12 research outputs found
Supplemental Material: cdem: A macOS program for discrete element modeling of tectonic structures
No full textIncludes cdem simulations for Figures 1–12. Notes from author: These are files with .cdem extension containing the parameters and settings for each simulation. In addition, Table 2 specifies the general settings that must be set for each simulation via the Preferences panel (Fig. 3). Please note that after opening any of these files in cdem, you will need to Initialize it and Run it to recreate the results. Use a powerful computer with as many cores as possible. </p
A two-scale contact model for collisions between blocks in CDEM
No full textContact detection between interacting blocks is of great importance to discontinuity-based numerical methods, such as DDA, DEM, and NMM. A rigorous contact theory is a prerequisite to describing the interactions of multiple blocks. Currently, the penalty method, in which mathematical springs with high stiffness values are employed, is always used to calculate the contact forces. High stiffness values may cause numerical oscillations and limit the time step. Furthermore, their values are difficult to identify. The intention of this study is to present a two-scale contact model for the calculation of forces between colliding blocks. In this new model, a calculation step taken from the moment of contact will be divided into two time stages: the free motion time stage and the contact time stage. Actually, these two time stages correspond to two real physical processes. Based on this, we present a new numerical model that is intended to be more precise and useful in calculating the contact forces without mathematical springs. The propagation of the elastic wave during collision is of a characteristic length, which determines the volume of material involved in the contact force calculation. In conventional contact models, this range is always regarded as the length of one element, which may lead to an inaccurate calculation of contact forces. In fact, the real scale of this range is smaller than the length of a single element, and subdivided elements, which are refined according to the characteristic length and are presented in the new contact model
2D particle contact-based meshfree method in CDEM and its application in geotechnical problems
No full textPurpose - Continuum-based discrete element method is an explicit numerical method, which is a combination of block discrete element method (DEM) and FEM. When simulating large deformation problems, such as cutting, blasting, water-like material flowing, the distortion of elements will lead to no convergence of the numerical system. To solve the convergence problem, a particle contact-based meshfree method (PCMM) is introduced in. The paper aims to discuss this issue. Design/methodology/approach - PCMM is based on traditional particle DEM, and use particle contacts to generate triangular elements. If three particles are contact with each other, the element will be created. Once elements are created, the macroscopic constitutive law could be introduced in. When large deformation of element occurs, the contact relationship between particles will be changed. Those elements that do not meet the contact condition will be deleted, and new elements that coincide with the relationship will be generated. By the deletion and creation of elements, the convergence problem induced by element distortion will be eliminated. To solve FEM and PCMM coupled problems, a point-edge contact model is introduced in, and normal and tangential springs are adopted to transfer the contact force between particles and blocks. Findings - According to the deletion and recreation of elements based on particle contacts, PCMM could simulate large deformation problems. Some numerical cases (i.e. elastic field testing, uniaxial compression analysis and wave propagation simulation) show the accuracy of PCMM, and others (i.e. soil cutting, contact burst and water-like material flowing) show the rationality of PCMM. Originality/value - In traditional particle DEM, contact relationships are used to calculate contact forces. But in PCMM, contact relationships are adopted to generate elements. Compared to other meshfree methods, in PCMM, the element automatic deletion and recreation technique is used to solve large deformation problems
A GPU accelerated continuous-based discrete element method for elastodynamics analysis
No full textThis paper presents a GPU computing algorithm, used to accelerate the Continuous-based Discrete Element Method (CDEM). Using a NVIDIA GTX VGA card, the computing speed achieved an average 650 times speedup ratio vs. Intel Core-Dual 2.66 GHz CPU. To parallelize the CDEM algorithm, the clone node force refreshing process is separated from the elemental calculation, and is replaced by a "Node Group" force assignment process, which ensures the data independence in parallel execution
Comparisons between centrifuge and numerical modeling results for slope toppling failure
No full textThis paper presents series studies on the toppling mechanism by centrifuge tests and numerical simulations. Two different discrete element methods, i.e., the continuum-based discrete element method (CDEM) and the discontinuous deformation analysis (DDA), are adopted. The modeling results show that both the methods can accurately capture the failure modes of the centrifuge tests, including three distinct zones and two failure surfaces. Comparisons are made between the physical test and numerical simulation results. The critical inclination angle of the tilting table where the slope models are fixed on can be moderately predicted by the two methods, with different degrees of precision. The error between the test results and the simulated results is within 1% for the slope models without rock-bridges by both CDEM and DDA. However, it is amplified for the staggered-joint models that simulate the rock-bridges. With DDA, the average error is about 5%, and the maximum error is up to 17%. While with CDEM, the errors for the aligned-joint models are ranged from 1% to 6%, and it is from 10% to 29% for the staggered- joint models. The two numerical methods show the capability in simulating toppling failure of blocky rock mass with and without rock-bridges. The model with rock-bridges which provides a certain bending resistance is more stable than the one without any rock-bridge. In addition, the two failure surfaces were observed, which is different from the common understanding that only one failure surface appears
