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Soft Matter and Biological Physics

Dr Pietro Cicuta

Reader in Physics
Fellow, Corpus Christi College

Telephone: 01223 337462
E-mail: pc245 [at] cam.ac.uk

We are interested in understanding soft materials and some problems that remain unresolved in biology. There is a strong synergy between these two themes, due to the fact that many experimental techniques and theoretical concepts can be applied in both. We work across most of the spectrum of BSS activity. For example, we use optical tweezers, microrheology, advanced confocal microscopy and image analysis methods to address dynamics both in colloidal and cellular systems. Another example are liquid interfaces and membranes, which play an important role in both complex fluids and biological systems.

Here is a brief video interview on our current red blood cell and malaria work:



Below is a very short summary of the three main current research lines. A complete publication list is here.

1. Model and Cell Membranes, Liquid interfaces and monolayers, particle rafts

granular layer

Diagram of customised Langmuir trough setup, used to study stress propagation in two dimensional layers. Images show rafts of large and rough-shaped rubber particles. Recent work has shown that stress is transmitted through these layers in a similar way as in piles of grains.

This is the longest running research line, we have addressed in particular the problem of how polymers form monolayered films on interfaces, and the physics properties of these structures. We are also working on protein films of industrial interest such as hydrophobin, and on the behavior of colloidal particles and grains (rafts) confined to two dimensions. Various new methods have been developed to characterise surface viscoelasicity, including modifications of the Langmuir trough and Surface Dynamic Light Scattering.

Model Membranes

vesicles

Ternary mixtures of phospholipids and cholesterol phase separate below a critical temperature. Phase separation is imaged in fluorescence, thanks to the preferential partitioning of a fluorescent dye into one phase. This process may have a role in regulating biological activity at membranes.

Membrane mechanics is characterised by bending, shear and compression moduli. Furthermore, multicomponent membranes can phase separate, and in this case each phase has different moduli, and there is a line tension between the coexisting phases. Working with giant vesicles that mimic the composition of biological cell membranes, we are trying to understand the coupling between the phase behavior and the membrane properties.

Cell Membranes

vesicles

An erythrocyte (red blood cell) is "grabbed" at opposite ends by a pair of colloidal particles held in optical traps. The cell is dynamically stretched, measuring its mechanical properties.

We have been studying the Red Blood Cell, which has a relatively simple membrane structure made of a phospholipid bilayer tethered to a thin cortical network of semiflexible filaments. We have observed very complex dynamics upon stretching the cell, which we have interpreted as a stress induced remodeling of the cytoskeletal network.

Biological applications of Optical Traps

vesicles

This animated gif shows a colloidal bead being dragged to the membrane of a macrophage cell. The interaction with beads of different coatings are being studied, as well as with bacteria.

Optical Traps allow to move objects in solution (typically cells or colloidal particles), and to exert forces of the order of a few tens of pico-Newtons. We have a very advanced optical trap system which is easily programmed to perform sets of measurements, or to automatically perform certain "actions" based on video feedback from the experiment. This powerful instrument is being used also in collaboration with a few biologists, to study interesting problems such as cell infection by bacteria and other parasites.

2. Hydrodynamic interaction

We have recently started studying the hydrodynamic coupling between colloidal particles in solution, with a view to understand better the mechanisms of propulsion and synchronisation that take place in many biological systems (e.g. motility of bacteria, metachronal waves).

Model system with driven colloids

sync

Illustration of the model experimental system we have developed to study the hydrodynamic interaction of colloidal oscillators.

An experimental model system has been developed using feedback-controlled optical tweezers. Driven oscillations of colloidal particles, of fixed amplitude but free inphase, are achieved. The trap alternates between two minima with a geometric switch triggered by the position of the colloidal particle. In the figure, (A) and (B) illustrate the experimental parameters. The distance between trap pairs is in the range 4 to 40 micron. (C) shows timelapse images of two particles locked in antiphase. Particle positions are overlayed on the image sequence. Antiphase motion can be seen. This result is from our first experiment, published in PNAS in 2010. Since then we have studied more general geometric conditions, including many oscillators, and the effect of changing the driving potential shape from harmonic to other forms.

