PHD Projects in Theoretical Soft Condensed Matter and Biophysics
I can suggest a variety of possible PhD projects in the general areas
of theoretical soft condensed matter and biological physics spanning
the research areas described below. If you are heading for a good
degree in physics or mathematics and are interested in any of these
(or have ideas about related) problems then drop me a line.
Note that most positions are funded for UK students, with some possibilities for European Union students. Students from elsewhere will have to apply for funding for overseas students, either from their own country or through other EU and UK schemes.
More details on funding possibilities and the application procedure can be found here.
Soft Matter and Complex Fluids
The physics of soft materials involves, (but is not restricted to) the
study of emulsions, gels, foams, colloids, synthetic and bio-polymer
melts and solutions, liquid crystals and other such systems. They are
characterised by geometric structures on a mesoscopic scale several
orders of magnitude bigger than the molecular scale but well below the
macroscopic (human) scale.
Over the last few decades, we have come to realise that by
understanding this structure (which can be described using simple
geometrical models with a small number of physical parameters) it is
possible to come up with a set of general principles, to understand
many features of their macroscopic behaviour. It turns out that many
microscopic details like detailed chemical structure can simply be
used to determine the specific values of the physical parameters of
the coarse-grained mesoscopic models. Of course this is not the whole
story, a current active area of research is the study of soft systems
to find out exactly those macroscopic properties cannot be separated
from the microscopic details.
The separation of this mesoscopic scale from the macroscopic allows
one to use the powerful techniques of statistical mechanics. The
study of complex fluids is an interdisciplinary field with many
fruitful interactions between physicists, chemists, and engineers and
mathematicians.
Dynamics of lipid membranes
Lipid membranes are thin sheets made up of layers of phospholipid
molecules. Phospholipids (e.g. 1-palmitoyl 2-oleoyl phosphatidyl
choline) are amphiphilic with the hydrocarbon tail of the molecule
being hydrophobic; its polar head hydrophilic. They form bilayers in
aqueous solution and mono-layers at the air-water or oil-water
interface. From a statistical mechanical point of view they represent
an interesting class of fluctuating two-dimensional (fluid) manifolds
(sort of a higher dimensional polymer) which can be characterised by a
small number of geometric quantities.
They has been much experimental and theoretical study of their
structure, self assembly, phase behaviour, transport and
elasticity, as well as their interactions with other
macromolecules.
Lipid membranes are also important model systems for biological
membranes, composite objects built from a large variety of lipids and
proteins. Bio-membranes are also not passive, actively controlling the
structures and environments of the cell suggesting that understanding
them requires a dynamic and not equilibrium description. Recently
there has been much interest in `rafts' and multicomponent lipid
membranes and the role they may play in cell signalling and function.
We are interested in dynamical models of inhomogeneous lipid
membranes. In particular, we are interested in the dynamics of objects
embedded in lipid membranes, the coupling to the dynamics of the
membrane as well as the coupling of the dynamics of the membrane to
the hydrodynamics of the fluid it is embedded in.
Polymer Physics
Polymers are long chain molecules made up of repeating units called
monomers linked together by (covalent) bonds. Typically a polymer is
synthesised out of a small number of repeating chemical groups which
are attached end-to-end. As well as linear polymers it is possible to
make branched objects, or objects with non-trivial topology. It turns
out that many (physical) properties of polymers and polymer solutions
can be understood without any knowledge of the chemical structure of
the polymers from which they are made. In fact this is what attracted
a number of physicists to the study of polymeric materials in the
first place. Rather it turns out that it is the geometry and topology
of the polymer chains that determine many of these properties.
Polymeric materials are characterised by the large role that Entropy
(Thermal Fluctuations) play in their physical properties. Typically
the elasticity of polymeric solids has the opposite temperature
behaviour as that of simple crystalline solids because long polymers have a
random-coil like structure at finite temperatures.
The dynamics of polymeric fluids is complicated and often displaying
what is called Non-Newtonian behaviour with complicated flow behaviour
as a function of deformation. In comparison water (the archetypal
Newtonian fluid) has a much simpler flow behaviour.
We are interested in predicting the macroscopic properties of polymer
solutions from simplified `mesoscopic' models of the polymers which
are defined using only geometrical and topological quantities.
Recently there has been much interest in semiflexible polymers who in
addition to the entropic contribution (leading to the random coil
conformations of flexible polymers) have an enthalpic bending energy
contribution to their free energy. As well as having very different
static and dynamic behaviour from classical flexible polymers, they
are important as good models for the behaviour of a number of
biological polymers. We are interested in developing models of the
dynamics of semiflexible polymer solutions to explain both scattering
and rheological experiments.
