Stanford’s Linac X-Rays capture Molecular Matter in Motion

A computer simulation of the LCLS Linac Injection Model showing molecular matter in motion.Super Fast, Super Bright…

Take one second and divide it a million times.  Then, take one millionth of that second and divide it again… by a billion!  All you’re left with is a femtosecond.  That’s how fast the Linac laser at Palo Alto can deliver burst of X-rays and track chemical reactions in living systems… as they happen.

For nearly 50 years, SLAC – Stanford Linear Accelerator Center – National Accelerator Laboratory‘s Linac has produced high-energy electrons for cutting-edge physics experiments.  Now, scientists continue this tradition of discovery by using the Linac to drive a new kind of laser, creating X-ray pulses of unprecedented brilliance.


X-Rays and Synchrotron Light Sources


Discovered in 1895 by German physicist Wilhelm Conrad Röntgen, X-rays are a high-energy, short-wavelength form of light that is invisible to the eye.  X-ray wavelengths are several thousand times shorter than those of visible light, and are comparable to the dimensions of atoms.


A diagram showing the whole electromagnetic spectrum, and highlighting the specific wavelengths corresponding to Xrays - 10^-10 metres.


The tiny wavelength of X-rays is ranging from 0.01-10 nanometres.

(1 nm = 1 nanometre 10-9 metre = 1000 picometres = 10 angstroms…)


Basically, this puts the Röntgen radiation wavelength on a par with the size of atoms.

X-rays with photon energies above 5-10 keV (i.e. below 0.2-0.1 nm in wavelength) are called hard X-rays – while those with lower energy are called soft X-rays.  Due to the penetrating ability of hard X-rays, they are widely used to image the inside of objects.

A photograph showing a surgeon, wearing scrubs and surgical mask, who is looking closely at a chest Xray.
Medical doctor looking at X-ray picture of lungs

X-rays can penetrate through many materials that visible light cannot.  Since their initial discovery, X-rays have been used in medicine and dentistry to reveal bones and dense tissues.  X-ray scanners are notably involved in airport security systems.  X-rays are also being used in the laboratory to study atomic structures.

A photograph showing the airport-style security Xray of a suspicious luggage.
Inside a suspect suitcase…  The key is in the density: – Blue colours equal hard materials.  Metal (blue/black), hard plastics, alloys etc.  A gun or metal knife will show up as blue-black mix.  So will wires in a sunglass case, batteries, etc. – Orange colours show biological/organic material.  Anything that is natural, and some things that are not.  Cotton, silk, rubber, leather and food, dynamite and other explosives (except plastique – that turns slightly blue-ish).  All liquids, gels and organic powders (like flour).  – Green colours are for plastics and alloys, where the density is not great enough to make it blue or black. This can also be ceramics, although only the densest types. Normally, ceramics (ceramic knives) will show up as orange.

Synchrotron light-source facilities are special types of cyclic particle accelerators, in which the guiding magnetic field (bending the particle trajectory into a closed path) is time-dependent, being synchronized to a particle beam of increasing kinetic energy.  Synchrotrons produce X-rays that are millions of times brighter than medical X-rays. 

Scientists use these highly focused, intense beams of X-rays to reveal the identity and arrangement of atoms in a wide range of materials.

X-rays can be used to resolve the arrangement of atoms in metals, semi-conductors, ceramics, polymers, catalysts, plastics, and biological molecules. 

However, atoms are constantly moving or vibrating, and synchrotron X-ray sources produce long pulses which yield only blurred images of these motions.


LCLS produces pulses of X-rays more than a billion times brighter than the most powerful existing sources, the so-called synchrotron sources which are also based on large electron accelerators.


LCLS – Linac Coherent Light Source

An aerial view of the site of the Stanford linear accelerator.SLAC’s two-mile-long linear accelerator (or linac) begun a new phase of its career, when the Linac Coherent Light Source (LCLS) began operating.  The first X-ray pulses streamed through the machine in April 2009. 

SLAC’s scientific mission has diversified since its creation, from an original focus on particle physics and accelerator science to include cosmology, materials and environmental sciences, biology, chemistry and alternative energy research.  Some of the first LCLS experiments imaged parts of the photosynthetic system found in plants.  Understanding how nature converts sunlight to energy could lead to the technology we need to ensure safe and efficient power generation for the future.  Other experiments have revealed the first images of an intact virus in its natural state as well as the 3-D structure of proteins that generate energy for life and play key roles in disease.

A computer model of the 3D X-ray structure of matter, as seen by the SLCS Linac.
A three-dimensional rendering of X-ray data obtained from over 15,000 single nanocrystal diffraction snapshots recorded at the Linac Coherent Light Source, the world’s first hard X-ray free-electron laser, located at SLAC National Accelerator Laboratory.  The 3-D structure of proteins – in this case Photosystem I, the biological factory in plant cells that converts sunlight to energy during photosynthesis – can be determined from these diffraction patterns.  Each nanocrystal was destroyed by the intense X-ray pulse, but not before information about its structure was revealed. Credit: Thomas White (DESY)

Transforming SLAC’s venerable linear accelerator into a next-generation X-ray light source has benefited from the efforts of hundreds of scientists from all over the world. The LCLS project is a collaboration among Department of Energy laboratories including SLAC, Argonne, Brookhaven, Los Alamos and Lawrence Livermore national laboratories, and the University of California, Los Angeles.