Synchronisation of colloidal rings

An open problem in biology and physiology is how the motile cilia coordinate their beating to generate fluid flow in the airways and other ciliated tissues, or to enable the motility of microorganisms. The difficulty and hence the challenge for physicists, lies in the fact that the dynamics is non-linear, both at the level of each cilium, and in the coupling between them. Solving this would have impact in medicine, since establishing a link between the behaviour of the single filament and the collective motion would allow us to diagnose readily between various cilia pathologies.

rings

Five colloidal beads are moved with optical traps, with fixed force. They start at random angular positions, and self-coordinate to rotate in-phase. Figure shows three moments of an experiment.


In the last few years we have been performing model experiments using systems of colloidal scale particles driven by optical traps [J.Kotar et al., Proc. Natl. Acad. Sci. 107, 7669-7673 (2010); N.Bruot et al., Phys.Rev.Lett. 107, 094101 (2011)].
As a development of our work, with Nicolas Bruot and Jurij Kotar we are investigating a new model system proposed in [T.Niedermayer et al., Chaos 18, 037128 (2008)] in which particles are pushed with constant force along pre-defined closed trajectories (orbits). Since only the force is constant, the phase at which the particle travels around the orbits is free: These are phase oscillators. Through the fluid flow, they are coupled, and we see that they exhibit synchronisation.
We have performed a variety of experiments on this system, which are being prepared for publication. One arrangement we have tested is particularly captivating and may be of general interest. The image shows three snapshots of how the configuration of five beads evolves in time: The five beads, each a few micrometers in diameter, are initially held by optical tweezers in random positions. Then each one is pushed, on a pre-defined circular trajectory, with constant force. In addition to the tweezers’ constant force, they feel the fluid flow from neighbours, and after a couple of orbits they are synchronised, and proceed to rotate thereafter in-phase (last panel).

See the full movie in real time here .

Studying the synchronized states in these simple model systems is helping us to understand the more complex behaviour observed in nature, and shows us getting ready for the Olympic Games.

3. Biological Physics of Bacteria

The most recent research line in our group aims to understand better the growth and the regulation processes within micro-organisms.

Local packing of the chromosome from loci motility

loci project

Left panel shows a schematic of the channel device used to grow and image bacteria. Sustained exponential growth is achieved, and can be maintained for a few days. Central panel shows an image in which fluorescent (green) dots are visible inside bacteria; the light is emitted from GFP bound to one particular chromosomal locus. The dots can be traced in time, and the mean square displacement is obtained (right hand panel). Watch this space for the results of this!

The main question we are facing, in an HFSP funded collaboration with Marco Cosentino Lagomarsino, Bianca Sclavi, Kevin Dorfman, and with Gillian Fraser in Pathology, concerns the physical structure of the bacterial nucleoid (the genome plus associated bound proteins), and how this in turn affects the fundamental biological processes. We focus particularly on gene expression. This research brings together a key biological processes (replication), with polymer physics, and cutting edge microfluidics and imaging technology.

With Madan Babu and Mario Nicodemi we organised in Sept 2011 a very successful meeting on Quantitative Methods in Gene Regulation and a second edition is being planned for December 2013... watch this space.

General Experimental Methodology

A first theme that spans across all our activities is the extraction of maximum information from image and video data. Microrheology is an example of this: the motion of tracer particles is tracked, and this information characterises the material in which the particles are embedded. Applications of this in our group are to study the mechanics of the cell cytoskeleton and the process of gelation in polymer and particulate systems. We are also actively developing new image analysis, for example for detection of cell edges and cell tracking.

A second general theme is instrument automation. We aim to automate as much as possible all our experiments, in order to improve data acquisition, and in some cases to enable experiments that it would simply not be possible to run manually. The optical tweezers and our imaging microscopes can be run through a custom scripting language, which includes the possibility of feedback control via real time video analysis.

A third general theme is microfluidics. We are very happy to make use of the University's Nanoscience Center, as well as facilities in our Physics Department, and to collaborate with Kevin Dorfman at the University of Minnesota. We can make micron scale incubators for continuous and controlled growth of bacteria, and we are developing devices to study other unicellular organisms.