Untangling Complex Systems, page 85
Process [12.28] is a photo-induced redox reaction. The carbohydrates that are the products in process
[12.28] become food for both the autotrophs and the heterotrophs. Molecular oxygen is the by-product
of the photosynthesis. The primordial atmosphere of our planet was devoid of oxygen because the first
photosynthetic organisms, probably living close to hydrothermal vents, were using H S and not H O as
2
2
reducing reagent of CO . The dominant photosynthetic process was
2
6CO2+12H S
2
+ hν → C6H12O6+12S + 6H2O [12.29]
producing S rather than O2 as a by-product. The appearance of oxygenic photosynthesis dates back
to 3.5 billion of years ago (Nisbet and Sleep 2001).18 It determined a radical change in the evolution of life on Earth. In fact, when O became a relevant component of the terrestrial atmosphere, it pro-2
tected the biosphere from the most harmful UV radiations by producing ozone and allowed life to
colonize the lands.19 Moreover, it opened a new chemical avenue for the exploitation of the chemical energy of carbohydrates. It made possible the breakdown of carbohydrates not only by fermentation
but also combustion, gaining more energy.
The oxygenic photosynthesis consists of two distinct phases (Blankenship 2002): the light-driven
and the dark phase, respectively. In the light-driven phase, the first step is the absorption of light
by specialized complexes that contain pigments and proteins. The absorption of light occurs on a
timescale of femtoseconds (10−15 s), and it is efficient due to the large absorption coefficients of pig-
ments (chlorophylls, carotenoids, and, in some bacteria, phycobilins), as well as to the high density
of pigments in the photosynthetic complexes (Figure 12.10).
If the light is absorbed by the antenna system consisting of an aggregate of pigments, an ultrafast
energy transfer process from the antenna to the chlorophyll present in the photosynthetic reaction
center follows. Due to the proximity of the antenna and reaction center pigments, the energy transfer
occurs coherently through the excitonic mechanism (Romero et al. 2017). Therefore, the first step
of the light-driven phase of photosynthesis is the formation of the excited state of the chlorophyll
(Chl*) present in the reaction center, by indirect or direct absorption. The photosynthetic reaction
center is a multi-subunit membrane protein complex that functions as a remarkable photochemical
device. In fact, Chl* participates in an ultrafast unidirectional electron transfer process within the
protein, which requires a few picoseconds and allows to separate two opposite charges: a positive
17 In complex living beings, such as humans, the dichotomy between life and death can be not so evident because the different organs can cease to work not all at the same time, but progressively. This evidence raises ethical issues (Aguilar, 2009).
18 The formation of the Earth dates back to 4.5 × 109 years (4.5 Gyr) ago. The geological evidence demonstrates that life has been present for at least 3.5 Gyr, and it is probable that life began before 3.8 Gyr.
19 At about 100–150 Km from the land, O is photo-dissociated by the solar radiations having the higher energies: 2
O2 + hν (λ ≤ 240 nm) → 2O. The oxygen atoms couple to form O , again, or they can bind to O molecules and give 2
2
O . The concentration of ozone reaches a maximum at a height of 20–30 Km over the equator. Ozone exerts a screening
3
action from solar radiation with wavelengths included between 250 and 350 nm. These radiations could be harmful for
the DNA of living beings.
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OH
HO
Carotenoid
CH3
ption
H C
3
N
N
Mg
N
N
H
CH3
H C
3
H
Relative absor
O
H CO C
O
2
2
CO H CO H
O
2
2
O
N
N
NH+
N
O
H
H
H
400
450
500
550
600
650
700
Chlorophyll
Wavelength (nm)
Phycobilin
FIGURE 12.10 Spectral profiles of chlorophyll, carotenoid, and phycobilin pigments. A chlorophyll mol-
ecule absorbs the violet and red (and it is responsible for the green color of leaves), a carotenoid absorbs the
violet and blue (it is responsible for the yellow color of fallen leaves in autumn), whereas a phycobilin absorbs
the green and yellow.
charge in Chl and a negative charge in another acceptor molecule (that can be a quinone). The
quantum efficiency of the charge-separation process is usually very high (close to 1), due to the well-
organized supramolecular structure of the reaction center that avoids recombination of the charges
having opposite signs. For the estimation of the maximum work that can be achieved from Chl *, it
is necessary to determine the Helmholtz free energy of the pigment: ∆ A = (∆ U − T∆ S). ∆ U is given by the energy of the absorbed photon ( hν ) minus that squandered in vibronic relaxation processes
( Esq) from the Franck-Condon state20 to the potential energy minimum of the electron donor state of Chl * (see Figure 12.11).
