Performance debugging using program profiling and tracing for scientific workflows can be extremely difficult for two reasons. 1) Existing performance tools lack the ability to automatically produce global performance data based on local information from coupled scientific applications of workflows, particularly at runtime. 2) Profiling/tracing with static instrumentation may incur high overhea...

The emergence of leadership class systems with nodes containing many-core accelerators, such as GPUs, has the potential to vastly increase the performance of distributed applications. Exploiting the additional parallelism that manycore accelerators offer is fraught with challenges. Developers and existing performance tools focus on a subset of these challenges, primarily the identification of C...

Graphene oxide (GO) nanoparticle is a high potential effective absorbent. Tetracycline (TC) is a broad-spectrum antibiotic produced, indicated for use against many bacterial infections. In the present research, a systematic study of the adsorption and release process of tetracycline on GO was performed by varying pH, sorption time and temperature. The results of our studies showed that tetracyc...

Anhydrous Hydrogen Fluoride (HF) at high temperatures and pressures is used to process manufacture nuclear fuel. As HF often directly with uranium, correct neutron thermal scattering cross sections are crucial criticality safety applications. Classical molecular dynamics (CMD) simulation of the flexible system was create law (TSL) sections. The initial 2-site model in LAMMPS, it can not capture...

In this paper we detail the key features, architectural design, and implementation of rCUDA, an advanced framework to enable remote and transparent GPGPU acceleration in HPC clusters. rCUDA allows decoupling GPUs from nodes, forming pools of shared accelerators, which brings enhanced flexibility to cluster configurations. This opens the door to configurations with fewer accelerators than nodes,...

Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within di...

This thesis describes an investigation of interactions between colloidal particles immersed in a liquid crystal. The presence of colloidal particles in the liquid crystal distorts the director field distorted from its uniform orientation. These elastic distortions produce topological defects around the particles, which induce anisotropic interactions between them, and these anisotropic interact...

a r t i c l e i n f o a b s t r a c t Molecular dynamics (MD) methods compute the trajectory of a system of point particles in response to a potential function by numerically integrating Newton's equations of motion. Extending these basic methods with rigid body constraints enables composite particles with complex shapes such as anisotropic nanoparticles, grains, molecules, and rigid proteins t...