Tesis Doctorado
Thermodynamic concepts in adaptive resolutión simulatións
Autor
Poblete, Simón
Institución
Resumen
This thesis work is devoted to the conceptual and technical development of
the Adaptive Resolution Scheme (AdResS), a molecular dynamics method that
allows the simulation of a system with different levels of resolution simultaneously.
The simulation domain is divided into high and low resolution zones and
a transition region that links them, through which molecules can freely diffuse.
The first issue of this work regards the thermodynamic consistency of the
method, which is tested and verified in a modelliquid of tetrahedral molecules.
The results allow the introduction of the concept of the Thermodynamic Force,
an external field able to correct spurious density fluctuations present in the
transition region in usual AdResS simulations. The AdResS is also applied to
a system where two different representations with the same degree of resolution
are confronted. This simple test extends the method from an Adaptive
Resolution Scheme toan Adaptive Representation Scheme, providing a way of
coupling different force fields based on thermodynamic consistency arguments.
The Thermodynamic Force is successfully applied to the example described in
this wor k as well.
An alternative approach of deducing the Thermodynamic Force from pressure
consistency considerations allows the interpretation of AdResS as a first
step towards a molecular dynamics simulation in the Grand Canonical ensemble.
Additionally, such a definition leads to a practical way of determining the
Thermodynamic Force, tested in the well studied tetrahedralliquid. The effects
of AdResS and this correction on the atomistic domain are analyzed by inspecting
the local distribution of velocities, radial distribution functions, pressure
and particle number fluctuation. Their comparison with analogous results coming
from purely atomistic simulations shows good agreement, which is greatly
improved under the effect of the external field.
A further step in the development of AdResS, necessary for several applications
in biophysics and material science, consists of its application to multicomponent
systems. To this aim, the high-resolution representation of a model
binary mixture is confronted with its coarse-grained representation systematically
parametrized. The Thermodynamic Force, whose development requires a
more delicate treatment, also gives satisfactory results.
Finally, AdResS is tested in systems including two-body bonded forces,
through the simulation of a model polymer allowed to adaptively change its
representation. It is shown that the distribution functions that characterize the
polymer structure are in practice not affected by the change of resolution.
The technical details of the implementation of AdResS in the ESPResSo
package conclude this thesis work. PFCHA-Becas Doctor en Ciencias 110p. PFCHA-Becas TERMINADA