Scalable HPC and AI Infrastructure for COVID-19 Therapeutics. - Hyungro Lee; André Merzky; Li Tan; Mikhail Titov; Matteo Turilli; Dario Alfè; Agastya Bhati; Alex Brace; Austin Clyde; Peter V. Coveney; Heng Ma; Arvind Ramanathan; et al. (CoRR, 2020)

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads. - Aymen Al Saadi; Dario Alfè; Yadu N. Babuji; Agastya Bhati; Ben Blaiszik; Alexander Brace; Thomas S. Brettin; Kyle Chard; Ryan Chard; Austin Clyde; Peter V. Coveney; Ian T. Foster; et al. (ICPP, 2021)

Stream-AI-MD: streaming AI-driven adaptive molecular simulations for heterogeneous computing platforms. - Alexander Brace; Michael Salim; Vishal Subbiah; Heng Ma; Murali Emani; Anda Trifan; Austin R. Clyde; Corey Adams; Thomas D. Uram; Hyun Seung Yoo; Andew Hock; Jessica Liu; et al. (PASC, 2021)

Scalable HPC & AI infrastructure for COVID-19 therapeutics. - Hyungro Lee; André Merzky; Li Tan; Mikhail Titov; Matteo Turilli; Dario Alfè; Agastya Bhati; Alex Brace; Austin Clyde; Peter V. Coveney; Heng Ma; Arvind Ramanathan; et al. (PASC, 2021)

Achieving 100X faster simulations of complex biological phenomena by coupling ML to HPC ensembles. - Alexander Brace; Hyungro Lee; Heng Ma; Anda Trifan; Matteo Turilli; Igor Yakushin; Todd S. Munson; Ian T. Foster; Shantenu Jha; Arvind Ramanathan (CoRR, 2021)

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. - Lorenzo Casalino; Abigail C. Dommer; Zied Gaieb; Emília P. Barros; Terra Sztain; Surl-Hee Ahn; Anda Trifan; Alexander Brace; Anthony T. Bogetti; Austin Clyde; Heng Ma; Hyungro Lee; et al. (Int. J. High Perform. Comput. Appl., 2021)

Coupling streaming AI and HPC ensembles to achieve 100-1000× faster biomolecular simulations. - Alexander Brace; Igor Yakushin; Heng Ma; Anda Trifan; Todd S. Munson; Ian T. Foster; Arvind Ramanathan; Hyungro Lee; Matteo Turilli; Shantenu Jha (IPDPS, 2022)

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. - Anda Trifan; Defne Gorgun; Michael Salim; Zongyi Li; Alexander Brace; Maxim Zvyagin; Heng Ma; Austin Clyde; David Clark; David J. Hardy; Tom Burnley; Lei Huang 019; et al. (Int. J. High Perform. Comput. Appl., 2022)

High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. - Austin Clyde; Stephanie Galanie; Daniel W. Kneller; Heng Ma; Yadu N. Babuji; Ben Blaiszik; Alexander Brace; Thomas S. Brettin; Kyle Chard; Ryan Chard; Leighton Coates; Ian T. Foster; et al. (J. Chem. Inf. Model., 2022)

Linking the Dynamic PicoProbe Analytical Electron-Optical Beam Line / Microscope to Supercomputers. - Alexander Brace; Rafael Vescovi; Ryan Chard; Nickolaus D. Saint; Arvind Ramanathan; Nestor J. Zaluzec; Ian T. Foster (SC Workshops, 2023)

DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies. - Shuaiwen Leon Song; Bonnie Kruft; Minjia Zhang; Conglong Li; Shiyang Chen 004; Chengming Zhang 006; Masahiro Tanaka; Xiaoxia Wu; Jeff Rasley; Ammar Ahmad Awan; Connor Holmes; Martin Cai; et al. (CoRR, 2023)

