Abstract:
This thesis has developed an understanding of the hydrodynamic behaviour of
Janus nanoparticles in
uids by using molecular dynamics simulations. The
molecular dynamics method is capable of modelling Janus particles with slipasymmetric
boundary conditions, where there is an asymmetry in the solidliquid
interactions over each particle's surface. The hydrodynamic behaviour
of the Janus particles under shear can be modelled correctly using a dissipative
particle dynamics thermostat. We begin this work by studying the force
and torque on a single amphiphilic Janus sphere in a
uid
ow. Then, we
investigate the stability and orientation of a Janus dimer. Finally, we use similar
methods to propose a new coarse-grained model for studying protein-like
structures which is capable of capturing the correct hydrodynamic behaviour
of proteins in
ows.
In order to study individual Janus particles in
ows, the slip length values
for uniform spheres with di erent hydrophobicities in a simple
uid
ow are
calculated. Then, the force and torque on a single Janus particle in a simulation
box with periodic boundary conditions are measured. There was good
agreement between the forces calculated from the simulations and rst order
corrections to the Stokes law from previous theoretical studies. Moreover, the
force and torque on a deformed sphere with uniform wettability is measured
and compared with the equivalent Janus sphere. The results demonstrate the
importance of understanding and applying slip boundary conditions, especially
on hydrophobic surfaces, to understand colloidal dynamics. A Janus dimer is the rst building block of any self-assembly process. The
thermal- and shear-induced break-up of Janus dimers in a
uid box was studied
by performing long time simulations. The simulations are examined from
energetic and entropic points of view to understand the thermodynamics of the
break-up. The orientation of Janus spheres in a dimer, and the rotation rate of
the dimer during shear simulations are investigated. We propose a theoretical
expression that gives a description of all e ective parameters contributing to
the break-up rate. The results indicate the importance of slip-asymmetric
boundary conditions to understanding the stability of Janus self-assembled
nanostructures.
Inspired by the unexpected results in the orientation of the Janus dimers
under shear, the favoured orientations of Janus dimers at rest were investigated.
Variations in the orientations are explored as a function of the potential,
temperature, hydrophobicity, patch size, and sphere design. In contrast
to initial assumptions in most previous studies, it is found that pole-to-pole
con gurations are unfavoured due to orientational entropy and the short-range
nature of the potential. Furthermore, the results show that solvent ordering
around the spheres in the dimer breaks azimuthal symmetry which has not
been observed previously.
Finally, the simulations of Janus dimers under shear led to a study of
the stability of more complex nanostructures in shear
ows. A molecular
dynamics modelling approach is developed to study amphiphilic proteins under
shear
ow. This approach enables us to observe folding of a model protein,
which is designed as a collection of spheres, to a lower energy `most stable'
state. By applying shear to this `most stable' state, the aggregate changes
the arrangement of its spheres. The common neighbour analysis is employed
to identify the metastable structures most commonly accessed from the most
stable state. Also, the gyration radius and rotation rate of the aggregate are
studied at di erent shear rates and hydrophobicities. The results show that
this approach can be extended to model the correct hydrodynamic behaviour
of simple proteins under shear.