∆ U = hν − Esq [12.30]
The entropy difference between the ground and the excited state of Chl may be assumed to be small
and negligible in the photoreaction center (thanks to the rigid structure of Chl). It is not necessary to
consider the contribution of mixing entropy (also called configurational entropy). In fact, each pho-
toreaction center is a separate thermodynamic system, and the free energy available is independent
of the relative positions of centers that are excited with respect to those in the ground state (Jennings
et al. 2014). Because of the short lifetime of the excited state, there is virtually no spreading out of
energy. Therefore, T S
∆ ≈ 0 and the maximum work that can be achieved from Chl * is
∆ A ≈ ( hν − E )
sq [12.31]
In the absorption process (Chl + hν → Chl*), ∆ H ≈ ∆ U because ∆( PV ) ≈ 0. Therefore, ∆ G ≈ ∆ A. It is possible to have work different from that of the type pressure-volume because the photosynthetic
organism has a different temperature with respect to the sun.
20 The Franck-Condon state is the electronically excited state obtained immediately after the absorption of light (occurring in 10−15 s) and having the same molecular conformation of the original ground state. In fact, in 10−15s, the nuclei do not have enough time to change their reciprocal position.
Complex Systems
435
400
Chl∗ ( S 2)
500
λ(nm)
600
FC state
Esq
700
Chl∗ ( S 1)
hv ( red)
Chl
FIGURE 12.11 Schematic representation of the formation of the Franck-Condon (FC) state of Chl, and
its relaxation after absorption of a red photon. In the primary electron transfer process occurring inside
the reaction center, the lowest excited state of Chl is converted into a charge-transfer state, character-
ized by the localization of the electron and hole on adjacent molecules (Romero, E. et al., Nature, 543,
355–365, 2017.).
The efficient transformation of solar energy into electrochemical energy, taking place in the
chlorophyll-based harvesting system, triggers redox chemical reactions that produce O (due to
2
the oxidation of water) and two other essential species, endowed with high chemical energy con-
tent. They are nicotinamide adenine dinucleotide phosphate (NADPH) and adenosine triphosphate
(ATP). ATP is the well-known energy vector of cells, whereas NADPH is a reducing agent. Both
species are involved in the dark phase of the overall photosynthetic process where reduction of
CO produces carbohydrates.
2
There are other circumstances wherein solar radiation is stored as electrochemical energy by
living beings. Some examples are reported in Table 12.1
Alternatively, solar radiation is exploited as heat. For instance, cold-blooded living beings
(such as the reptiles) bask in the morning sun to raise their internal body temperature and stimu-
late their metabolism. In thermodynamic terms, the sun is a heat reservoir at Ts = 5,777 K that
transfers thermal radiation to a cold body, the living being at T . According to the Carnot effi-
c
ciency, the maximum Helmholtz free energy gained by the cold body absorbing a photon of
frequency ν is:
T
∆ A = h
c
ν 1−
[12.32]
Ts
12.4.2.4.1 Human Activities
Of course, solar radiation is an inexhaustible energy source also useful for the human activities.
According to the International Energy Outlook 2016 (EIA 2016), the total world consumption of
marketed energy should expand to 1.84 × 1014 KWh in 2020. The sun releases an amount of energy
that is ten thousand larger than that required by human activities, every year. However, solar energy
has one principal drawback if we think about its exploitation. That is its inhomogeneous distribution
in time and space. In fact, solar radiation is discontinuous in time, and it is spread over a broad area.
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Untangling Complex Systems
TABLE 12.1
Examples of Exploitation of Solar Radiation as Electrochemical Energy by Living Beings
Living Beings
Photo-induced Processes
Absorption Features
Purposes
Halobacteria
In the protein Bacterio-
Green-yellow (max at
Bacterio-rhodopsin is a transmembrane
living in water
rhodopsin, the chromophore
568 nm)
proton-pump: it generates a
saturated with
all- trans retinal photo-
trans-membrane H+ gradient that
salts
isomerizes to 13-cis retinal
triggers the synthesis of ATP
Halobacteria
In the protein Halo-rhodopsin,
Green-yellow (max at
Halo-rhodopsin is a transmembrane
living in water
the all- trans retinal photo-
578 nm)
anion-pump: it controls the cellular
saturated with
isomerizes to 13-cis retinal
concentration of salts.
salts
All living
Photo-sensitization is, usually, an
It depends on the
It can be a harmful oxidation reaction
beings
oxidation reaction of a substrate
absorption spectrum of
for the living being, or it can be a
induced by a sensitizer that
the sensitizer. Usually,
strategy of defense against
absorbs solar radiation
it absorbs visible light
undesirable guests.
