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discrete element method

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https://www.readbyqxmd.com/read/27915232/quantitative-profiling-of-selective-sox-pou-pairing-on-hundreds-of-sequences-in-parallel-by-coop-seq
#1
Yiming K Chang, Yogesh Srivastava, Caizhen Hu, Adam Joyce, Xiaoxiao Yang, Zheng Zuo, James J Havranek, Gary D Stormo, Ralf Jauch
Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements...
December 2, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27882468/discrete-element-modelling-of-sediment-falling-in-water
#2
Dong Wang, Dao Ho-Minh, Danielle S Tan
The Discrete Element Method (DEM) is a discrete, particle-based method commonly used in studies involving granular media, e.g. sediment transport, and geomechanics. It is heavily dependent on particle properties, and one important component is the force model, which relates the relative positions and velocities of the simulated particles to the forces they experience. In this paper we model a collection of lightly compacted granular material, released at a short distance above a flat base in a quiescent fluid --similar to the process whereby sediment tailings are released back into the sea during nodule harvesting...
November 2016: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/27865921/community-detection-in-weighted-brain-connectivity-networks-beyond-the-resolution-limit
#3
Carlo Nicolini, Cécile Bordier, Angelo Bifone
Graph theory provides a powerful framework to investigate brain functional connectivity networks and their modular organization. However, most graph-based methods suffer from a fundamental resolution limit that may have affected previous studies and prevented detection of modules, or "communities", that are smaller than a specific scale. Surprise, a resolution-limit-free function rooted in discrete probability theory, has been recently introduced and applied to brain networks, revealing a wide size-distribution of functional modules (Nicolini and Bifone, 2016), in contrast with many previous reports...
November 16, 2016: NeuroImage
https://www.readbyqxmd.com/read/27855228/the-devil-is-in-the-details-incomplete-reporting-in-preclinical-animal-research
#4
Marc T Avey, David Moher, Katrina J Sullivan, Dean Fergusson, Gilly Griffin, Jeremy M Grimshaw, Brian Hutton, Manoj M Lalu, Malcolm Macleod, John Marshall, Shirley H J Mei, Michael Rudnicki, Duncan J Stewart, Alexis F Turgeon, Lauralyn McIntyre
Incomplete reporting of study methods and results has become a focal point for failures in the reproducibility and translation of findings from preclinical research. Here we demonstrate that incomplete reporting of preclinical research is not limited to a few elements of research design, but rather is a broader problem that extends to the reporting of the methods and results. We evaluated 47 preclinical research studies from a systematic review of acute lung injury that use mesenchymal stem cells (MSCs) as a treatment...
2016: PloS One
https://www.readbyqxmd.com/read/27853896/discrete-mesh-approach-in-morphogenesis-modelling-the-example-of-gastrulation
#5
J Demongeot, A Lontos, E Promayon
Morphogenesis is a general concept in biology including all the processes which generate tissue shapes and cellular organizations in a living organism. Many hybrid formalizations (i.e., with both discrete and continuous parts) have been proposed for modelling morphogenesis in embryonic or adult animals, like gastrulation. We propose first to study the ventral furrow invagination as the initial step of gastrulation, early stage of embryogenesis. We focus on the study of the connection between the apical constriction of the ventral cells and the initiation of the invagination...
November 16, 2016: Acta Biotheoretica
https://www.readbyqxmd.com/read/27845929/electroencephalography-eeg-forward-modeling-via-h-div-finite-element-sources-with-focal-interpolation
#6
S Pursiainen, J Vorwerk, C H Wolters
The goal of this study is to develop focal, accurate and robust finite element method (FEM) based approaches which can predict the electric potential on the surface of the computational domain given its structure and internal primary source current distribution. While conducting an EEG evaluation, the placement of source currents to the geometrically complex grey matter compartment is a challenging but necessary task to avoid forward errors attributable to tissue conductivity jumps. Here, this task is approached via a mathematically rigorous formulation, in which the current field is modeled via divergence conforming H(div) basis functions...
December 21, 2016: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/27779140/integral-equations-and-boundary-element-solution-for-static-potential-in-a-general-piece-wise-homogeneous-volume-conductor
#7
Matti Stenroos
Boundary element methods (BEM) are used for forward computation of bioelectromagnetic fields in multi-compartment volume conductor models. Most BEM approaches assume that each compartment is in contact with at most one external compartment. In this work, I present a general surface integral equation and BEM discretization that remove this limitation and allow BEM modeling of general piecewise-homogeneous medium. The new integral equation allows positioning of field points at junctioned boundary of more than two compartments, enabling the use of linear collocation BEM in such a complex geometry...
