The framework of the heterogeneous multiscale method (HMM) is used to develop numerical methods for the study of macroscale dynamics of fluids in situations, where either the constitutive relation or the boundary conditions are not explicitly available and have to be inferred from microscopic models such as molecular dynamics. Continuum hydrodynamics is used as the macroscopic model, while mole...

Detailed agreements between the predictions of the coupling model and the results of Monte Carlo simulations and a molecular dynamics simulation on the dynamics of the center-of-mass diffusion of entangled multichain systems are pointed out. These are further discussed in conjunction with real experimental data.

For many practical cases, such as gas-wall interactions, molecular dynamics simulations are a perfect tool. Here we use such molecular dynamics simulation to study the micro heat transfer of gas in a nanochannel. However, to study larger microchannels molecular dynamics is computationally too expensive. Within the GASMEMS project, firstly an efficient parallel code will be developed and a metho...

In this work, we present a seamless, energy-conserving method to couple atomistic and continuum representations of a temperature field in a material. This technique allows a molecular dynamics simulation to be used in localized regions of the computational domain, surrounded and overlaid by a continuum finite element representation. Thermal energy can pass between the two regions in either dire...

This supporting information contains three sections with details on the mathematical model for the pace-making circuit of segmentation clock, parameter value/range selection, numerical methods. In the section on the mathematical model, we provide details about modeling the dynamics of Hes7 mRNA and protein. In the section on parameter selection, we describe how we In the section on numerical me...

Under certain kinetic or thermodynamic conditions, proteins make large conformational changes, formally called state transitions, resulting in significant changes in their chemical or biological functions. These dynamic properties of proteins can be studied through molecular dynamics simulation. However, in contrast to conventional dynamics simulation protocols where an initial-value problem is...

A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab-initio molecular dynamics simulations with full wave functions. It extends and combines the traditions of existing augmented wave methods and the pseudopotential approach. Without sacrificing efficiency, the PAW...

A continuum model of nanocrystalline copper was developed based on results from independent atomistic calculations on 11 bicrystals containing high angle grain boundaries. The relationship between grain boundary structure and its mechanical response was investigated. Based on the atomistic calculations; a constitutive law for grain boundary interfaces was implemented within a finite element cal...

Article history: Received 1 March 2013 Accepted 30 June 2013 Available online 12 July 2013

Very few works exist to date on development of a consistent energy-based coupling of atomistic and continuum models of materials in more than one dimension. The difficulty in constructing such a coupling consists in defining a coupled energy whose minimizers are free from uncontrollable errors on the atomistic/continuum interface. In this paper a consistent coupling in three dimensions is propo...