John Stone

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne… Show more

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized. Show less

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular… Show more

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale. Show less

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows… Show more

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems. Show less

An Accessible Visual Narrative for the Primary Energy Source of Life from the Fulldome Show Birth of Planet Earth.
https://sc19.supercomputing.org/proceedings/sci_viz/sci_viz_pages/svs110.html

Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. An explanatory visualization depicting this process is presented in the form of an excerpt from the fulldome show Birth of Planet Earth. This accessible visual narrative shows a lay… Show more

An Accessible Visual Narrative for the Primary Energy Source of Life from the Fulldome Show Birth of Planet Earth.
https://sc19.supercomputing.org/proceedings/sci_viz/sci_viz_pages/svs110.html

Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. An explanatory visualization depicting this process is presented in the form of an excerpt from the fulldome show Birth of Planet Earth. This accessible visual narrative shows a lay audience, especially children, how the energy of sunlight is captured, converted, and stored through a chain of proteins to power living cells. The visualization is the result of a multi-year collaboration among biophysicists, visualization scientists, and artists, which, in turn, is based on a decade-long experimental-computational collaboration on structural and functional modeling that produced an atomic detail description of a bacterial bioenergetic organelle, the chromatophore. The energy conversion steps depicted feature an integration of function from electronic to cell levels, spanning nearly 12 orders of magnitude in time scales modeled with multi-scale computational approaches. This atomic detail description uniquely enables a modern retelling of one of humanity's earliest stories---the interplay between light and life.

Authors: Melih Sener, Stuart Levy, AJ Chistensen, Robert Patterson, Kalina Borkiewicz, John E. Stone, Barry Isralewitz, Jeffrey Carpenter, Donna Cox. (University of Illinois at Urbana-Champaign) Show less

John Stone of University of Illinois was awarded as an IBM Champion for Power along with 13 other new, and 27 returning Champions for 2017.
The IBM Champion program recognizes innovative thought leaders in the technical community – and rewards these contributors by amplifying their voice and increasing their sphere of influence.

Our research article: Molecular dynamics-based refinement and validation for sub-5A cryo-electron microscopy maps., eLife, 2016 (http://dx.doi.org/10.7554/eLife.16105) has been recommended in F1000Prime as being of special significance in its field by F1000 Faculty Member Jose-Maria Carazo:
http://f1000.com/prime/726488409?bd=1

My work on molecular visualization using interactive ray tracing on VR HMDS using remote clouds and supercomputers was a finalist for NVIDIA's 2016 GPU Center of Excellence Achievement Award:
https://blogs.nvidia.com/blog/2016/04/12/oxford-gpu-center-of-excellence-achievement-award/

http://blogs.nvidia.com/blog/2015/03/12/how-gpus-keep-pace-with-viruses/

The NVIDIA Global Impact Award is an annual grant for groundbreaking work that addresses the world's most important social and humanitarian problems. It will go to a researcher or institution using NVIDIA technology to achieve breakthrough results with broad impact. This includes – but is not limited to – the areas of disease research, drug design & development, medical imaging, energy & fuel efficiency, weather… Show more

http://blogs.nvidia.com/blog/2015/03/12/how-gpus-keep-pace-with-viruses/

The NVIDIA Global Impact Award is an annual grant for groundbreaking work that addresses the world's most important social and humanitarian problems. It will go to a researcher or institution using NVIDIA technology to achieve breakthrough results with broad impact. This includes – but is not limited to – the areas of disease research, drug design & development, medical imaging, energy & fuel efficiency, weather prediction, natural disaster response and cyber security. Show less

"Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail"
Melih Sener, John E. Stone, Angela Barragan, Abhishek Singharoy, Ivan Teo, Kirby L. Vandivort, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten.
Proceedings of the 2014 International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'14), 2014.

Fighting HIV with CUDA
Researchers from University of Illinois at Urbana-Champaign received the Third Annual Achievement Award for CUDA Centers of Excellence, for their research on Fighting HIV with CUDA. Each of the world’s 22 CUDA Centers were asked to submit an abstract describing their top achievement in GPU computing over the past year.

