Biophysics Research Group

sitefiles/Image/48/2050/theoreticalbanner.jpg


Announcements

 

  • The studies of Michal Gwizdala and Prof. Krüger in the Namib Desert have been featured in Physics Today! Here is a link to the article.

  • Prof. Krüger has been elected to serve as a topic editor of the Journal of Physical Chemistry Letters!

  • Prof. Krüger has been featured by the faculty

  • Our cross-disciplinary project on hypoliths in the Namib Desert has culminated in the first publication. See also the accompanying Newsletter article on page 23 here

  • Bertus passed his MSc cum laude! Congratulations, Bertus!

  • Prof. Krüger received the Meiring Naudé Medal from the Royal Society of South Africa for his research

  • We look back on a series of very stimulating Solar Energy and Photosynthesis Schools:

  • 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!

 

 

For more news you can follow Prof. Krüger on twitter: @TjaartKrueger

Direct link below:


 

What are we doing?

 

We investigate the energy and structural dynamics of light-harvesting molecular machines and how they can inspire the next generation of solar cells.

 

The light-harvesting protein complexes of photosynthetic organisms are amazing molecular machines. They use quantum mechanics to optimise their functions, a property that has captivated physicists for the past few decades. They also feature as light-sensitive nano-switches to maintain a delicate balance between their light-harvesting and photoprotective functions. There are a plethora of organisms performing photosynthesis and the light-harvesting complexes of each photosynthetic organism are different, sometimes entirely different! Despite the broad variety in structure and composition, the light-harvesting complexes have one thing in common: they absorb sunlight very effectively and transport the excitation energy to the photosynthetic reaction centre, where it is converted into chemical energy, the full process of which has a quantum efficiency of almost 100%. This property is already one great source of inspiration for finding green, sustainable energy solutions for humankind.

We want to understand the fundamental properties of these intriguing molecular machines, especially the transport and regulation of excitation energy. Our state-of-the-art spectroscopic techniques enable us to unravel many of the otherwise hidden dynamics of these complex systems. We also investigate to what extent we can improve their properties, using light, chemistry, and gold or silver nanoparticles as parts of our toolkit. Using photon correlation spectroscopy, we can get an indication of the “quantumness” of the light-harvesting complexes as a function of their complexity.

 

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.

 

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.

 

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 Gwizdala:

““I am exploring how various organisms sustain photosynthesis under stress conditions. I want to unravel how different molecular components of the photosynthetic apparatus work together and how these interactions impact the photosynthetic processes, organisms and environment. I am using biochemical and molecular biology tools combined with spectroscopy and protein design to investigate the molecular mechanisms in natural and engineered photosynthetic systems.”

“I have also founded a biotech research start-up project that will develop next-generation foods based on photosynthetic microorganisms“

 

Cosmas Mafusire:

“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.”

 
Farooq Kyeyune:

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.

Luke Ugwuoke:

“Biophysics of photosynthesis features lots of interesting nanoscale phenomena that can be mimicked and manipulated in the design of sensors, solar cells, light-emitting plants, and so on, to achieve desired results. Through theoretical studies via open quantum systems and experimental work via single molecule spectroscopy, biophysicists have shown that some of these phenomena; especially single molecule fluorescence, and resonance energy transfer, can be controlled using plasmonic nanoantennas of noble metals. By combining theory with simulations, my project aims to elucidate some prevalent results such as metal-enhanced and quenched fluorescence, plexciton formation, and increased rate of non-radiative resonance energy transfer in hybrid structures comprising light-harvesting photosynthetic complexes of higher plants and metal nanoparticles, due to exciton-plasmon interactions.

