Biomolecular & Chemical Physics (BCP) group

 

Mesoscopic structure in complex liquids: microscopy & ultrafast studies

SUPA theme: Physics and the Life Sciences, Condensed Matter
Supervisors: Klaas Wynne, Jan Karolin (Physics), and Jan Sefcik (Chemical Engineering)

Liquids are enormously important as media for chemical and biological reactions. Water is probably the most crucial in particular for the function of proteins and other biomolecules. Water has numerous poorly understood strange properties such as the well-known density maximum at 4° C and many crystalline and solid amorphous phases. Amorphous (glassy) water is the most common form of water in interstellar space.

Liquids are generally considered to be homogeneous media (except for liquid crystals). However, there are numerous hints that this might not be true. A number of liquids (such as liquid carbon, germanium, phosphorous, and possibly water) show liquid–liquid transitions in which the liquid undergoes a phase transition between two amorphous phases. (1, 2) Mesoscopic nanoscale structuring has been seen in room-temperature ionic liquids (3) and even more controversially in liquid mixtures and solutions. (4, 5) Recent imaging experiments have shown that such liquid structuring can affect other (solute) molecules (6) suggesting that these effects may be of critical importance for nanoscale self-assembly. The project proposed here will investigate these very important but mysterious phenomena.

In this project, we will use a group of collaborators to bring multiple modern experimental techniques to bear on the problem. Phase contrast microscopy will be used to directly image mesoscopic structures and the dynamics of their formation. (7) Static and dynamic light scattering experiments will be used to gain access to slow dynamics and sizes of structures on 10 nm-10 mm length scales. Confocal fluorescence microscopy will allow us to determine distributions of dye molecules in structured liquids. (6) Ultrafast spectroscopy will be used to probe the dynamics of small clusters and local viscosity through the Stokes-Einstein-Debye relation. (3) If things progress well, we may be able to use dynamic differential microscopy, (8) small-angle X-ray/neutron scattering (SANS/SAXS), and Raman microscopy. These techniques will be used to study a variety of promising liquids, mixtures, and solutions, while (phase) transition are induced by varying the temperature in a special liquid-nitrogen cooled microscopy stage.

The project is of a fundamental nature while having many realistic practical applications in chemical engineering. Ionic liquids may be used in new types of batteries and are of importance to green chemistry where their mesoscopic structuring is very important in understanding their properties and reactivities. Solutions and their concentration fluctuations are of great importance to the pharmaceutical and chemical industries.

More information about the Ultrafast group can be found here. Formal applications can be made through online application. Applications should be made as soon as possible.

References

1. R. Kurita, H. Tanaka, Science 306, 845-848 (2004).
2. C. A. Angell, Science 319, 582-587 (2008).
3. D. A. Turton et al., J. Am. Chem. Soc. 131, 11140-11146 (2009).
4. S. Dixit, J. Crain, W. Poon, J. Finney, A. Soper, Nature 416, 829-832 (2002).
5. M. Sedlak, J. Phys. Chem. B 110, 13976-13984 (2006).
6. T. Xia, L. Xiao, M. Orrit, J. Phys. Chem. B 113, 15724-15729 (2009).
7. R. Kurita, K.-I. Murata, H. Tanaka, Nat Mater 7, 647-652 (2008).
8. R. Cerbino, V. Trappe, Phys. Rev. Lett. 100, 188102 (2008).

Ultrafast terahertz spectroscopy of supercooling, phase transitions, hydrogen bonding, and peptides

SUPA theme: Physics and the Life Sciences, Condensed Matter
Supervisor: Klaas Wynne

This project is based on a recent £623k EPSRC grant entitled “Two-dimensional terahertz/IR spectroscopy: a unique probe of ultrafast hydrogen-bond dynamics of liquid water and model systems”. A brand new laboratory has been built including three climate-controlled laser labs, a chemical lab, and a prep room. For this project, we have taken delivery of a state-of-the-art Coherent Legend Elite USX-HE femtosecond regenerative amplifier system producing ~23-fs laser pulses.

