444 citations · 1.5k across the 10 of their papers we have counts for
11 papers
General Principles of Secondary Active Transporter Function
Oliver Beckstein, Fiona Naughton
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 driv…
Parallel Performance of Molecular Dynamics Trajectory Analysis
Mahzad Khoshlessan, Ioannis Paraskevakos, Geoffrey C. Fox +2
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output…
Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation
Geoffrey Fox, James A. Glazier, JCS Kadupitiya +10
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…
Task-parallel Analysis of Molecular Dynamics Trajectories
Ioannis Paraskevakos, Andre Luckow, Mahzad Khoshlessan +5
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…
Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways
Sean L. Seyler, Avishek Kumar, Michael F. Thorpe +1
Diverse classes of proteins function through large-scale conformational changes; sophisticated enhanced sampling methods have been proposed to generate these macromolecular transit…
Opening a hydrophobic gate: the nicotinic acetylcholine receptor as an example
Sarah E. Rogers, Kaihsu Tai, Oliver Beckstein +1
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 nAC…