Department of Physics John Anderson Research Colloquia

Wednesday's at 3.00pm (unless otherwise stated) 

Colloquia will usually be held in JA3.14
John Anderson Building 
107 Rottenrow, Glasgow

Coffee and Tea served at 4.00 pm.

All Welcome

Coordinated with the Colloquia at the Department of Physics and Astronomy of the University of Glasgow. (They may have donuts but we have free chocolate covered biscuits and coffee!)

Colloquia Schedule 2017-2018

Semester I

  • 20/09/17 - Oliver Henrich (Dept of Physics, University of Strathclyde)
  • 01/11/17 - Sebastian Van De Linde (Dept of Physics, University of Strathclyde)
  • 08/11/17 - Nick Kelly (Dept of Mechanical and Aerospace Engineering, University of Strathclyde) *
  • 14/11/17 - Peter Mulser (TQE: Theoretical Quantum Electronics, Tech. Univ. Darmstadt) *
  • 15/11/17 - Frederique Vanholsbeeck (The University of Auckland, New Zealand)
  • 01/12/17 - Robert Fedosejevs (University of Alberta, Edmonton) *

Semester II

* Note: Outside of regular schedule.

Mesoscopic Simulation of Soft Condensed Matter

Oliver Henrich (Dept of Physics, University of Strathclyde) 20 September 2017, JA3.14, 3pm

Soft condensed matter is an interdisciplinary field at the interface of physics, chemistry and biology. It comprises a huge variety of materials that we know from our everyday lives, for instance colloidal suspensions, glasses, amphiphilic mixtures, polymeric liquids, foams, gels, granular matter, liquid crystals, and a vast number of biologically relevant substances.

All these materials share the common feature that their generic physical behaviour occurs at energy scales that are comparable to thermal energies at room temperature, which is why we call them ‘soft’. As deformability often entails flow, hydrodynamics plays a particularly important part in their dynamical behaviour.

Another characteristic feature is their propensity to self-assemble into more complex structures on intermediate time and length scales that are well above the molecular level, but also much smaller than the macroscopic lab scale. Both aspects have led to the development of specialised, mesoscopic simulation methods for soft matter.

Starting from Landau’s phenomenological theory of a binary, phase-separating fluid, I will outline a thermodynamically consistent description of complex fluids that is based on so-called free energy models. I will introduce into the lattice Boltzmann method, which solves a discretised version of the Boltzmann equation from statistical mechanics, and show how these concepts can be applied to study novel composite materials for tuneable optical filters and encryption devices.

Single-molecule based super-resolution imaging

Sebastian Van De Linde (University of Strathclyde) 1 November 2017, JA3.14, 3pm

Fluorescence microscopy is the method of choice to study biological samples in a comparatively non-invasive way. The field has received a powerful boost with the development of super-resolution imaging methods, which overcome the limitations imposed by optical diffraction.

A very strong class of these novel techniques can be merged under the generic term single-molecule localization microscopy (SMLM), which relies on the detection of single-molecules, their precise localization and the reconstruction of an artificial super-resolution image. It can improve on the ~200 nm resolution limit by a factor of ten and more, and thus have opened the door for the study of finer cellular ultrastructure.

While in the beginning the driving force in SMLM was methodological advancements, such as development and characterization of fluorophores, multicolour and 3D imaging capabilities, in recent years SMLM is increasingly applied in biology and medicine. Besides its high spatial resolution SMLM also provides access to quantitative information and thus enables the study of structure-function relationships.

I will provide a concise overview of the development and underlying principles of SMLM with an emphasis on dSTORM, describe novel technical developments and conclude with applications in the field of neurobiology.


Fig. 1 Super-resolution image of active zones in Drosophila, comparison of conventional wide-field fluorescence image and SMLM.

Introducing the New Energy Strategic Theme and Exploring Collaborative Opportunities

Nick Kelly (Mechanical and Aerospace Engineering, University of Strathclyde) 8 November 2017, JA5.05, 3pm

The talk will provide an overview of the University’s Energy Strategic Theme, detailing the theme objectives; the various areas of energy research activity covered; funding opportunities and upcoming activities. There will also be an opportunity for discussion, to identify possible areas of collaboration between Physics and other university energy researchers and how these could be taken forward.

