Isolating water's impact on vibrations within DNA

http://phys.org/news/2015-12-isolating-impact-vibrations-dna.html

In a biological system, the ratio of water-to-non-water molecules, known as the hydration level, influences both the arrangement of biomolecules and the strength of the electric interactions that occur between biomolecules, free ions, and functional groups, which are groups of atoms within molecules that strongly influence the molecules' chemical properties. To isolate the contribution of water to the vibrational fluctuations that occur between DNA, bulk water, and the charged biomolecular interface between the two, researchers at the Max-Born Institute for Nonlinear Optics and Short Pulse Spectroscopy in Berlin have performed two-dimensional spectroscopic analyses on double-stranded DNA helices at different hydration levels.

The analysis gives insight into the way water and DNA interact, which could ultimately help scientists understand how biological systems function at the molecular level and what goes wrong when adverse conditions cause the systems to fail.

Two-dimensional infrared spectroscopy is a laser technique used to map correlated vibrations, the basic oscillatory motions of atoms, and their fluctuations into observable data.

The researchers used an amplified titanium-sapphire laser system to generate a sequence of four femtosecond infrared pulses in the low-frequency range that corresponds to the vibrational modes of DNA's sugar-phosphate backbones between 920 and 1120 cm-1. They found that the spectra give evidence of both ultrafast structural fluctuations and a broadening of vibrational transitions, which reflects the structural disorder and variation of hydrogen bonding at the DNA-water interface.

"We were looking for probes which are most sensitive to dynamics at the [DNA-water] interface and noninvasive, leaving the structure of the interface unchanged," said Thomas Elsaesser, director of the institute and a professor of experimental physics at Humboldt University of Berlin. "We concluded that [DNA] backbone modes would be interesting candidates, as their elongations are at the interface and they should be sensitive to local electric fields."

Elsaesser and his colleagues at the Max-Born Institute detail their investigations this week in Structural Dynamics.

Their current work builds on a seminal paper published in Nature in 2005 - with the collaboration of Dwayne Miller's group at the University of Toronto - which reported the first two-dimensional spectra of bulk water and established the basic time scales of the structural fluctuations that determine the lineshapes of vibrations.

For DNA, dehydration induces a transition from the traditional B-helix form to the A-helix form, the second most common shape. To determine the vibrational contribution of a system's hydration level, Elsaesser and his colleagues spectroscopically examined DNA strands at 0% humidity and 92% humidity, which correspond to around 2 and 20 water molecules per base pair, respectively.

By analyzing the two-dimensional spectral lineshapes, the researchers found that the hydrated DNA strands display structural fluctuations on a sub-picosecond time scale - less than a trillionth of a second - and that the structural disorder of local arrangements of water and DNA functional groups persists for time scales longer than 10 picoseconds, leaving water-DNA hydrogen bonds intact. Additionally, they found that although the arrangement of interfacial water molecules fluctuates at a slower rate compared to bulk water, it makes a substantial contribution to the sub-picosecond fluctuations, along with the low-frequency motions of the DNA helix.

They also noticed a pronounced coupling of the different, partly delocalized backbone modes. According to Elsaesser, this results in an energy transfer between the modes on a time scale of a few picoseconds.

Future work for Elsaesser and his colleagues includes extending their investigation toward longer natural DNA and RNA systems, such as DNA from salmon testes in a full water environment, as well as investigating the terahertz spectroscopy of low frequency motions and electric interactions.

 Explore further: Water molecules characterize the structure of DNA genetic material

More information: Biswajit Guchhait et al. Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy, Structural Dynamics (2016). DOI: 10.1063/1.4936567

Scientists create mini linac prototype, could alter radiation therapy

                               Terahertz accelerator modules easily fit into two fingers.
                                   Credit: DESY/Heiner Mueller-Elsner                                                                                  

by Lisa Chamoff 
http://www.dotmed.com/news/story/27370

A team of scientists has built a prototype for a miniature particle accelerator with a single module that is 1.5 centimeters long and 1 millimeter thick, which could enable new diagnostic imaging and radiation therapy techniques. 

The researchers, part of the Hamburg-based Center for Free-Electron Laser Science — a joint enterprise of DESY, the Max Planck Society and the University of Hamburg — presented the prototype in the journal Nature Communications. The prototype, which was set up in DESY scientist Franz Kärtner's lab at the Massachusetts Institute of Technology (MIT), uses terahertz radiation instead of radio frequency structures, which the scientists say has the potential to miniaturize the entire accelerator by at least a factor of 100. 

