Nov. 18 - 19, 2021 / 9am - 2pm EST
Zoom ID: https://cuboulder.zoom.us/j/2251625831 Passcode: cyberloop |
AIM |
The workshop aims at sharing new science contributions and perspectives on challenges in the ease of use of cyber-infrastructure, development of inter-atomic potentials and model databases, input/output generation, validation of simulations, and needs to integrate software tools. We plan to identify capabilities, issues, and user needs for the simulation of processes from atoms to micrometers. |
Background: The NSF-supported project “Cyberloop for Accelerated Bionanomaterials Design” aims at creating cyberinfrastructure for the simulation of bionanomaterials from atoms to the large nanometer scale, including compounds across the periodic table, and developing community standards for testing and validation. Initial building blocks include CHARMM-GUI, the Interface Force Field (IFF), and OpenKIM.
Cyberloop for Accelerated Bionanomaterials Design
The understanding of the dynamical evolution of biological and materials systems from the atomic scale to the microscale is essential for groundbreaking advances in the health sciences, materials sciences, energy conversion, sustainability, and overall quality of life. Molecular simulations using sophisticated force fields and complex configuration databases play an increasing role in such efforts by addressing the limitations of experiments in probing phenomena over very small time and length scales. However, such simulations require a very high level of expertise to do correctly due to the complexity of the systems being studied and the simulation tools being used. This is particularly true for models systems containing both inorganic and biological materials at nanometer scales, so called “bionanomaterial systems.” This project will assist researchers to correctly and rapidly set up complex bionanomaterial simulations, carry out the simulations with high accuracy, and assess uncertainties in the results by developing the “Cyberloop” computational infrastructure. Cyberloop aims to dramatically reduce the time and errors involved in performing state-of-the-art bionanomaterial simulations and help to educate the next generation of researchers in this important field.
Cyberloop will integrate three existing successful platforms for soft matter and solid state simulations (IFF, OpenKIM, and CHARMM-GUI) into a single unified framework. The systems will work together to enable users to set up complex bionanomaterial configurations, select reliable validated force fields, generate input scripts for popular simulation platforms, and assess the uncertainty in the results. The integration of these tools requires a host of technological and scientific innovations including: automated charge assignment protocols and file conversions, expansion of the Interface force field (IFF) to new systems, generation of new surface models, extension of the Open Knowledgebase of Interatomic Models (OpenKIM) to bonded force fields, development of machine learning based force field selection and
uncertainty tools, and development of new Nanomaterial Builder and Bionano Builder modules in CHARMM-GUI. Cyberloop fulfils a critical need in the user community to discover and engineer new multi-component bionanomaterials to create the next generation of therapeutics, materials for energy conversion, and ultrastrong composites. The project facilitates the training of graduate students, undergraduate students, and postdoctoral scholars, including underrepresented and minority students, at the participating institutions to prepare an interdisciplinary scientific workforce with significant experience in cyber-enabled technology.
Online educational materials and tutorials aim at lowering the barrier and increasing participation in bionanomaterial research.
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Cyberloop will integrate three existing successful platforms for soft matter and solid state simulations (IFF, OpenKIM, and CHARMM-GUI) into a single unified framework. The systems will work together to enable users to set up complex bionanomaterial configurations, select reliable validated force fields, generate input scripts for popular simulation platforms, and assess the uncertainty in the results. The integration of these tools requires a host of technological and scientific innovations including: automated charge assignment protocols and file conversions, expansion of the Interface force field (IFF) to new systems, generation of new surface models, extension of the Open Knowledgebase of Interatomic Models (OpenKIM) to bonded force fields, development of machine learning based force field selection and
uncertainty tools, and development of new Nanomaterial Builder and Bionano Builder modules in CHARMM-GUI. Cyberloop fulfils a critical need in the user community to discover and engineer new multi-component bionanomaterials to create the next generation of therapeutics, materials for energy conversion, and ultrastrong composites. The project facilitates the training of graduate students, undergraduate students, and postdoctoral scholars, including underrepresented and minority students, at the participating institutions to prepare an interdisciplinary scientific workforce with significant experience in cyber-enabled technology.
Online educational materials and tutorials aim at lowering the barrier and increasing participation in bionanomaterial research.
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Organizers: Hendrik Heinz, University of Colorado Boulder (Lead Organizer); Wonpil Im, Lehigh University; Ellad Tadmor, University of Minnesota
Website created by Krishan Kanhaiya, University of Colorado Boulder
Contact: [email protected] and [email protected]
Website created by Krishan Kanhaiya, University of Colorado Boulder
Contact: [email protected] and [email protected]