Adiabatic invariants and generalized ponderomotive force

Peter Mulser (TQE: Theoretical Quantum Electronics, Tech. Univ. Darmstadt) 14 November 2017, JA 3.14, 1pm

The ponderomotive force embraces a realm of physics: collisionless shock wave generation, novel schemes of particle acceleration, stimulated Brillouin and Raman scattering in solids, liquids, gases and plasmas, ac Stark effect in atoms, and the Lamb shift. In the introduction the standard expressions of the ponderomotive force, or wave pressure, are presented and their derivations and physical interpretations are indicated.

In the central part of the talk its connection with the adiabatic invariants is established. Conservation of action is illustrated by various, also historical examples to begin with Lord Rayleigh, and are verified by simple arguments. The adiabatic theorem is formulated and its connection with the Poincaré-Cartan invariant is shown. On this Hamiltonian basis we are prepared for generalized expressions of the ponderomotive potential and force. A fundamental difference between the forces from a longitudinal and a transverse wave will appear. Adiabatic particle trapping, detrapping and acceleration in the electron plasma wave will result as a byproduct. The results will be illustrated by simple case studies.

In the conclusion a survey on conservation of action in various disciplines of physics and applied mathematics: in optics, thermodynamics, quantum physics, time scale methods and linearization, will be briefly discussed. The principle unifying them lies in one property of alternating series of mathematics.

Biophotonics at the University of Auckland

Frederique Vanholsbeeck (The University of Auckland, New Zealand) 15 November 2017, JA3.14, 3pm

Our research projects focus on different imaging modalities such as fluorescence quantification using the optrode, an all-fibre real time spectroscopic optical probe and optical coherence tomography (OCT) imaging.

OCT is a non-invasive imaging technique based on low coherence interferometry that provides high resolution 3D images of samples with a depth range of a few mm. The depth resolution is inversely proportional to the light source bandwidth and can be as good as 1 µm in some recent experiments. Recently, we have been working on new swept sources to get a better imaging depth. We also use these sources to map chromatic dispersion in tissue in order to differentiate tissue type. Lately, we have been working on polarisation sensitive OCT to detect early signs of osteoarthritis.

We are using spectroscopic fluorescence to detect and classify bacteria or monitor their activity. This work has a particular focus on food safety where bacterial enumeration is important.

During the talk, I will present our recent results on these topics obtained by the University of Auckland biophotonics group.

High Intensity Laser-Plasma Interactions in the Relativistic Regime

Robert Fedosejevs (Department of Electrical and Computer Engineering, University of Alberta, Edmonton) 1 December 2017, JA3.14, 2pm 

Using Chirped Pulse Amplification (CPA) technology it is now possible to amplify laser pulses to instantaneous power levels of several petawatts in ultrashort pulses with durations of 20 to 1000 fs. Facilities exist and are being built with such capabilities around the world, opening up a range of exciting and challenging opportunities in particle acceleration, tunable x-ray sources and table top nuclear physics sources.  The focused intensities currently range from 1018 W/cm2 to 1022 W/cm2 where the motion of electrons in the EM laser field is strongly relativistic. Applications range from 100 MeV class ion sources for cancer therapy to ignition sources for laser fusion energy. Recently, we have been involved in studies of MeV electron generation for applications in Fast Ignition Fusion Energy and the study and development of laser wakefield acceleration sources of electrons up to the GeV energy level. These studies have been carried out at the Titan Laser Facility in Lawrence Livermore National Laboratory and using 200 TW laser facilities located at INRS in Montreal, Canada, and at CLPU in Salamanca, Spain. The wakefield accelerated electrons, in turn, generate synchrotron-like betatron radiation which can be used as a broadband femtosecond x-ray probe pulse. We have applied these ultrashort probe pulses to study the ionization dynamics of warm dense solid aluminium at electron temperatures of 20 eV to 30 eV, using x-ray k-shell absorption spectroscopy. Results from a number of these experiments will be presented and discussed.

