EPJ D Highlight - Folding biomolecule model shows how form dictates function
- Published on 25 August 2017
New theoretical calculations of the conformation of very large biomolecules helps in understanding interactions with DNA strands as part of biological functions
Proteins are fundamental macromolecules for life, with a diversity of functions, like acting as channels through cellular walls, catalysers, DNA benders, etc. When it comes to these functions, what matters is the layout of the secondary branches, made up of each protein’s amino acids, such as alanine, glutamine, arginine, phenylalanine and tyrosine. These are stabilised mainly by weak interactions-- such as hydrogen bonds, intramolecular interactions, and inter molecular dispersive forces, -- between the backbone and the lateral chain of their amino acids. In a new study published in EPJ D, Jorge González from the University of the Basque Country, in Leioa, Spain and colleagues have developed a theoretical method to calculate the most stable disposition that biomolecules try to adopt when they are together, or in close contact in cases where the bonding is weak. They also demonstrate that their model is consistent with our understanding of the same systems gained from experiments, such as spectroscopic analysis.
New Editor-in-Chief for EPJD – Prof Tommaso Calarco
- Published on 25 July 2017
The publishers of European Physical Journal D: Atomic, Molecular, Optical and Plasma Physics are delighted to announce the appointment of a new Editor-in-Chief, Professor Tommaso Calarco of the University of Ulm, Germany.
As Director of the Institute for Complex Quantum Systems and of the Centre for Integrated Quantum Science and Technology at Ulm, Prof Calarco’s research interests cover a broad range of topics in quantum and atom optics, quantum control and quantum information, and he is a member of the High-Level Steering Committee for the Quantum Flagship of the EC.
Prof Calarco has recently joined the Editorial Board for EPJD, and will take on the Editor-in-Chief role from January 2018, succeeding Prof Vladimir Buzek, who comes to the end of his five-year term.
EPJ D Highlight - First aid kit in some living organisms helps fix DNA after lengthy sun exposure
- Published on 26 June 2017
New study unveils the binding mechanisms of enzymes capable of repairing DNA damaged by UV light before any risk of cellular malfunction sets in
Sunburn in living organisms is caused by ultraviolet (UV) light from the sun damaging the DNA in the cells. Many organisms, however, have an in-built mechanism for repairing the sun damage. This is possible thanks to an enzyme called DNA photolyase, which is so specialised that cryptochrome, a structurally similar molecule, is unable to do the same job. By comparing both types of molecule, physicists can understand precisely how the ability of our enzymes to repair DNA boils down to the most minute structural details. In a study published in EPJ D, Katrine Aalbæk Jepsen from the University of Southern Denmark, in Odense, and her colleague Ilia Solov'yov pinpoint the mechanism by which repair enzymes bind to the damaged site.
EPJ D Highlight - Zig-zagging device focuses high-energy radiation emissions
- Published on 23 May 2017
Physicists have found a way to better control high-energy particle emissions in an undulator device that could potentially be used as a source of radiation for cancer treatment or nuclear waste processing
There’s no substitute for using the right tool for the job at hand. Using low-energy radiation sources simply isn’t suitable for certain tasks: equipment used in cancer treatment requires a strong, monochromatic source of radiation to produce hard X-rays. Other similar radiation sources find applications in nuclear waste processing. To design devices that steadily emit a specific type of radiation, physicists use a special kind of crystal, referred to as a crystalline undulator. In a recent study published in EPJ D, a team has demonstrated the ability to control radiation emissions from a particle travelling through such a device. Tobias Wistisen from Aarhus University, Denmark, and colleagues have shown how to manipulate the emitted radiation by selecting a combination of incoming particle charge and energy, oscillation amplitude and period of the undulator’s crystalline lattice.
EPJ D Colloquium: From nuclear to meso systems: how small is simple and how large is complex?
- Published on 25 April 2017
How small is simple and how large is complex? This is the question asked in a new Colloquium article by Jean-Patrick Connerade of Imperial College, published as part of the Topical Issue of EPJ D on Dynamics of Systems at the Nanoscale.
