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Palabos: Parallel Lattice Boltzmann Solver
2020
Computers and Mathematics with Applications
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Palabos is a C++ software platform developed since 2010 for Computational Fluid Dynamics simulations and Lattice Boltzmann modeling, which specifically targets applications with complex, coupled physics ...
We present the scope, concepts, data structures and application programming models of the open-source Lattice Boltzmann library Palabos. ...
Introduction Palabos (Parallel Lattice Boltzmann Solver) is a software library developed since 2010, which serves as a modeling platform for lattice Boltzmann (LB) schemes and as a reference implementation ...
doi:10.1016/j.camwa.2020.03.022
fatcat:y3n7gxmvjbatrnbwmcbjzcrjou
Lattice–Boltzmann simulations for complex geometries on high-performance computers
2020
CEAS Aeronautical Journal
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Simulations on large-scale meshes are performed by a high-scaling lattice-Boltzmann method using the second-order accurate interpolated bounce-back boundary conditions for no-slip walls. ...
Hierarchical Cartesian boundary-refined meshes for complex geometries are obtained by a massively parallel grid generator. In this process, the geometry is parallelized for efficient computation. ...
A promising numerical method for the efficient simulation of flows are lattice-Boltzmann (LB) methods [3, 27, 31] . ...
doi:10.1007/s13272-020-00450-1
fatcat:tblfyydgyjgbfcztqjs5egp5gq
Do we have to explicitly model the ions in Brownian dynamics simulations of proteins?
2012
Journal of Chemical Physics
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the bond is fully desolvated, respectively. ...
B 134, 4570 (1999)] and improves upon previous lattice models based on it. ...
Langevin dynamics for the transport of flexible biological macromolecules in confined geometries. Peters MH. ...
doi:10.1063/1.3698593
pmid:22462897
fatcat:i4ewhl25evf2zoesdifstzfgge
A new GPU implementation for lattice-Boltzmann simulations on sparse geometries
[article]
2017
arXiv
pre-print
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We describe a high-performance implementation of the lattice Boltzmann method (LBM) for sparse 3D geometries on graphic processors (GPU). ...
We show that by using a uniform mesh of small three-dimensional tiles and a careful data placement it is possible to utilise more than 70% of maximum theoretical GPU memory bandwidth for D3Q19 lattice ...
This work was supported by Wroc law University of Science and Technology, Faculty of Electronics, Chair of Computer Engineering statutory funds. ...
arXiv:1611.02445v2
fatcat:ahyx3idx3ne43alrtwtrkduwqy
Structural properties of the chelating agent 2,6-bis(1-(3-hydroxypropyl)-1,2,3-triazol-4-yl)pyridine: a combined XRD and DFT structural study
2020
RSC Advances
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Dispersion corrected DFT analysis in combination with single crystal X-ray structural analysis provides insights into the ability of to chelate metal ions of radiotoxic waste from nuclear fuel. ...
Acknowledgements We acknowledge the CINECA award under the ISCRA initiative, for the availability of high performance computing resources and support. A. ...
F. thanks MIUR for the Fondo Finanziamento delle Attività Base di Ricerca (FFARB). G. C. D. thanks Politecnico di Milano for her Inter-Departments PhD scholarship. J. M. ...
doi:10.1039/d0ra04142d
pmid:35515445
pmcid:PMC9054079
fatcat:dhsyyqyoivamzb6b5macddxt2q
A neural network-based algorithm for high-throughput characterisation of viscoelastic properties of flowing microcapsules
2021
Soft Matter
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Microcapsules, consisting of a liquid droplet enclosed by a viscoelastic membrane, have a wide range of biomedical and pharmaceutical applications and also serve as a popular mechanical model for biological ...
Immersed-boundary lattice Boltzmann method We first use a well-tested immersed-boundary lattice Boltzmann method to simulate the transient deformation of the capsule in the branched channel. ...
The fluid flow is solved by a three-dimensional nineteen-velocity (D3Q19) lattice Boltzmann method (LBM). ...
doi:10.1039/d0sm02121k
pmid:33480936
fatcat:7b5qbkw6ebeqfocxurlzuoee4u
A High-Performance Interactive Computing Framework for Engineering Applications
[chapter]
2013
Lecture Notes in Computational Science and Engineering
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2018 pre-print arXiv:1807.00769v1 fatcat:ssfrmww6wzgqtlngafb2vmmwou
Namely, the regular course of the simulation coupled to our framework is interrupted in small, cyclic intervals followed by a check for updates. ...
To leverage the concept for a broader scope of applications, it is essential that a user receives an immediate response from the simulation to his or her changes. ...
The work related to SCIRun PSE was made possible in part by software from the NIH/NIGMS Center for Integrative Biomedical Computing, 2P41 RR0112553-12. ...
doi:10.1007/978-3-642-38762-3_9
fatcat:rzfsctjperdete4hwo4dgnlogy
On Automation and Medical Image Interpretation, With Applications for Laryngeal Imaging
[article]
2013
arXiv
pre-print
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and quite possibly other areas of biomedical image analysis. ...
