We theoretically investigate the strong coupling between a single molecule and a single metallic nanoparticle. A theory suited for the quantum-mechanical description of surface plasmon polaritons SPPs is developed. The coupling between these SPPs and a single molecule, and the modified molecular dynamics in the presence of the nanoparticle are described within a combined Drude and boundary-elem...

Analysis of a variety of dynamic phenomena requires simultaneous resolution at both atomistic and continuum length scales. A combined molecular dynamics and finite element method approach, which we discuss in this paper, allows us to find the balance between the necessary level of detail and computational cost. The combined method is applied to the propagation of a laser-induced pressure wave i...

Recent attempts to investigate the properties of dense and semidilute polymer systems are reviewed. Both molecular dynamics (MD) and Monte Carlo (MC) methods provide direct evidence for the reptation model and give a rather detailed picture of the motion of linear polymers at high density. Mapping the results onto various chemical polymers allow one to predict the time and length scale for the ...

The idea of acoustic activation of surface diffusion is explored theoretically and in atomistic simulations. It is found that a substantial diffusion enhancement by surface acoustic waves is possible via (1) transient surface straininduced modification of the diffusion barriers, (2) adiabatic variation in the surface temperature, and (3) dynamic coupling of the acoustic waves with vibrational s...

We discuss several post-processing issues in molecular dynamics (MD) calculation of lattice thermal conductivity using the Green–Kubo formula. For crystals with high thermal conductivity such as SiC, converting the MD raw data on heat current fluctuations into thermal conductivity result is non-trivial. One can accelerate the process using Fast Fourier Transform and the spectral method. A few m...

Variable high order finite difference methods are applied to calculate the action of molecular Hamiltonians on the wave function using centered equi-spaced stencils, mixed centered and one-sided stencils, and periodic Chebyshev and Legendre grids for the angular variables. Results from one-dimensional model Hamiltonians and the three-dimensional spectroscopic potential of SO2 demonstrate that a...

The assessment of the ability of a mechanical system to tolerate defects is a typical multi-scale problem where the property of flaw tolerance emerges from the nonlinear interactions between the material constituents at the different scales, a common feature of complex systems. In the present talk, a critical analysis of the factors influencing flaw tolerance of continuum and discrete mechanica...

Ehrenfest, Born-Oppenheimer, Langevin and Smoluchowski dynamics are shown to be accurate approximations of time-independent Schrödinger observables for a molecular system avoiding caustics, in the limit of large ratio of nuclei and electron masses, without assuming that the nuclei are localized to vanishing domains. The derivation, based on a Hamiltonian system interpretation of the Schrödinger...

The Poisson-Boltzmann equation is widely used to describe the electrostatic potential of molecules in an ionic solution that is treated as a continuous dielectric medium. The linearized form of this equation, applicable to many biologic macromolecules, may be solved using the boundary element method. A single-layer formulation of the boundary element method, which yields simpler integral equati...