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High Performance Computing in Biomedical Applications

S. Bastrakov, I. Meyerov, V. Gergel, A. Gonoskov, A. Gorshkov, E. Efimenko, M. Ivanchenko, M. Kirillin, A. Malova, G. Osipov, V. Petrov, I. Surmin (+1 others)
2013 Procedia Computer Science  
The software system is aimed at large-scale simulation on cluster systems with high efficiency and scalability.  ...  We consider four main fields: plasma simulation, heart activity simulation, brain sensing simulation, molecular dynamics simulation.  ...  PICADOR [3] is a tool for large-scale three-dimensional Particle-in-Cell plasma simulation on heterogeneous cluster systems.  ... 
doi:10.1016/j.procs.2013.05.164 fatcat:6hzmpjn35zfihapdwr4l3qyita

Stochastic simulations of ErbB homo and heterodimerisation: potential impacts of receptor conformational state and spatial segregation

M.-Y. Hsieh, B. Wilson, J.S. Edwards, D.G. Vlachos, W. Shu, M.A. Raymond-Stinz, S. Steinberg, S. Yang
2008 IET Systems Biology  
The impact of ErbB receptor clustering patterns on hetero and homodimerisation rates is also considered, using immunoelectron microscopy data derived from SKBR3 breast cancer cells that expresses ErbB2  ...  First, ligandindependent homodimerisation, is considered, based upon constitutive oligomerisation estimates (14%) in A431 cells that overexpress EGFR.  ...  However, as shown in Fig. 2b , resting EGFRs are highly clustered on the A431 cell surface.  ... 
doi:10.1049/iet-syb:20070073 pmid:19045821 fatcat:q62mlo5rwnbttkzbdor3tnywhm

Influenza A viruses use multivalent sialic acid clusters for cell binding and receptor activation

Christian Sieben, Erdinc Sezgin, Christian Eggeling, Suliana Manley, Yoshihiro Kawaoka
2020 PLoS Pathogens  
Intriguingly, quantitative cluster analysis revealed that AFs and EGFR are organized in partially overlapping submicrometer clusters in the plasma membrane of A549 cells.  ...  Using our experimentally measured cluster characteristics, we simulated virus diffusion on a flat membrane.  ...  Acknowledgments We would like to thank Katharina Horst for support and Andreas Herrmann for helpful discussions on the manuscript.  ... 
doi:10.1371/journal.ppat.1008656 pmid:32639985 pmcid:PMC7371231 fatcat:5kzimokbkzgovffsigmaovmwwm

A discrete-particle model of blood dynamics in capillary vessels

Witold Dzwinel, Krzysztof Boryczko, David A. Yuen
2003 Journal of Colloid and Interface Science  
The blood plasma is represented by a system of dissipative fluid particles. We have simulated the flow of cells of different shapes, such as normal and "sickle" cells.  ...  The cluster of "sickle" cells formed in the necking of the conduit efficiently decelerates the flow, while normal cells can pass through.  ...  Thanks are due to Dr R de Roeck and Professor Dr M.R.Mackley from Department of Chemical Engineering, University of Cambridge, for the pictures from their laboratory findings included in this paper.  ... 
doi:10.1016/s0021-9797(02)00075-9 pmid:12600784 fatcat:ajpatdxq6bcdze3d55sf64zl6u

A Grid-Based Distributed Simulation of Plasma Turbulence [chapter]

S. Briguglio, Beniamino di Martino, G. Fogaccia, G. Vlad, Salvatore Venticinque
2006 High-Performance Computing  
In this paper the porting on a Globus equipped platform of a hierarchically distributed-shared memory parallel version of an application for particle-in-cell (PIC) simulation of plasma turbulence is described  ...  , based on the hierarchical integration of MPI and OpenMP, and originally developed for generic (non Grid) clusters of SMP nodes. i ii  ...  of an application for particle-in-cell (PIC) simulation of plasma turbulence, based on the hierarchical integration of MPI and OpenMP [2] , originally developed for generic (non Grid) clusters of SMP  ... 
doi:10.1002/0471732710.ch27 fatcat:3sddvloltza5fhaob7e53thz7u

