Biophysics Research Group

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Announcements

 

  • We have published a few new exciting papers! In PNAS, JPCL, BBA-Bioenergetics. This is quite a range of photosynthetic organisms. Congratulations to Michal for his JPCL work!

  • Alex’s first paper has been published! Have a look here. This is our first paper on ultrafast kinetics in a semiconductor. It’s great to see the fruit of departmental collaboration.

  • And don’t forget our invited Topical Review and another review on single molecule spectroscopy

  • Congratulations to Farooq who was awarded a travel grant by Nature Journal to attend the GRC meeting on Single-Molecule Approaches to Biology

  • Congratulations to Luke and Tesfaye for their PhD bursaries. They will soon be joining the group.

 

"Light and Life"

The light-harvesting complexes of photosynthetic organisms are amongst the most complex systems in the universe – trying to understand how they work is a fascinating playground for a physicist’s creativity! And the plethora of organisms performing photosynthesis means there will always be something new and exciting to explore! Apart from the fascinating science on which the primary steps of photosynthesis are based, there is also potential commercial value in understanding their intricate details. We can gain a lot of inspiration from the smart ways in which these systems convert solar energy into biologically useful forms for making more efficient solar panels. Not to mention the remarkable level of light-harvesting regulation – by tweaking or controlling the underlying molecular mechanisms we can improve crop yield. Cyanobacteria may also become part of mankind’s food supply in the near future.

 

What are we doing?

1. Resolve - manipulate - full control

a. We firstly want to have a molecular understanding of energy transfer and its regulation in isolated light-harvesting complexes from various photosynthetic organisms. There is still so much not yet known. We then want to connect our observations to functions and properties of physiological significance. This means that we’re ultimately after finding protein structure–function relationships.

b. Our second step is to see how much we can improve some specific properties, for example the light-harvesting efficiency. For this purpose we use light, chemistry and nanoparticles to manipulate the complexes.

c. Our ultimate goal is to fully control the photosynthetically relevant parameters in isolated light-harvesting complexes.

2. More realistic environments

Taking protein complexes out of their native environment is quite a reductionistic approach. How do we know they behave the same as in their native environment when they’re isolated and placed in a test tube? The natural environment is too complex to mimic entirely, so in our test tube the protein complexes will always experience a different environment. We are therefore developing experimental methods that will enable us to investigate the protein complexes in more realistic environments, whilst not sacrificing the level of molecular detail we’re after.

3. Artificial photosynthesis

Every second the earth is lavished with an enormous amount of energy from the sun. So why doesn’t the whole world switch immediately to solar energy resources? One major challenge is in the area of light harvesting. We need to think differently about light harvesting technologies. Photosynthetic organisms use cheap and clean materials for diverse applications in a remarkably fine-tuned, regulated and economic fashion. There are many remarkable principles that underlie their function. For example, photosynthetic light-harvesting complexes (which we may call ‘natural’ solar panels) use a ‘bad’ thing like disorder for a ‘good’ purpose. Our current solar technologies need a paradigm shift and learn from nature! Does this mean that our solar panels should be green? Not quite, but it means that we should apply the design principles gleaned from research on the ‘natural’ solar panels.

What we’re doing with this idea is to synthesise and explore donor-acceptor assemblies, semiconductor–biological hybrid systems, and our own pigment-protein complexes – all in a multidisciplinary collaborative setting.

 

How do we do this?

We use optical spectroscopy as the main experimental tool and strongly back the experimental work by theoretical modelling. To gain as much from the data as possible we’re pushing the resolution to the extremes:

1. Femtosecond laser spectroscopy

Using a state-of-the-art setup we can resolve and control processes on timescales down to tens of femtoseconds. With this resolution one can see how energy flows from one part of the system to another part.

2. Single-molecule spectroscopy

That’s right: we perform spectroscopy on one molecule at a time! This approach avoids all sorts of averaging processes, which reveals a lot of new information. We have built (from scratch) the first single molecule spectroscopy setup on the continent! See the articles here and here.

