Synchrotrons lighting life

Caterina Biscari


Synchrotron radiation produced by electrons in particle accelerators is a powerful instrument for investigating properties of matter from biological samples to material science ones. It extends from infrared to X-rays of energies above 100 keVs. The excellent energy definition, together with the high fluxes, the properties of spatial and temporal coherence, the variable polarization, opens the utilization of the photon sources to multiple applications. Among the users of the synchrotron light infrastructures stand communities of life science, pharmacology, materials science, cultural heritage, environment, production and conservation of energy. A constant evolution of the photon sources, of the detection techniques and of the analysis of the light interaction with materials, puts this area at the frontier of knowledge. Many synchrotron light sources are around the world, and new facilities are being built, also in countries which are betting on their future evolution starting with such a flexible and wide-range instrument. One of these projects, SESAME in Jordan, is on top of that also an instrument of peace. Under the UNESCO umbrella several countries in the Middle East are collaborating through their scientific representatives in the construction of a common infrastructure. It has already become, even before its operation, a common field for exchanging science, technological advances and people aiming at the progress of life.

1 Introduction

Erwin Schrödinger published in 1944 the book “What is life?”(see fig. 1) whose main subject is how physics and chemistry can explain life mechanisms, introducing the idea of the genetic information contained in crystals. Lawrence and William Bragg had already explained in 1913 how crystals can reveal their structures through the diffraction patterns, and this was the method used by Rosalind Franklin in her research on DNA. The first image was obtained in 1952, the famous Photo 51 reported in fig. 2. Watson, Crick and Wilkins developed from there the chemical model of the DNA. They were awarded the Nobel Prize in 1962, four years after Franklin’s death.
Decades of development in the production and utilization of X-rays have given scientists the capacity of obtaining from a diffraction pattern the precise information of the position of the tens of thousands of the atoms which form a protein, like in fig. 3, which represents the result from an experiment carried out at the XALOC Beamline at ALBA [1], showing the DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factor.
Synchrotron radiation was detected for the first time in 1946 at General Electric, USA, when the light emitted by the 70 MeV electron beam stored in the second synchrotron ever built (from there its name) was seen. In fact the phenomenon was already predicted, as can be deduced from Maxwell equations, but the frequency range of the emitted radiation was not yet clear. The fact that it included visible light was a surprise, and at a first glance the light was confused with a discharge in the vacuum chamber. It took some time to determine that its origin were the electrons travelling in the synchrotron.
For the lepton storage rings dedicated to High Energy Physics (HEP) the synchrotron light has been a characteristic to fight, since it implies unwanted loss of energy which must be compensated by RF power. The energy emitted per turn by a particle is proportional to the magnetic field of the bending magnets and to the fourth power of the electron energy. This is the reason of the need of increasing circumferences of HEP colliders by lowering the bending magnetic field. LEP is the largest and last example, as predecessor of LHC in the 27 km tunnel under the Genève region.
On the other hand, the synchrotron light is a wonderful instrument for a wide range of scientific communities, who profits from its extraordinary resolving power in investigating the matter down to atomic dimensions.
Researchers from the academic world, universities, research institutions, and researchers from those private companies who invest in innovation are the users of the light sources.

2 Synchrotron radiation facilities

Once the synchrotron radiation was detected and its potential understood, the path towards what today represents the instrument for thousands of scientists was drawn. Synchrotron radiation facilities begun to appear in the most advanced laboratories already in the seventies. The evolution of these facilities is usually schematized into generations, being the photon beam brilliance the parameter which marks their difference. The brilliance Bγ is the number of photons per time and phase space unit and energy bandwidth, which reflects the sharpness of the photon probe to interact with the matter:

$B_{\gamma} = \frac{N_{\gamma}}{4 \pi^{2}(\Delta\lambda/\lambda) \Delta t \Sigma_{x}\Sigma_{x'}\Sigma_{y}\Sigma_{y'}}$

