Archive for the 'bio' Category

au courant

Friday, October 5th, 2012

image by Curtis Neveu on wikipedia

About five years ago there was on randform a question regarding the possibility to study the electron transport in a pigment-protein complex via some optical methods in the attosecond regime. Understanding this may be important for the development of new types of solar cells. From the randform post:

It would be interesting to know wether such high temporal resolution could also be used for investigating electron tranfer in pigment-protein complexes such as in a photosynthetic reaction center (see image above)(correction 05.10.2012: in a FMO complex (the reaction center seems to be a part of this complex)), which was done by researchers in Berkeley e.g. in a 3 pulse two-color electronic photon echo experiment with 750 and 800 nm pulses in the femtosecond range (science 316 (5830)) or wether the high energies of the corresponding laser pulses would alter the corresponding structures, which apparently happenes if one shoots with gamma rays on a pigment.

In a press release which reports about measurements at the photosystem 1 (PS 1) protein (which appears to be even more complex than the above mentioned FMO complex) it seems that one can at least measure the speed of charges in a photosystem with the help of optical devices.

Not only the press release but even the article itself:
Photocurrent of a single photosynthetic protein, by Daniel Gerster, Joachim Reichert, Hai Bi, Johannes V. Barth, Simone M. Kaniber, Alexander W. Holleitner, Iris Visoly-Fisher, Shlomi Sergani & Itai Carmeli
is actually still currently available on the nature nanotechnology website.

The results of their research makes the researchers write (see article):

Our results demonstrate that individual PS I units can be integrated and selectively addressed in nanoscale photovoltaic devices while retaining their biomolecular functional properties. They act as light-driven, highly efficient single-molecule electron pumps that can function as current generators in nanoscale electric circuits.

Instead of directly shooting with lasers the researchers were here however “exciting the PS 1 with a “633 nm laser light with a power of ~4 mW “from the back of the tip” (see figure 1 in the article), which I understand as that the laser light went through the glass of the tip of a scanning near-field optical microscope before it entered the PS 1 (the PS 1 was “glued” via cysteine mutation groups to the glass tip). Moreover the light makes electrons travel through the protein (as I understand with the help of a voltage through the protein i.e. between the tip and the ground) and this can be measured as a current:

The photocurrent was measured by means of a gold-covered glass tip employed in a scanning near-field optical microscopy set-up. The photosynthetic proteins are optically excited by a photon flux guided through the tetrahedral tip that at the same time provides the electrical contact.

The researchers sketched out the whole reaction-centre electron transfer chain and showed electron transfer and recombination times (see figure 2). I didn’t understand where the detailled knowledge for this figure came from, however their measurement seems to be in good agreement with this knowledge, they write:

One of the most significant results in our experiment is the intriguingly large value of ~10 pA for Iphoto. This translates into a turnover time of ~16 ns; in other words, every ~16 ns, an electron transverses the PS I covalently bound between the two electrodes.

(remark: with electrodes the researchers mean here probably the tip and the ground)

The wavelength in the experiment was 633 nm laser light with a power of ~4 mW but I have no feeling how the light is altered by the scanning near-field optical microscope. In particular I still don’t know wether one could use the high resolution laser pulses to investigate the traveling electrons within a photo system without destroying the photo systems.

Because in principle it seems one could make interesting films with this, similar to what had been done for topological insulators.

addition 090113:

It seems there are already some applications underway, which use PS1, which seems also to be up for a patent. I can’t read the original article , but there is some english description e.g. on nanowerk. Found via Sascha Peters on Liligreen.

I haven’t written this explicitly, but may be I should. PS1 is interesting not only because it has a high quantum efficiency (here a current record for quantum efficiency in quantum dots) and because it is usually available in ecofriendly materials like spinach but amongst others also because it seems that the charge carrier separation works rather well. The above work seems to be amongst others probably concerned with studying the involved mechanisms of charge carrier separation, i.e. last but not least it is concerned with the mechanisms of electron transfer.
On that issue I had written five years ago: “electron transfer in the photosynthetic reaction center of Rhodobacter sphaeroides in the above experiment seems to be highly efficient due to the long coherence between the exiton states of two chromophores corresponding to the bacteriochlorophyll b (BChl-b) molecules and bacteriophaeophytin b molecules (BPh) of a photosynthetic reaction center.”” (the comment was based on observations of the Fleming group) but I haven’t found the time and means to look into these mechanisms much further.

addition 24072014:

There is a new article in nature concerned with some of the above questions, in which Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser is used to investigate the catalytic processes in photosystems. I can’t read the article, but only the abstract and look the images, but that is already quite interesting. In particular concerning the above comment about the correlations one sees in image c how the spatial configuration of the molecules in the electron transfer chain looks like. After the photosystem II primary donor P680 one sees achlorophyll Chl_A and then a pheophytin Pheo_A. In the Wikipedia description of P680 it is written:

The primary donor receives excitation energy either by absorbing a photon of suitable frequency (colour) or by excitation energy transfer from other chlorophylls within photosystem II. During excitation, an electron is excited to a higher energy level. This electron is subsequently captured by the primary electron acceptor, a pheophytin molecule located within photosystem II near P680.