This laser will be used to revive a neglected technique called terahertz-field-induced second-harmonic generation (TFISH). (1) In TFISH, a terahertz field (2) lines up dipoles in an initially isotropic sample such as a liquid, making it non-centrosymmetric and allowing an 800-nm probe pulse to be frequency doubled to 400 nm. As the probe pulse is delayed, the non-centrosymmetry decays, and the TFISH signal vanishes. In effect, TFISH takes a dielectric spectrum. However, the key difference is that this dielectric spectrum can be taken from ~100 fs to ~4 ns, covering the range 250 MHz to 10 THz in one single uninterrupted spectrum. This will make this set-up unique and unrivalled. If all goes well, we may be able to extend the standard TFISH technique into a multi-dimensional spectroscopy (2D-TFISH) that can be used to measure non-equilibrium dynamics. In addition, we will be able to perform optical Kerr effect (OKE) studies as described in many of our recent papers. (3-7)

TFISH and OKE will be used to study hydrogen-bond dynamics in water and protein model systems such as N-methylacetamide. (6) We are particularly interested in supercooling, the formation of glasses, and the influence of nano-confinement on supercooling. For example, a debate has been raging for years about a liquid-liquid phase transition in water at about 220 K, which may or may not be visible in nanoconfined water samples. (8) Our new techniques described above will provide completely new insights into these phenomena.
The ideal candidate for this position is either a chemical physicist, physical chemist, or somebody with knowledge of soft condensed matter. Either way, the student will be working alongside a team of people with experience in ultrafast techniques (Kerr, terahertz, 2D-IR, etc.), chemical physics, and biochemistry.

More information about the Ultrafast group can be found here. Formal applications can be made through online application. Applications should be made as soon as possible.

References

1. D. Cook, J. Chen, E. Morlino, R. Hochstrasser, Chem. Phys. Lett. 309, 221-228 (1999).
2. G. H. Welsh, N. T. Hunt, K. Wynne, Phys. Rev. Lett. 98, 026803 (2007).
3. D. A. Turton, K. Wynne, J. Chem. Phys. 131, 201101 (2009).
4. D. A. Turton et al., J. Am. Chem. Soc. 131, 11140-11146 (2009).
5. D. A. Turton, J. Hunger, G. Hefter, R. Buchner, K. Wynne, J. Chem. Phys. 128, 161102 (2008).
6. D. A. Turton, K. Wynne, J. Chem. Phys. 128, 154516 (2008).
7. N. T. Hunt, L. Kattner, R. P. Shanks, K. Wynne, J. Am. Chem. Soc. 129, 3168-3172 (2007).
8. C. A. Angell, Science 319, 582-587 (2008).

Ultrafast Biophysics

SUPA theme: Physics and the Life Sciences
Supervisor: Neil Hunt, Nicholas Tucker (SIPBS)

Understanding the relationship between molecular structure and biological function of proteins and enzymes is of importance in many areas of scientific research from drug design and medicine to nanotechnology and green energy production. Obtaining the level of comprehension required often involves multidisciplinary research spanning a range of disciplines. An opportunity for a PhD project exists jointly between the groups of Dr Neil Hunt (Physics) and Dr Nick Tucker (Strathclyde Institute for Pharmaceutical and Biomedical Sciences) to investigate the structure, dynamics and reactivity of nitric oxide (NO) sensing proteins.

NO is a water-soluble radical gas that is of considerable biological importance in both eukaryotic and prokaryotic systems. Mammals utilise NO at relatively low concentrations as a signaling molecule to control processes such as vasodilation, the mechanism by which blood flow is controlled. NO is also produced by the macrophage cells of the mammalian immune system in response to infection by disease causing bacteria. In this latter example, NO is produced at much higher concentrations so that it becomes toxic to the invading bacterium by disrupting the metal centres of respiratory enzymes. Many pathogenic bacteria have evolved a number of proteins to detect and counteract the toxic effects of this macrophage derived NO.

Ultrafast 2D-IR spectroscopy is a new technique using state of the art ultrafast lasers to examine the rapid fluctuations in structure that are present in every biological molecule. These fluctuations are thought to play a key role in determining both the overall shape of the molecule and the mechanism by which they react. We will apply this approach to NO sensing systems and ultimately use it to make real time molecular movies of reacting proteins.