EPJ D Highlight - Reading between the lines of highly turbulent plasmas
- Published on 29 March 2017
Study shows how to identify highly turbulent plasma signatures in the broadening of the shapes of lines emitted by ions and atoms within
Plasma, the ionised state of matter found in stars, is still not fully understood, largely due to its instability. Astrophysicists have long-since sought to develop models that can account for the turbulent motions inside plasma, based on observing line shapes emitted by atoms and ions in the plasma. Turbulences are typically detected through the observation of broadened lines due to the Doppler effect, similar to the principle behind radar. In a new study published in EPJ D, Roland Stamm from the CNRS and Aix-Marseille University, France, and colleagues develop an iterative simulation model that accurately predicts, for the first time, the changes to the line shape in the presence of strong plasma turbulence. Ultimately, the authors aim to provide a system for assessing plasma turbulence that is valid for both a stellar atmosphere and the ITER tokamak designed to generate fusion energy. Line shapes are extensively employed as a powerful diagnostic tool for detecting turbulences in stable gases and plasmas. For many years now, astrophysicists have developed and employed models that gauge the effect of turbulent motions in the broadening of line shapes due to the Doppler effect. Such models are now also being employed to understand the role of turbulences in plasmas created to harvest energy from fusion.
EPJ D Highlight - Ionisation mechanisms of captive atoms struck by light matter
- Published on 01 March 2017
Physicists elucidate the effects of light rays falling onto hydrogen atoms trapped in a carbon atom cage
Light interacting with hydrogen atoms enclosed in hollow cages composed of carbon atoms - referred to as fullerene material - produces ionisation. This phenomenon, which has been the subject of intense theoretical scrutiny, is particularly interesting because the light rays can have dramatic effects in inducing small external energy potentials. Specifically, they alter the structural and dynamic properties of the atoms confined within the fullerene molecule. Ana Frapiccini from the CONICET research centre at the Universidad Nacional del Sur, in Bahía Blanca, Argentina, and colleagues have just published a study in EPJ D explaining the theory behind the ionisation. Applications of this process include drug delivery, quantum computation, photovoltaics and hydrogen storage.
EPJ D Highlight - Novel plasma jet offshoot phenomenon explains blue atmospheric jets
- Published on 08 February 2017
Russian physicists identify mysterious right-angle side-jet occurring off the plasma arc in air at ambient pressure conditions
Ionised matter, like plasma, still holds secrets. Physicists working with plasma jets, made of a stream of ionised matter, have just discovered a new phenomenon. Indeed, Eduard Sosnin from the Institute of High Current Electronics, Russian Academy of Sciences in Tomsk, Russia, and colleagues found a new type of discharge phenomenon in an atmospheric pressure plasma. It has been dubbed apokamp—from the Greek words for ‘off’ and ‘bend’, because it appears at a perpendicular angle to where plasma jets bend. Their findings have been recently published in EPJ D and are particularly relevant for the development of novel applications in medicine, health care and materials processing because they involve air at normal atmospheric pressure, which would make it cheaper than applications in inert gases or nitrogen.
EPJ D Colloquium: Non-equilibrium in low-temperature plasmas
- Published on 28 November 2016
The wide range of applications that have been found for cold plasmas stems from the fact that they are physical systems out of thermodynamic equilibrium. This property enhances their reactivity at low gas temperature, and allows macroscopic effects to be obtained with only moderate energy consumption.
In this EPJ D review, the basic concepts of ionised gases in a non-equilibrium state are treated by showing how and why the non-equilibrium functions of the degrees of freedom are formed in a variety of natural and man-made plasmas, with particular emphasis on the progress that has been made in the last decade. A modern perspective of the molecular basis of non-equilibrium and of a state-to-state kinetic approach is adopted. Computational and diagnostic techniques that have been used to investigate the non-equilibrium conditions are also surveyed.
EPJ D Highlight - Better than milk on breakfast cereals: new precision coating method for industrial granular material
- Published on 23 November 2016
Deposition of a thin film catalyst of a predicted thickness on the surface of novel hydrogen storage microbeads helps release hydrogen
As anyone who eats their cereal with milk in the morning knows: coating large volumes of granular material homogeneously is no mean feat. In a recent paper published in EPJ D, an Austrian team has developed a new method, based on physical vapour deposition, to upscale the quantity of coating without affecting the quality and homogeneity of the film. In this study, Andreas Eder from Vienna University of Technology and colleagues also developed a model capable of predicting the film thickness. This represents a major step forward for industrial materials, as previous approaches relied on optical measurement after the coating had been deposited. Because this coating system is capable of implementing a plasma close to the granular substrate, it opens the door to new surface treatment and modification possibilities.