All living
Formation of dimers of
UVB (320–280 nm)
Harmful effect by UVB on DNA
beings
pyrimidine bases in DNA
Humans
Photo-induced production of
UVA (400–320 nm)
Melanin screens cells from noxious
the protective pigment melanin
effect of solar radiation (especially
UVB).
Humans
7-dehydrocholesterol is
UVB
Previtamin D thermally isomerizes to
3
converted in previtamin D
Vitamin D that is important for
3
3
skeletal health
Many living
Photolyase destroys dimers of
Violet and blue
Photolyase repairs DNA that has been
beings but not
pyrimidine bases by a
damaged by the formation of dimers
humans
photo-induced electron transfer
of pyrimidine bases
involving a flavin.
Source: Björn, L.O. (ed.), Photobiology. The Science of Light and Life. 3rd ed., Springer, New York, 2015.
Nevertheless, it can be exploited as a source of both electrochemical energy and heat. Examples of
techniques that use solar radiation as a source of electrochemical energy are:
• Photovoltaics when solar radiation is converted to electricity.
• Solar fuels when solar radiation is converted into chemical energy. An example is natural
photosynthesis. It is possible to use the biomass as fuel. Alternatively, it is possible to exploit
secondary fuels that are produced by biomass in their metabolism. Examples of secondary
metabolites are ethanol, methanol, methane, and hydrogen. Such fuels are renewable, and
by burning them, we release oxidized carbon (mainly, CO ), which is already within the
2
biosphere. When we burn petrol, coal, and natural gas, we indirectly exploit solar energy
because fossil fuels are fossilized solar radiation. However, they are exhaustible because
their formation required millions of years. Moreover, by burning fossil fuels, we release
carbon (mainly, like CO ), which was sequestered from the biosphere.
2
Examples of techniques to exploit solar radiation as a source of heat are:
• Heating environments or fluids.
• Heating thermocouples to produce electrical energy by the Seebeck effect.
• Hydroelectric energy grounds on the kinetic energy of water, whose cycle is triggered by
solar thermal energy.
Complex Systems
437
• Wind energy grounds on the kinetic energy of air, whose winds are generated by the asym-
metric heating of the atmosphere due to the sun.
• By using solar concentrators (lenses and/or mirrors), it is possible to reach high tempera-
tures (thousands of degrees Kelvin), induce thermal reactions, and store solar energy into
chemicals
It is worthwhile striving to improve the techniques that exploit the renewable solar energy to respond
to the ever-growing energy demand.
12.4.2.5 Solar Radiation as Information Source for Life on Earth
Biological systems collect, process, store, and send information to accomplish their functions of
surviving and reproducing. Information exists only in the presence of life forms (or devices, such
as robots, built by intelligent beings). In fact, the interactions between inanimate objects are driven
by force-fields. On the other hand, the interactions between biological systems are information-
based (Roederer 2003). 21 Aware of this fundamental difference, the sharp question about the origin of life on Earth can be re-formulated as it follows: “How was it possible that from an inanimate
world, devoid of agents able to process information, matter self-organized in forms able to make
decisions?” Life’s emergence appears as a phase transition, as a sudden change in how chemis-
try can process and use information and free energy (Cronin and Walker 2016). If we consider a
living being, there are three distinct types of natural (not man-made) information systems. First,
the Biomolecular Information Systems (BISs); second, the Immune Information System (IIS) and,
third, the Neural Information System (NIS). All unicellular organisms, plants, and fungi, devoid
of a nervous system, are driven by BISs22 and protected by IISs. On the other hand, every animal
(except for sponges) relies on BISs at the cellular level, on IISs for protection against pathogens,
and on NISs to make decisions as a whole.23 In a BIS (see Figure 12.12), the intelligence relies on three elements. First, the multiple sensory proteins that collect information. Second, the signaling
network, based on proteins, which transduce, amplify, and process the received data. Third, the epi-
genetic events, such as the activation and/or inhibition of the expression of specific genes in DNA,
which are the actuators. The output of computation might have repercussions in the metabolic net-
work of the cell. In an IIS, receptors of B-cells and T-cells bind to specific antigens (Ishida 2004).
Intra- and inter-lymphocytes have cooperative signaling events to induce the expression of antibod-
ies and killer T-cells that are the actuators to combat the infection. In a NIS (see Figure 12.12), there are sensory cells that collect and transduce physical and chemical messages; their content is sent to
the brain where the information is processed, and decisions are made. Such decisions are signals
sent to the effectors, i.e., muscles and glands.
All living beings, except those living permanently under the dark,24 exploit solar light for their spatial and temporal orientation. For example, plants, which are sessile organisms, have specialized
modules to sense their environmental light and adjust their form, orientation, metabolism, and flow-
ering. The phenomena of photomorphogenesis, phototropism, and photoperiodism optimize plants’