More information about the Ultrafast group can be found here. Formal applications can be made through online application. Applications should be made as soon as possible.

References

N. T. Hunt, Chem Soc Rev 38, 1837 (2009).

 

Femtosecond Two-Dimensional Infrared (2D-IR) Spectroscopy - A New Approach to Understanding Enzyme Chemistry

SUPA theme: Physics and the Life Sciences
Supervisor: Neil Hunt

Two dimensional infrared (2D-IR) spectroscopy is an exciting new ultrafast laser technique which gives access to a wealth of new information from the infrared spectrum of a molecule, including real-time structural information and vibrational dynamics.

We aim to observe the structural changes that occur at in bio molecules, such as at the active site of enzymes during their catalytic cycle and during the action of drug molecules. Using our state-of-the-art 2D-IR spectrometer and novel techniques capable of observing chemical reactions in real time and in unprecedented detail we will use physics to gain a greater understanding of important biological processes.

A PhD position is available working on a project studying the hydrogenase family of enzymes, which catalyse the reversible activation of molecular hydrogen. It is anticipated that a thorough understanding of the mechanism by which this is achieved will lead to the development of new catalysts for use in hydrogen fuel cells. The objective of the project is to use ultrafast 2D-IR spectroscopy to determine the structure of the enzyme active site and transient changes of this structure during the reactive cycle.

The project will be based mainly around obtaining and analyzing femtosecond 2D-IR spectra using brand new, state of the art laser equipment but will incorporate elements of computational modeling and the opportunity exists for some synthetic chemistry and biochemistry if desired. This is a collaborative project between several UK institutions and the opportunity to work at another University learning new skills is an important part of the project.

More information about the Ultrafast group can be found here. Formal applications can be made through online application. Applications should be made as soon as possible.

References

For more info on 2D-IR, see:

• N. T. Hunt, Chem Soc Rev 38, 1837 (2009).

or our recent publications:

• R. Kania, A. I. Stewart, I. P. Clark, G. M. Greetham, A. W. Parker, M. Towrie, and N. T. Hunt, PhysChemChemPhys in press DOI: 10.1039/B919194A  (2010).
• G. M. Bonner, A. R. Ridley, S. K. Ibrahim, C. J. Pickett, and N. T. Hunt, Faraday Discussions in press [doi:10.1039/b906163k] (2009).
• A. I. Stewart, I. P. Clark, M. Towrie, S. Ibrahim, A. W. Parker, C. J. Pickett, and N. T. Hunt, J Phys Chem B 112, 10023 (2008).

Photophysics

SUPA theme: Physics and the Life Sciences
Supervisors: David Birch, Olaf Rolinksi, Jan Karolin, Yu Chen

In Photophysics, we offer a range of research studentships within its three core areas and these can usually be tuned to match the interests of individual students to give a bespoke training in leading edge research. The primary phenomenon used in all the research is fluorescence and in particular when time-resolved. This is because fluorescence is extremely sensitive (even down to the single molecule/photon level), has Å structural resolution, offers temporal resolution of molecular dynamics, is non-destructive and can be performed in-situ. Moreover fluorescence is widespread and occurs naturally in the life sciences and in materials, for example in proteins in plasma, chlorophyll in plants and melanin in skin. Indeed fluorescence phenomena and techniques form an important core research area in the Group in their own right. Our three main areas are:

Medicine and life sciences interfaces

The Group has specialised in solving physics problems related to understanding the behaviour and detecting the presence of molecules relevant to the very origins and care of life itself. Several aspects of metabolic and structural monitoring are under investigation and the approaches we are developing and challenges to be overcome have generic application well beyond these specific examples.

Glucose sensing

The interest in glucose stems from the need to measure it in-vivo for the management of diabetes. To date no truly non-invasive sensor is available and the problem still remains one of the holy-grails of medical sensing. This is because of the sheer scale of the problem. Statistics such as 200 million diabetics worldwide predicted by 2010 and 9% of the present UK health care cost bear this out. In collaboration with Guy’s Hospital we are investigating two approaches. Firstly assays based on glucose binding proteins and secondly an analysis of NADH fluorescence, a fluororohore which occurs naturally in cells. In recent work we have modelled the kinetics and observed the structural changes in the glucose-protein complex for the first time (for a popular review of the work see the article by David Bradley in EPSRC Newsline Autumn 2002).

