David J Hardy | University of Illinois at Urbana-Champaign (original) (raw)

Papers by David J Hardy

Research paper thumbnail of GPU-Accelerated Computation and Interactive Display of

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Research paper thumbnail of GPU Algorithms for Molecular Modeling

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Research paper thumbnail of Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus

Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the ... more Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the SARS-CoV-2 virion, its spike protein, and other structures related to the viral infection cycle has led biomedical researchers worldwide to urgently seek out all available biomolecular structure information, appropriate molecular modeling and simulation software, and the necessary computing resources to conduct their work. We describe our experiences from several COVID-19 research collaborations and the challenges they presented in terms of our molecular modeling software development and support efforts, our laboratory’s local computing environment, and our scientists’ use of non-traditional HPC hardware platforms such as public clouds for large scale parallel molecular dynamics simulations.

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Research paper thumbnail of High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

Journal of Physical Chemistry Letters, Dec 23, 2010

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Research paper thumbnail of Multilevel Summation Method for Electrostatic Force Evaluation

Biophysical Journal, 2015

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Research paper thumbnail of Experiences Porting NAMD to the Data Parallel C++ Programming Model

International Workshop on OpenCL, May 10, 2022

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Research paper thumbnail of Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

Journal of Chemical Physics, Mar 21, 2016

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Research paper thumbnail of Computer modeling in biotechnology: a partner in development

Methods in molecular biology, 2008

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Research paper thumbnail of Application Experiences on a GPU-Accelerated Arm-based HPC Testbed

Proceedings of the HPC Asia 2023 Workshops

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Research paper thumbnail of Multilevel summation for the fast evaluation of forces for the simulation of biomolecules

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Research paper thumbnail of NAMD Version 2.9

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Research paper thumbnail of Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action

ABSTRACTThe severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcriptio... more ABSTRACTThe 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 ...

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

The International Journal of High Performance Computing Applications, 2021

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explo... 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 i...

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Research paper thumbnail of Experiences Porting NAMD to the Data Parallel C++ Programming Model

International Workshop on OpenCL

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Research paper thumbnail of Multilevel summation for periodic electrostatics using B-splines

The Journal of Chemical Physics, 2021

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Research paper thumbnail of Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus

2021 IEEE/ACM HPC for Urgent Decision Making (UrgentHPC)

Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the ... more Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the SARS-CoV-2 virion, its spike protein, and other structures related to the viral infection cycle has led biomedical researchers worldwide to urgently seek out all available biomolecular structure information, appropriate molecular modeling and simulation software, and the necessary computing resources to conduct their work. We describe our experiences from several COVID-19 research collaborations and the challenges they presented in terms of our molecular modeling software development and support efforts, our laboratory’s local computing environment, and our scientists’ use of non-traditional HPC hardware platforms such as public clouds for large scale parallel molecular dynamics simulations.

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Research paper thumbnail of #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

ABSTRACTWe seek to completely revise current models of airborne transmission of respiratory virus... more ABSTRACTWe 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 ob-scure 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.ACM Reference FormatAbigail Dommer1†, Lorenzo Casalino1†, Fiona Kearns1†, Mia ...

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Research paper thumbnail of Scalable molecular dynamics with NAMD on the Summit system

IBM Journal of Research and Development, 2018

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Research paper thumbnail of Practical Construction of Modified Hamiltonians

SIAM Journal on Scientific Computing, 2001

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Research paper thumbnail of Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations

Journal of Computational Physics, 2007

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Research paper thumbnail of GPU-Accelerated Computation and Interactive Display of

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Research paper thumbnail of GPU Algorithms for Molecular Modeling

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Research paper thumbnail of Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus

Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the ... more Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the SARS-CoV-2 virion, its spike protein, and other structures related to the viral infection cycle has led biomedical researchers worldwide to urgently seek out all available biomolecular structure information, appropriate molecular modeling and simulation software, and the necessary computing resources to conduct their work. We describe our experiences from several COVID-19 research collaborations and the challenges they presented in terms of our molecular modeling software development and support efforts, our laboratory’s local computing environment, and our scientists’ use of non-traditional HPC hardware platforms such as public clouds for large scale parallel molecular dynamics simulations.

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Research paper thumbnail of High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

Journal of Physical Chemistry Letters, Dec 23, 2010

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Research paper thumbnail of Multilevel Summation Method for Electrostatic Force Evaluation

Biophysical Journal, 2015

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Research paper thumbnail of Experiences Porting NAMD to the Data Parallel C++ Programming Model

International Workshop on OpenCL, May 10, 2022

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Research paper thumbnail of Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

Journal of Chemical Physics, Mar 21, 2016

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Research paper thumbnail of Computer modeling in biotechnology: a partner in development

Methods in molecular biology, 2008

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Research paper thumbnail of Application Experiences on a GPU-Accelerated Arm-based HPC Testbed

Proceedings of the HPC Asia 2023 Workshops

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Research paper thumbnail of Multilevel summation for the fast evaluation of forces for the simulation of biomolecules

Bookmarks Related papers MentionsView impact

Research paper thumbnail of NAMD Version 2.9

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Research paper thumbnail of Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action

ABSTRACTThe severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcriptio... more ABSTRACTThe 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 ...

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

The International Journal of High Performance Computing Applications, 2021

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explo... 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 i...

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Research paper thumbnail of Experiences Porting NAMD to the Data Parallel C++ Programming Model

International Workshop on OpenCL

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Research paper thumbnail of Multilevel summation for periodic electrostatics using B-splines

The Journal of Chemical Physics, 2021

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Lessons Learned from Responsive Molecular Dynamics Studies of the COVID-19 Virus

2021 IEEE/ACM HPC for Urgent Decision Making (UrgentHPC)

Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the ... more Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the SARS-CoV-2 virion, its spike protein, and other structures related to the viral infection cycle has led biomedical researchers worldwide to urgently seek out all available biomolecular structure information, appropriate molecular modeling and simulation software, and the necessary computing resources to conduct their work. We describe our experiences from several COVID-19 research collaborations and the challenges they presented in terms of our molecular modeling software development and support efforts, our laboratory’s local computing environment, and our scientists’ use of non-traditional HPC hardware platforms such as public clouds for large scale parallel molecular dynamics simulations.

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Research paper thumbnail of #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

ABSTRACTWe seek to completely revise current models of airborne transmission of respiratory virus... more ABSTRACTWe 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 ob-scure 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.ACM Reference FormatAbigail Dommer1†, Lorenzo Casalino1†, Fiona Kearns1†, Mia ...

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Research paper thumbnail of Scalable molecular dynamics with NAMD on the Summit system

IBM Journal of Research and Development, 2018

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Research paper thumbnail of Practical Construction of Modified Hamiltonians

SIAM Journal on Scientific Computing, 2001

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations

Journal of Computational Physics, 2007

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