, by 10.5%, 36.9%, 10.3%, and 11.0%, respectively, than in the males (p < 0.05). After normalization, no significant difference was found in the condylar height between the genders. However, the female subjects had a significantly larger value of approximately 7.9% for the normalized trochlear width. Male subjects had greater condylar heights and widths than the female subjects. Although the trajectory of the trochlear groove varied greatly among the subjects, the trochlear groove appeared to be wider and shallower in the female subjects than in the male subjects. These results provide important information for the design of femoral trochlea to fit Asian female patients. III.

Additive manufacturing process creates local surface roughness modifications leading to variation in cell adhesion on multifaceted TiAl6V4 samples

This work looks at the effect of the surface texture variability on cell adhesion and cell morphology of an osteoblastic linage (MC3T3) using a multifaceted TiAl6V4 (stem-like) specimen produced by selective laser melting.We produced a Ti6Al4V anchoring component presenting de facto surfaces with different inclinations with respect to the build plate. Surfaces had different complex surface textures composed of submicroscale groove tracks induced by the laser beam, and partially melted particles varying with the inclination of the surface in the SLM chamber. We measured the adhesion of cells on the specimen, having previously tested any cytotoxic effect of the material on a fibroblastic linage. Our multifaceted geometric specimens made it possible to compare potential effects of different surface textures on the same specimen. We found that cell attachment increased on surfaces with microscale grooves, and that partially melted powders were the least appreciated zones for adhesion (26-fold increase in the number of cells from a zone containing 1192 particles/mm2 compared to 188,3 particles/mm2). The ratio of the number of submicroscale grooves to the number of partially melted particles can be controlled by the inclination of the surface with respect to the build plate. Surfaces with a lower inclination (upskin surfaces) had fewer partially melted particles than downskin surfaces (200 particles/mm2 at 35° compared to 1200 particles/mm2 at 125°).Based on our results, we propose an approach to better understand and therefore control the inherent heterogeneities of AM-based implants in order to reduce potentially costly post-processing for osseous interface implant.

Do size, shape, and alignment parameters of the femoral condyle affect the trochlear groove tracking? A morphometric study based on 3D- computed tomography models in Chinese people

BackgroundOur study aimed to investigate whether geometrical features (size, shape, or alignment parameters) of the femoral condyle affect the morphology of the trochlear groove.MethodsComputed tomography models of 195 femurs (97 and 98 knees from male and female subjects, respectively) were reconstructed into three-dimensional models and categorised into four types of trochlear groove morphology based on the position of the turning point in relation to the mechanical axis (types 45°, 60°, 75°, and 90°). Only subjects with healthy knees were included, whereas individuals with previous knee trauma or knee pain, soft tissue injury, osteoarthritis, or other chronic diseases of the musculoskeletal system were excluded. The size parameters were: radius of the best-fit cylinder, anteroposterior dimension of the lateral condyles (AP), and distal mediolateral dimension (ML). The shape parameters were: aspect ratio (AP/ML), arc angle, and proximal- and distal- end angles. The alignment parameters were: knee valgus physiologic angle (KVPA), mechanical medial distal femoral angle (mMDFA), and hip-knee-ankle angle (HKA). All variables were measured in the femoral condyle models, and the means for each groove type were compared using one-way analysis of variance.ResultsNo significant difference among groove types was observed regarding size parameters. There were significant differences when comparing type 45° with types 60°, 75°, and 90° regarding aspect ratio and distal-end angle (p < 0.05), but not regarding proximal-end angle. There were significant differences when comparing type 90° with types 45°, 60°, and 75° regarding KVPA, mMDFA, and HKA (p < 0.05).ConclusionAmong size, shape, and alignment parameters, the latter two exhibited partial influence on the morphology of the trochlear groove. Shape parameters affected the trochlear groove for trochlear type 45°, for which the femoral condyle was relatively flat, whereas alignment parameters affected the trochlear groove for trochlear type 90°, showing that knees in type 90° tend to be valgus. The morphometric analysis based on trochlear groove classification may be helpful for the future design of individualized prostheses.

