Lab Partnering Service Discovery
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Title: HPC Application Architect
- Molecular dynamics
- Density Functional Theory Code Development
- Parallel programming (GNU parallel, MPI, OpenMP, PGAS models, etc.)
Hubertus (Huub) van Dam is a computational chemist with expertise in docking and molecular dynamics simulations. In prior work he has collaborated on improving the accuracy of docking calculations by using ab-initio molecular potentials for the electrostatic part of docking scores (DOI: 10.1063/1.2793399). He is currently supporting the National Virtual Biotechnology Laboratory (NVBL) effort to find COVID-19 drug candidates using Autodock 4.2, Dock 6 and DeepDriveMD. He also has extensive expertise in writing and supporting large parallel quantum chemistry packages. Currently, he serves as Testing and Assessment Task Lead on the Exascale Computing Project’s NWChemEx effort. NWChemEx is providing a community infrastructure for computational chemistry that takes full advantage of exascale computing technologies.
Energy research represents a major focus for BNL over the next decade. We are using a multifaceted approach driven by the unique state-of-the art laboratory facilities and the inter-disciplinary expertise of our scientific staff to solve fundamental questions regarding U.S. energy independence and to translate discoveries into deployable technologies. The laboratory has identified several energy focus areas – including biofuels, complex materials, catalysis, and solar energy.
BNL's one-of-kind user facilities include the National Synchrotron Light Source II NSLS-II, which produces extremely bright beams of x-ray, ultraviolet, and infrared light for scientists exploring materials—including superconductors, catalysts, geological samples, and proteins—to accelerate advances in energy, environmental science, and medicine. Scientists at our Center for Functional Nanomaterials create materials and explore their unique structure and properties at the nanoscale, with a focus on more efficient solar and energy storage materials. And at BNL's Northeast Solar Energy Research Center, where researchers from labs, academia, and industry study test new solar technologies, working to make solar "power plants" more efficient and economical
In addition to fundamental research, the laboratory actively collaborates with industry and other academic institutions to bring the benefits of scientific discoveries to the marketplace. Brookhaven's Office of Strategic Partnerships integrates Brookhaven Lab's industry engagement, technology licensing, and economic development functions to expand the impact of collaborative research and technology commercialization. Strategic Partnerships supports the Laboratory's science mission through identifying, pursuing and managing partnerships with a broad set of private-sector companies, federal agencies, and non-federal entities. For information on licensing and industry.
- Basic science: seeks to understand how nature works. This research includes experimental and theoretical work in materials science, physics, chemistry, biology, high-energy physics, and mathematics and computer science, including high performance computing.
- Applied science and engineering helps to find practical solutions to society’s problems. These programs focus primarily on energy resources, environmental management and national security.
Amy Sims, Ph.D. is a Senior Research Scientist in the Chemical and Biological Signatures Division of the National Security Directorate at Pacific Northwest National Laboratory (PNNL) in Richland, WA. She earned her Ph.D. from Vanderbilt University Medical Center and worked with Professor Ralph Baric at the University of North Carolina at Chapel Hill (UNC) during her postdoctoral studies. Dr. Sims spent an additional 15 years at UNC as faculty in a continued collaboration with Dr. Baric to understand the pathogenesis of highly pathogenic human coronaviruses and to identify novel vaccination strategies and therapeutic targets. Dr. Sims has published over 50 peer-reviewed publications on antivirals that are efficacious against human coronaviruses, using reverse genetic platforms to characterize coronavirus protein functions, and how coronaviruses prevent transcription factor nuclear translocation to regulate host gene expression, and recently joined PNNL to continue a decade long collaboration on the use of computational modeling and bioinformatics approaches in analyses of kinetic ‘omics data from studies of severe acute respiratory syndrome coronavirus 2003 (SARS-CoV 2003) and Middle East respiratory syndrome coronavirus (MERS-CoV) infected samples. The overall goal of her research is to understand the detailed molecular mechanisms by which CoVs manipulate host pathways and processes to evade the innate immune response and to enhance viral replication and spread.
Michael Connolly is a Principal Scientific Engineering Associate at the Molecular Foundry at Lawrence Berkeley National Laboratory and an organic chemist with 20+ years of expertise in combinatorial and automated synthesis methods and nanomaterial discovery. His research focus is the development of combinatorial discovery technologies and new biopolymer nanomaterials. He has developed a class of bio-inspired polymer called ‘peptoids’ that have found utility in drug discovery, drug delivery, diagnostics, and materials science. Key contributions included the development of new synthetic methods, new sequencing, and characterization methods for peptoids.
Additional information available at this link.
COVID-19-related research: "Scientists Aim Gene-Targeting Breakthrough against COVID-19" (cellular delivery system/anti-viral agent)
Lawrence Berkeley National Laboratory (Berkeley Lab), a U. S. Department of Energy Office of Science national lab managed by the University of California, delivers science solutions to the world – solutions derived from hundreds of patented and patent pending technologies plus scores of copyrighted software tools and published, peer-reviewed manuscripts.
Berkeley Lab has more than one hundred cutting-edge research projects using AI to find new scientific solutions to national problems. Through this effort, computer scientists, mathematicians, and domain scientists are collaborating to turn burgeoning datasets into scientific insights. Visit Berkeley Lab’s Machine Learning for Science site for more information.
Berkeley Lab’s advanced materials expertise is applied to innovation in batteries and other energy storage technologies, semiconductors, and photovoltaics. Additional energy-related areas of expertise include grid modernization and security, bio-based fuels and chemicals and building energy and demand response. Several National User Facilities are available for collaborative engagement: the Advanced Light Source, Molecular Foundry, National Energy Research Scientific Computing Center (NERSC), Energy Sciences Network, and the Joint Genome Institute. Other specialized facilities include FLEXLAB for building energy research and the Advanced Biofuels Process Demonstration Unit.
Ernest Orlando Lawrence, the lab's founder, believed team science yielded the greatest discoveries. That belief is reflected today in interdisciplinary teams and collaborative projects connecting Berkeley Lab, industry, and other research organizations. Berkeley Lab's Intellectual Property Office, connects industry partners with lab innovations and unique facilities to enable lab-to-market transition.