This sounds as if Chl_A is rather in charge of the excitation energy transfer to P680 than as part of the electron transfer from P680 to Pheo_A, which seems different from what the little orange arrows in image c indicates. So a question which arises here is wether one can here observe a long coherence between exiton states of Chl_A and Pheo_A (as it seems it exists for the case of BChl-b and BPh) and wether this involves P680 or not. It seems as if the grid like bubbles in the images g,h,i are eventually charge carrier configurations (? that is those seem to be electron density bubbles upon making a survey on the results of googleing what is an omit map). However I can’t even identify Pheo_A in those images.

addition 19092014:
The question about how the concrete energy transport pathway looks like concretely was raised also on the Azimuth forum

addition 04102017:
I detected an article which explains:
Why Quantum Coherence Is Not Important in the Fenna–Matthews–Olsen Complex

The authors, who apparently use certain Hierarchical equations of motion techniques claim:

Our exact results are then compared to calculations using the incoherent Förster theory, and it is found that the time scale of energy transfer is roughly the same, regardless of whether or not coherence is considered. This means that coherence is not likely to improve the efficiency of the transfer. In fact, the incoherent theory often tends to overpredict the rates of energy transfer, suggesting that, in some cases, quantum coherence may actually slow the photosynthetic process.

Remark: There exists now a Förster resonance energy transfer on Wikipedia, but I don’t know in how far this is related to (incoherent) “Förster theory”.

focus and context, part II-2: brain childs and their evolution

Monday, February 20th, 2012

This post is a follow-up to the last post. There is also a copy of this essay at the Azimuth project.
If you read the essay you will in particular understand that I profoundly disagree with most of the key concepts as formulated in the video by Kirby Ferguson, who also investigated intellectual property in the context of evolution.

Feb22: some additions to the essay in orange more additions eventually on Azimuth

diversity maintenance

Saturday, November 19th, 2011

“Dreimäckriges Blauquallendrachengespenst verwandelt sich in einen Kugelblitz um die ausgecyborgte, zweigebeinigte “Jeanne die Arge”, zu töten”. Artwork by Hugo Buster, acrylic paint and pencil

Just a quick link to what seems to be an interesting study about biodiversity with the title Experiment gives insight into how species maintain diversity (via In the study it was investigated how biodiversity could be maintained despite dominance. Experiments with male voles, ordered by testesterone level, were performed:

when they released just a few of the high testosterone males and lots of low testosterone males into the same area, the males once again reigned supreme with the ladies. But when they released lots of high testosterone males with lots of lots of low testosterone males, the males with the lower levels actually did better than those with the high levels, indicating that there was something clearly at play. The researchers suggest that such results came about because the high testosterone level males spent more time fighting or showing off than mating, which gave the low testosterone males more of a chance to mate.

Holograms Reveal Brain’s Inner Workings

Wednesday, August 17th, 2011

“HirniKoppic”, Copic Markers on paper, by artist “nettwürg” on the occasion of the rumors about the possibility of closing the Medizinhistorisches Museum (Berlin Medical Historical Museum) of the Charité.

Using Digital Holographic Microscopy (DHM) researchers of EPFL gathered quite some interesting images from inside the brain:

->Holograms Reveal Brain’s Inner Workings.

When do we get to see brain images from image imaginations? and when can others recognize these?

plastic surgery

Monday, June 20th, 2011

Photography: Pal Lindlund

This post is like the previous post a comment to the discussion about human-machine hybrids in the recently uploaded game-scheme article.
In a passage from human to a human-machine hybrid the tolerance towards body modifications plays an important role.
There was recently an interesting interview in the english newspaper “The Guardian” wether cosmetic surgery does help or damage people.
The interview however didn’t really touch the issue of how strongly plastic surgery (and other body modifications) is influenced by cultural predispositions (which are of course often influenced by economic considerations, but not only by these). In particular it also didn’t touch upon the question in how far the design of the human outer appearance via cosmetic surgery (especially its current boom) etc. might be seen as a step in a human-machine-hybrid transition.

