We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program N...
Robert Brunner, James C. Phillips, Laxmikant V. Ka...
With advances in reconfigurable hardware, especially field-programmable gate arrays (FPGAs), it has become possible to use reconfigurable hardware to accelerate complex applicatio...
Ronald Scrofano, Maya Gokhale, Frans Trouw, Viktor...
Abstract We discuss data production rates and their impact on the performance of scientific applications using parallel computers. On one hand, too high rates of data production c...
Terry W. Clark, L. Ridgway Scott, Stanislaw Wloked...
Aligning structures, often referred to as docking or registration, is frequently required in fields such as computer science, robotics and structural biology. The task of alignin...
Johannes Jansen van Vuuren, Michelle Kuttel, James...
—This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) for characterization of molecular elastic joints for bio nanorobotic prototyping. Simp...
Mustapha Hamdi, Gaurav Sharma, Antoine Ferreira, C...