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pro vyhledávání: '"Beckstein, Oliver"'
Autor:
Beckstein, Oliver, Naughton, Fiona
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondar
Externí odkaz:
http://arxiv.org/abs/1912.06275
Autor:
Khoshlessan, Mahzad, Paraskevakos, Ioannis, Fox, Geoffrey C., Jha, Shantenu, Beckstein, Oliver
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations is becomi
Externí odkaz:
http://arxiv.org/abs/1907.00097
Autor:
Fox, Geoffrey, Glazier, James A., Kadupitiya, JCS, Jadhao, Vikram, Kim, Minje, Qiu, Judy, Sluka, James P., Somogyi, Endre, Marathe, Madhav, Adiga, Abhijin, Chen, Jiangzhuo, Beckstein, Oliver, Jha, Shantenu
The convergence of HPC and data-intensive methodologies provide a promising approach to major performance improvements. This paper provides a general description of the interaction between traditional HPC and ML approaches and motivates the Learning
Externí odkaz:
http://arxiv.org/abs/1902.10810
Akademický článek
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Autor:
Paraskevakos, Ioannis, Luckow, Andre, Khoshlessan, Mahzad, Chantzialexiou, George, Cheatham, Thomas E., Beckstein, Oliver, Fox, Geoffrey C., Jha, Shantenu
Different parallel frameworks for implementing data analysis applications have been proposed by the HPC and Big Data communities. In this paper, we investigate three task-parallel frameworks: Spark, Dask and RADICAL-Pilot with respect to their abilit
Externí odkaz:
http://arxiv.org/abs/1801.07630
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America, 2020 Oct . 117(41), 25517-25522.
Externí odkaz:
https://www.jstor.org/stable/26969624
Publikováno v:
PLoS Comput Biol 11(10): e1004568 (2015)
Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transition paths. As such paths are curves in a high-dimensional space, they
Externí odkaz:
http://arxiv.org/abs/1505.04807
To what extent must a hydrophobic gate expand for the channel to count as open? We address this question using the nicotinic acetylcholine receptor (nAChR) as the exemplar. The nAChR is an integral membrane protein which forms a cation selective chan
Externí odkaz:
http://arxiv.org/abs/0902.1417
Akademický článek
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