 

 

 

 

 

Group Leader

     

Tjaart Krüger        

“The deeper I understand physics, the more fascinated I become by the molecular processes of life: their beauty, extraordinary detail, remarkable efficiency, robustness, variety and elegance.”

 

Postdoctoral Fellows

     

Michal:

“I am passionately exploring the excitation energy flow regulatory mechanisms in photosynthetic light harvesting complexes and their impact on photosynthetic processes, organisms and the environment. I use biochemical and advanced spectroscopic methods combined with molecular biology to investigate molecular mechanisms in natural photosynthetic complexes and to design and study artificial pigment-protein complexes for artificial photosynthesis and imaging.”

 

Cosmas:

“I am working on the study of continuous-wave light propagation for application in image formation. I enjoy this work because it allows for a symbiotic relationship between theory and experiment which has resulted in the rapid development of computational optics.”

 

 

PhD Students

     
Josh:

“I am investigating how energy is transferred within and between photosynthetic proteins by using different spectroscopic techniques such as single molecule spectroscopy and fluorescence streak camera measurements. I’m also the main developer of the single molecule spectroscopy experiment that has been built at the University of Pretoria. Biophysics offers a platform to study fascinating processes using tools from a vast range of different fields of science. Multidisciplinary scientific endeavours, such as these, I believe is the way forward; working together to explore and develop exciting new avenues of science.”

Towan:

“During the process of photosynthesis, light energy is absorbed by pigment molecules that are embedded in protein complexes called light-harvesting complexes (LHCs). In plants, the LHCs, in turn, form part of two photosystems (called PSI and PSII). My research project focuses on understanding the energy flow and regulation, after photon absorption, in PSI, and in three separable LHCs (called CP29, CP24, and CP26) of the more complex PSII. I approach my research using a combination of experimental techniques and computer simulation. I enjoy setting up models to simulate molecular energy transfer events, as this process requires one to think critically in order to gain a fundamental understanding of our complex, beautiful world.”
“Biophysics offers the best of two fields: the complex beauty of Biology and the rigour of Physics”

 

 
Huzifa:

"I am a Ph.D. candidate with the Biophysics group. My project involves spectroscopy and control of ultrafast energy dynamics in natural light-harvesting complexes. In this project, I exploit ultrashort laser pulses to investigate non-photochemical quenching-related mechanisms in natural light-harvesting complexes. Moreover, I use manipulated shapes of these pulses to control the energy flow pathways in these complexes in order to understand the underlying quantum-physical processes.

Farooq:

It is the desire to tackle a challenging puzzle at the interface of biology and physics that motivated me to pursue a Ph.D. in Biophysics. Though I had never attended any biophysics class, understanding how biological systems function in nature was enough to capture my imagination. For example, how plants can survive under stressful environmental conditions, such as high levels of irradiation. Plants have developed various specialised mechanisms through which they are able to protect themselves against high light intensities. One set of mechanisms occurs during the initial steps of light harvesting and energy transfer and is known as non-photochemical quenching, NPQ. Although in recent years there have been many reports about the pigment-protein complexes that are involved with NPQ, dominant mechanisms responsible for such a process are not satisfactorily understood.


My project aims at contributing towards the understanding of NPQ via a unique combination of spectroscopy with plasmonic effects. Here, plasmonic nanostructures of different morphologies and shapes are synthesized via chemical reactions. The hybrid systems are constructed using either spin-assisted layer-by-layer technique or electrostatic adhesion of pigments on functionalized plasmonic nanostructures. Experiments include a thorough characterization of the hybrid systems using both ensemble and single molecule spectroscopy.

Alex:

“I am a devoted PhD Physics student in Biophysics. Biophysics study is essential as it brings together knowledge from Physics, Life Sciences and other exact sciences. My study aims at adding knowledge on the processes of excitation energy transfer in the early stages of Photosynthesis. Knowledge in this Biophysics sub-discipline is essential for bio-solar cells design – green energy.”

MSc students

     

Justin:

“I am currently working on building/developing a femtosecond transient absorption spectroscopy (FTAS) experimental setup, which will measure in the VIS-NIR region (400-1000 nm) with a micro-OD resolution, in order to accurately characterize energy pathways of various photosensitive samples.”