Hybrid CPU + Xeon Phi implementation of the Particle-in-Cell method for plasma simulation

2016 Supercomputing Frontiers and Innovations  
This paper presents experimental results of Particle-in-Cell plasma simulation on a hybrid system with CPUs and Intel Xeon Phi coprocessors.  ...  We consider simulation of two relevant laserdriven particle acceleration regimes using the Particle-in-Cell code PICADOR.  ...  PICADOR code PICADOR [13, 14] is a tool for 3D plasma simulation based on the Particle-in-Cell method.  ... 
doi:10.14529/jsfi160301 fatcat:hrferh6rwvhlvpaqhuzbghi6ci

Fluctuating Topological Defects in 2D Liquids: Heterogeneous Motion and Noise

C. Reichhardt, C. J. Olson Reichhardt
2003 Physical Review Letters  
We measure the defect density as a function of time at different temperatures in simulations of a two dimensional system of interacting particles.  ...  We demonstrate this heterogeneity both in systems interacting with a short ranged screened Coulomb interaction, as well as in systems with a long range logarithmic interaction between the particles.  ...  Most of the studies of heterogeneities in 2D and 3D have focused on systems that are supercooled near the glass transition in simulations [2] and experiments [3, 4, 5] .  ... 
doi:10.1103/physrevlett.90.095504 pmid:12689235 fatcat:kj4ph25uaza5bgr2q75ym45pwq

Scalable Multi-Platform PIC Simulations as an Open Science Service

Axel Huebl, Richard Pausch, René Widera, Marco Garten, Alexander Debus, Ilja Goethel, Alexander Matthes, Felix Meyer, Benjamin Worpitz, Sebastian Starke, Jeffrey Kelling, Sophie Rudat (+6 others)
2018 Zenodo  
PIConGPU is a fully open, community-driven, 3D and 2D3V particle-in-cell code for the age of heterogeneous, many-core driven supercomputing.  ...  PIConGPU has shown to be suitable for production runs on the full system size of TOP5 clusters such as Titan (ORNL) and Piz Daint (CSCS).  ...  This research used resources of the Oak Ridge Leadership Computing Facility located in the Oak Ridge National Laboratory, which is supported by the Office of Science of the Department of Energy under Contract  ... 
doi:10.5281/zenodo.1345079 fatcat:rg4nhdlqp5gcxa3ldgzq4l4a5e

A Model for Membrane Patchiness: Lateral Diffusion in the Presence of Barriers and Vesicle Traffic

Levi A. Gheber, Michael Edidin
1999 Biophysical Journal  
Patches (lateral heterogeneities) of cell surface membrane proteins and lipids have been imaged by a number of different microscopy techniques.  ...  Our computer model takes into account lateral diffusion, barriers to lateral diffusion, and vesicle traffic to and from the plasma membrane.  ...  One such assumption is that the concentration of particles in an arriving vesicle is the same as the concentration of the particles on the plasma membrane.  ... 
doi:10.1016/s0006-3495(99)77147-x pmid:10585938 pmcid:PMC1300587 fatcat:yx2ldbu42zhjnkueamwvqrj6du

Particle-in-Cell laser-plasma simulation on Xeon Phi coprocessors

I.A. Surmin, S.I. Bastrakov, E.S. Efimenko, A.A. Gonoskov, A.V. Korzhimanov, I.B. Meyerov
2016 Computer Physics Communications  
This paper concerns development of a high-performance implementation of the Particle-in-Cell method for plasma simulation on Intel Xeon Phi coprocessors.  ...  Direct porting with no code modification gives performance on Xeon Phi close to 8-core CPU on a benchmark problem with 50 particles per cell.  ...  Heterogeneous cluster systems are based not only on convenient CPUs, but also on different types of accelerators, including GPUs and the recently introduced Intel Xeon Phi coprocessors.  ... 
doi:10.1016/j.cpc.2016.02.004 fatcat:zsv5qljeurah5glzzbov2po3my