New economic schemes in games

Friday, March 25th, 2011

In the blogpost on the return of investments I proposed to use games for testing new economical scenarious. I currently try to make an article out of that.
In the draft I sofar have given an overview about games and roughly motivated why I think that it may be a good idea to introduce new economical schemes. In particular I talk about the limitations of this planet, design and in particular about something that I dubbed “recycling-run-away effect”.

Amongst others I also try to line out why I think that the nuclear waste problem may be a worse problem than the safety of reactors (see also the first post on Fukushima).

Comments are appreciated, here is the draft:
update (06072015) :
It currently looks as if an article format is rather not suited for the writings and findings made within the context of the game draft article. It is also still not clear wether this project will ever be finished and if in which form. You may though still find on and off some informations in this context, likethis blog post is an example.

update (06072011) : This blog post is now used as a referrer URL for the game scheme article, thus newer versions of the article and comments will be uploaded more or less regularily. Please note that this offer to our randform readers costs our private money. Since randform is currently purely financed by Tim Hoffmanns income as a math professor, we may eventually be forced to reduce or close this offer, depending on download rate, inflation, etc. Most of the content of the article is also spread on the Azimuth project like the section about the Game environment. The Azimuth updates are usually more current.

->version July 06, 2011

The most essential content article of the article was presented on July 1st at the open knowledge conference 2011 in Berlin:

Talk: “Testing new toy economies/political structures in MMOGs” at

older versions of the article:

->version May 25, 2011

->version april 26, 2011

-> New economical schemes in games, version march 25, 2011

about competition, part III

Wednesday, January 26th, 2011


around teufelsee

Tuesday, October 19th, 2010

On the occasion of the current convention on biodiversity some images from a green part of Berlin, called Teufelsee (the “satanic lake”) in the district of Köpenick.


phytoplankton decline

Thursday, July 29th, 2010


In todays nature magazine there was an article about the “Global phytoplankton decline over the past century”. I have no access to the article however in an article by Markus Becker – a reporter from the german news magazine Spiegel Online – it was reported that since 1950 on average the mass of phytoplankton declined globally by 40%. Since phytoplankton are amongst others a major food source for food webs this affects e.g. the abundance of fish. Moreover phytoplankton are responsible for much of the oxygen present in the earth’s atmosphere. A main reason for the decline of phytoplankton is climate change.

-> related article on randform about oceans and climate change
->related article on randform on microorganisms and oxygen supply
-> see also here
update 30.7.10: You might also want to kick into the subject by reading
about the decline in fish occurence:
->Elizabeth Kolbert on overfishing on Azimuth
-> randform post about fish consumption and nutrition

some koi after the click

Bright Green Design

Thursday, June 24th, 2010


BerliNordik is a rather new forum for sustainable design, it is

“an international platform that brings together young talented designers from Berlin with their colleagues from the Nordic countries on the subject of sustainable design. “

The berliNordik blog informs amongst others about activities of BerliNordik. Recently BerliNordik coorganized an exhibition called “Bright green design” where I attended the opening. For the exhibition few product design objects were chosen. I actually had also sent in a proposal but unfortunately –again– it wasn’t chosen (maybe I write later about that project in product design). Below some images from the opening.

There are images from three projects in the images. One project is featuring a partially wooden bike called “Holzweg”. Here I was asking myself how good the different material components can be dissassembled. Another project is the Yellowone Needle Cap – a protective cap that turns an empty soft drink can into a safe depository for used needles, by Hân Pham. The third project is “Spot on the BUOY” by Adrian Paulsen. In this envisaged project a buoy is supplied with a paper towel for oil spills and e.g. lights so that the buoy acts as a kind of sensor for oil spills. Clearly the buoy would only be appropriate for rather “light” spills it would certainly not be addaped for the recent oil spills in the gulf of Mexico. Any paper would be totally overstrained with this spill.

(Images of the other projects from create berlin )

In the below images you can see also the discussion of jury members and organizers about “what is green design“. One key issue here was the quandary of eco-designers, which is that to a great extend the task of a designer is to communicate a product and thus in part to encourage more consumption, which is against sustainability. It is also in part the task of an eco-designer to greenwash a product. Last but not least sustainability is often in conflict with economic interests, i.e. due elaborate production methods and materials and e.g. longer durability often only small profits can be made which is a problem in our economic system. Moreover next to the demand of incorproating new green technologies, questions about certification of eco-efficiency, compliance to new standards etc. are making the design process difficult.

->Video of the opening
Interview by Lilli Green with visitors of the exhibition about “what is green design” (-> video)