Protein structure

There are nearly 100,000 proteins in the human body, each with a specific task, which is achieved by each protein being in a unique conformation. Yet how a given protein folds into its unique structure is one of the key mysteries to be overcome in the early detection, prevention and treatment of many diseases. For example protein mis-folding is implicated in the prion disorders of BSE, Creutzfeld-Jacob disease and possibly Alzheimer's and Parkinson's diseases. We are studying protein folding by using proteins labelled with extrinsic fluorophores and using intrinsic amino acids such as tryptophan in a range of novel environments including silica nano-pores in order to shed new light on the kinetics involved. In separate work in collaboration with Ineos Silicas Ltd we have been investigating the fining of haze and foam forming proteins by silica for use by the brewing industry.

Metal ion sensing

The important role of metal ions and in particular transition metal ions such as copper and cobalt in cell physiology has recently become to be realised, for example in influencing protein function. We have developed methods for detecting metal ions using fluorescence resonance energy transfer (FRET) in both synthetic vesicles and polymer sensor matrices. Our efforts are presently focused on determining the distribution of metal ions and the flurorophores which detect them using FRET in such microheterogeneous media.

Melanin

Melanin is the ubiquitous skin pigment responsible for protecting tissue from the harmful effects of ultra-violet radiation. Melanin itself is a polymer with an indole non-repeating basic structure. Although it can be synthesized in the laboratory, its in-vivo structure is still as yet unknown. Melanin has taken on renewed importance because of the increasing incidence of skin cancer so a better understanding of the photophysical dissipative pathways in melanin could have widespread benefits to all aspects of skin-care. We are interested in understanding the correlation between the size of melanin aggregates and the fluorescence spectra, lifetimes and depolarisation as they are clear pointers to its unusual and fascinating properties.

Sol-gel nano-morphology

We are using the sol-gel process to produce amorphous and ordered structures. The sol-gel process is a room temperature method of preparing oxide gels, glasses and ceramics based on hydrolysis and condensation reactions. By controlling the reactions a diverse range of end products such as powders, thin films, fibres and bulk monoliths can be obtained. Applications span traditional uses of silica gel (SiO2) as an absorptive, abrasive, carrying and surface coating agent to the more recent production of photonics, bio-compatible materials and nano-structures. Our interests span the underlying kinetics of formation, charactering the pore structure and fabricating ordered nano-structures and sensor media.

Nano-particle growth dynamics

Traditional techniques for studying sol-gel glass formation include small angle scattering of neutrons or x-rays. We have introduced a new and advantageous approach based on using fluorescence probe depolarisation to dually report on the silica nanoparticle size and microviscosity. By this means we can study the high silica concentrations more usually encountered. So far we have been able to monitor the aggregation of the nanometre size silica particles, which lead to gelation with near Å resolution, but there is much more to be done in exploring the limits of the technique. This work is in collaboration with Ineos Silicas Ltd.

Pore morphology

To date no instrument capable of measuring pore size during gelation has reached industrial practice despite the global amorphous silicas market being in excess of $2 billion. At present pore measurement by industry is not done in-situ, but on the final dried gel using such as mercury porosimetry or nitrogen adsorption. FRET has been used previously to measure pore size in the final dry gel, but all these techniques have hitherto shared a common limitation, namely, they require assumptions to be made about pore morphology before interpretation i.e. spheres, cylinders etc. We are researching how donor-acceptor distance distribution functions can be determined from FRET measurements without assuming the form of the distribution (and hence pore geometry). Success would enable better control to be achieved over the manufactured end product and may lead to new silicas based on controlled pore size distributions.

Nano-structures

Sol-gels ceramics are amorphous solids, which can exist in various forms including powder and bulk glass at almost infinitely varying levels of porosity. We are interested in the extent to which order and controlled porosity can be introduced into such structures for use as sensor matrices to encapsulate fluorescent dyes, the radiative lifetime of which being the sensor measurand. Such structures could have many multidisciplinary applications including controlled drug release, metabolic sensing, environmental monitoring, etc.