where Nγ is the number of photons, and in the denominator the wavelength resolution Δλ/λ, the pulse length Δt and the transverse phase space size (Σx Σx’ Σy Σy’) appear. The first generation, developed in the seventies, corresponds to the HEP rings used parasitically for X-ray production. In the eighties the second generation appeared with dedicated rings, followed in the nineties by the third generation based on rings with lower emittance and filled with insertion devices, these last producing special modulated magnetic fields where emission is enhanced. A debate on which is the fourth generation is in course: the Diffraction-Limited Storage Rings, whose first example, MAX IV in Lund, is nowadays in commissioning, and the Free Electron Lasers (FELs) driven by linear accelerators and providing photons since the beginning of the century, are both step forwards in the quest for higher brilliance. FELs are not the subject of this review, but it must be mentioned that synergies and complementarities are copious between the two communities.
Figure 4 shows the spectacular increase of the brilliance of X-ray sources since the appearance of X-ray tubes at the end of the nineteenth century.
When a charged-particle beam travels in the magnetic field its trajectory is bent and emits photons covering a wide range of frequencies. The synchrotron radiation is emitted in a continuous spectrum, from infrared to hard X-rays up to 100 keV, depending on the electron energy, magnetic field strength and structure. Synchrotron light emitted in accelerators is distinguished by the high brilliance of the source due to small cross section of the electron beam and high degree of collimation of the radiation, the high degree of polarization which can be tuned by variable-orientation magnetic fields and the pulsed time structure defined by the electron bunches frequency and length.
In the world there are presently about fifty synchrotron light sources in operation, half of them belonging to the third generation. They can also be classified according to the electron beam energy: the low-energy ones, about five sources in the world with beam energy between 1.5 and 2 GeV, the medium energy which represents the great majority (energies between 2.5 and 3 GeV) and few highenergy ones, two in Europe, one in Asia and another one in the United States, from 6 to 8 GeV. Another set of sources is in construction or already in the commissioning phase. Figure 5 summarizes the present panorama of the light sources, as obtained from the information extracted from www.lightsources.org (the figure does not claim to be fully exhaustive or completely updated). The heart of the light source is the accelerator, with an injector which produces and accelerates the electron beam, injecting it into the storage ring. Here, beam ports around the circumference are open to receive the light which is then redirected towards several beamlines, each of them dedicated to a special technique and focused on specific scientific communities.
The photon sources in a dedicated synchrotron are of three different types: dipoles, wigglers and undulators. The vertical fields of the dipoles are used to bend the electron beam and make it follow the nominal orbit inside the vacuum chamber. The bendings are part of the so-called lattice which defines the electron beam size.
The spectrum of the emitted photon is centered on the critical energy, which is given by

$E_{crit} [keV] = 0.665 E^{2} [GeV]B[T]$

where E is the electron energy and B the magnetic field strength. The total power is emitted fifty per cent with energies above the critical one, the other fifty below. The lowest frequency is the revolution one, of the order of the MHz, the highest of the order of ten times the critical frequency, which is related to Ecrit by

$\omega_{crit} = \frac{E_{crit}}{\hbar}$

or written in terms of the bending radius and of the relativistic gamma of the electrons:

$\omega_{crit} =\frac{3}{2} \frac{c}{\rho} \gamma^{3}$

Dipoles are normal-conducting electromagnets, with magnetic fields in the range 1–1.6 T. The critical energy is therefore usually few keV for the medium energy synchrotrons, reaching therefore the range of hard X-rays. Figure 6 shows the emitted spectra of the phase-I ALBA beamlines.
The power emitted per turn is much higher for light particles and strongly depending on the energy of the emitting particles. For the same kinetic energy electrons emit much more power than protons and therefore all synchrotron light sources use the electrons as emitting particles. As an example the energy emitted per turn by synchrotron radiation by the 3 GeV electrons in Alba (~1 MeV) is about three orders of magnitude larger than the one emitted by protons in LHC, at the present energy of 6.5 TeV. The photon beam has an opening angle which decreases with the electron energy E:

$ \theta [rad] = \frac{1}{\gamma} = \frac{0.51}{E[MeV]}$

The light is polarized in the orbital plane and maintains the same temporal structure of the electron beam.
The two types of insertion devices which appeared in the third light sources generation to enhance and tune the radiation are wigglers and undulators. They are magnetic structures with longitudinally alternating magnetic fields, where electrons follow sinusoidal trajectories and emit in each one of the insertion poles. The characteristic parameter of an insertion device is K:

$ K = \frac{eB_{0}\lambda_{ID}}{2\pi m_{b}c} $

where B0 is the peak field at the pole center and λID is the pole length.
When K is larger than 1, the device is a wiggler. The total power adds incoherently and the critical frequency has the same expression of the dipolar case.
When K is smaller due to the short period, the insertion device is considered an undulator. In this case the radiation adds up to a large extent coherently, and is highly enhanced at a specified frequency and its harmonics which reflect the natural periodicity of the undulator:

$ \lambda_{n} = \frac{\lambda_{\nu}}{2n\gamma^{2}}( 1+ \frac{K^{2}}{2}) \approx \frac{\lambda_{\nu}}{n\gamma^{2}}$

The bandwidth is

$ \frac{\Delta \omega}{\omega} = \frac{1}{2N_{\nu}} $

The photon beam parameters are strongly related to the electron beam producing them. The newest generation of synchrotrons is advancing in the production of always brighter photon beams by lowering the electron beam phase space size, its emittance.
The emittance of the electrons in a storage ring is the result of the equilibrium between two opposite phenomena. One is the damping due to the effect of the RF cavity which tends to damp the oscillations of the particles around the nominal orbit, and the other is the excitation of transverse oscillations associated to the photon emission when passing through a magnetic field. The shorter are the dipoles, the lower the magnetic field, the weaker the noise effect and the smaller the total emittance of the beam. The easiest way for decreasing the emittance is increasing the number of dipoles i.e., lengthen the circumference, which means increasing the total cost of the infrastructure, strongly dependent on the storage ring size. An example of this strategy is the latest light source come into operation in 2014, NSLS-II. With its 620 m circumference has an emittance a factor of four smaller than ALBA, whose circumference is 270 m.
Decreasing further the emittance is what will happen soon, in the so-called Ultimate Storage Rings or Diffraction-Limited Storage Rings. A light source is referred to as “diffraction limited” when the electron beam emittance is less than that of the radiated photon beam at the desired X-ray wavelength:

$ \epsilon (photon) \le \frac{\lambda}{4 \pi} = 0.159 \lambda = 98.66 [pm \ rad] E_{\gamma} [keV] $

A combination of new magnet designs in the Multi Bend Achromats schemes, advanced vacuum technology, precise simulation codes which use genetic algorithms for optimizing the full design of the accelerator, high-resolution diagnostic, powerful feedback systems fighting against instabilities and vibrations, are squeezing the electron bunches to dimensions never reached before in circular accelerators. MAX-IV (www.maxlab.lu.se/maxiv) is the first Diffraction- Limited Storage Ring, now in commissioning, which has been built following the visionaries ideas of Mikael Eriksson. Its example is being followed by the new projects now in construction like Sirius in Brazil, or Solaris in Poland. Some of the synchrotrons which have been in operation since the nineties are also moving toward the diffraction limit by realizing or planning upgrades. ESRF (www.esrf.eu), the European synchrotron sited at Grenoble, will be shut down during 2019–2020 for the installation of new magnets and vacuum chambers in the ring, maintaining its circumference and its beamlines. At the startup these beamlines will receive much brighter photon beams, opening fields not available nowadays and possibly not even thought up to now.

3 Synchrotron light use

The beamlines around the synchrotron storage rings are specialized laboratories where different techniques of detection and data analysis can be used according to the phenomenon of interaction between the light and the matter for which they have been designed. The products of the interaction carry information on the matter structure and composition. Hundreds of beamlines around the world are being visited by thousands of users, who light up their samples, characterize them and contribute to key advances in life, material, environmental, food, energy, and cultural heritage sciences.
The white beam produced by the electrons encounters, still inside the ring tunnel, the front-end, a series of elements which define the beam aperture, block part of the radiation which will not be used in the specific beamline, and measure the photon beam position. The beam then enters the optical hutch, where monochromators are able to select with high resolution the wavelength needed for the experiment. These are systems mainly based on high reflectivity mirrors and crystals, and make extensive use of the radiation diffraction. We can group the characterization techniques in three large categories: elastic scattering, spectroscopy and imaging methods. Each one of them includes a set of techniques, sometimes available at the same beamline as complementary procedures. Figure 7 shows a simplified scheme of the usual available techniques in a synchrotron light source.
Beamlines based on scattering extract information on the inner structure of the matter thanks to its deviating capacity on the incident photons. Bragg law, in its simplicity, is the bone of the diffraction based techniques: given a structure where successive atomic layers are separated by a distance d, and an incident photon beam with wavelength λ at an angle θ, there will be constructive interference if the following relationship is satisfied:

$ 2d \ sin\theta = n\lambda $

where n is an integer number.
Diffraction patterns obtained illuminating crystals by synchrotron radiation are one of the most powerful tools in understanding basic properties of proteins. In the last twenty years more than 80000 protein structures have been deposited in the PDB (Protein Data Bank) database, resolved in the 130 beamlines which are operating around the world, with an ever increasing trend, as shown in fig. 8. Some of these have been the instrument of Nobel Prize winners, as for example the Chemistry Prizes granted in 1997 to Boyer and Walker, in 2003 to Agre and MacKinnon, in 2006 to Kornberg, in 2009 to Ada Yonath, together with Venkatraman Ramakrishnan, Thomas A. Steitz, for their studies of the structure and function of the ribosome and lately in 2012 to Lefkowitz and Kobilka or the Medicine Prize in 2013 to Rothman, Schekman and Südhof.
The extensive use of protein crystallography in the pharmaceutical industry can be summarized quoting Peter Doherty, Nobel Prize of Medicine “Synchrotron light is presently fundamental for 80% of research and development of drugs”.
Diffraction is also employed to investigate samples which are not single crystals. An example is the powder diffraction, widely used in environmental sciences, metallurgy, archaeology, pharmaceutical sciences, mineralogy, and condensed-matter physics. High pressure and high temperatures are often available in powder diffraction beamlines, to submit samples to extreme conditions, mimicking environmental or special situations. The noncrystalline diffraction is applied to the study of large molecular assemblies like polymers, colloids, proteins and fibers in SAXs or WAXs (Small or Wide Angle X-ray Scattering) specialized beamlines.
The capacity of absorption, transmission, reflectivity, etc. of the sample as a function of the photon energy is the basis of Spectroscopy methods, related to the capacity of valence and core electrons to absorb or release energy. This energy is a well-known characteristic of each atom, as well as the different possible phenomena (photoelectron emission, Auger electron emission, fluorescence ...). By tuning the incident photon energy and detecting the information of the absorption or of the information on the resulting emission of photons or electrons, the composition and chemical status of the sample are beautifully determined.
A good energy resolution of the photon beam enhances the capability of obtaining clean spectra and of disclosing characteristics otherwise masked by the spectral blurring.
Energy scanning methods can be based on the source modification or on the photon beam manipulation, or on combination of both. Figure 9 shows an example of a XANES the K shell of iron containing samples (left panel) and the Fourier transform of an EXAFS (Extended X-Ray Absorption Fine Structure) spectrum revealing the distances between the absorbing Fe atoms and their neighbors (right panel) obtained at the ALBA CLÆSS beamline for an experiment devoted to study catalyst for cleaner oil production.
Absorption spectroscopy is often used in cultural heritage to determine the composition of art works, to help in the process of their conservation, restoring and identification. Imaging methods are based on the differential absorption of X-rays by materials of different nature and electron densities. The transmitted X-rays across an heterogeneous sample allow to map its morphology or internal structure.
Radiographies, 3D reconstructions, computer-assisted tomographies, are all expression of the possibilities of using the light to see the details which are under the surface of matter and not visible to our eyes, with the power of transforming opaque sample in transparent ones.
It is possible to visualize the inner structure of a cell, like in the example shown in fig. 10, referred to the study on hepatocytes at the ALBA MISTRAL beamline, the soft X-rays microscope. By a precise selection of the photon energy, water may become transparent to X- rays and carbon atoms opaque. Cryo nano-tomography in water window and multikeV spectral regions are available at MISTRAL.
As the penetration for the X rays is of several micrometers which is comparable to the thickness of the cells, these may be imaged intact without sectioning as it is always done in electron microscopy due to the much shorter penetration of the electrons.
The beamline is also used in material science for viewing the orientation of magnetic domains in the buried layers of magnetic materials.
Hard X-rays imaging beamlines, as those present at ESRF in Grenoble or SLS in VIllingen, are being used to reconstruct large samples in non-invasive way. The experiment being carried out at ESRF, to read the Hercolaneum Papiri is one example. Over 1800 papyri, containing a full library, were completely covered by the Vesuvius eruption in AD 79 which destroyed Pompei and Hercolaneum. It represents the only surviving library from antiquity, and the writings in the papyri are books otherwise lost in the history of the literature and of the philosophy. Trials to read the papyri have been done since their discovery in the eighteen century, but the carbonization status has always prevented the possibility of opening them in a noninvasive way. At ESRF a group is using hard X-rays which cross the papyrus, being able to detect the micro difference in width in each layer of the roll due to the presence of the ink used to write. Precise reconstruction methods, assisted by powerful computers, are able to transform a black scroll in words which come to us from two thousand years ago.
Figure 11 shows some of the reconstructed words. A long way is in front of the team in order to be able to read the scrolls, but these have waited two thousand years to be unveiled and are not in a hurry to reveal their secrets.