 

PhD Students

     
Joshua Botha:

“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 Nothling:

“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”

 

 
Tesfaye Assefa:

“Photosynthesis is the fundamental mechanism by which almost all life forms get their energy from sunlight either directly or directly. An important property in photosynthesis, which is also the focus of my PhD project, is photoprotection. Photoprotection is performed by a complex set of mechanisms that organisms employ to prevent damage of their photosynthetic apparatus under conditions of high solar light intensities. A detailed study of the different kinds of photoprotection mechanisms will not only enhance our understanding of photosynthesis but will also contribute to the development of new bioinspired solar cells that realise artificial photosynthesis. I am studying photoprotection in the main light harvesting protein complex of cyanobacteria, known as phycobilisomes, using single-molecule spectroscopy.”

Bertus van Heerden:

“My research focusses on extending the current single-molecule spectroscopy setup in order to perform single-particle tracking, allowing us to study freely diffusing photosynthetic proteins – in solution and eventually in a natural membrane. This is important as it brings us closer to performing single-molecule experiments in vivo. I am also interested in the theoretical side of single-particle tracking, as well as the use of photon correlations to study light harvesting. This includes picosecond correlations, like the quantum optical effect known as photon antibunching, as well as fluorescence correlation spectroscopy, which is used to study diffusion and dynamics such as protein aggregation.”

Leonato Nchinda:

“Photosynthesis, an indispensable process, is the most important biological process on earth. By liberating oxygen and consuming carbon dioxide, it has transformed the world into the hospitable environment we have today. The light-harvesting protein complexes of photosynthetic organisms are intriguing molecular machines. They use the principles of quantum mechanics and switch between light-harvesting and photoprotective functions. The photoprotective state is established through a complex mechanism known as non-photochemical quenching (NPQ) during which excitation energy is thermally dissipated in a clean and safe manner. Since the photosynthetic light-harvesting process is dominated by the laws of quantum mechanics, precise control of the switch between light-harvesting and NPQ demands a technique based on quantum control; an approach that has not yet been utilised. In this light, I am using laser coherent control to observe and actively manipulate the course of physical and chemical processes immediately after photoexcitation of LHCII, the main light-harvesting complex of plants. Through the wavefront shaping of ultrashort laser pulses under the instruction of a genetic algorithm, the quenching process can be optimised or minimised. The 4f setup, which forms part of an ultrafast transient absorption spectroscopy setup, contains a Spatial Light Modulator (SLM), which will be used for shaping the pump pulse in phase and amplitude, while a genetic algorithm will be implemented to manipulate the laser pulses until an optimal pulse shape is achieved. At the end of this interesting adventure, we believe that the results obtained will be able to guide agricultural biotechnologies to develop high-light tolerant crops through genetic modification. Finally, with the advent of Biomimicry, a perfect understanding of the fundamental properties of these intriguing molecular machines (like LHCII), will serve as a great inspiration for finding green, sustainable energy solutions for our planet.

 

 

 

Alumni

 

  • Dr Hufiza Elnour (PhD)

  • Dr Alexander Paradzah (PhD)

  • Asmita Singh (MSc)

  • Justin Harrison (Hons and MSc)

  • Sifiso Mpapane (Hons)

  • Carrie-Anne Rubidge (Hons)

 


Publications

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

Orcid
Google Scholar
 

 

If you are new to this field, have a look at our popular science articles first:

 

Photosynthetic light-harvesting complexes

Plants

  1. T. P. J. Krüger, V. I. Novoderezhkin, C. Ilioaia, R. van Grondelle, “Fluorescence Spectral Dynamics of Single LHCII Trimers.” Biophys J, 98:3093–3101 (2010). DOI: 10.1016/j.bpj.2010.03.028

  2. T. P. J. Krüger, C. Ilioaia, R. van Grondelle, “Fluorescence Intermittency from the Main Plant Light-Harvesting Complex: Resolving Shifts between Intensity Levels.” J Phys Chem B 115:5071–5082 (2011). DOI: https://doi.org/10.1021/jp201609c