Charged Polymers: Polyelectrolytes
Polyelectrolytes are macromolecules with ionisable groups which
dissociate into a charged polymer and oppositely charged counter-ions
in polar solvents. Most bio-polymers are charged polymers ( DNA, RNA
are negatively charged and proteins have both positive and negative
charges). There are also many examples of synthetic charged polymers
(e.g. Polystyrene-sulphonate) which have many industrial applications
because they are water soluble.
Charged polymer systems have a rich spectrum of physical behaviour
with dramatically different properties from neutral polymers. This is
due to the long range nature of the Coulomb interactions between
monomers. In addition they are always associated with small charged
mobile counter-ions which dissociate from their backbones and interact
strongly with the polymer chains. The physics of the counter-ions plays
a central role in determining the properties of polyelectrolyte
solutions. Charged polymer systems cannot be understood without
understanding their counter-ions.
We study various aspects of charged polymer systems particularly the
role of counter-ion fluctuations in the attractions between highly
charged macromolecules.
Microrheology
Soft materials are often viscoelastic meaning that their response to
deformation has aspects that are like solids (elastic) and liquids
(viscous). Conventional rheology measures this viscoelasticity by
studying the response of the material to a macroscopic deformation
requiring large (macroscopic) samples. If you have a limited amount of
your soft material or wish to look at the short time behaviour, it is
difficult to perform such experiments. The new experimental technique
of microrheology looks at the (thermal) motion of small particles
embedded in a material and tries to extract the bulk rheological
properties. Only small amounts of material are need and high frequency
(short time) behaviour can be easily probed. We try to understand the
relation between the microscopic rheological behaviour and the bulk
rheology.
Biological Physics
The sub-cellular world has many components in common with soft
condensed matter systems (polymers, amphiphilic molecules, colloids,
and liquid crystals). But (and this is what makes it so fascinating)
it has novel properties which are not present in traditional complex
fluids. These new features include a number of specific interacting
elements present that are crucial for biological function. The
addition of these elements which can be both active and passive, lead
to a highly non-equilibrium system with a rich spectrum of behaviours.
A new generation of experiments using physical probes are giving us an
unprecedented view of this non-equilibrium system at work. The search
is on for an as yet undiscovered hierarchy of organisational
principles which will enable us to understand these exceedingly
complex systems!
The Eukariotic Cell Cytoskeleton
The cytoskeleton provides both the supporting structure of the cell
and the vehicle for internal transport processes. It is a network of
long protein filaments, mainly microtubules, actin filaments and
intermediate filaments, coupled by smaller proteins, such as molecular
motors and cross-linkers. Motor proteins are molecular machines that
convert chemical energy derived from the hydrolysis of ATP (Adenosine
TriPhosphate) into mechanical work, generating forces and motion of
the filaments relative to each other in this{\em active} complex
fluid. We study the mechanics and organisation of the cell
cytoskeleton viewing it as a solution of filaments interacting with
active cross-links.
Bio-polymers
Many biological molecules are polymers (long chain molecules made up
of a variety of repeating units called monomers). Examples are DNA (
monomers are nucleotides, adenine and thymine, guanine and
cytosine[A-T,C-G]), RNA ( monomers are nucleotides adenine, guanine,
cytosine, and uracil [AGCU]), proteins ( whose monomers are
amino-acids), filamentous protein aggregates (e.g. F-Actin) whose
monomers are globular proteins (e.g. G-Actin).
We study the response of single bio-polymers to mechanical force.
Molecular Machines
Molecular motors are machines that convert chemical energy to
mechanical work. Examples are the cytoplasmic motors that move along
biological (protein) tracks in the cell by converting the energy
released upon ATP hydrolysis into mechanical work. These complex
machines act as the inspiration for the design of macromolecular
devices with the ability to sort, sense and transport material in
chip-sized laboratories. We are interested in models for the design of
both biological and synthetic molecular machines driven by chemical
reactions.
Single Molecule Mechanics
New experimental developments have meant that it is now possible to
manipulate man bio-polymers one molecule at a time. This can lead to
important insights about how they function in-vivo. The
conformational dynamics of single molecules can be studied
experimentally using atomic force microscopy, fluorescence probes and a
number of other techniques. We try to model the statistical mechanics
and dynamics of single molecules of proteins and DNA using
coarse-grained models.