RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures

The 3D architectures of RNAs are essential for understanding their cellular functions. While an accurate scoring function based on the statistics of known RNA structures is a key component for successful RNA structure prediction or evaluation, there are few tools or web servers that can be directly used to make comprehensive statistical analysis for RNA 3D structures. In this work, we developed RNAStat, an integrated tool for making statistics on RNA 3D structures. For given RNA structures, RNAStat automatically calculates RNA structural properties such as size and shape, and shows their distributions. Based on the RNA structure annotation from DSSR, RNAStat provides statistical information of RNA secondary structure motifs including canonical/non-canonical base pairs, stems, and various loops. In particular, the geometry of base-pairing/stacking can be calculated in RNAStat by constructing a local coordinate system for each base. In addition, RNAStat also supplies the distribution of distance between any atoms to the users to help build distance-based RNA statistical potentials. To test the usability of the tool, we established a non-redundant RNA 3D structure dataset, and based on the dataset, we made a comprehensive statistical analysis on RNA structures, which could have the guiding significance for RNA structure modeling. The python code of RNAStat, the dataset used in this work, and corresponding statistical data files are freely available at GitHub (https://github.com/RNA-folding-lab/RNAStat).

IFC TO CITYGML CONVERSION ALGORITHM BASED ON GEOMETRY AND SEMANTIC MAPPING

Geographic information system (GIS) is known traditionally for the modelling of two-dimensional (2D) geospatial analysis and therefore present information about the extensive spatial framework. On the other hand, building information modelling (BIM) is digital representation of building life cycle. The increasing use of both BIM and GIS simultaneously because of their mutual relationship, as well as their similarities, has resulted in more relationships between both worlds, therefore the need for their integration. A significant purpose of these similarities is importing BIM data into GIS to significantly assist in different design-related issues. However, currently this is challenging due to the diversity between the two worlds which includes diversity in coordinate systems, three-dimensional (3D) geometry representation, and semantic mismatch. This paper describes an algorithm for the conversion of IFC data to CityGML in order to achieve the set goal of sharing information between BIM and GIS domains. The implementation of the programme developed using python was validated using an IFC model (block HO2) of a student’s hostel, Kolej Tun Fatima (KTF). The conversion is based on geometric and semantic information mapping and the use of 3D affine transformation of IFC data from local coordinate system (LCS) to CityGML world coordinate system (WCS) (EPSG:4236). In order to bridge the gap between the two data exchange formats of BIM and GIS, we conducted geometry and semantic mapping. In this paper, we limited the conversion of the IFC model on level of details 2 (LOD2). The conversion will serve as a bridge toward the development of a software that will perform the conversion to create a strong synergy between the two domains for purpose of sharing information.

Fatigue Strength Evaluation of Welded Structure on Aluminum Alloy Car Body Based on Multi-Axial Stress

With the continuous development of the subway, the demand for its safety and stability is getting higher and higher. It is of great significance to accurately evaluate the fatigue life of the carbody to ensure the subway's safe operation. In this paper, the finite element model of a subway head carbody was established, and the fatigue strength of the welded structure on the carbody was evaluated based on Multi-axial stress. The local coordinate system was defined according to the geometrical characteristics of the welds. Local stresses perpendicular and parallel to the weld seam were obtained to calculate the stress ratio, stress range, and allowable stress value corresponding to the stress component. According to the joint fatigue resistance, the components of the degree of utilization and comprehensive degree of utilization are calculated to evaluate the structural fatigue strength under the survival rate of 97.5% and load cycles of 10 7 . The evaluation of the fatigue strength of the pivotal weld joints shows that the fatigue strength of the aluminum alloy carbody meets the design requirements, the weld of the carbody has a strong ability to resist fatigue damage. The fatigue strength of the weld is mainly affected by the normal stress component, while the shear stress has little effect on the fatigue strength of the structure. In addition, compared with the filleted weld joint and the butt-welded joint, the normal stress parallels to and perpendicular to the weld direction and shear stress have the greatest effect on the lap-welded joint. Meanwhile, the comprehensive degree of utilization of the lap-welded joint is the largest at 0.49. The introduction of multi-axial stress for the fatigue strength evaluation is beneficial when considering the material utilization degree in multiple structural directions. This research results provide a reference for fatigue strength evaluation of subway carbody's welded structure.