  3. T. P. J. Krüger, C. Ilioaia, L. Valkunas, R. van Grondelle, “Fluorescence Intermittency from the Main Plant Light-Harvesting Complex: Sensitivity to the Local Environment.” J Phys Chem B 115:5083–5095 (2011). DOI: https://doi.org/10.1021/jp109833x

  4. T. P. J. Krüger, E. Wientjes, R. Croce, R. van Grondelle, “Conformational Switching Explains the Intrinsic Multifunctionality of Plant Light-Harvesting Complexes.” Proc Natl Acad Sci USA, 108:13516-13521 (2011). DOI: https://doi.org/10.1073/pnas.1105411108

  5. T. P. J. Krüger, C. Ilioaia, M. P. Johnson, A. V. Ruban, E. Papagiannakis, P. Horton, R. van Grondelle, “Controlled Disorder in Plant Light-Harvesting Complex II Explains its Photoprotective Role.” Biophys J 102: 2669–2676 (2012). DOI: 10.1016/j.bpj.2012.04.044

  6. T. P. J. Krüger, C. Ilioaia, M. P. Johnson, E. Belgio, P. Horton, A. V. Ruban, R. van Grondelle, “The Specificity of Controlled Protein Disorder in the Photoprotection of Plants” Biophys J 105:1018–1026 (2013). DOI: 10.1016/j.bpj.2013.07.014 *Selected for editor's choice

  7. T. P. J. Krüger, C. Ilioaia, M. P. Johnson, A. V. Ruban, R. van Grondelle, “Disentangling the Low-Energy States of the Major Light-Harvesting Complex of Plants and their Role in Photoprotection.” Biochim Biophys Acta 1837:1027-1038 (2014). DOI: https://doi.org/10.1016/j.bbabio.2014.02.014

  8. C. Ramanan, J. M. Gruber, P. Maly, M. Negretti, V. I. Novoderezhkin, T. P. J. Krüger, T. Mančal, R. Croce, R. van Grondelle, “Site Specific Mutation Elucidates the Role of Exciton Delocalization in the Lowest Energy State Cluster of LHCII Monomer.” Biophys J 108 (5): 1047-1056 (2015).
    DOI:
    https://doi.org/10.1016/j.bpj.2015.01.019

  9. G. S. Schlau-Cohen, H.-Y. Yang, T. P. J. Krüger, P. Xu, M. Gwizdala, R. van Grondelle, R. Croce, W. E. Moerner. “Single-molecule Identification of Quenched and Unquenched States of LHCII.” J Phys Chem Lett 6: 860-867 (2015). DOI: https://doi.org/10.1021/acs.jpclett.5b00034

  10. J.M. Gruber, J. Chmeliov, T.P.J. Krüger, L. Valkunas, R. van Grondelle, “Singlet–triplet annihilation in single LHCII complexes.” Phys Chem Chem Phys 17 (30): 19844-19853 (2015).
    DOi:
    https://doi.org/10.1039/C5CP01806D

  11. J.M. Gruber, P. Xu, J. Chmeliov, T.P.J. Krüger, M.T.A. Alexandre, L. Valkunas, R. Croce and R. van Grondelle, “Dynamic quenching in single photosystem II supercomplexes.” Phys Chem Chem Phys 18: 25852-25860 (2016). DOI: https://doi.org/10.1039/C6CP05493E


 

Cyanobacteria (Phycobilisomes)

  1. M.S. Gwizdala, R. Berera, D. Kirilovsky, R. van Grondelle, T.P.J. Krüger, “Controlling light harvesting with light.” J Am Chem Soc 138 (36): 11616-11622 (2016).
    DOI:
    https://doi.org/10.1021/jacs.6b04811

Accompanying Conversation article: https://theconversation.com/a-smart-switch-in-photosynthesis-holds-lessons-for-solar-technology-66602

  1. M.S. Gwizdala, T.P.J. Krüger, Md. Wahadoszamen, J.M. Gruber, D. Kirilovsky, R. van Grondelle, “Phycocyanin: one complex, two states, two functions.” J Phys Chem Lett 9:1365-1371 (2018).
    DOI: https://doi.org/10.1021/acs.jpclett.8b00621