A case study integrating numerical simulation and GB-InSAR monitoring to analyze flexural toppling of an anti-dip slope in Fushun open pit
No full textToppling failure of rock slopes is a complicated mode due to a combination of both continuous and discontinuous deformation, especially in dealing with anti-dip rock slopes. In this paper, a novel continuum-based discrete element method (CDEM), which is useful in modeling the entire progressive process from continuous to discontinuous deformation, is proposed to analyze the deformation characteristics, the failure mechanism and the evolution process of a large-scale open pit slope with a typical anti-dip structure. To simulate the slope deformation, the shear strength reduction method (SSR) is adopted to represent the strength degradation of rock mass in the deterioration process. The simulated results are validated using data obtained from a field investigation and continuous monitoring by employing an advanced remote sensing technique called ground-based interferometric synthetic aperture radar (GB-InSAR). To analyze the evolution trend of the anti-dip slope, the subsequent toppling failure mode is predicted using the validated CDEM models. Based on a case study of a slope at the Fushun open pit mine (in Fushun, China), the unique geological structure with various joints and discontinuities, ground-water, intense rainfall, and mining activities are identified as the main triggers for different failure stages. The comparison between the field data and the simulation shows that CDEM accurately depicts the rock deformation and the failure pattern of the studied slope. The proposed numerical modeling techniques can be used for predicting failures of other similar excavated rock slopes. The simulated evolution process and the recorded deformation patterns help engineers to gain a better understanding of rock mass movement of anti-dip slopes, and the presented methodology could be utilized for similar studies and engineering designs. (C) 2015 Elsevier B.V. All rights reserved
Artificial membranes for membrane protein purification, functionality and structure studies
No full textMembrane proteins represent one of the most important targets for pharmaceutical companies. Unfortunately, technical limitations have long been a major hindrance in our understanding of the function and structure of such proteins. Recent years have seen the refinement of classical approaches and the emergence of new technologies that have resulted in a significant step forward in the field of membrane protein research. This review summarises some of the current techniques used for studying membrane proteins, with overall advantages and drawbacks for each method
A GPU-Based Parallel Procedure for Nonlinear Analysis of Complex Structures Using a Coupled FEM/DEM Approach
No full textThis study reports the GPU parallelization of complex three-dimensional software for nonlinear analysis of concrete structures. It focuses on coupled thermomechanical analysis of complex structures. A coupled FEM/DEM approach (CDEM) is given from a fundamental theoretical viewpoint. As the modeling of a large structure by means of FEM/DEM may lead to prohibitive computation times, a parallelization strategy is required. With the substantial development of computer science, a GPU-based parallel procedure is implemented. A comparative study between the GPU and CPU computation results is presented, and the runtimes and speedups are analyzed. The results show that dramatic performance improvements are gained from GPU parallelization
Stability analysis of underground oil storage caverns by an integrated numerical and microseismic monitoring approach
No full textUnderground storage in unlined caverns is of great significance for storing energy resources. Construction of underground storage caverns is an extremely complex process, involving extensive multi-bench excavation and strong unloading. Excavation-induced damage of surrounding rock masses may lead to instability of underground storage caverns. The aim of this paper is to put forward a method by integrating numerical simulation and microseismic monitoring for evaluation of cavern stability. A novel numerical method called Continuous-Discontinuous Element Method (CDEM) is applied to simulate micro-cracks under excavation-induced unloading conditions. Meanwhile, a microseismic (MS) monitoring system is employed to monitor real-time MS events during construction of storage caverns. Numerical results are validated using the monitoring data from the MS monitoring system. The integrated method is proved to be successful in capturing micro-cracks in underground storage caverns. Local instability, potential unstable zones and micro-crack evolution are analyzed, and cracking mechanisms are also discussed. (C) 2016 Elsevier Ltd. All rights reserved
Golgi-dependent transport of vacuolar sorting receptors is regulated by COPII, AP1, and AP4 protein complexes in tobacco.
No full textThe cycling of vacuolar sorting receptors (VSRs) between early and late secretory pathway compartments is regulated by signals in the cytosolic tail, but the exact pathway is controversial. Here, we show that receptor targeting in tobacco (Nicotiana tabacum) initially involves a canonical coat protein complex II-dependent endoplasmic reticulum-to-Golgi bulk flow route and that VSR-ligand interactions in the cis-Golgi play an important role in vacuolar sorting. We also show that a conserved Glu is required but not sufficient for rate-limiting YXX-mediated receptor trafficking. Protein-protein interaction studies show that the VSR tail interacts with the μ-subunits of plant or mammalian clathrin adaptor complex AP1 and plant AP4 but not that of plant and mammalian AP2. Mutants causing a detour of full-length receptors via the cell surface invariantly cause the secretion of VSR ligands. Therefore, we propose that cycling via the plasma membrane is unlikely to play a role in biosynthetic vacuolar sorting under normal physiological conditions and that the conserved Ile-Met motif is mainly used to recover mistargeted receptors. This occurs via a fundamentally different pathway from the prevacuolar compartment that does not mediate recycling. The role of clathrin and clathrin-independent pathways in vacuolar targeting is discussed