Automatic mapping of traffic signs

Nowadays, people easily can get into their cars and drive hundreds of kilometers in a few hours, but for that to work efficiently a system of rules must be applied and those rules have to be communicated transparently. This is why traffic signs are an influential part of our lives and every kind of information about each is helping the government, the community, and the drivers. This paper presents a novel and cost-efficient method for acquiring information on traffic signs, such like the category and the 3D position. The former can be gained using camera images and a Convolutional Neural Network model. The latter can be obtained using positioning devices.With the help of a GNSS device the absolute position of the vehicle can be learned and based on that a local coordinate system can be established. From the vehicle’s point of view the coordinates and the orientation of the traffic sign can be acquired by applying a stereo camera and an IMU (Inertial Measurement Unit) sensor. Then, with the help of these attributes a large database can be built, maintained, and updated. This project displays that adequately precise data can easily be accessible using a few cheap devices and sensors.

Pose Normalization of Indoor Mapping Datasets Partially Compliant with the Manhattan World Assumption

Due to their great potential for a variety of applications, digital building models are well established in all phases of building projects. Older stock buildings however frequently lack digital representations, and creating these manually is a tedious and time-consuming endeavor. For this reason, the automated reconstruction of building models from indoor mapping data has arisen as an active field of research. In this context, many approaches rely on simplifying suppositions about the structure of buildings to be reconstructed such as, e.g., the well-known Manhattan World assumption. This however not only presupposes that a given building structure itself is compliant with this assumption, but also that the respective indoor mapping dataset is aligned with the coordinate axes. Indoor mapping systems, on the other hand, typically initialize the coordinate system arbitrarily by the sensor pose at the beginning of the mapping process. Thus, indoor mapping data need to be transformed from the local coordinate system, resulting from the mapping process, to a local coordinate system where the coordinate axes are aligned with the Manhattan World structure of the building. This necessary preprocessing step for many indoor reconstruction approaches is also frequently known as pose normalization. In this paper, we present a novel pose-normalization method for indoor mapping point clouds and triangle meshes that is robust against large portions of the indoor mapping geometries deviating from an ideal Manhattan World structure. In the case of building structures that contain multiple Manhattan World systems, the dominant Manhattan World structure supported by the largest fraction of geometries was determined and used for alignment. In a first step, a vertical alignment orienting a chosen axis to be orthogonal to horizontal floor and ceiling surfaces was conducted. Subsequently, a rotation around the resulting vertical axis was determined that aligned the dataset horizontally with the axes of the local coordinate system. The performance of the proposed method was evaluated quantitatively on several publicly available indoor mapping datasets of different complexity. The achieved results clearly revealed that our method is able to consistently produce correct poses for the considered datasets for different input rotations with high accuracy. The implementation of our method along with the code for reproducing the evaluation is made available to the public.

TOF-Based Fast Self-Positioning Algorithm for UWB Mobile Base Stations

To solve the problem of heavy workload and high cost when acquiring the position of Ultra-Wideband (UWB) mobile base stations in sports fields, a fast self-positioning algorithm for UWB mobile base stations algorithm based on Time of Flight (TOF) is proposed. First, according to the layout of the base stations in the sports field, the local coordinate system is determined, and an equation based on the ranging information between the base stations is established; the Least Square method is used to calculate the coordinates of each base station, and the Newton Iteration method is used to converge the positioning results. Then the origin and propagation law of positioning error, as well as the method of reducing the positioning error are analyzed. The simulation data and experimental results show that the average positioning accuracy of the mobile base station is within 0.05 m, which meets the expected accuracy of the base station position measurement. Compared with traditional manual measurement methods, base station self-positioning can effectively save deployment time and reduce workload.

STRESS AND FAILURE ANALYSIS OF WOVEN COMPOSITES USING AN AUTOMATED CONFORMAL MESH METHOD

This paper presents a progressive damage modeling study to investigate the damage and failure behaviors of woven composites using an automated structured conformal meshing model developed by the authors. The composite domain consists of two materials: yarns and matrix. Yarns impregnated by matrix are considered to be homogenous and transversely isotropic. Each yarn element has its local coordinate system oriented according to the yarn’s centroid path. Properties of yarn are obtained using a micromechanics-based homogenization method. The matrix is considered to be homogenous and isotropic. Maximum stress is used as the damage initiation criteria under tensile loading. Damage evolution is governed by the material property degradation method. The meshing algorithm is based on a realistic micro-geometry generated using the Digital Fabric Mechanics Analyzer (DFMA), and thus is applicable to a wide variety of woven architectures. Numerical damage predictions are discussed and compared with previous numerical studies and experimental data to support the validity of the proposed model.