Theoretical Studies of Dust-Raising Characteristics of Heading Machines

The paper studies how the design parameters of the development machines affect the generation intensity of the explosive coal dust. At present, there are about 20 different types of development machines operating in underground coal mines. The operation of these machines produces coal dust in explosive concentrations. When working on improving the design parameters of the development machines, their dust-generating properties must be accounted for. The organic part of coal dust of 30-50 µm size is considered explosive. The article proposes an index of dust-generating intensity for the development machines. The value of this index equals the total length of grooves which are produced by hard-alloy inserts of the machine’s cutter picks within 1 minute. The article presents the dependency relations for calculating the amount of dust produced from 1 m of groove, including its explosive properties. We have also provided a dependency relation between the total length of grooves and the number of cutter picks, the average diameter of the cutter head and revolutions per minute. The underground field research has confirmed the presence of groove tracks at the face and the interrelation of their size and the type of cutter picks used. The article provides estimates of the intensity of dust generation for the currently utilized types of development machines.

Morphological classification of the femoral trochlear groove based on a quantitative measurement of computed tomographic models.

This study aimed to investigate the natural morphology of the femoral trochlear groove based on quantitative measurement. Computed tomographic femur models of 50 male and 50 female healthy Chinese adults (30-60years) were analysed using three-dimensional software. Coaxial cutting planes (15° increments) rotating about the trochlear groove axis from the proximal to distal point were created, followed by the deepest point of the trochlear groove marked at each cross section. The shape, position, and orientation of the trochlear groove were analysed. The trochlear groove was located laterally relative to the mechanical axis and consisted of the laterally oriented proximal part and medially oriented distal part. Based on the turning points located on different cross sections, the trochlear groove was classified into four types: types 45°, 60°, 75°, and 90°. The mediolateral position relative to the mechanical axis was types 45°, 60°, 75°, and 90°, from the lateral to medial side, while the distal parts of them extended along the same path. The orientation of the trochlear groove was relatively consistent and smooth, which oriented at approximately 1° medially between two adjacent segments, except at approximately 10° medially at the turning point. The trochlear groove tracking varies greatly amongst a population that is mainly categorized into four types. This study may be helpful for better understanding of the natural trochlear groove anatomy, prosthetic design modification, and provide the reference value for studying patellofemoral diseases such as patellar maltracking and trochlear dysplasia. Prospective study, Level II.

New Wobble-Address Format for an Optical Disc with a Separated Guide Layer

We propose a physical address format suitable for the separated guide layer of a multilayered optical disc. Since the track format of the guide layer is different from that of conventional multilayered discs, a novel address format is required. The proposed format adopts a land-and-groove-track structure to generate a stable tracking signal. The address information for land and groove tracks is physically premastered by the wobbling and width-modulating of grooves. We fabricated a replicated disc sample with the proposed format and demonstrated a sufficiently low bit error rate by an experiment. Consequently, we considered that the format is a promising solution for the physical format for multilayered discs with a separated guide layer.

Relationship Between Three-Dimensional Geometry of the Trochlear Groove and In Vivo Patellar Tracking During Weight-Bearing Knee Flexion

It is widely recognized that the tracking of patella is strongly influenced by the geometry of the trochlear groove. Nonetheless, quantitative baseline data regarding correlation between the three-dimensional geometry of the trochlear groove and patellar tracking under in vivo weight-bearing conditions are not available. A combined magnetic resonance and dual fluoroscopic imaging technique, coupled with multivariate regression analysis, was used to quantify the relationship between trochlear groove geometry (sulcus location, bisector angle, and coronal plane angle) and in vivo patellar tracking (shift, tilt, and rotation) during weight-bearing knee flexion. The results showed that in the transverse plane, patellar shift was strongly correlated (correlation coefficient R=0.86, p<0.001) to mediolateral location of the trochlear sulcus (raw regression coefficient β(raw)=0.62) and the trochlear bisector angle (β(raw)=0.31). Similarly, patellar tilt showed a significant association with the trochlear bisector angle (R=0.45, p<0.001, and β(raw)=0.60). However, in the coronal plane patellar rotation was poorly correlated with its matching geometric parameter, namely, the coronal plane angle of the trochlea (R=0.26, p=0.01, β(raw)=0.08). The geometry of the trochlear groove in the transverse plane of the femur had significant effect on the transverse plane motion of the patella (patellar shift and tilt) under in vivo weight-bearing conditions. However, patellar rotation in the coronal plane was weakly correlated with the trochlear geometry.

RNA polymerase can track a DNA groove during promoter search.

