Research Topic

[Cyberloop Project] Topic: Cyberloop for Accelerated Bionanomaterials Design

Minnesota Team: Yaser Afshar, Daniel Karls, Ryan Elliott, Ellad Tadmor

Colorado Team: Krishan Kanhaiya, Hendrik Heinz

Lehigh Team: Wonpil Im

Funding: National Science Foundation (CSSI Framework)

Figure: Cyberloop combines IFF (the interface force field for nano/bio systems), CHARMM-GUI (a graphical front end for setting up bio/nano material simulations), and OpenKIM (Open Knowledgebase of Interatomic Models framework) into a single unified cyberinfrastructure for accelerated simulations and discovery of bionanomaterials. Developments are released on the KIM project website at https://openkim.org

Description: The Cyberloop for Accelerated Bionanomaterials Design integrates three existing successful platforms for soft matter and solid state simulations (IFF, OpenKIM, and CHARMM-GUI) into a single unified framework. These 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.


For more information, see also our collaborators IFF project at CU Boulder and the CHARMM-GUI Nanomaterial Modeler at Purdue.

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