This issue’s cover doesn’t look like the beautiful protein structures or micrographs that often grace the front of Biophysical Journal—it might just look like layers of brightly-colored candy. But it is drawn from real data and represents a real (and really colorful) biophysical system: the photosynthetic light-harvesting and charge conversion apparatus in stacked thylakoid membranes. Our computational model of the protein-protein interactions within and between these membrane layers is simple enough to access large length scales (the image represents hundreds of nanometers), yet rich enough to capture structural motifs such as inter-membrane correlations and to predict thermodynamic phase behavior that could affect photosynthetic function.
While building and studying this model, we found visualization to be indispensible for extracting insight from data; visualization came before discovery, not just after. The multilayered structure of our configurations was difficult to visualize clearly using traditional software, prompting us to develop a suite of tools for reproducibly creating graphics that illuminate particular research questions. For the image on the cover, I collaborated with Lester Hedges (a fellow statistical mechanician and my boyfriend) to connect the existing scripts to POV-Ray, a command-line raytracing program that he has used to create other journal cover art. He and I both enjoyed the challenge of creating a computer-generated image that is at once visually striking and scientifically meaningful.
Anna Schneider is a grad student in the Geissler group and an editor of the Berkeley Science Review.
– Written by Anna Schneider
Alán Aspuru-Guzik and his group in the Department of Chemistry and Chemical Biology at Harvard University describe the image they created for the cover of the current issue of Biophysical Journal.
Photosynthesis is the fundamental biological process in many organisms for the energy conversion from sunlight into other forms to be used in cellular processes. Recent experiments have provided evidence that interesting quantum coherence effects persist in several plant, algae, and bacterial light-harvesting complexes even at ambient temperatures.
Green sulfur bacteria have adapted to extreme environmental conditions and low exposure to light. The cover art shows a part of this organism’s highly efficient photosynthetic apparatus which consists of Fenna-Matthews-Olson (FMO) complexes and reaction centers. When light hits the organism the energy is absorbed in the form of an electronic excitation in one of the many chlorophyll molecules of an antenna complex (called the chlorosome, not shown). This energy then moves through the antenna complex onto the FMO complex, from which it is transported to the reaction center. In the reaction center the energy
conversion takes place. In our research, we focus on the FMO complex and its distinct biological role and perform atomistically precise simulations of the energy transport.
Two FMO complexes are prominently displayed in the image. For each complex, the chlorophyll molecules colored in yellow are shown nested inside a blue-green protein scaffolding. The FMO complexes sit on top of the reaction center, which is rendered with less detail and provides an artistic background in light blue-green. The bottom part of the image shows the ultrafast movement of one of the excitations inside a seven-molecule subsystem of the FMO complex. The presence of an excitation on a molecule is represented by a yellow irradiating glow, where the strength of the glow is based on our quantitative
calculations of excitation populations. This allows for the visualization of the quantum nature of the process which makes the excitation spatially delocalize and oscillate between the molecules.
We have used the atomistic structure information from the Protein Databank for the Fenna-Matthews-Olson complex (3EOJ) and taken the reaction center from (3DSY). We have used Autodesk Maya for the rendering and composited the image in Adobe After Effects and Adobe Photoshop.
We are happy that our image was chosen as the cover of Biophysical Journal. We hope that the image conveys our excitement about quantum effects in photosynthesis and the broad appeal of this field of research.
The interested reader can find further research by the Aspuru-Guzik group in the areas of quantum chemistry, clean energy, quantum computation and simulation, excitation energy transfer, and more at http://aspuru.chem.harvard.