Fluorescence techniques

Many of the fluorescence techniques and instrumentation in widespread use around the world have their origins in the Strathclyde Photophysics Group. In recent years our techniques research has concerned the use of femtosecond laser excitation and fluorescence resonance energy transfer (FRET). Multiphoton excited fluorescence lifetime measurements using time-correlated single-photon timing and nanotomography based on FRET were developed in the Group. These two areas now add to our capabilities across all of our projects and in their own right are still being researched.

Multiphoton excitation

Multiphoton excitation offers the unusual opportunity of exciting at longer wavelengths than that of fluorescence. This has potential in medical sensing since it makes use of the spectral window in tissue and skin in the near infra-red between 650 and 950 nm. Our efforts in this area are focused on finding and characterising new sources of fluorescent probes, particularly intrinsic ones, which become possible under multiphoton conditions. For examples we have excited fluorescence from saturated carbon-carbon bonds and ketones under such conditions.

Nanotomography

FRET is one of the most widely used techniques in fluorescence because it enables the location of labelled sites to be measured and tracked with Å resolution. We have developed methods of achieving this, which extend the capabilities of FRET beyond that of random donor-acceptor distance distributions by enabling determination of the distribution function itself. Hence we are exploring the capabilities of this approach across our interests in biomolecular systems and ceramics by exploring different donor-acceptor pairs, different micro-geometries and molecular structures.

Ph.D. Studentship In Molecular Nanometrology
“Nanotechnology of noble metal nanoparticles”

An EPSRC PhD studentship is available from October 2007 to undertake frontier research in nanotechnology of noble metal nanoparticles.

The aim of this project is to explore the great potentials of noble metal nanoparticles for applications in biological systems and to address fundamental scientific questions on the photoluminescence of nanoparticles and their surface plasmon resonance characteristics. This is a multidisciplinary project, involving state-of-the-art optical and electron spectroscopic and microscopic analysis at the interface of nanotechnology and life science.

The student will be based in Photophysics Group in the Department of Physics, with access to outstanding laboratories and facilities, including the Centre of Molecular Nanometrology.  This centre was launched jointly by the Department of Physics and the Department of Pure and Applied Chemistry with £2M investment in 2005 and has been awarded a further £5M under the EPSRC Science and Innovation Initiative. The centre has strong collaborations with other research groups, industry and biomedical practitioners.

The applicant should have, or expected to receive, an upper second class or a first class honours degree or an MSc in physics, chemistry, or a related subject.  Informal enquires may be directed to Dr. Yu Chen ( y.chen strath.ac.uk) or Prof. David Birch ( djs.birch strath.ac.uk).  Formal applications can be made through online application. Applications should be made as soon as possible.

Marine Optics and Remote Sensing physics

Supervisors: Alex Cunningham, David McKee

The Marine Optics and Remote Sensing theme is interested in problems of radiance transfer in seawater, light utilisation by phytoplankton, optical monitoring of ecological processes, and remote sensing in the marine environment. These problems all involve the application of physical principles in an interdisciplinary context.

This is an exciting field to work in because 1. Optical oceanography has undergone a rapid expansion in recent years, with six ocean colour satellites currently in orbit and growing networks of moored optical sensors in the Atlantic and Pacific oceans. 2. Optical techniques are applied on a wide range of spatial scales: they can be used to detect phytoplankton blooms from space (using satellite radiometers to measure patterns of ocean colour extending over hundreds of kilometres) and to measure the fluorescence of single cells under water (using laser-based flow cytometers with a resolution of the order of one micron). 3. A theoretical framework is emerging that links the absorption and scattering characteristics of individual suspended particles to the colour of the sea measured by remote sensing reflectance. This theoretical framework is the key to deriving information on ecological processes in the marine environment from remotely sensed data. 4. It is an area where physics research can make a direct contribution to our understanding of the way the earth’s life-support systems function, and help assess the vulnerability of these mechanisms to changes brought about by human activity.

