We welcome contributions from anyone to our library which should be sent to the editor by email. We will accept contributions in any format, but prefer LaTeX, MSWord, pdf or HTML. As far as is practicable, we will publish information on infoweb in HTML and .pdf formats.


Masahiro Takenaga, who is undertaking a Master of Research (MRes) degree at Imperial College London, has been awarded a prize for his talk at a Molecular Science & Engineering MRes Symposium.

His presentation was on the ‘Investigation of viscosity in ionic liquids’, a project which he has been working on with scientists from Collaborative Computational Project 5 (CCP5) at STFC’s Daresbury Laboratory.Masahiro went to the Daresbury Laboratory to learn the science and art of molecular modelling. Under the supervision of Professor Ilian Todorov and Dr Vlad Sokhan, he was able to gain valuable experience and knowledge in modelling methodology. In his research with ionic liquids*, Masahiro used DL_POLY, a molecular dynamics software suite, developed by Professor Todorov’s group at Daresbury through CCP5.

Dr Sokhan imparted knowledge and know-how through one-to-one training, enabling Masahiro to apply advanced simulation methods to ionic liquids, giving him first-hand experience of DL_POLY’s capability and setting milestones for his research.

This helped Masahiro (pictured beside with Dr Patricia Hunt from Imperial College) to give a confident and entertaining presentation of his work at the MRes Symposium.

The MRes students competed to give the best talk and were assessed by judges from both academia and industry against pre-defined criteria, including quality of slides and figures, pacing of the presentation, ability to explain clearly and concisely, how engaging the speaker was, and their ability to answer questions well.

Masahiro is delighted to have won the prize, and thanked his tutors for their guidance and support.

He said, “Thanks to the support from Daresbury Lab I have learned how to use the DL_POLY software, from generating input files to analysing the computed results. I started by learning about Linux shell, commands and directory structure before going on to the more advanced work with atomistic models, equations of motion and electrostatic interactions.

He added, “These new skills enabled me to understand the properties of materials, which were difficult to study experimentally, and will enable me to design and create novel materials in my future work.

Masahiro is continuing his MRes studies within the Hunt Research Group at Imperial College, under the supervision of Dr Patricia Hunt and Professor George Jackson.


*Ionic liquids are a new type of solvent with many benefits to industry. For example, industrial machinery might run at a very high temperature, causing lubricants to boil off or chemically react with steel components. Ionic liquids remain stable and unreactive, so can enable devices to run at a wider range of temperatures. (Source: Hunt Research Group)

Researchers at UCL use DL_POLY_4 to study mystery of bones and teeth tissues via molecular dynamics. The research of featured recently on the cover of Journal of Materials Chemistry B
Bones and teeth are composite materials made of an organic component, a helical protein named collagen and an inorganic component, calcium phosphate. Although calcium phosphate is found in nature as a variety of polymorphs, the most stable one is hydroxyapatite (Ca10 (PO4 )6(OH)2
Our research consisted in simulating the behaviour of calcium and phosphate ions in water at body temperature using classical Molecular Dynamics with the aid of a supercomputing facility. We observed the aggregation of the ions to form large clusters; a thorough examination of the latter showed the presence of several Posner’s clusters within them. Afterwards, we simulated a series of solutions with different composition: a change in pH was achieved tuning the ratio among the phosphate species (HPO42 – , H2 PO4 – and PO43 – ); in physiological conditions (pH ≈ 7.4) the phosphate ions are mainly present in the protonated form. We also added sodium ions, which are abundantin the body fluids, to see how their presence affects the calcium phosphate aggregation. The Posner’s clusters were
also detected altering the composition of the initial solution, hence we were able to validate the assumption that these clusters form spontaneously in water and play a fundamental role in calcium phosphate formation in the body fluids.

The interface between organic (molecular) and inorganic (crystals) is most seen in biominerals – the mineral structures living creatures produce, for example eggshells. Researchers at Sheffield and York Universities teamed up to study the proteins found in ostrich eggshells. Archaeologists had shown that particular sequences of amino acids in particular proteins (struthiocalcin 1 and 2) survived in the fossil record for millions of years – far longer than other proteins. Using DL_POLY the Sheffield team modelled these proteins interacting with calcite (the main mineral component of eggshells) and demonstrated that the long surviving amino acid sequences were those sections of the protein that bound most strongly to the calcite. Further analysis demonstrated that the amino acid sequence in contact with the calcite is stabilised by the surface. This will make it less volatile and therefore increase the lifetime of the region protecting it from hydrolysis. Published in eLife DOI: 10.7554/eLife.17092.
More info on BBC website Proteins from ‘deep time’ found in ostrich eggshell

Emergence and evolution of k-gap in spectra of liquid and supercritical states C Yang, M T Dove, V V Brazhkin and K Trachenko Physical Review Letters
  We are all familiar with the concept of waves. Waves can be visible on the surface of water, audible as sound and music or detectable by electronic devices as electromagnetic signals. We have good theories of waves in solids and gases but, surprisingly and despite many decades of research, not in the third state of matter, liquids. Liquids is the least understood state of matter – this is why textbooks are often silent about their most basic properties. For long time, it has been contemplated that liquids can sustain both gas-like waves with long wavelengths and solid-like waves with short wavelengths. In other words, liquids can be thought of as an interesting mixture of solids and gases. However, we had no idea just how solid-like waves can propagate in liquids. Physicists at Queen Mary University of London have discovered that liquids are capable of supporting solid-like waves but these waves start only with short wavelengths. In other words, there is an interesting gap in the liquid wave spectrum. Researchers have used DL_POLY to perform extensive modelling study to ascertain the gap and discuss its properties. Kostya Trachenko says, “The difference between liquids and solids is that particles rearrange in liquids with a certain frequency – this enables liquids to flow. These rearrangements disrupt the propagating waves but they do so in an interesting way. You can think about these motions as microscopic demons living in the liquid which eat all low-energy (long-wavelength) solid-like waves but leave high-energy waves intact. In other words, flowing liquid particles act as wave filters – the insight not hitherto anticipated. Kostya Trachenko continues, “This result is important for fundamental understanding of liquids and gives us hope that we are getting close to constructing a consistent theory of this elusive third state of matter, liquids.”