Furthermore, discuss some applications for processing medical images of the vocal folds, and discuss some of the exhilarating directions the art of automation will take vocal-fold image interpretation ...
Dimitar Deliyski and the NIH R01 grant DC007640 on the efficacy of laryngeal imaging. Thanks to the University of South Carolina Department of Computer Science. ...
arXiv:1212.6933v3
fatcat:rsbzafx5cfe7rc6st2xjek7c3a
Applications of machine learning for simulations of red blood cells in microfluidic devices
2020
BMC Bioinformatics
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For optimization of microfluidic devices for the analysis of blood samples, it is useful to simulate blood cells as elastic objects in flow of blood plasma. ...
While for uncomplicated box channels there is no advantage in using a system of bases instead of a simple prediction using fluid streamlines, in a more complicated geometry, the neural network is significantly ...
About this supplement This article has been published as part of BMC Bioinformatics Volume 21 Supplement 2, 2020: Selected articles from the 6th International Work-Conference on Bioinformatics and Biomedical ...
doi:10.1186/s12859-020-3357-5
pmid:32164547
fatcat:g57ag2v3evafhjhdoqn3vpk3y4
Evaluating Broader Impacts of Nanoscale Thermal Transport Research
2015
Nanoscale and Microscale Thermophysical Engineering
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, building and vehicle heating and cooling, manufacturing, and biomedical devices. ...
The past two decades have witnessed the emergence and rapid growth of the research field of nanoscale thermal transport. ...
In order to circumvent the experimental difficulties involved in making parallel-plate measurements, researchers have exploited the sphere-plane geometry [82] [83] [84] or the tip-plane geometry [100 ...
doi:10.1080/15567265.2015.1031857
fatcat:msum5zmzczcf7ddwemr4a3ej4a
Sorting of Particles Using Inertial Focusing and Laminar Vortex Technology: A Review
2019
Micromachines
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The capability of isolating and sorting specific types of cells is crucial in life science, particularly for the early diagnosis of lethal diseases and monitoring of medical treatments. ...
Among all the micro-fluidics techniques for cell sorting, inertial focusing combined with the laminar vortex technology is a powerful method to isolate cells from flowing samples in an efficient manner ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/mi10090594
pmid:31510006
pmcid:PMC6780945
fatcat:jjzhhcuqxrb4bjncytt2crnwxa
Multicriteria Optimization in Intensity Modulated Rediotherapy Planning
[chapter]
2008
Handbook of Optimization in Medicine
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Kehrwald
Parallel lattice Boltzmann simulation
of complex fl ows
). ...
Zeiser
After a short introduction to the basic ideas of lattice Boltzmann methods and a brief description of a modern parallel computer, it is shown how lattice Boltzmann schemes are successfully applied ...
After fitting the model, the flow is computed in digitized realizations of the stochastic geometric model using the lattice Boltzmann method. ...
doi:10.1007/978-0-387-09770-1_5
fatcat:yimhx7gxdfcptj7buqxnm7svlq
The role of morphology and coupling of gold nanoparticles in optical breakdown during picosecond pulse exposures
2016
Beilstein Journal of Nanotechnology
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For this purpose we used a fully coupled electromagnetic, thermodynamic and plasma dynamics model for a laser pulse interaction with gold nanospheres, nanorods and assemblies, which was solved using the ...
The thresholds of optical breakdown for off-and on-resonance irradiated gold nanosphere monomers were compared against nanosphere dimers, trimers, and gold nanorods with the same overall size and aspect ...
Vogel for their fruitful discussions. ...
doi:10.3762/bjnano.7.79
pmid:27547604
pmcid:PMC4979631
fatcat:n5oqoua7jbhjrph5rysbywkycy
Advances in High-Resolution Microscale Impedance Sensors
2017
Journal of Sensors
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of Things), it also presents new challenges for the detection electronics, reaching the zeptoFarad domain. ...
In this tutorial review, a selection of examples is illustrated with the purpose of distilling key indications and guidelines for the design of high-resolution impedance readout circuits and sensors. ...
Caviglia (Denmark Technical University) for microfluidics and cell detection, and with T. Albrecth (Imperial College London) for nanopores are gratefully acknowledged. ...
doi:10.1155/2017/7638389
fatcat:l4ltfpipljcxjlyxxseuwd3fui
Interactive Geometry Modification of High Performance Finite Element Simulations
[article]
2021
arXiv
pre-print
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In the context of high performance finite element analysis, the cost of iteratively modifying a computational domain via re-meshing and restarting the analysis becomes time prohibitive as the size of simulations ...
We employ existing in situ visualization techniques to rapidly inform the user of simulation progression, enabling computational steering. ...
Acknowledgements The authors would like to thank Cameron Smith for his continued assistance with SCOREC tools. This material is based ...
arXiv:2005.00202v2
fatcat:ia7lq6ztzvgyjfcwmdrsyme3i4
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