In the Marine Optics and Remote Sensing Laboratory, we are tackling these issues through the following research projects:

Measuring the mass-specific inherent optical properties of particle suspensions in shelf seas

Most algorithms which invert reflectance measurements to provide information on seawater composition assume that the mass-specific inherent optical properties (the absorption and attenuation coefficients and the scattering phase function) are constant for a given class of suspended material. We are gathering evidence to show that this assumption is not valid in shelf seas, and devising alternative approaches to formulating inversion algorithms. (in collaboration with the School of Ocean Sciences, Bangor)

Underwater light fields and photosynthesis

We are using a combination of direct measurements and radiance transfer calculations to quantify the variation in intensity and spectral distribution of underwater light fields in the Clyde Sea. The relationship between phytoplankton light absorption and photosynthesis has been determined by short term 14C incubations at sea. By combining these sources of information, it is possible to construct a mathematical model of the potential primary productivity of Clyde Sea water columns, and to explore diurnal and seasonal variations. We are currently using this approach to assess the degree to which the rate of photosynthetic carbon incorporation in the Firth of Clyde (and by implication other regions with similar hydrography) is limited by light availability even under nutrient-rich conditions during spring bloom development. (in collaboration with Dunstaffnage Marine Laboratory)

Remote sensing

Data from the SeaWiFS satellite radiometer is processed in our laboratory and the water leaving radiance values recovered are compared with those measured at the sea surface in UK coastal waters. The physical factors that determine water leaving radiances are studied by radiance transfer modelling using parameter values constrained by in-situ measurements.(in collaboration with the School of Ocean Sciences, Bangor)

Submersible flow cytometry

In flow cytometry, samples are entrained in a fluid stream and passed through a tightly focused laser beam so that the optical properties of individual cells and colonies can be determined. We have recently completed field work on a project in which a specially constructed flow cytometer was deployed on an autonomous underwater vehicle (Autosub) in order to study phytoplankton in the Celtic sea. This is an exciting new technical development that makes it possible to analyse single cells and colonies in their natural environment. The results of the first cruise are providing new insights into the optical properties of coccolithophore blooms. (in collaboration with Plymouth Marine Laboratory and Southampton Oceanography Centre)

Phytoplankon fluorescence lifetimes

The lifetime of fluorescence from intact phytoplankton cells is a complex function of light exposure and physiological status. We are studying the factors that influence fluorescence lifetimes (and the quantum yield of fluorescence) using phytoplankton cells grown under different regimes of illumination and nutrient availability

 

Astrochemistry - From laboratory to telescope to space

SUPA theme: Astronomy
Supervisor: Helen Fraser

PhD studentships will be available for research in ASTROCHEMISTRY in the group of Dr. Helen Fraser at the University of Strathclyde, starting October 2006. At least one studentship will be based at Strathclyde and will focus on laboratory studies of interstellar ices, combined with observation work on ice mapping with SPITZER, ESO VLT and (potentially) ASTRO F data.

The potential exists for a second position (funding pending), in collaboration with RAL, the Rutherford Appelton Laboratories in Didcot, Oxfordshire, and will focus on laboratory studies of photon and electron induced chemistry and physics in Interstellar Ices, and utilizing this laboratory data in ASTROCHEMICAL models of disks, YSOs and HH objects. This student will split their time 30:70 % (approximately) between research on CCLRC facilities and the laboratory / theory work at Strathclyde.

For both positions students will be required to formally apply via Strathclyde University, but in the first instance may contact Dr. Helen Fraser (h.fraser phys.strath.ac.uk) for further information and an informal chat. For further information about PhD study in the Physics Department at Strathclyde, and for an online application form go to the postgraduate page.

Students will be able to collaborate with colleagues in the USA, Holland, France, Germany, Japan and the UK, as well as have the option to participate in PUS and outreach activities. EU candidates (who have been resident in the UK for the last 3 years) may be eligible to apply - if you are interested but come from outside the EU please contact me - there are options.

PhD positions are available for suitably qualified candidates, a least a good (2:1 / 1st class honours (usually MSci)) degree in Physics, Astronomy or Chemistry is required.

30 September, 2011 | information | research | study physics | undergrad | postgrad | schools