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. - Abigail C. Dommer; Lorenzo Casalino; Fiona L. Kearns; Mia A. Rosenfeld; Nicholas Wauer; Surl-Hee Ahn; John Russo 003; A. Sofia F. Oliveira; Clare Morris; Anthony T. Bogetti; Anda Trifan; Alexander Brace; et al. (Int. J. High Perform. Comput. Appl., 2023)

GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics. - Maxim Zvyagin; Alexander Brace; Kyle Hippe; Yuntian Deng; Bin Zhang; Cindy Orozco Bohorquez; Austin Clyde; Bharat Kale; Danilo Perez-Rivera; Heng Ma; Carla M. Mann; Michael W. Irvin; et al. (Int. J. High Perform. Comput. Appl., 2023)

High Performance Binding Affinity Prediction with a Transformer-Based Surrogate Model. - Archit Vasan; Ozan Gökdemir; Alexander Brace; Arvind Ramanathan; Thomas S. Brettin; Rick Stevens; Venkatram Vishwanath (IPDPS (Workshops), 2024)

MProt-DPO: Breaking the ExaFLOPS Barrier for Multimodal Protein Design Workflows with Direct Preference Optimization. - Gautham Dharuman; Kyle Hippe; Alexander Brace; Sam Foreman; Väinö Hatanpää; Varuni Katti Sastry; Huihuo Zheng; Logan T. Ward; Servesh Muralidharan; Archit Vasan; Bharat Kale; Carla M. Mann; et al. (SC, 2024)

LSHBloom: Memory-efficient, Extreme-scale Document Deduplication. - Arham Khan; Robert Underwood; Carlo Siebenschuh; Yadu N. Babuji; Aswathy Ajith; Kyle Hippe; Ozan Gökdemir; Alexander Brace; Kyle Chard; Ian T. Foster (CoRR, 2024)

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery. - Peter St. John; Dejun Lin; Polina Binder; Malcolm Greaves; Vega Shah; John St. John; Adrian Lange; Patrick D. Hsu; Rajesh Illango; Arvind Ramanathan; Anima Anandkumar; David H. Brookes; et al. (CoRR, 2024)

HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights. - Ozan Gökdemir; Carlo Siebenschuh; Alexander Brace; Azton Wells; Brian Hsu; Kyle Hippe; Priyanka Setty; Aswathy Ajith; J. Gregory Pauloski; Varuni Sastry; Sam Foreman; Huihuo Zheng; et al. (PASC, 2025)

Employing artificial intelligence to steer exascale workflows with colmena. - Logan T. Ward; J. Gregory Pauloski; Valérie Hayot-Sasson; Yadu N. Babuji; Alexander Brace; Ryan Chard; Kyle Chard; Rajeev Thakur; Ian T. Foster (Int. J. High Perform. Comput. Appl., 2025)

Connecting Large Language Model Agent to High Performance Computing Resource. - Heng Ma; Alexander Brace; Carlo Siebenschuh; J. Gregory Pauloski; Ian T. Foster; Arvind Ramanathan (CoRR, 2025)

Object Proxy Patterns for Accelerating Distributed Applications. - J. Gregory Pauloski; Valérie Hayot-Sasson; Logan T. Ward; Alexander Brace; André Bauer 001; Kyle Chard; Ian T. Foster (IEEE Trans. Parallel Distributed Syst., 2025)

AdaParse: An Adaptive Parallel PDF Parsing and Resource Scaling Engine. - Carlo Siebenschuh; Kyle Hippe; Ozan Gökdemir; Alexander Brace; Arham Khan; Khalid Hossain; Yadu N. Babuji; Nicholas Chia; Venkatram Vishwanath; Rick Stevens; Arvind Ramanathan; Ian T. Foster; et al. (CoRR, 2025)

HiPerRAG: High-Performance Retrieval Augmented Generation for Scientific Insights. - Ozan Gökdemir; Carlo Siebenschuh; Alexander Brace; Azton Wells; Brian Hsu; Kyle Hippe; Priyanka Vasanthakumari; Aswathy Ajith; J. Gregory Pauloski; Varuni Katti Sastry; Sam Foreman; Huihuo Zheng; et al. (CoRR, 2025)