The first scientific breakthrough achieved with the Blue Waters supercomputer at the University of Illinois was the determination of the… Show more

Fighting HIV with CUDA
Researchers from University of Illinois at Urbana-Champaign received the Third Annual Achievement Award for CUDA Centers of Excellence, for their research on Fighting HIV with CUDA. Each of the world’s 22 CUDA Centers were asked to submit an abstract describing their top achievement in GPU computing over the past year.

The first scientific breakthrough achieved with the Blue Waters supercomputer at the University of Illinois was the determination of the structure of the complete HIV capsid in atomic-level detail, a collaborative effort of experimental groups, at the University of Pittsburgh and Vanderbilt University, and the NIH center for Macromolecular Modeling and Bioinformatics, led by Prof. Klaus Schulten at the University of Illinois. The breakthrough was enabled by the NIH Center’s popular and freely available programs NAMD and VMD, both of which incorporate CUDA technology to enable and accelerate the computationally intensive large-scale biomolecular modeling, simulation, and analysis required to perform the 64-million-atom HIV capsid simulation. The process through which the capsid disassembles, releasing its genetic material, is a critical step in HIV infection and a potential target for antiviral drugs. The work was featured on the cover of Nature and recognized by an HPCwire Editors’ Choice Award for “Best use of HPC in life sciences” at SC13.
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GPU Supercomputing in Blue Waters
The Blue Waters supercomputer at the University of Illinois contains 3072 Kepler GPUs, totaling about 4 PetaFLOPS of peak compute throughput. There are a total of 25,712 nodes in Blue Waters. 22,480 of them are Cray XE6 nodes that contain two AMD Interlagos CPUs each, totaling
7.1 PetaFLOPS. 3,072 of these nodes are Cray XK7 nodes that consist of one AMD Interlagos CPU and one NVIDIA Kepler GPU, totaling 4 PetaFLOPS.

As part of an agreement with… Show more

GPU Supercomputing in Blue Waters
The Blue Waters supercomputer at the University of Illinois contains 3072 Kepler GPUs, totaling about 4 PetaFLOPS of peak compute throughput. There are a total of 25,712 nodes in Blue Waters. 22,480 of them are Cray XE6 nodes that contain two AMD Interlagos CPUs each, totaling
7.1 PetaFLOPS. 3,072 of these nodes are Cray XK7 nodes that consist of one AMD Interlagos CPU and one NVIDIA Kepler GPU, totaling 4 PetaFLOPS.

As part of an agreement with NSF, the UIUC CCoE PI (Wen-mei Hwu) agreed to assemble and
lead a task force to prove that the GPUs in XK7 nodes provide at least 3x full-application performance advantage over using CPUs alone in these nodes when run ning NSF-designated
Blue Waters applications (NAMD, QMCPACK, Chroma, and GAMESS), at a scale no less than 600 nodes. This was part of the Blue Waters acceptance criteria. Show less

John E. Stone, Sr. Research Programmer for the Theoretical and Computational Biophysics Group in the University of Illinois Beckman Institute for Advanced Science and Technology, is among three research and academic leaders appointed to the NVIDIA CUDA Fellows Program in 2010. The program recognizes early adopters of the CUDA architecture who have made exceptional advances in the use of GPUs in high-performance computing. “Each of these individuals has demonstrated a passion and commitment to… Show more

John E. Stone, Sr. Research Programmer for the Theoretical and Computational Biophysics Group in the University of Illinois Beckman Institute for Advanced Science and Technology, is among three research and academic leaders appointed to the NVIDIA CUDA Fellows Program in 2010. The program recognizes early adopters of the CUDA architecture who have made exceptional advances in the use of GPUs in high-performance computing. “Each of these individuals has demonstrated a passion and commitment to leveraging CUDA and the power of GPU computing to help solve some of the worlds’ most challenging computational problems,” said Bill Dally, chief scientist at NVIDIA. Show less

Awarded for the paper "An Asymmetric Distributed Shared Memory Model for Heterogeneous Parallel Systems" presented at ASPLOS 2010.

Tachyon, the ray tracing package I originally wrote for my Master's Thesis and continue to maintain today, was selected as a finalist for the SPEC MPI benchmark and is now part of the SPEC MPI2007 benchmark suite.