An Enhanced Ubiquitous-Joint Model for a Rock Mass With Conjugate Joints and Its Application on Excavation Simulation of Large Underground Caverns

A conjugate jointed rock mass (CJRM) is a rock mass with two sets of intersecting joints formed from intact rock under shear. Its mechanical properties and excavation-induced hazards of large underground caverns are different from those of common rock masses because of the unique geological origin thereof. To demonstrate numerically the excavation responses of CJRM, the ubiquitous-joint model is enhanced by consideration of the specific mechanical behaviors of the rock mass. In the enhanced model, CJRM is considered as the composite of columns of rock and two sets of weak planes of joints. The local coordinates, failure modes, and failure sequences of the rock columns and joints are redefined based on the composite characteristics of CJRM, and the failure criteria and plastic potential functions are accordingly modified. The enhanced model is verified numerically by triaxial compression tests and then employed to simulate the excavation of large underground caverns of a pumped storage power station in China. Results show that the modification of the local coordinate system, failure modes, and failure sequences made in the enhanced model is suited to the simulation of the mechanical behaviors of CJRM. Compared with the original ubiquitous-joint model, the enhanced model allows better predictions of the distribution of plastic zones and magnitudes of deformations in simulating underground excavations in CJRM and helps to assess the excavation-triggered hazards more accurately.

On the Effective Implementation and Capabilities of the Least-Squares Collocation Method for Solving Second-Order Elliptic Equations

Исследованы возможности численного метода коллокации и наименьших квадратов (КНК) на примерах кусочно-полиномиального решения задачи Дирихле для уравнений Пуассона и типа диффузии-конвекции с особенностями в виде больших градиентов и разрыва решения на границах раздела двух подобластей. Предложены и реализованы новые hp-варианты метода КНК, основанные на присоединении внутри области малых и/или вытянутых нерегулярных ячеек, отсекаемых криволинейной границей раздела от исходных прямоугольных ячеек сетки, к соседним самостоятельным ячейкам. Выписываются с учетом особенности условия согласования между собой кусков решения в ячейках, примыкающих с разных сторон к границе раздела. Проведено сравнение результатов, полученных методом КНК и другими высокоточными методами. Показаны преимущества и достоинства метода КНК. Для ускорения итерационного процесса применены современные алгоритмы и методы: предобуславливание; свойства локальной системы координат в методе КНК; ускорение, основанное на подпространствах Крылова; операция продолжения на многосеточном комплексе; распараллеливание. Исследовано влияние этих способов на количество итераций и время расчетов при аппроксимации полиномами различных степеней. The capabilities of the numerical least-squares collocation (LSC) method of the piecewise polynomial solution of the Dirichlet problem for the Poisson and diffusion-convection equations are investigated. Examples of problems with singularities such as large gradients and discontinuity of the solution at interfaces between two subdomains are considered. New hp-versions of the LSC method based on the merging of small and/or elongated irregular cells to neighboring independent cells inside the domain are proposed and implemented. They cut off by a curvilinear interface from the original rectangular grid cells. Taking into account the problem singularity the matching conditions between the pieces of the solution in cells adjacent from different sides to the interface are written out. The results obtained by the LSC method are compared with other high-accuracy methods. Advantages of the LSC method are shown. For acceleration of an iterative process modern algorithms and methods are applied: preconditioning, properties of the local coordinate system in the LSC method, Krylov subspaces; prolongation operation on a multigrid complex; parallelization. The influence of these methods on iteration numbers and computation time at approximation by polynomials of various degrees is investigated.

Kinematic Modeling of Six-Axis Industrial Robot and its Parameter Identification: A Tutorial

In advanced industrial applications, like machining, the absolute positioning accuracy of a six-axis robot is indispensable. To improve the absolute positioning accuracy of an industrial robot, numerical compensation based on positioning error prediction by the Denavit and Hartenberg (D-H) model has been investigated extensively. The main objective of this study is to review the kinematic modeling theory for a six-axis industrial robot. In the form of a tutorial, this paper defines a local coordinate system based on the position and orientation of the rotary axis average lines, as well as the derivation of the kinematic model based on the coordinate transformation theory. Although the present model is equivalent to the classical D-H model, this study shows that a different kinematic model can be derived using a different definition of the local coordinate systems. Subsequently, an algorithm is presented to identify the error sources included in the kinematic model based on a set of measured end-effector positions. The identification of the classical D-H parameters indicates a practical engineering application of the kinematic model for improving a robot’s positioning accuracy. Furthermore, this paper presents an extension of the present model, including the angular positioning deviation of each rotary axis. The angular positioning deviation of each rotary axis is formed as a function of the axis’ command angles and the direction of its rotation to model the effect of the rotary axis backlash. The identification of the angular positioning deviation of each rotary axis and its numerical compensation are presented, along with their experimental demonstration. This paper provides an essential theoretical basis for the error source diagnosis and error compensation of a six-axis robot.