Analysing the distribution patterns of membrane constituents on the cell plasma membrane based on inhomogeneity

Sebastian Munck (VIB-KU Leuven Center for Brain and Disease Research, Belgium) 8 January 2018, JA3.26, 11am

The plasma membrane is the outer limit of the cell and plays an essential role in signal transduction, transport of molecules, and adhesion to substrates or other cells. Plasma membrane constituents, proteins, and lipids are organized in complex organizations ranging from random to clustered, as part of signaling platforms during dynamic events including endocytosis or distribute into gradients on polarized cells. These distributions are key to multiple signaling events at the cell surface, including migration, differentiation, proliferation, and extracellular stress.

We have developed an approach that allows quantifying the overall spatial organization of proteins and lipids on the cell surface and that, unlike current tools, is compatible with the diverse organization types of the cell membrane, including polarity. To quantify the distribution of plasma membrane constituents, we make use of a tool called tessellation to divide the space surrounding each detected membrane component. Consequently, we quantify the distribution of areas surrounding the identified constituents to describe various spatial patterns in degrees of inhomogeneity. We have integrated an intensity-based correction to be able to analyze images stemming from devices with a wide range of resolutions. We call our method Quantitative Analysis of the Spatial distributions in Images using Mosaic segmentation and Dual parameter Optimization in Histograms (QuASIMoDOH). We demonstrate that QuASIMoDOH can be used to assess protein and lipid patterns, quantifying distribution changes and spatial reorganization at the cell surface. An ImageJ/Fiji plugin of this analysis tool is available.

Animal magnetoreception – a non-trivial effect of quantum mechanics on biology?

Alex R. Jones (Biometrology Group, National Physical Laboratory), 24th January 2018, JA3.14, 3pm

Many animals can sense the Earth’s magnetic field (MF) to aid with behaviours such has migration, but the biophysical origin of this remarkable ability has confounded scientists for decades. Considerable evidence indicates the primary magnetoreceptor is the flavoprotein, cryptochrome (CRY), which has been proposed to provide geomagnetic information via a quantum effect of MF on photochemical radical pair intermediates.

Although the sub-atomic description of any biological system necessarily encounters the quantum domain, it has been argued that in the vast majority of cases these quantum effects are incidental or ‘trivial’. Why bother with a quantum description of the macroscopic world of biology when invariably a classical one will suffice?

The radical pair model of animal magnetoreception might be different, however. Research to elucidate its biophysical basis encompasses almost the entire spectrum of scientific endeavour, from theoretical quantum mechanics to animal behaviour. In this lecture I will give an overview of this field of research, with particular focus on my own interest in the interplay between CRY structure and the transduction of magnetic signals. In doing so, I hope to go some way to answering the question: is animal magnetoreception an example of a non-trivial effect of quantum mechanics on biology?

Correlative Imaging: From Cells to Stars

Lucy M. Collinson (The Francis Crick Institute) 31 January 2018, JA3.14, 3pm 

Correlative light and electron microscopy (CLEM) combines the benefits of fluorescence and electron imaging, revealing protein localisation against the backdrop of cellular architecture. The correlative imaging field is expanding rapidly, and encompasses workflows that link many different imaging modalities, to answer scientific questions in the biological and physical sciences. We link fluorescence microscopes (widefield, confocal, super-resolution and light-sheet) with electron microscopes (scanning, transmission, serial block face and focused ion beam) and X-ray microscopes (microCT and soft X-ray) to analyse a range of biological samples, from single cells to whole model organisms.

Our technology development work has focused on improving the speed, accuracy and accessibility of CLEM. During this development work, it became clear that the technical challenges associated with correlative imaging are exaggerated when working in 3D. To increase protein localisation precision, we developed an ‘In-Resin Fluorescence’ (IRF) protocol that preserves the activity of GFP and related fluorophores in resin-embedded cells and tissues. The sample preparation is relatively fast, and also introduces electron contrast so that cell structure can be visualised in the electron microscope. Once the resin blocks have been cut into ultrathin sections, out-of-plane fluorescence is removed resulting in physical ‘super-resolution’ light microscopy in the axial direction, which increases the accuracy of the LM-EM overlays. Localisation precision is further increased by imaging the IRF sections in vacuo in the next generation of commercial integrated light and electron microscopes (ILEM). We were able to further improve accuracy by developing integrated super-resolution light and electron microscopy, using the remarkable blinking properties of GFP and YFP in-resin in vacuo.

