title: Scalable nanohelices for predictive studies and enhanced 3D visualization.
abstract: Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing applications. For predictive simulations, it has become increasingly important to be able to model the structure of nanohelices accurately. To study the effect of local structure on the properties of these complex geometries one must develop realistic models. To date, software packages are rather limited in creating atomistic helical models. This work focuses on producing atomistic models of silica glass (SiO₂) nanoribbons and nanosprings for molecular dynamics (MD) simulations. Using an MD model of "bulk" silica glass, two computational procedures to precisely create the shape of nanoribbons and nanosprings are presented. The first method employs the AWK programming language and open-source software to effectively carve various shapes of silica nanoribbons from the initial bulk model, using desired dimensions and parametric equations to define a helix. With this method, accurate atomistic silica nanoribbons can be generated for a range of pitch values and dimensions. The second method involves a more robust code which allows flexibility in modeling nanohelical structures. This approach utilizes a C++ code particularly written to implement pre-screening methods as well as the mathematical equations for a helix, resulting in greater precision and efficiency when creating nanospring models. Using these codes, well-defined and scalable nanoribbons and nanosprings suited for atomistic simulations can be effectively created. An added value in both open-source codes is that they can be adapted to reproduce different helical structures, independent of material. In addition, a MATLAB graphical user interface (GUI) is used to enhance learning through visualization and interaction for a general user with the atomistic helical structures. One application of these methods is the recent study of nanohelices via MD simulations for mechanical energy harvesting purposes.
authors.affiliation: Materials Science and Engineering, School of Engineering, University of California Merced.
authors.forename: Kwyn A
authors.initials: KA
authors.lastname: Meagher
authors.affiliation: Materials Science and Engineering, School of Engineering, University of California Merced.
authors.forename: Benjamin N
authors.initials: BN
authors.lastname: Doblack
authors.affiliation: Computer Science and Engineering, School of Engineering, University of California Merced.
authors.forename: Mercedes
authors.initials: M
authors.lastname: Ramirez
authors.affiliation: Materials Science and Engineering, School of Engineering, University of California Merced; ldavila@ucmerced.edu.
authors.forename: Lilian P
authors.initials: LP
authors.lastname: Davila
mesh_terms: D021621:Imaging, Three-Dimensional / Q000379:methods*; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology / Q000379:methods*; D012822:Silicon Dioxide / Q000737:chemistry*; D012984:Software
chemical_list: D012822:Silicon Dioxide