Abstract
In many biology, chemistry and physics applications molecular simulations can be used
to study material and process properties. The level of detail needed in such simulations
depends on the application. In some cases quantum mechanical simulations are indispensable.
However, traditional abinitio methods, usually employing plane waves or a
linear combination of atomic orbitals as a basis, are extremely expensive in terms of
computational as well as memory requirements. The wellknown fact that electronic
wave functions vary much more rapidly near the atomic nuclei than in interatomic regions
calls for a multiresolution approach, allowing one to use low resolution and to
add extra resolution only in those regions where necessary, so limiting the costs. This
is provided by an alternative basis formed of wavelets. Using such a wavelet basis, a
method has been developed for solving electronic structure problems that has been applied
successfully to 2D quantum dots and 3D molecular systems. In other cases, it
suffices to use effective potentials to describe the atomic interaction instead of the use
of the electronic structure, enabling the simulation of larger systems. Molecular dynamics
simulations with such effective potentials have been used for a systematic study of
surface wettability influence on particle and heat flow in nanochannels, showing that the
effects at the solidgas interface are crucial for the behavior of the whole nanochannel.
Again in other cases even coarse grained models can be used where the average behavior
of several atoms is combined into a single particle. Such a model, refraining from
as much detail as possible while maintaining realistic behavior, has been developed for
lipids and with this model the dynamics of membranes and vesicle formation have been
studied in detail. A disadvantage of molecular dynamics simulations with effective potentials
is that no reactions are possible. Therefore a new method has been developed,
where molecular dynamics is coupled with stochastic reactions. Using this method, both
unilamellar and multilamellar vesicle formation, and vesicle growth, bursting, and healing
are shown. Still larger systems can be simulated using other methods, like the direct
simulation Monte Carlo method. However, as shown for nanochannels, these methods
are not always accurate enough. But, exploiting again that the finest level of detail is
often only needed in part of the domain, a hybrid method has been developed coupling
molecular dynamics, where needed for accuracy, and direct simulation Monte Carlo,
where possible in order to speed up the calculation. Further development of such hybrid
simulations will further increase molecular simulation’s scientific role.
Original language  English 

Qualification  Doctor of Philosophy 
Awarding Institution 

Supervisors/Advisors 

Award date  14 Mar 2006 
Place of Publication  Eindhoven 
Publisher  
Print ISBNs  9038630379 
DOIs  
Publication status  Published  2006 
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Cite this
Markvoort, A. J. (2006). Towards hybrid molecular simulations. Technische Universiteit Eindhoven. https://doi.org/10.6100/IR601609