Mathematical Simulation of Membrane Protein Clustering for Efficient Signal Transduction

Krishnan Radhakrishnan, Ádám Halász, Meghan M. McCabe, Jeremy S. Edwards, Bridget S. Wilson
2012 Annals of Biomedical Engineering  
Initiation and propagation of cell signaling depends on productive interactions between signaling proteins at the plasma membrane.  ...  This review considers the experimental and mathematical evidence that protein clustering impacts cell signaling in complex ways.  ...  Key concepts and definitions relevant to the consideration of protein clustering in the plasma membrane In this brief review, we focus attention on the mathematical simulation of protein clustering in  ... 
doi:10.1007/s10439-012-0599-z pmid:22669501 pmcid:PMC3822010 fatcat:knpuxe2sdraynlsfa4ufpnuyye

Influenza a Viruses use Multivalent Sialic Acid Clusters for Cell Binding and Receptor Activation

Christian Sieben, Suliana Manley
2016 Biophysical Journal  
Intriguingly, 40 quantitative cluster analysis revealed that AF and EGFR are organized in partially overlapping 41 submicrometer clusters in the apical plasma membrane of A549 cells.  ...  We find that molecules 69 are organized in submicrometer nanodomains and, in combination with virus diffusion simulations, 70 present a mechanistic view for how IAV first engages with AFs in the plasma  ...  In both cases, we simulate a spherical virus 352 particle and project its size as a landing spot on the simulated molecule surface.  ... 
doi:10.1016/j.bpj.2015.11.2843 fatcat:pxfycnk7ljgxja3sr3gv4tokny

VPIC 2.0: Next Generation Particle-in-Cell Simulations

Robert Bird, Nigel Tan, Scott V Luedtke, Stephen Harrell, Michela Taufer, Brian Albright
2021 IEEE Transactions on Parallel and Distributed Systems  
VPIC is a general purpose particle-in-cell simulation code for modeling plasma phenomena such as magnetic reconnection, fusion, solar weather, and laser-plasma interaction in three dimensions using large  ...  VPIC's capacity in both fidelity and scale makes it particularly well-suited for plasma research on pre-exascale and exascale platforms.  ...  INTRODUCTION Many plasma physics phenomena can only be understood through the use of kinetic particle-in-cell (PIC) simulations.  ... 
doi:10.1109/tpds.2021.3084795 fatcat:375qqzr5dfdljkec6id6hhhxoy

Live Programming in Scientific Simulation

2016 Supercomputing Frontiers and Innovations  
Through a set of examples using a Particle-In-Cell (PIC) simulation framework we show how the real-time, human-in-the-loop interactivity of liveprogramming can be incorporated into traditional "offline  ...  We demonstrate that a live-programming environment can be used to harness and add runtime interactivity to scientific simulation codes.  ...  in Cell and Kinetic Simulation Center (PICKSC), funded by the US National Science Foundation, NSF Grant ACI-1339893, for their support of this work.  ... 
doi:10.14529/jsfi150401 fatcat:aryakl5bxfgplfzmckewrswa7i

VPIC 2.0: Next Generation Particle-in-Cell Simulations [article]

Robert Bird, Nigel Tan, Scott V. Luedtke, Stephen Lien Harrell, Michela Taufer, Brian Albright
2021 arXiv   pre-print
VPIC is a general purpose Particle-in-Cell simulation code for modeling plasma phenomena such as magnetic reconnection, fusion, solar weather, and laser-plasma interaction in three dimensions using large  ...  VPIC's capacity in both fidelity and scale makes it particularly well-suited for plasma research on pre-exascale and exascale platforms.  ...  INTRODUCTION Many plasma physics phenomena can only be understood through the use of kinetic Particle-in-Cell (PIC) simulations.  ... 
arXiv:2102.13133v1 fatcat:tozit2tlvzbuvamizwpdofpw34
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