Accompanying Conversation article: https://theconversation.com/how-the-discovery-of-a-proteins-secret-function-could-boost-solar-tech-98407

  1. M.S. Gwizdala, J.L. Botha, A. Wilson, D. Kirilovsky, R. van Grondelle, T.P.J. Krüger, “Switching an individual phycobilisome off and on.” J Phys Chem Lett 9:2426-2432 (2018).
    DOI: https://doi.org/10.1021/acs.jpclett.8b00767

Accompanying Conversation article: https://theconversation.com/proteins-reveal-intricate-details-about-life-under-the-microscope-106886)

  1. T.P.J. Krüger, R. van Grondelle, M.S. Gwizdala, “The role of far-red spectral states in the energy regulation of phycobilisomes.” Biochim. Biophys. Acta – Bioenergetics 1860:341-349 (2019).
    DOI: 10.1016/j.bbabio.2019.01.007

  2. Md. Wahadoszamen*, T.P.J. Krüger*, A.M Ara, R. van Grondelle, M.S. Gwizdala, “Charge-transfer states in phycobilisomes.” Biochim. Biophys. Acta – Bioenergetics 1861:148187 (2020).
    DOI: https://doi.org/10.1016/j.bbabio.2020.148187

  3. G.T. Assefa, T.P.J. Krüger, and M. Gwizdala, "Phycobilisomes’ secret life unravelled with single molecule spectroscopy", Proc. SPIE 11650, Single Molecule Spectroscopy and Superresolution Imaging XIV, 1165006 (5 March 2021). DOI: https://doi.org/10.1117/12.2583009


 

Diatoms

  1. T.P.J. Krüger, P. Maly, M.T.A. Alexandre, T. Mančal, C. Büchel, R. van Grondelle, “How reduced excitonic coupling enhances light harvesting in the main photosynthetic antennae of diatoms” Proc Natl Acad Sci USA 114: E11063-E11071 (2017). DOI: https://doi.org/10.1073/pnas.1714656115

Accompanying Conversation article: https://theconversation.com/water-dwelling-organisms-show-new-ways-to-harvest-light-for-solar-tech-88801

  1. H.M.A.M. Elnour, C. Ramanan, L. Dietzel, C. Büchel, R. van Grondelle, T.P.J. Krüger, “Energy dissipation mechanisms in the FCPb light-harvesting complex of the diatom Cyclotella meneghiniana.” Biochim Biophys Acta – Bioenergetics 1859:1151-1160 (2018). DOI: 10.1016/j.bbabio.2018.07.009


 

Bacteria

  1. A. Gall, C. Ilioaia, T.P.J. Krüger, B. Robert, R. van Grondelle, “Conformational Changes in a Single Light-Harvesting Protein as Followed by Fluorescence Spectroscopy.” Biophys J 108 (11): 2713-2720 (2015). DOI: 10.1016/j.bpj.2015.04.017

  2. C. Ilioaia, T.P.J. Krüger, O. Ilioaia, B. Robert, R. van Grondelle, A. Gall, “Apoprotein heterogeneity increases spectral disorder and a step-wise modification of the B850 fluorescence peak position.” Biochim Biophys Acta – Bioenergetics 1859:137-144 (2018). DOI: 10.1016/j.bbabio.2017.11.003


 

Hypoliths

  1. M. Gwizdala P.H. Lebre, G. Maggs-Kölling, E. Marais, D.A. Cowan, T.P.J. Krüger, “Sub-lithic photosynthesis in hot desert habitats.” Environ Microbiol 23:3867–3880 (2021). DOI: https://doi.org/10.1111/1462-2920.1550

Accompanying Newsletter article: See page 23 here: https://bit.ly/3yd2xeT


 

