Molecular dynamics simulations and applications in computational toxicology and nanotoxicology

C Selvaraj, S Sakkiah, W Tong, H Hong - Food and Chemical Toxicology, 2018 - Elsevier
Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical
researches to explore toxicity of various biological systems. Investigating biological systems …

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

AP Thompson, LP Swiler, CR Trott, SM Foiles… - Journal of …, 2015 - Elsevier
We present a new interatomic potential for solids and liquids called Spectral Neighbor
Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine …

86 PFLOPS deep potential molecular dynamics simulation of 100 million atoms with ab initio accuracy

D Lu, H Wang, M Chen, L Lin, R Car, E Weinan… - Computer Physics …, 2021 - Elsevier
We present the GPU version of DeePMD-kit, which, upon training a deep neural network
model using ab initio data, can drive extremely large-scale molecular dynamics (MD) …

Design, modeling, and evaluation of a scalable multi-level checkpointing system

A Moody, G Bronevetsky, K Mohror… - SC'10: Proceedings …, 2010 - ieeexplore.ieee.org
High-performance computing (HPC) systems are growing more powerful by utilizing more
hardware components. As the system mean-time-before-failure correspondingly drops …

Toward exascale resilience

F Cappello, A Geist, B Gropp, L Kale… - … Journal of High …, 2009 - journals.sagepub.com
Over the past few years resilience has became a major issue for high-performance
computing (HPC) systems, in particular in the perspective of large petascale systems and …

Adapting a message-driven parallel application to GPU-accelerated clusters

JC Phillips, JE Stone, K Schulten - SC'08: Proceedings of the …, 2008 - ieeexplore.ieee.org
Graphics processing units (GPUs) have become an attractive option for accelerating
scientific computations as a result of advances in the performance and flexibility of GPU …

Processor design for soft errors: Challenges and state of the art

T Li, JA Ambrose, R Ragel… - ACM Computing Surveys …, 2016 - dl.acm.org
Today, soft errors are one of the major design technology challenges at and beyond the
22nm technology nodes. This article introduces the soft error problem from the perspective …

A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer

F Di Natale, H Bhatia, TS Carpenter, C Neale… - Proceedings of the …, 2019 - dl.acm.org
Computational models can define the functional dynamics of complex systems in
exceptional detail. However, many modeling studies face seemingly incommensurate …

Flux: Overcoming scheduling challenges for exascale workflows

DH Ahn, N Bass, A Chu, J Garlick, M Grondona… - Future Generation …, 2020 - Elsevier
Many emerging scientific workflows that target high-end HPC systems require complex
interplay with the resource and job management software (RJMS). However, portable …

Richtmyer–Meshkov instability: theory of linear and nonlinear evolution

K Nishihara, JG Wouchuk… - … of the Royal …, 2010 - royalsocietypublishing.org
A theoretical framework to study linear and nonlinear Richtmyer–Meshkov instability (RMI) is
presented. This instability typically develops when an incident shock crosses a corrugated …