November 21, 2016: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/27775523/example-based-subspace-stress-analysis-for-interactive-shape-design
#8
Xiang Chen, Changxi Zheng, Kun Zhou
Stress analysis is a crucial tool for designing structurally sound shapes. However, the expensive computational cost has hampered its use in interactive shape editing tasks. We augment the existing example-based shape editing tools, and propose a fast subspace stress analysis method to enable stress-aware shape editing. In particular, we construct a reduced stress basis from a small set of shape exemplars and possible external forces. This stress basis is automatically adapted to the current user edited shape on the fly, and thereby offers reliable stress estimation...
October 19, 2016: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27761107/design-of-microfluidic-channels-for-magnetic-separation-of-malaria-infected-red-blood-cells
#9
Wei-Tao Wu, Andrea Blue Martin, Alberto Gandini, Nadine Aubry, Mehrdad Massoudi, James F Antaki
This study is motivated by the development of a blood cell filtration device for removal of malaria-infected, parasitized red blood cells (pRBCs). The blood was modeled as a multi-component fluid using the computational fluid dynamics discrete element method (CFD-DEM), wherein plasma was treated as a Newtonian fluid and the red blood cells (RBCs) were modeled as soft-sphere solid particles which move under the influence of drag, collisions with other RBCs, and a magnetic force. The CFD-DEM model was first validated by a comparison with experimental data from Han et al...
2016: Microfluidics and Nanofluidics
https://www.readbyqxmd.com/read/27722051/discrete-element-modeling-of-a-mining-induced-rock-slide
#10
JianJun Zhao, JianGuo Xiao, Min Lee Lee, YunTao Ma
Slopes are subjected to stress redistributions during underground mining activities, and this may eventually cause deformation or landslide. This paper takes Madaling landslide in Guizhou Province, China as a case study to investigate the failure mechanism and its run-out behaviours by using discrete element method. Previous qualitative analysis indicated that the slope experienced four stages of failure mechanisms: (1) development of tension cracks, (2) development of stepped-like creep cracks, (3) development of potential rupture surfaces, and (4) occurrence of the landslide...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27720592/sonochemical-synthesis-and-structural-determination-of-novel-the-nano-card-house-cu-ii-metal-organic-coordination-system
#11
Faeze Mojtabazade, Babak Mirtamizdoust, Ali Morsali, Pejman Talemi
A sonochemical method by using various time and concentrations of initial reagents and power of irradiation, was used to synthesize nano-card house of a new copper(II) metal-organic coordination system, {[Cu2(p-2yeinh)2Cl2]·(H2O)}n (1), where p-2yeinh=pyridin-2-yl ethylidene-isonicotinohydrazide. The compound was characterized by scanning electron microscopy (SEM), elemental analysis, IR spectroscopy, X-ray powder diffraction (XPRD), and single crystal X-ray analysis. The X-ray structure revealed that the Cu(II) atom is coordinated by one oxygen and three nitrogen atoms from two p-2yeinh ligands and one chloride anion with a CuN3OCl donor set with square pyramid geometry...
March 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/27713659/stress-concentration-in-periodically-rough-hertzian-contact-hertz-to-soft-flat-punch-transition
#12
R Ledesma-Alonso, E Raphaël, L Léger, F Restagno, C Poulard
We report on the elastic contact between a spherical lens and a patterned substrate, composed of a hexagonal lattice of cylindrical pillars. The stress field and the size of the contact area are obtained by means of numerical methods: a superposition method of discrete pressure elements and an iterative bisection-like method. For small indentations, a transition from a Hertzian to a soft-flat-punch behaviour is observed when the surface fraction of the substrate that is covered by the pillars is increased. In particular, we present a master curve defined by two dimensionless parameters, which allows one to predict the stress at the centre of the contact region in terms of the surface fraction occupied by pillars...
September 2016: Proceedings. Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/27706076/modeling-and-control-of-the-redundant-parallel-adjustment-mechanism-on-a-deployable-antenna-panel
#13
Lili Tian, Hong Bao, Meng Wang, Xuechao Duan
With the aim of developing multiple input and multiple output (MIMO) coupling systems with a redundant parallel adjustment mechanism on the deployable antenna panel, a structural control integrated design methodology is proposed in this paper. Firstly, the modal information from the finite element model of the structure of the antenna panel is extracted, and then the mathematical model is established with the Hamilton principle; Secondly, the discrete Linear Quadratic Regulator (LQR) controller is added to the model in order to control the actuators and adjust the shape of the panel...