Review articles

  1. T.P.J. Krüger, R. van Grondelle, “Design principles of natural light-harvesting as revealed by single molecule spectroscopy.” Physica B: Condensed Matter, 480:7-13 (2016). DOI: 10.1016/j.physb.2015.08.005

  2. T.P.J. Krüger, R. van Grondelle, “The role of energy losses in photosynthetic light harvesting” J Phys B: At Mol Opt Phys 50: 132001 (2017) DOI: 10.1088/1361-6455/aa7583. *Invited review

  3. J.M. Gruber, P. Maly, T.P.J. Krüger, R. van Grondelle, “From isolated light-harvesting complexes to the thylakoid membrane:a single-molecule perspective” Nanophotonics 7:81-92 (2018). DOI: https://doi.org/10.1515/nanoph-2017-0014

  4. Headline Review on Quantum Biology: A. Marais, B. Adams, A. Ringsmuth, M. Ferretti, J.M. Gruber, R. Hendrikx, M. Schuld, S.L. Smith, I. Sinayskiy, T.P.J. Krüger, F. Petruccione, R. van Grondelle, “The future of quantum biology.” J R Soc Interface 15: 20180640 (2018). DOI: https://doi.org/10.1098/rsif.2018.0640

Accompanying blog article: https://royalsociety.org/blog/2019/02/the-future-of-quantum-biology/


 

Theory

  1. L. Valkunas, J. Chmeliov, T. P. J. Krüger, C. Ilioaia, R. van Grondelle, “How Photosynthetic Proteins Switch.” J Phys Chem Lett 3:2779–2784 (2012). DOI: https://doi.org/10.1021/jz300983r

  2. J. Chmeliov, L. Valkunas, T. P. J. Krüger, C. Ilioaia, R. van Grondelle, “Fluorescence Blinking of Single Major Light-Harvesting Complexes.” New J Phys 15:085007 (2013). DOI: 10.1088/1367-2630/15/8/085007

  3. J.A. Nöthling, T.P.J. Krüger, T. Mančal, “A phenomenological description of the bath and its effect in photosynthetic light-harvesting systems” in The Proceedings of the 60th Annual Conference of the South African Institute of Physics (SAIP2015), edited by Makaiko Chithambo (RU) and André Venter (NMMU) (2015), pp. 527 - 531. ISBN: 978-0-620-70714-5 (2016).


 

Method development: SPT

  1. B. van Heerden, T.P.J. Krüger, "Theoretical comparison of real-time single-particle tracking techniques", Proc. SPIE 11650, Single Molecule Spectroscopy and Superresolution Imaging XIV, 116500K (5 March 2021). DOI: https://doi.org/10.1117/12.2582974


 


 

Solar-cell materials

  1. A.T. Paradzah, M. Diale, K. Maabong, T.P.J. Krüger, “Use of interfacial layers to prolong hole lifetimes in hematite probed by ultrafast transient absorption spectroscopy” Physica B: Condensed Matter 535:138-142 (2018). DOI: https://doi.org/10.1016/j.physb.2017.06.088

  2. A.T. Paradzah, K. Maabong, H.M.A.M. Elnour, A. Singh, M. Diale, T.P.J. Krüger, "Identification of exciton-exciton annihilation in hematite thin films." J Phys Chem C 123:18676-18684 (2019). DOI: 10.1021/acs.jpcc.9b04664

  3. J.S. Nyarige, T.P.J. Krüger, M. Diale. “Structural and optical properties of hematite and L-arginine/hematite nanostructures prepared by thermal spray pyrolysis.” Surfaces and Interfaces 18:100394 (2020). DOI: 10.1016/j.surfin.2019.100394

  4. J.S. Nyarige, T.P.J. Krüger, M. Diale. “Eects of L-arginine concentration on hematite nanostructures synthesized by spray pyrolysis and chemical bath deposition.” Physica B: Condensed Matter 581:411924 (2020). DOI: https://doi.org/10.1016/j.physb.2019.411924