Many proteins select special DNA sequences to form functional complexes. In one possible mechanism, protein molecules would scan DNA sequences by tracking a groove without complete dissociation. Upon dragging single molecules of DNA over a surface carrying fixed Escherichia coli RNA polymerase holoenzyme, we detected rotation of individual DNA molecules, providing direct evidence that a DNA-binding protein can track a DNA groove. These results confirm our previous observations of longitudinal movement of RNA polymerase along fixed, extended DNA and, moreover, imply that groove tracking facilitates scanning of DNA sequences.

Wobble-Address Format of the Blu-ray Disc

We explain a new address format that is adapted in the Blu-ray Disc Rewritable format. The address information is prerecorded by wobbling the groove track. It is based on a single tone carrier to obtain a stable and accurate write clock. The modulation scheme is a combination of minimum shift keying (MSK) that is strong for media noise and saw tooth wobble (STW) that is strong for wobble shift. The robustness of the format is demonstrated by measurement of the system margins.

Simulations of Marks Formed on Phase-change, Land/Groove Disks*

Finite-difference time-domain (FDTD) simulation was used to determine the amount of absorption of light propagating inside a land/groove optical disk. The results showed that three-dimensional geometry influenced absorption. Furthermore, heat conduction inside the disk depended on its geometry, so the temperature profiles of land and groove tracks were not equal. Therefore, the spatial and historic profiles of temperature must be investigated in three dimensions. These temperature profiles can then be input into a phase-change simulator in order to carry out a simulation of the process of writing marks in land and groove tracks. To predict the optical and thermal effects of a land/groove structure on the writing process, we integrated an FDTD and phase-change simulation. The integrated simulation effectively evaluated the differences between the marks formed in land and groove tracks. As well, we applied the FDTD simulation to a blue-laser recording and found that groove-track recording showed higher light convergence than land-track recording. This inclination was explained the convex/concave effect of the structure of the disk surface.

Measurement of the thermal coefficients of rewritable phase-change optical recording media.

We describe a method to estimate the heat capacity of the substrate, the dielectric layer, and the phase-change layer of phase-change optical recording media as well as the thermal conductivity of the phase-change layer in its crystalline state. Measurements were carried out on spinning disks with the beam of light focused and locked onto the groove track. The method relies on the identification of the solid-to-liquid phase transition that occurs in the phase-change layer and takes advantage of the dependence of thermal diffusion on track velocity and irradiation time.

Wobble Addressing Method for Land and Groove Structured Optical Storage

In this paper, two wobble addressing methods for land and groove structured optical discs are proposed. These methods use only modulated wobble signals for addressing, while excluding the need for an embossed prepit. As a consequence, the overhead associated with the proposed methods is less than that of the conventional addressing method for rewritable digital versatile discs. In addition, the proposed methods enable the use of a one-beam mastering machine for making discs. This is possible because a signal from a land track is optically added to two signals from adjacent groove tracks, which are produced by a single laser beam for each signal, while maintaining its phase relationship for signal decoding. The advantages of the proposed methods have been demonstrated through computer simulation as well as through evaluation of test discs.

Thermal cross-track cross talk in phase-change optical disk data storage

We have investigated the temperature distribution in land/groove phase-change optical disks. The incident beam is linearly polarized either parallel to track (E∥ polarization) or tangential to track (E⊥ polarization). Calculations have shown that temperature profiles in the medium are dependent on the wavelength of light, the state of polarization, the geometry of the grooved structure, and the multilayer stack. The temperature profiles are quite different between the land track and the groove track. Thermal cross-track cross talk from a land track to its neighboring groove tracks is higher than that from a groove track to its neighboring land tracks. The interaction between the E⊥ electric field and the grooved structure is mainly responsible for thermal cross-track cross talk.

Analysis of Read-out Signals in Land/Groove Recording of a Phase-Change Optical Disc

We have analyzed the read-out signal obtained from a phase-change optical disc. The marks were recorded both on land tracks and in groove tracks with the focused laser beam of a wavelength of 685nm and a numerical aperture (NA) of 0.6. Characteristics of the read-out signal of marks recorded both on land tracks and in groove tracks were understood by considering the land/groove configuration of the substrate, the reflectance difference and the phase difference between amorphous and crystalline states of a recording layer. By comparing the measured carrier levels obtained from the land and groove tracks with the simulation results based on the diffraction theory, we found that the measured carrier level difference between land and groove recordings resulted mainly from the effects of groove geometry and the phase difference which was estimated to be 20° for our sample disc. For this work, the groove geometry of the substrate and mark sizes were precisely estimated from transmission electron microscopy (TEM) micrographs.