Bayesian uncertainty quantification and propagation in molecular dynamics simulations: A high performance computing framework

2012 ◽  
Vol 137 (14) ◽  
pp. 144103 ◽  
Author(s):  
Panagiotis Angelikopoulos ◽  
Costas Papadimitriou ◽  
Petros Koumoutsakos
2021 ◽  
Author(s):  
Mohsen Hadianpour ◽  
Ehsan Rezayat ◽  
Mohammad-Reza Dehaqani

Abstract Due to the significantly drastic progress and improvement in neurophysiological recording technologies, neuroscientists have faced various complexities dealing with unstructured large-scale neural data. In the neuroscience community, these complexities could create serious bottlenecks in storing, sharing, and processing neural datasets. In this article, we developed a distributed high-performance computing (HPC) framework called `Big neuronal data framework' (BNDF), to overcome these complexities. BNDF is based on open-source big data frameworks, Hadoop and Spark providing a flexible and scalable structure. We examined BNDF on three different large-scale electrophysiological recording datasets from nonhuman primate’s brains. Our results exhibited faster runtimes with scalability due to the distributed nature of BNDF. We compared BNDF results to a widely used platform like MATLAB in an equitable computational resource. Compared with other similar methods, using BNDF provides more than five times faster performance in spike sorting as a usual neuroscience application.


Author(s):  
Arturo Schiaffino ◽  
V. M. Krushnarao Kotteda ◽  
Vinod Kumar ◽  
Arturo Bronson ◽  
Sanjay Shantha-Kumar

Abstract In the manufacturing of metal matrix composites (MMC), liquid-metal reactive infusion with a solid mesh or particles composed of ceramic or metal may be used. The objective of this study is to determine the uncertainty quantification of the modeling of liquid hafnium infusion to expedite the processing and improve properties of MMCs ultimately. Uncertainty quantification (UQ) characterized the uncertainty scientifically especially for high-performance computing with observed physics and/or chemistry of the phenomena and predicted from estimated parameters. In this work, molten hafnium infusing through a boron carbide packed bed is modeled to optimize the manufacturing of components used for a hypersonic vehicle. The creation of molten matrix composites by the infiltration of molten metal represents a formidable challenge to be accurately modeled. First, the structural randomness associated with porous mediums complicates the prediction of the flow passing through it. Secondly, the properties of the molten metal could vary inside our control volume, since the temperature inside the control volume is not constant. Also, there are several chemical reactions and solidification rates occurring in during the impregnation. Given the recent advances in high-performance computing, an in-house pore network simulator are implemented along with Dakota, an open-source, exascale software, to determine the optimal parameters (e.g., porosity and temperature) and uncertainty quantification for the modeling.


2009 ◽  
Vol 5 (10) ◽  
pp. e1000528 ◽  
Author(s):  
Noriaki Okimoto ◽  
Noriyuki Futatsugi ◽  
Hideyoshi Fuji ◽  
Atsushi Suenaga ◽  
Gentaro Morimoto ◽  
...  

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