  5. S. Congolo, M.J. Madito, A.T Paradzah, A.J. Harrison, H.M.A.M. Elnour, T.P.J. Krüger, M. Diale. “Reduction of recombination rates due to volume increasing, annealing, and tetraethoxysilicate treatment in hematite thin films.” Appl Nanosci 10, 1957–1967 (2020). DOI: https://doi.org/10.1007/s13204-020-01264-7

  6. J.S. Nyarige, T.P.J. Krüger, M. Diale. “Influence of precursor concentration and deposition temperature on the photoactivity of hematite electrodes for water splitting.” Mater Today Commun 25: 101459 (2020). DOI: https://doi.org/10.1016/j.mtcomm.2020.101459

  7. A.T. Paradzah, K. Maabong-Tau, M. Diale, T.P.J. Krüger,.”Photoelectrochemical Performance and Ultrafast Dynamics of Photogenerated Electrons and Holes in Highly Titanium-Doped Hematite” Phys Chem Chem Phys 22:27450-27457 (2020). DOI: https://doi.org/10.1039/D0CP04954A


 

Plasmonics

  1. F. Kyeyune, J.L. Botha, B. van Heerden, P. Maly, R. van Grondelle, M. Diale, T.P.J. Krüger. “Strong plasmonic fluorescence enhancement of individual plant light-harvesting complexes.” Nanoscale 11:15139-15146 (2019). DOI: https://doi.org/10.1039/C9NR04558A

  2. L.C. Ugwuoke, T. Mančal, T.P.J. Krüger, “Localized Surface Plasmon Resonances of simple tunable plasmonic nanostructures.” Plasmonics 15:189–200 (2020). DOI: https://doi.org/10.1007/s11468-019-01019-3

  3. L.C. Ugwuoke, T. Mančal, T.P.J. Krüger, “Plasmonic Quantum Yield Enhancement of a Single Molecule Near a Nanoegg.” J Appl Phys 127: 203103 (2020).
    DOI: 
    https://doi.org/10.1063/5.0007985 (arXiv:2002.09399)

  4. L.C. Ugwuoke, T. Mančal, T.P.J. Krüger, “Optical Properties of a Nanoegg-Nanorod Heterodimer: A Quasi-Static Analysis” J Opt Soc Am B 37: A293-A303 (2020) https://doi.org/10.1364/JOSAB.399015

  5. L.C. Ugwuoke, F. Kyeyune, T. Mančal, T.P.J. Krüger, "Modelling of plasmon-enhanced fluorescence in a single light-harvesting complex near a gold nanorod", Proc. SPIE 11661, Plasmonics in Biology and Medicine XVIII, 116610E (5 March 2021). DOI: https://doi.org/10.1117/12.2583000


 

Optics Theory

  1. C. Mafusire, T.P.J. Krüger, “Strehl ratio and amplitude-weighted generalized orthonormal Zernike-based polynomials”, Appl Opt 56:2336-2345 (2017). DOI: https://doi.org/10.1364/AO.56.002336

  2. C. Mafusire, T.P.J. Krüger, “Orthonormal vector polynomials in general pupils derived from the Cartesian gradient of the orthonormal Zernike-based polynomials using the Gauss-Jordan elimination method” J Opt Soc Am A 35:840-849 (2018). DOI: 10.1364/JOSAA.35.000840

  3. C. Mafusire, T.P.J. Krüger, “Local and curvature divergence in first order optics.” J. Opt. 20:0965603 (2018). DOI: 10.1088/2040-8986/aabf06

  4. C. Mafusire, T.P.J. Krüger. “Zernike coefficients of a circular Gaussian pupil.” J Mod Opt. 67:7, 577-591 (2020), DOI: 10.1080/09500340.2020.1759712


 

  Other

  1. R. A. Burger, T. P. J. Krüger, M. Hitge, N. E. Engelbrecht, “A Fisk-Parker Hybrid Heliospheric Magnetic Field with A Solar-Cycle Dependence.” Astrophys J 674:511–519 (2008).

