AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics

L Casalino, AC Dommer, Z Gaieb… - … Journal of High …, 2021 - journals.sagepub.com
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC
resources to explore the time-dependent dynamics of molecular systems. We use this …

Investigating a Novel Neurodegenerative Disease Toxic Mechanism Involving Lipid Binding Specificity of Amyloid Oligomers

SS Hirschbeck, ET Lindberg, JH Jang… - ACS Chemical …, 2024 - ACS Publications
Exploring the mechanisms underlying the toxicity of amyloid oligomers (AOs) presents a
significant opportunity for discovering cures and developing treatments for …

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication …

A Trifan, D Gorgun, M Salim, Z Li… - … journal of high …, 2022 - journals.sagepub.com
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication
transcription complex (RTC) is a multi-domain protein responsible for replicating and …

Intelligent resolution: Integrating cryo-em with ai-driven multi-resolution simulations to observe the sars-cov-2 replication-transcription machinery in action

A Trifan, D Gorgun, Z Li, A Brace, M Zvyagin, H Ma… - bioRxiv, 2021 - biorxiv.org
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication
transcription complex (RTC) is a multi-domain protein responsible for replicating and …

Distributed Continuation Stealing is More Scalable than You Might Think

S Shiina, K Taura - 2022 IEEE International Conference on …, 2022 - ieeexplore.ieee.org
The need for load balancing in applications with irregular parallelism has motivated
research on work stealing. An important choice in work-stealing schedulers is between child …

Scaling neural simulations in STACS

F Wang, S Kulkarni, B Theilman… - Neuromorphic …, 2024 - iopscience.iop.org
As modern neuroscience tools acquire more details about the brain, the need to move
towards biological-scale neural simulations continues to grow. However, effective …

A scalable elliptic solver with task-based parallelism for the SpECTRE numerical relativity code

NL Vu, HP Pfeiffer, GS Bonilla, N Deppe, F Hébert… - Physical Review D, 2022 - APS
Elliptic partial differential equations must be solved numerically for many problems in
numerical relativity, such as initial data for every simulation of merging black holes and …

High-accuracy numerical models of Brownian thermal noise in thin mirror coatings

NL Vu, S Rodriguez, T Włodarczyk… - … and Quantum Gravity, 2023 - iopscience.iop.org
Brownian coating thermal noise in detector test masses is limiting the sensitivity of current
gravitational-wave detectors on Earth. Therefore, accurate numerical models can inform the …

[PDF][PDF] A task-based parallel elliptic solver for numerical relativity with discontinuous Galerkin methods

NL Vu - 2022 - inspirehep.net
My work also has applications beyond numerical relativity, since elliptic PDEs are common
in many areas of physics. One such application is the simulation of thermal noise in thin …

Unified data movement for offloading Charm++ applications

M Diener, L Kale - 2020 IEEE International Parallel and …, 2020 - ieeexplore.ieee.org
Data movement between host and accelerators is one of the most challenging aspects of
developing applications for heterogeneous systems. Most existing runtime systems for …