Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structu...

Motivated by recent work in density matrix embedding theory, we define exact link orbitals that capture all quantum mechanical (QM) effects across arbitrary quantum mechanics/molecular mechanics (QM/MM) boundaries. Exact link orbitals are rigorously defined from the full QM solution, and their number is equal to the number of orbitals in the primary QM region. Truncating the exact set yields a ...

Results of molecular-mechanics simulations of axial and torsional deformations of a single wall carbon nanotube are used to find Young’s modulus, the shear modulus, and the wall thickness of an equivalent continuum tube made of a linear elastic isotropic material. These values are used to compare the response of the continuum tube in bending and buckling with that obtained from the molecular me...