October 1, 2016: Sensors
https://www.readbyqxmd.com/read/27697855/proteome-wide-structural-analysis-of-ptm-hotspots-reveals-regulatory-elements-predicted-to-impact-biological-function-and-disease
#14
Matthew P Torres, Henry Dewhurst, Niveda Sundararaman
Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al...
November 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27692112/is-cannulated-screw-fixation-an-alternative-to-plate-osteosynthesis-in-open-book-fractures-a-biomechanical-analysis
#15
Ángel Lázaro Gonzálvez, Javier Martínez Reina, Pedro Cano Luis, Juan Jiménez Baquero, José Sueiro Fernández, Miguel Ángel Giráldez Sánchez
OBJECTIVES: The current biomechanical work compares the symphyseal and sacroiliac stability obtained with two systems of bone osteosynthesis. The two methods of fixation compared were the 6-hole suprapubic non-locked plate and pubic fixation with two cannulated screws, a novel technique that can be applied percutaneously in the clinical practice. The aim of this study was to examine the validity of the use of two-cannulated-screws osteosynthesis in order to minimize the secondary effects of open fixation, especially in patients in whom an open reduction is contraindicated...
September 2016: Injury
https://www.readbyqxmd.com/read/27681417/super-enhancers-at-the-nanog-locus-differentially-regulate-neighboring-pluripotency-associated-genes
#16
Steven Blinka, Michael H Reimer, Kirthi Pulakanti, Sridhar Rao
Super-enhancers are tissue-specific cis-regulatory elements that drive expression of genes associated with cell identity and malignancy. A cardinal feature of super-enhancers is that they are transcribed to produce enhancer-derived RNAs (eRNAs). It remains unclear whether super-enhancers robustly activate genes in situ and whether their functions are attributable to eRNAs or the DNA element. CRISPR/Cas9 was used to systematically delete three discrete super-enhancers at the Nanog locus in embryonic stem cells, revealing functional differences in Nanog transcriptional regulation...
September 27, 2016: Cell Reports
https://www.readbyqxmd.com/read/27643816/estimating-colloidal-contact-model-parameters-using-quasi-static-compression-simulations
#17
Vincent Bürger, Heiko Briesen
For colloidal particles interacting in suspensions, clusters, or gels, contact models should attempt to include all physical phenomena experimentally observed. One critical point when formulating a contact model is to ensure that the interaction parameters can be easily obtained from experiments. Experimental determinations of contact parameters for particles either are based on bulk measurements for simulations on the macroscopic scale or require elaborate setups for obtaining tangential parameters such as using atomic force microscopy...
October 5, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/27627377/machine-learning-framework-for-analysis-of-transport-through-complex-networks-in-porous-granular-media-a-focus-on-permeability
#18
Joost H van der Linden, Guillermo A Narsilio, Antoinette Tordesillas
We present a data-driven framework to study the relationship between fluid flow at the macroscale and the internal pore structure, across the micro- and mesoscales, in porous, granular media. Sphere packings with varying particle size distribution and confining pressure are generated using the discrete element method. For each sample, a finite element analysis of the fluid flow is performed to compute the permeability. We construct a pore network and a particle contact network to quantify the connectivity of the pores and particles across the mesoscopic spatial scales...
August 2016: Physical Review. E
https://www.readbyqxmd.com/read/27627376/formation-mechanism-of-shock-induced-particle-jetting
#19
K Xue, L Sun, C Bai
The shock dissemination of granular rings or shells is characterized by the formation of coherent particle jets that have different dimensions from those associated with the constituent grains. In order to identify the mechanisms governing the formation of particle jets, we carry out the simulations of the shock dispersal of quasi-two-dimensional particle rings based on the discrete-element method. The evolution of the particle velocities and contact forces on the time scales ranging from microseconds to milliseconds reveals a two-stage development of particle jets before they are expelled from the outer surface...
August 2016: Physical Review. E
https://www.readbyqxmd.com/read/27597789/understanding-hydraulic-fracturing-a-multi-scale-problem
#20
REVIEW
J D Hyman, J Jiménez-Martínez, H S Viswanathan, J W Carey, M L Porter, E Rougier, S Karra, Q Kang, L Frash, L Chen, Z Lei, D O'Malley, N Makedonska
Despite the impact that hydraulic fracturing has had on the energy sector, the physical mechanisms that control its efficiency and environmental impacts remain poorly understood in part because the length scales involved range from nanometres to kilometres. We characterize flow and transport in shale formations across and between these scales using integrated computational, theoretical and experimental efforts/methods. At the field scale, we use discrete fracture network modelling to simulate production of a hydraulically fractured well from a fracture network that is based on the site characterization of a shale gas reservoir...
October 13, 2016: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
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