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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.”


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