 

Abrie:

“I am currently characterizing transparent conducting oxide, Fluorinated Tin Oxide (FTO for short), with the aim of doing Stark spectroscopy on the single molecule level. Stark spectroscopy is spectroscopy done with an externally applied electric field over the sample. This shifts the energy level of each electron and hole and gives rise to a spectral shift or broadening. We hope to investigate the change in electric dipole moment as well as polarizability of some samples to determine the causation of some dark states.


I have always felt passionate about alternative, sustainable energy harvesting methods, as I believe that fossil fuels have a devastating effect on our planet and want my children’s children to still be able to experience the wonders of our habitat as I and all the people before me have.”

 
 

Sipho:

“What I enjoy most about my research project is the technique I use, which is pump-probe spectroscopy. It allows me to study my materials at the nanoscale and the processes that occur once light interacts with the materials at very short time scales (faster than picoseconds). Which I think is truly amazing.”

 

 


Publications

For a complete list of publications, see the following links:

Orcid
Google Scholar
 

Book Chapters

T. P. J. Krüger, V. I. Novoderezhkin, E. Romero, R. van Grondelle, “Photosynthetic Energy Transfer and Charge Separation in Higher Plants”, In: “The Biophysics of Photosynthesis”, Vol 11, pp. 79-118, J. Golbeck and A. van der Est (Eds.); (Series: “Biophysics for the Life Sciences”), Springer, Dordrecht, (2014). ISBN 978-1-4939-1147-9. Link: http://www.springer.com/physics/biophysics+%26+biological+physics/book/978-1-4939-1147-9

T. P. J. Krüger, C. Ilioaia, M. Alexandre, P. Horton, and R. van Grondelle, “How Protein Disorder Controls NPQ”, In: “Non-Photochemical Quenching and Energy Dissipation in Plants, Algae and Cyanobacteria”, B. Demmig-Adams, G. Garab, W. Adams III, and Govindjee (Eds.) (“Advances in Photosynthesis and Respiration”; Series Editors: Govindjee and T. D. Sharkey), Springer, Dordrecht (2014). ISBN 978-94-017-9031-4. Link: http://www.springer.com/life+sciences/plant+sciences/book/978-94-017-9031-4


What is Biophysics?

Biophysics is much more than biology + physics. It’s in fact the confluence of several scientific disciplines: physics, biology, chemistry, mathematics, statistics, computer modelling, and engineering – all are integrated to solve some of nature’s big problems.


Personally, I like to put a stronger emphasis on physics (otherwise my physics colleagues tend to erroneously think I’m doing biology). This would be my definition: “Biophysics is the branch of physics that applies the methods and theories of physics to study biological systems. In short, biophysicists study the physics of living systems.”

But BPS prefers a broader definition.

For more information, have a look at our “World of Biophysics” booklet.

If you are new to the world of Biophysics, have a look at the following pages:


South African Biophysics Initiative
Careers in Biophysics (from the Biophysical Society) [pdf]
Biophysicist Profiles (from the Biophysical Society)


Student Projects

Please contact Dr. Krüger for the availability of funding and a list of projects.

We particularly invite above-average students with a passion for science to apply. Please send Dr. Krüger your CV, academic record and two recommendation letters. If possible, come to our lab and introduce yourself in person.

A strong background in Physics or Physical Chemistry is recommended. Applicants with a different background may also be considered, but this needs to be strongly motivated. Some experience with lasers and/or chemistry is favourable but not obligatory. Computer programming is a requirement for most of the projects.

 

Past Student Projects

Asmita Singh (MSc): “Illuminating the ultrafast excited state dynamics of protein-bound carotenoids in plants” [pdf]

Joshua Botha (MSc): “Using single molecule spectroscopy to study fast photoprotective processes in plants” [pdf]

Ashton Dingle (Hons): “Determining the Energy Pathways in Light Harvesting Complex II using Femtosecond Laser Techniques at Two Excitation Wavelengths” [pdf]

Towan Nöthling (MSc): “Exciton Dynamics in Photosynthetic Molecular Aggregates” [pdf]

 

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