Intra-molecular coupling as a mechanism for a liquid-liquid phase transition

We study a model for water with a tunable intra-molecular interaction $J_\sigma$, using mean field theory and off-lattice Monte Carlo simulations. For all $J_\sigma\geq 0$, the model displays a temperature of maximum density.For a finite intra-molecular interaction $J_\sigma > 0$,our calculations support the presence of a liquid-liquid phase transition with a possible liquid-liquid critical point for water, likely pre-empted by inevitable freezing. For J=0 the liquid-liquid critical point disappears at T=0.Comment: 8 pages, 4 figure

Representation of protein secondary structure using bond-orientational order parameters

Structural studies of proteins for motif mining and other pattern recognition techniques require the abstraction of the structure into simpler elements for robust matching. In this study, we propose the use of bond-orientational order parameters, a well-established metric usually employed to compare atom packing in crystals and liquids. Creating a vector of orientational order parameters of residue centers in a sliding window fashion provides us with a descriptor of local structure and connectivity around each residue that is easy to calculate and compare. To test whether this representation is feasible and applicable to protein structures, we tried to predict the secondary structure of protein segments from those descriptors, resulting in 0.99 AUC (area under the ROC curve). Clustering those descriptors to 6 clusters also yield 0.93 AUC, showing that these descriptors can be used to capture and distinguish local structural information

Discrete element modelling approach to assessment of granular properties in concrete

This paper presents the technological relevance of a concurrent algorithm-based discrete element modelling (DEM) system, HADES. This new system is the successor of SPACE that is limited to spherical grains only. It can realistically simulate the packing of arbitrary-shaped particles up to the fully compacted state. Generation of families of such particles, i.e., generally representing aggregate of fluvial origin and crushed rock, respectively, and the forming way of particulate structure are described. Similarly shaped particles are proposed for simulation of cement paste because of conformity with experimental results obtained by the X-ray tomography method. Technologically relevant territories inside and outside concrete technology are presently explored in this efficient, reliable, and economic way. Some results obtained by this DEM approach are presented