“The compact accelerator we are building enables the construction of very bright and potentially fully coherent X-ray sources, which enable also new medical diagnostic imaging techniques, like phase contrast imaging and potentially also new radiation therapy techniques like image-guided small tumor radiation therapy and micro-beam radiation therapy or brain tumors,” Kärtner, a professor at the University of Hamburg and at MIT, as well a member of the Hamburg Centre for Ultrafast Imaging, told HCB News. “Currently, high brightness X-ray beams are only available from large synchrotron or free-electron laser facilities, which is not practical for health care. A compact highly coherent X-ray source would address this shortcoming.” 

For the prototype, the physicists used a type of electron gun to fire fast electrons into an accelerator module that was tailored to be used with terahertz radiation, which was fed into the module, further accelerating the electrons. The prototype was able to increase the energy of the particles by 7 kiloelectronvolts, according to the scientists. While not a particularly large acceleration, the experiment demonstrated that the principle works in practice, said co-author Arya Fallahi of CFEL in a press release. 

"The theory indicates that we should be able to achieve an accelerating gradient of up to one gigavolt per meter,” Fallahi said in the release. This is more than 10 times what can be achieved with the top conventional accelerator modules currently available, the scientists said. Plasma accelerators could product higher accelerations, but the scientists said this experimental technology requires much more powerful lasers than the ones needed for terahertz accelerators. 

Recently, scientists from the European Organization for Nuclear Research (CERN) built a miniature linear accelerator made up of four modules that are each roughly 20 inches long, for a total size of a little more than 6.5 feet. They doubled the operating frequency used for the radiofrequency quadrupole (RFQ), a linear accelerator component used in the acceleration of low-velocity ion beams. 

Kärtner said his group’s prototype works at an even higher frequency, roughly 100 times the usual frequency of 1.3 gigahertz, and generates electrons, which Kärtner said is good for making accelerator-driven X-ray sources. 

The scientists are looking to make a 20 mega-electronvolt accelerator within the next three to four years, Kärtner said.

Team shrinks particle accelerator: Prototype demonstrates feasibility of building terahertz accelerators

http://phys.org/news/2015-10-team-particle-prototype-feasibility-terahertz.html

An interdisciplinary team of researchers has built the first prototype of a miniature particle accelerator that uses terahertz radiation instead of radio frequency structures. A single accelerator module is just 1.5 centimetres long and one millimetre thick. The terahertz technology holds the promise of miniaturising the entire set-up by at least a factor of 100, as the scientists surrounding DESY's Franz Kärtner from the Center for Free-Electron Laser Science (CFEL) point out. They are presenting their prototype, that was set up in Kärtner's lab at the Massachusetts Institute of Technology (MIT) in the U.S., in the journal Nature Communications. The authors see numerous applications for terahertz accelerators, in materials science, medicine and particle physics, as well as in building X-ray lasers. CFEL is a cooperation between DESY, the University of Hamburg and the Max Planck Society.

In the electromagnetic spectrum, terahertz radiation lies between infrared radiation and microwaves. Particle accelerators usually rely on electromagnetic radiation from the radio frequency range; DESY's particle accelerator PETRA III, for example, uses a frequency of around 500 megahertz. The wavelength of the terahertz radiation used in this experiment is around one thousand times shorter. "The advantage is that everything else can be a thousand times smaller too," explains Kärtner, who is also a professor at the University of Hamburg and at MIT, as well as being a member of the Hamburg Centre for Ultrafast Imaging (CUI), one of Germany's Clusters of Excellence.

For their prototype the scientists used a special microstructured accelerator module, specifically tailored to be used with terahertz radiation. The physicists fired fast electrons into the miniature accelerator module using a type of electron gun provided by the group of CFEL Professor Dwayne Miller, Director at the Max Planck Institute for the Structure and Dynamics of Matter and also a member of CUI. The electrons were then further accelerated by the terahertz radiation fed into the module. This first prototype of a terahertz accelerator was able to increase the energy of the particles by seven kiloelectronvolts (keV).

"This is not a particularly large acceleration, but the experiment demonstrates that the principle does work in practice," explains co-author Arya Fallahi of CFEL, who did the theoretical calculations. "The theory indicates that we should be able to achieve an accelerating gradient of up to one gigavolt per metre." This is more than ten times what can be achieved with the best conventional accelerator modules available today. Plasma accelerator technology, which is also at an experimental stage right now, promises to produce even higher accelerations, however it also requires significantly more powerful lasers than those needed for terahertz accelerators.

The physicists underline that terahertz technology is of great interest both with regard to future linear accelerators for use in particle physics, and as a means of building compact X-ray lasers and electron sources for use in materials research, as well as medical applications using X-rays and electron radiation. "The rapid advances we are seeing in terahertz generation with optical methods will enable the future development of terahertz accelerators for these applications," says first author Emilio Nanni of MIT. Over the coming years, the CFEL team in Hamburg plans to build a compact, experimental free-electron X-ray laser (XFEL) on a laboratory scale using terahertz technology. This project is supported by a Synergy Grant of the European Research Council.