Primary Processes of Photosynthesis

Fig. 1: Photosynthesis is always a process on membranes. Photosynthetic bacteria involve their cellular walls to create two membrane separated environments.

Essentially all energy, which the biosphere and the humanity uses, comes from the Sun. Living organisms convert light into chemical energy in the process of photosynthesis. We study the so-called primary processes of photosynthesis, which include light-energy captures (excitation of photosynthetic pigments), excitation energy transfer, and subsequent charge transfers. Excitation energy drives electron and proton transfers through a membrane (the cellular wall on the picture), and creates proton gradient between the two sides of the membrane. Although clear divisions do not exist, the processes up to this point can be well understood as physics (no chemical transformation so far), whereas processes beyond this point are better characterised as chemistry.

Our group studies the process of energy transfer in photosynthetic antenna and the experimental methods used to investigate this process. Description of the natural excitation energy transfer and simulation of the experiments performed to investigate it requires to employ quantum mechanics. Because the systems in which these processes occur are composed of a macroscopically large number of molecular systems, they cannot be treated in full. We always have to select a part of the whole machinery which which we treat explicitly, and describe the processes and experiments on this very small chosen system as if it undergoes interaction with a large (but otherwise invisible) background. Such a small system embedded in something else is called an open system.  

Correspondingly, we always deal with open systems in our work. Because these systems are very small, they behave quantum mechanically. The very strange quantum behaviour of these basic parts of the photosynthetic machinery has consequences all the way to the macroscopic behaviour of photosynthetic mechanisms. We can say that without quantum mechanics, there would be no light-harvesting, not photo-synthesis, and consequently no life on Earth.

To learn  how quantum mechanics changes the picture of excitation energy transfer, read our paper on classical description of excitation energy transfer here.

Non-linear and Single Molecule Spectroscopy

Fig. 2: Scheme of a three pulse time resolved non-linear experiment.

Most of our knowledge about primary processes in photosynthesis originates from time resolved spectroscopic experiments. In these experiments, molecular systems are subject to investigation by very short laser pulses. The duration of the pulses is on the order of tens of femto-seconds (one femotosecond = 10-15 sec, one milionth of a bilionth of a second). When several such pulses are sent with precise timing into a cuvette with photosynthetic molecules, one can observe how the light is excited and the corresponding excitation energy is transferred within and between photosynthetic antennae.  

Interestingly, the experiments are performed in the conditions that the observed signals are non-linear. In linear optics two beams which cross continue unaffected. In non-linear optics, crossing beams generate other beams going into directions different from the original beams. This effect is used in our most sophisticated experiments to generate a background free signal beam out of crossing of three beams. Various non-linear signals carrying different information about the studied molecules can be measured in different directions with respect to the three generated beams. 

In ur group we develop methods of computer simulations of experiments with ultra-short laser pulses. We help chemists, biologists and other users of time-resolved spectroscopy tools to understand their results. Our simulations enable them to connect the dots between the observed behavior of spectra, and the behavior of molecular systems on nano-scale. 

Biomimetic Materials

FIG. 3: Bacterial photosynthetic antenna (upper figure) and a section of a bio-inspired artificial antenna based on fluorographene.

Recently,  we have embarked on a mission to translate design principles of photosynthetic antennae into artificial materials. Primary target of our initial research is fluorographene, a two-dimensional teflon, which we believe can act as a supporting material for artificial light-harvesting structures.

The essence of our idea is that the so-called pi-electron states which are responsible for visible light absorption of aromatic molecules (and also for absorption of molecules like chlorophyll) can be constructed in a pure fluorographen sheet by removing some of its fluorine atoms. Defects in fluorographene created by such removal of fluorines have properties very similar to the ones of molecules with the similar shape. We therefore call these defects moleculoids (entities similar to molecules). We study how to best construct artificial light harvesting antennas out of these moleculoids.

Our research so far shows that the moleculoids have properties favorable for construction of artificial antenna, and we look out for research who would be able to construct our antenna by manipulating fluorographene on atomic scale. We have also recently measured properties of moleculoids in nearly pure fluorographene by single molecule spectroscopy. We now know they exists and our intuition is turning to reality.



Theory of Open Quantum Systems

Fig. 4: Open quantum systems have to be described by the so-called reduced density operator. Wavefunction description can be used only for isolated quantum systems.

Quantum theory is the fundamental theory of the micro world. In fact it is probably the fundamental theory of the macro world, too (see below). The laws of classical physics, which govern the world as we know it, often break down when we deal with processes involving electrons in molecular systems. Quantum theory gives us means for describing electrons in molecules and their interaction with light. 

Theoretical description and simulation of both the photosynthetic energy transfer and the spectroscopic experiments require open quantum systems theory. Molecular excitations are small quantum mechanical objects interacting with a large bath consisting of protein vibrations, water environment and ultimately also the vacuum of electromagnetic field. This makes them open systems. 

Open quantum systems theory gives answers not only to questions related to function of microscopic living machines we meet in photosynthesis, but also to the fundamental question about the emergence of classical world from the quantum one. Is the classical world a separate level of reality for whose explanation we need to invoke some yet unknown physics of "wavefunction collaps" or other unknown phenomena which "make" quantum world classical?