The Linac Coherent Light Source is now being used to see how atoms and molecules move in living systems.

Each X-ray pulse has as much power as the national grid of a large country, and a hundred are produced every second.

Researchers at Palo Alto in the state of California, U.S. have developed the most powerful X-ray laser in the World – a billion times brighter than the previous generation of lasers.

An aerial view with superimposed diagram, of the Stanford Linear Accelerator site.

Scientists flock to use lab facilities for an even broader spectrum of experiments, from archaeology to drug development, industrial applications and even the analysis of dinosaur fossils and art objects.  Much of this diversity in World-class experiments is based on continuing modernizations at Stanford Synchrotron Radiation Lightsource (SSRL) and the unique capabilities of LCLS.

The laser was developed at the SLAC National Accelerator Laboratory.  Its systems were adapted from a particle collider.

But instead of smashing atoms, it enables researchers to see what is going on in living systems and to track chemical reactions, literally as they happen.

The researchers at the LCLS explore extraordinary possibilities.  The short-time structure of the source permits a range of novel time-dependent experiments in which femtosecond spectroscopy can be combined with very fast structural studies (e.g. femtochemistry).

While certain key reactions in life are photochemical, most enzymes participate in diffusion-dominated processes with their reactants and partners.  Time-resolved structural studies on diffusive processes in crystalline enzymes are difficult due to problems with mixing enzyme and reactant in the crystal.  With submicron-sized samples, the vast majority of solution techniques and methodologies will suddenly become available for time-resolved structural investigations at the LCLS.

X-ray diffraction tomography will be performed with the unfocused LCLS beam on whole cells at “intermediate” resolutions.  With non-reproducible structures (e.g. living cells) or with reproducible but small structures (e.g., single protein molecules), higher resolutions could only be reached with a focused beam and with shorter pulses than the pulses planned initially at the LCLS.



Super Powerful and Super Fast… 

The LCLS is the first source to produce X-rays that are both very intense and clumped into ultrafast pulses.

Thus, ultra-short and high-intensity x-ray pulses from the LCLS, in combination with novel container-free nanoscale sample handling methods, open up amazing new possibilities for structural determinations with X-rays and may lead eventually to high-resolution experiments on non-repetitive and non-reproducible structures like cells.


Muybridge’s Stereoscopic Horse in Motion


What’s with the horse you may ask…?

In 1878, Eadweard Muybridge used a series of 12 stereoscopic cameras spaced at 21-inch intervals over 20 feet to capture a single horse stride, taking pictures at one thousandth of a second.  These pictures (animated here), taken on what is now the Stanford University campus, resolved a hotly debated topic of the day: whether all four of a horse’s hooves left the ground at the same time during a gallop.



The Palo Alto LCLS’ femtosecond camera uses a similar technique.

The LCLS fires extremely fast bursts of X-rays.

A table indicating the subdivision units of a second: the millisecond $ ($time for a housefly's wing flap$ )$, the microsecond $ ($length of time of a high-speed, strobe light flash$ )$, the nanosecond $ ($time for molecules to fluoresce$ )$, the picosecond $ ($switching time of the world's fastest transistor$ )$, the femtosecond $ ($pulse width on world's fastest lasers$ )$ and the attosecond $ ($shortest time now measurable by scientists$ )$.Of course, X-ray sources of different scales have been used before.  But this takes even faster snapshots of chemical reactions and the processes of life…

  1. Take 1 second  and divide it a million times 1 s / 106 = 10-6 s.
  2. Then take one of these divisions and divide it a billion times = 10-6 s / 109 = 10-15 s.


What you’re left with is a femtosecond 10-15 s.

That’s exactly how fast the bursts of X-rays are.


The Mechanisms of Life at Unprecedented Speed 

The laser uses hard X-rays, 109 times the relative brightness of traditional synchrotron sources and is the most powerful X-ray source in the World.  LCLS enables a variety of new experiments and provides enhancements for existing experimental methods. 

As atoms are constantly moving or vibrating, and synchrotron X-ray sources produce long pulses which yield only blurred images of these motions.  Often, X-rays are used to take “snapshots” of objects on the nearly atomic level before obliterating samples.

An animation showing the scattering of Cyanobacteria seen using conventional X-ray tools compared to LCLS technique.The laser’s wavelength in LCLS is similar in width to that of an atom, providing extremely detailed images for objects previously unattainable.  Additionally, the laser is capable of capturing images with a shutter speed measured in femtoseconds, or million-billionths of a second, necessary because the intensity of the beam is often high enough so that the sample explodes on the femtosecond timescale.


A Femto-Camera for Molecular Movies

By sequencing together images of the ultra-small, taken with the ultra-fast pulses of the LCLS, scientists are for the first time creating molecular movies, revealing the frenetic action of the atomic world for us to see.

Understanding the precise dynamics at work on these scales will forever change our understanding of chemistry, physics and materials science.



For the first time, we can now look deep inside an atom on the space scale and the time scale at which chemistry and biology processes really happen.

This technology transforms our ability to view the real World.


Branching Out…

The ground-breaking speed with which the Linac can fire bursts of energy opens a new “never seen” regime of making science with the LCLS, where only predictions and simulations exist today.  A chemist’s dream, in other words!

The LCLS has been so successful that the Japanese government has built a similar system. Europe is constructing its own version in Hamburg, Germany.