AVS 60th International Symposium and Exhibition
    Biomaterial Interfaces Thursday Sessions
       Session BI+AS+BA+NS+SS-ThA

Paper BI+AS+BA+NS+SS-ThA4
Development of Molecular Modeling Capabilities in LAMMPS Specifically Designed for the Efficient and Accurate Simulation of Biomolecule-Surface Interactions

Thursday, October 31, 2013, 3:00 pm, Room 102 B

Session: Biomolecules at Interfaces
Presenter: R.A. Latour, Clemson University
Authors: R.A. Latour, Clemson University
C.D. Lorenz, King's College-London, UK
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The ability to understand and predict the interactions of tethered or adsorbed biomolecules (e.g., protein, DNA, carbohydrates) at material interfaces represents a critical need for many applications in bionanotechnology and biomedical engineering. Experimental methods alone are typically very limited in terms of their ability to probe the molecular level of detail needed to quantitatively understand these types of complex interfacial interactions. As a result, biomaterial systems must often largely be designed by trial-and-error approaches. Molecular simulation methods provide an excellent means to complement experimental studies to provide theoretical assessment and predictive capability of the behavior of biomolecules at interfaces with atomic-scale resolution. These methods, however, must be specifically designed and developed for biomaterial applications. The Latour group has focused on the development of molecular simulation methods for the efficient and accurate simulation of protein-surface interactions over the past two decades, mostly involving the CHARMM molecular simulation program. Over the past year, we have focused on transitioning from CHARMM to the LAMMPS molecular simulation program for our continued development work in collaboration with the Lorenz group at King’s College-London. LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a fast, versatile, and highly parallelizable molecular simulation program with excellent capabilities for materials modeling. It is also freely available for download from the primary developer’s website (Sandia National Laboratory, <http://lammps.sandia.gov/>). Over the past year, we have been developing new LAMMPS modules that are specifically being designed to support the efficient and accurate simulation of protein-surface interactions, with planned extension to other biomolecule systems. In this presentation, we will provide an overview of the developed capabilities in the LAMMPS program, with demonstrated applications to simulate protein-surface interactions at the atomic level. The development of these molecular simulation modules in LAMMPS has the potential to revolutionize current capabilities to accurately simulate, predict, and understand mechanisms governing biomolecule interactions at material interfaces and to serve as a valuable tool for system design.