Cyberloop

Cyberloop for Accelerated Bionanomaterials Design

This collaborative project (NSF OAC 1931587) aims at building a sustainable computational infrastructure for all-atom simulations of compounds and multiphase materials across the periodic table in high accuracy up to the 1000 nm scale.

cyberloop

Progress Update at 2022 NSF CSSI PI Meeting – July 25 & 26, 2022

Combined annual usage of our new cyberinfrastructure in this project has reached over 30,000 page views and over 10,000 job submissions per year. Please see our citable summary and poster here:

https://doi.org/10.5281/zenodo.6842341

CSSI Poster Heinz Im Tadmor 2022 v21

Cyberloop Workshop & Talks – November 18 & 19, 2021

A workshop on “Nano/Biomaterial Modeling and Validation” on November 18 and 19, 2021 highlights recent developments by the community and our team:

https://cyberloopworkshop.weebly.com/

Please see below available recordings and slide sets for talks, excluding unpublished discussions:

Welcome and Introduction to Cyberloop Capabilities: Integration of IFF, CHARMM-GUI, OpenKIM
Hendrik Heinz, University of Colorado, Wonpil Im, Lehigh University, Ellad Tadmor, University of Minnesota (3 Talks)
Combined PDF of the 3 Talks
Recording of Heinz: Workshop Opening and Introduction to IFF (15 min)
Recording of Im: What can CHARMM-GUI do for you? (15 min)
Recording of Tadmor: Introduction to OpenKIM (15 min)

Multiscale, Multiphysics Simulation Meets AI-Based Science for Advanced Materials Design
Peter Coveney, University College London
PDF of Talk
Recording of Talk (30 min)

Understanding the Self-Assembly of Skin Lipids from Molecular Dynamics Simulations: A Multiscale Perspective
Clare McCabe, Vanderbilt University (unpublished data, no recording available)

Identification of Bioprivileged Molecules: Expansion of a Computational Approach to Broader Molecular Space
Lauren “Ren” Lopez, Northwestern University (Linda Broadbelt Lab)
Recording of Talk (15 min)

Direct Molecular Dynamics Using the Reactive Explicit Polarization (ReX-Pol) Method
Jiali Gao, University of Minnesota and Shenzhen Bay Laboratory (unpublished data, no recording available)

Density Functional Theory and Multiconfiguration Pair-Density Functional Theory for Strongly Correlated Systems
Donald G. Truhlar, University of Minnesota (unpublished data, no recording available)

CHARMM-GUI Nanomaterials Modeler for Modeling and Simulation of Nanomaterial Systems
Yeolkyo Choi, Lehigh University (Im Lab)
PDF of Talk
Recording of Talk (20 min)

Automated Comparison of Bonded Force Fields and Reactive Interatomic Potentials in OpenKIM
Moon-Ki Choi, University of Minnesota (Tadmor Lab)

PDF of Talk
Recording of Talk (20 min)

Accurate Atomistic Simulations of Metals, Oxides and Hydroxides up to the Large Nanometer Scale
Krishan Kanhaiya, University of Colorado (Heinz Lab)
PDF of Talk
Recording of Talk (20 min)

Leveraging Advanced Simulations and Machine Learning to Overcome Free Energy Barriers in Molecular Systems
Sapna Sarupria, University of Minnesota
Recording of Talk (30 min)

Integrative Computational/Experimental Approaches to Study the Interaction of Peptides with Mineral Surfaces
Massimiliano “Max” Bonomi, Institute Pasteur (CNRS), Paris
PDF of Talk
Recording of Talk (30 min)

Force Field Development and Molecular Dynamics Studies of LiCoO2-Water Interfaces
Dongyue Liang, University of Chicago (Juan De Pablo/UC and Qiang Cui/BU Labs)
PDF of Talk
Recording of Talk (15 min)

Opportunities and Challenges in Simulating Biomolecules at Interfaces
Jim Pfaendtner, University of Washington
Recording of Talk (30 min)

Progress

From 2019 to-date, we doubled the coverage of IFF to include further metals, oxides, 2D and other materials. Most IFF developments since 2005 using 12-6 LJ potential options have been incorporated into the new CHARMM-GUI Nanomaterials Modeler, see charmm-gui.org nanomaterial modeler (after required user registration). The Nanomaterials Modeler is a unique resource to generate inputs for a variety of nanostructures in different input formats, ready to use with CHARMM, NAMD, GROMACS, OpenMM, and LAMMPS. OpenKIM now includes the first simulator models for bonded force fields (such as IFF and CHARMM) and is being extended to incorporate new validation protocols for force fields at room temperature, and include key properties such as surface/cleavage energies and hydration energies.

Motivation

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 will 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 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. 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 will facilitate 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 will help increase participation in bionanomaterial research across academia and government.

Links for further information:

CHARMM_GUI
IFF
OpenKIM

Open Knowledgebase of Interatomic Models (OpenKIM)

OpenKIM is a cyberinfrastructure for improving the reliability of molecular and multiscale simulations of materials. It includes a repository of interatomic potentials that are exhaustively tested, tools to help select among existing potentials and develop new ones, and standard integration methods for using potentials in major simulation codes. Visit the OpenKIM Website.

We are grateful for support from the National Science Foundation (OAC 1931587).