With the advent of dual contrast samples comes the potential to locate and track fluorescent cells during sample preparation and automated 3D EM image acquisition. We designed and built two new locator tools – a fluorescence microscope designed to integrate with an ultramicrotome to locate cells during trimming and sectioning (the ultraLM), and an even smaller version that fits into the extremely tight space of the SBF SEM vacuum chamber for on-the-fly tracking of fluorescent cells during long automated imaging runs (the miniLM).

As electron microscopes become more automated, data outputs are increasing astronomically, and so the bottleneck in our work is shifting from data acquisition to data analysis. I will describe the ideas and workflows we are developing to deal with big data, and describe our Citizen Science collaboration with the Zooniverse platform, which is helping us to develop automated detection and segmentation of cell structures in EM images.

Group-III-nitride-based hetero structures for sensor and UV-LED applications: Research activities at Ulm University

Ferdinand Scholz (Ulm) 28 February 2018, JA3.14, 3pm

GaN and related compounds have attracted immense research interest world-wide since the first presentation of very bright blue LEDs in 1992. At Ulm University, we have focused on the epitaxial growth and characterization of GaN-based hetero structures for optoelectronic devices since more than 20 years, contributing in particular to studies of semipolar LED structures over the last 10 years. Currently, we focus our efforts on two other topics which will be taken as main subjects for this talk.

Owing to the excellent chemical stability of GaN, such materials are regarded as bio-compatible and hence they are good candidates to act as chemical and bio-medical sensors. In our current studies, polar GaInN quantum well structures are applied for sensing different molecules adsorbed on the sample surface. Adsorbate-caused changes of the band bending near the surface and hence the photoluminescence signal of near-surface GaInN quantum wells are taken as chemical sensing signal. This optical read-out makes electrical contacts obsolete, which might be problematic in chemically harsh environments. The sensitivity depends on the design of the hetero structures like QW and cap layer thickness, as evaluated by band structure simulations. Besides gases such as oxygen and hydrogen, also biomolecules can be adsorbed on the semiconductor surface and studied by PL. As an example, we have studied the protein “ferritin”. Its concentration in blood is an important indicator for the iron storage state in our body. Ferritins with and without iron-load (the latter corresponds to apoferritin) are immobilized on hydroxylated polar GaInN quantum well surfaces and lead to a distinct spectral shift of the quantum well PL. In order to selectively detect such proteins, we investigate possibilities to functionalize the GaN surface by other specific organic molecules.

Another focus of our work is set on AlGaN-based hetero structures for LED applications in the UV-C spectral range (around 270 nm). Such LEDs still suffer from relatively poor external quantum efficiencies, which is discussed to be caused at least partly by the fairly large lattice mismatch between the various materials forming these hetero structures. Therefore, we investigate the incorporation of boron (B) into AlGaN layers, which reduces the lattice constant and hence may help to manage the strain in such hetero structures. Unfortunately, the miscibility of B in AlGaN is very low. For total boron contents of about 5% in AlBN epitaxially grown by MOVPE, we see strong indications for phase separation between AlN and boron. For lower boron contents, phase separation could not be observed in thin layers. However, strong 3D growth developed for thicker or multi layers (Fig. 1) resulting in tilted facets and surface roughening, certainly a consequence of the low mobility of B on the growing surface. Hence, further optimization of the MOVPE growth conditions has to be done.

These studies are done in cooperation with K. Thonke et al., Inst. of Quantum Matter, T. Weil et al., Inst. of Organic Chemistry III, and U. Kaiser et al., Central Facility of Electron Microscopy, all at Ulm University.

Fig.1: Cross-section Transmission electron micrograph of an AlN/AlBGaN superlattice structure.

Quantum mechanics of light-matter and system-bath interactions in photosynthesis

Fred Manby (University of Bristol) 14 March 2018, JA3.14, 3pm

Almost all of the biomass in the world derives from the harvesting of solar energy through photosynthesis. A great deal is known about the structure and dynamics of the machinery responsible for this process, but mysteries remain. Photosynthesis in purple bacteria is amazingly efficient: chemical change is induced almost every time a photon is absorbed. This is curious because it implies very efficient transport of the energy through a disordered system. Here we will explore the quantum mechanics of the light-matter interaction, and of the energy-transport processes involved, to try to arrive at a clear picture of how photosynthetic light harvesting really works.