title: Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures.
abstract: The potential energy of molecules and nanostructures is commonly calculated in the molecular mechanics formalism by superimposing bonded and nonbonded atomic energy terms, i.e. bonds between two atoms, bond angles involving three atoms, dihedral angles involving four atoms, nonbonded terms expressing the Coulomb and Lennard-Jones interactions, etc. In this work a new, generalized numerical simulation is presented for studying the mechanical behavior of three-dimensional nanostructures at the atomic scale. The energy gradient and Hessian matrix of such assemblies are usually computed numerically; a potential energy finite element model is proposed herein where these two components are expressed analytically. In particular, generalized finite elements are developed that express the interactions among atoms in a manner equivalent to that invoked in simulations performed based on the molecular dynamics method. Thus, the global tangent stiffness matrix for any nanostructure is formed as an assembly of the generalized finite elements and is directly equivalent to the Hessian matrix of the potential energy. The advantages of the proposed model are identified in terms of both accuracy and computational efficiency. In the case of popular force fields (e.g., CHARMM), the computation of the Hessian matrix by implementing the proposed method is of the same order as that of the gradient. This analysis can be used to minimize the potential energy of molecular systems under nodal loads in order to derive constitutive laws for molecular systems where the entropy and solvent effects are neglected and can be approximated as solids, such as double stranded DNA nanostructures. In this context, the sequence dependent stretch modulus for some typical base pairs step is calculated.
authors.affiliation: Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens , 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece.
authors.forename: Stavros
authors.initials: S
authors.lastname: Chatzieleftheriou
authors.affiliation: Laboratory of Computational Biology & Biophysics, Department of Biological Engineering, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, United States.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Adendorff
authors.affiliation: Institute of Structural Analysis & Antiseismic Research, Department of Structural Engineering, School of Civil Engineering, National Technical University of Athens , 9 Heroon Polytechniou Street, Zografou Campus, GR-15780 Athens, Greece.
authors.forename: Nikos D
authors.initials: ND
authors.lastname: Lagaros
mesh_terms: D004247:DNA / Q000737:chemistry; D019277:Entropy; D020342:Finite Element Analysis; D056004:Molecular Dynamics Simulation; D049329:Nanostructures / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D012997:Solvents; D004247:DNA