  2. D. C. Onwudiwe, T. P. J. Krüger, O. S. Oluwatobi, C. A. Strydom, “Nanosecond Laser Irradiation Synthesis of CdS Nanoparticles in a PVA System”, Appl Surface Sci 290:18-26 (2014). DOI: https://doi.org/10.1016/j.apsusc.2013.10.165

  3. D. C. Onwudiwe, T. P. J. Krüger, C. A. Strydom, Laser Assisted Solid State Reaction for the Synthesis of ZnS and CdS Nanoparticles from Metal Xanthate, Mater Lett 116, 154-159 (2014). DOI: 10.1016/j.matlet.2013.10.118

  4. L. Sitole, F. Steffens, T. P. J. Krüger, D. Meyer, “Mid-ATR-FTIR Spectroscopic Profiling of HIV/AIDS Sera for Novel Systems Diagnostics in Global Health.” OMICS: A Journal of Integrative Biology 18:1-11 (2014). DOI: 10.1089/omi.2013.0157

  5. D. C. Onwudiwe, T. P. J Krüger, A. Jordaan, C. A. Strydom. Laser-Assisted Synthesis, Structural, and Thermal Properties of ZnS Nanoparticles Stabilized in Polyvinyl Pyrrolidone”, Appl Surface Sci, 321:197-204 (2014). DOI: https://doi.org/10.1016/j.apsusc.2014.10.022

 

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

 

Book

Emil Roduner, Tjaart Krüger, Patricia Forbes, Katharina Kreß, “Optical Spectroscopy – Fundamentals and Advanced Applications” World Scientific Publishing Europe Ltd (2018). Link: https://www.worldscientific.com/worldscibooks/10.1142/q0182


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

We strive to pursue a balanced mixture of methodology development, application of established techniques and challenging and slightly more adventurous new projects. You may choose between experimental and theoretical/computational 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

Luke Ugwuoke (PhD, 2020): “Local spectroscopic properties of certain plasmonic and plexcitonic systems”

Bertus van Heerden (MSc, 2020): “'n Ondersoek na enkeldeeltjie-nasporingsmetodes vir fotosintetiese komplekse”

Farooq Kyeyune (PhD, 2019): “Single molecule spectroscopy on photosynthetic light-harvesting complexes”

Stephen Brookes (Hons, 2019): “Implementation of real-time auto-refocussing into a confocal microscope”

Johann Smith (Hons, 2019): “Investigating the effects of constrained protein motion on the fluorescence blinking behavior of light-harvesting complex II.”

Alexander Paradzah (PhD, 2018): “Resolving ultrafast dynamics of photoexcited plant antennas and hematite nanostructures”

Huzifa Elnour (PhD, 2018): “Spectroscopy and control of ultrafast energy dynamics in natural light–harvesting complexes”

Justin Harrison (MSc, 2018): “Investigating electron-transfer processes of supramolecular donor-acceptor complexes using femtosecond transient absorption spectroscopy”

Bertus van Heerden (Hons, 2018): “Investigation of Fluorescence Intensity and Lifetime Dynamics of Single LHCII Complexes”

Carrie-Anne Rubidge (Hons, 2018): “Coherent control in light-harvesting complex II”

Johanette Staats (Hons, 2018): “Intensity dynamics of single light-harvesting complexes from cryptophyte algae”

Marissa Boshoff (Hons, 2018): “A comparative study of plasmonic-enhanced fluorescence of the main plant light-harvesting complex induced by gold nanostructures”

Sifiso Mpapane (Hons, 2018): “Calculating and measuring the size and other properties of apertured laser beams”

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]

 

Published by Konstantinos Zoubos

Copyright © University of Pretoria 2021. All rights reserved.

FAQ's Email Us Virtual Campus Share Cookie Preferences