4 Light for peace

The need of a synchrotron light source in the Middle East was obvious already in the eighties, and now the dream has become a reality. Not giving credit to all the people who have participated to the birth of SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East, [6] ) let me mention the Nobel Laureate Abdus Salam, Gustaf-Adolf Voss from DESY, Herman Winick of SLAC, Herwig Schopper from CERN, actively pursuing the project.
Following the model of CERN birth, when European scientists joined to work together and reconstruct the link among the countries badly ruined by the war using science as a common language, in 2004 SESAME was funded under the UNESCO umbrella, to be hosted in Jordan. Today nine countries are SESAME members (Bahrain, Cyprus, Egypt, Iran, Israel, Jordan, Pakistan, the Palestinian Authority, and Turkey), and sixteen observers (Brazil, China, the European Union, France, Germany, Greece, Italy, Japan, Kuwait, Portugal, Russian Federation, Spain, Sweden, Switzerland, the United Kingdom, and the United States of America) complete the group which is actively working for science and peace.
The project has slowly come into shape, navigating through the unavoidable social and political difficulties.
SESAME is one of the third-generation light sources. With a circumference of 133 m, its 2.5 GeV electron beam can deliver photons to several beamlines of which two are being built and five more have been defined. The first beamlines to come into operation will be dedicated to Infrared Microscopy and XAFS Spectroscopy. The building and infrastructures are completed; the injector system is already commissioned, and represents the first ever working accelerator in the Middle East. The installation of the storage ring is in progress and the first beam is expected in one year.
The team working on the site is diverse and gathers scientists, engineers and technicians from the member countries, together with few well experienced experts from Europe who are leading the project. The European Commission has funded a project, CESSAMag, which has been led by CERN, for the production of the synchrotron magnets and to which ALBA has participated measuring all dipoles of the storage ring. Figure 12 shows the first arc just installed in the storage ring tunnel. The project has been a great success and has boosted the construction of all systems, also calling on board several research institutions now committed to continue the collaboration with SESAME and train its staff.
SESAME is the result of hard work and determination on the part of Governments in the Middle East and neighboring countries, but also that of Governments of the Observer countries of the Centre and scientists at large. It is also the result of goodwill and generosity on the part of international organizations and synchrotron radiation sources worldwide. The impact of a light source in developing countries is worldly accepted as an extremely powerful tool for the transformation into advanced societies. In Africa a group of scientists from several countries is now leading the proposal for a future AFrican Light Source (AFLS), with the aim that African countries take control of their destinies and become major players in the international community, promoting peace and collaborations among African nations and the wider global community. A workshop in Grenoble, which took place in November 2015, was the starting point for the future African project, with the outcome of the so-called “Grenoble Resolutions”. A roadmap has also been depicted, with three different goals: a short-term one, for the next three years, to build up awareness of the benefits of lightsource– based research, promoting education, mobility and access to current light sources, to develop a Strategic Plan for submission to African Ministries, and to study the feasibility of constructing African multinational beamlines at existing Light Sources, then a medium term one for the next five years aiming at a feasibility study and a governance model definition, and finally a long-term one for a Conceptual Design Report to be ready after five years.
The Grenoble workshop was attended by representatives from the different light sources and several African scientists representing the backbone of the future source.

5 Conclusions

Summarizing, synchrotron radiation considered initially as a side effect by accelerator physicists has become a largely developed tool across our planet to study the structure of matter in its different forms, dimensions and length scales, including the dynamical evolution of material systems to its fantastic temporal structure.
Each large infrastructures centered on a synchrotron represents not only scientific progress, but also technical development, industrial evolution, social and economic impact, training center for young people and above all a world of collaboration among diverse communities.

Acknowledgments

Let me thank the organizers of the Light & Life Conference at Varenna, for the opportunity of participating to the enlightening event, and my colleagues Salvador Ferrer and Ramon Pascual for their comments on the manuscript.