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Palabos: Parallel Lattice Boltzmann Solver

Jonas Latt, Orestis Malaspinas, Dimitrios Kontaxakis, Andrea Parmigiani, Daniel Lagrava, Federico Brogi, Mohamed Ben Belgacem, Yann Thorimbert, Sébastien Leclaire, Sha Li, Francesco Marson, Jonathan Lemus (+7 others)
2020 Computers and Mathematics with Applications  
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

Andreas Lintermann, Wolfgang Schröder
2020 CEAS Aeronautical Journal  
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?

Melanie J. Zimmer, Tihamér Geyer
2012 Journal of Chemical Physics  
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]

Tadeusz Tomczak, Roman G. Szafran
2017 arXiv   pre-print
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

Greta Colombo Dugoni, Alberto Baggioli, Antonino Famulari, Alessandro Sacchetti, Javier Martí-Rujas, Mario Mariani, Elena Macerata, Eros Mossini, Andrea Mele
2020 RSC Advances  
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

Tao Lin, Zhen Wang, Wen Wang, Yi Sui
2021 Soft Matter  
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]

Jovana Knežević, Ralf-Peter Mundani, Ernst Rank
2013 Lecture Notes in Computational Science and Engineering  
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]

H. J. Moukalled
2013 arXiv   pre-print
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

Hynek Bachratý, Katarína Bachratá, Michal Chovanec, Iveta Jančigová, Monika Smiešková, Kristína Kovalčíková
2020 BMC Bioinformatics  
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

Li Shi, Chris Dames, Jennifer R. Lukes, Pramod Reddy, John Duda, David G. Cahill, Jaeho Lee, Amy Marconnet, Kenneth E. Goodson, Je-Hyeong Bahk, Ali Shakouri, Ravi S. Prasher (+4 others)
2015 Nanoscale and Microscale Thermophysical Engineering  
, 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

Annalisa Volpe, Caterina Gaudiuso, Antonio Ancona
2019 Micromachines  
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]

Karl-Heinz Küfer, Michael Monz, Alexander Scherrer, Philipp Süss, Fernando Alonso, Ahmad Saher Azizi Sultan, Thomas Bortfeld, Christian Thieke
2008 Handbook of Optimization in Medicine  
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

Yevgeniy R Davletshin, J Carl Kumaradas
2016 Beilstein Journal of Nanotechnology  
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

Marco Carminati
2017 Journal of Sensors  
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]

Corey Wetterer-Nelson, Kenneth E. Jansen, John A. Evans
2021 arXiv   pre-print
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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