<center><b>Latest Papers in Condensed Matter Physics</b></center>
# <center>Soft Condensed Matter</center>
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### [Molecular Dynamics Investigation of the Influence of the Shape of Cation on the Structure and Lubrication Properties of Ionic Liquids](http://arxiv.org/abs/1811.12512v2) (1811.12512v2)
<b>Miljan Dašić, Igor Stanković, Konstantinos Gkagkas</b>
<i>2018-11-29</i>
> We present a theoretical study of the influence of the molecular geometry of the cation on the response of ionic liquid (IL) to confinement and mechanical strain. The so-called {\it tailed} model includes a large spherical anion and asymmetric cation consisting of a charged head and neutral tail. Despite its simplicity, this model recovers a wide range of structures seen in IL: simple cubic lattice for the small tails, liquid-like state for symmetric cation-tail dimers, and molecular layer structure for dimers with large tails. A mutual feature of all investigated model ILs is a formation of the fixed (stable) layer of cations along solid plates. We observe single anionic layer for small gap widths, double anionic layer for intermediate, and tail--to--tail layer formation for wide gaps. The normal force evolution with the gap size can be related to the layer formed inside the gap. The low hysteretic losses during the linear cyclic motion suggest the presence of strong slip inside the gap. In our model specific coefficient of friction is low and friction force decreases with the tail size.
### [Structural similarity between dry and wet sphere packings](http://arxiv.org/abs/1808.04342v2) (1808.04342v2)
<b>Simon Weis, Gerd Schröder-Turk, Matthias Schröter</b>
<i>2018-08-13</i>
> The mechanical properties of granular materials change significantly in the presence of a wetting liquid which creates capillary bridges between the particles. Here we demonstrate, using X-ray tomographies of dry and wet sphere packings, that this change in mechanical properties is not accompanied by structural differences between the packings. We characterize the latter by the average numbers of contacts of each sphere  and the shape isotropy  of the Voronoi cells of the particles. Additionally, we show that the number of liquid bridges per sphere  is approximately equal to , independent of the volume fraction of the packing. These findings will be helpful in guiding the development of both particle-based models and continuum mechanical descriptions of wet granular matter.
### [Understanding the effect of the base oil on the physical adsorption process of organic additives using molecular dynamcis](http://arxiv.org/abs/1808.08666v2) (1808.08666v2)
<b>Masakazu Konishi, Hitoshi Washizu</b>
<i>2018-08-27</i>
> Organic friction modifiers (OFMs) are widely added to oil to reduce the boundary friction in many kinds of lubricants such as vehicle engine oils. At the contact area in machine elements, the OFMs form a self-assembled organic monolayer. Although the friction properties of the monolayer are widely studied on a molecular level, the formation process is not well-known. In this study, the initial adsorbing process of additive molecules in explicit base oil molecules are calculated using molecular dynamics. The adsorption time depends on the structure of the base oils. Another effect of the base oil other than "chain matching" is found.
### [Universal dynamics of dilute and semidilute solutions of flexible linear polymers](http://arxiv.org/abs/1901.07116v1) (1901.07116v1)
<b>J. Ravi Prakash</b>
<i>2019-01-21</i>
> Experimental observations and computer simulations have recently revealed universal aspects of polymer solution behaviour that were previously unknown. This progress has been made possible due to developments in experimental methodologies and simulation techniques, and the formulation of scaling arguments that have identified the proper scaling variables with which to achieve data collapse, both for equilibrium and nonequilibrium properties. In this review, these advances in our understanding of universal polymer solution behaviour are discussed, along with a brief overview of prior experimental observations and theoretical predictions in order to provide a context for the discussion. Properties for which the existence of universality is still unclear, and those for which it has not yet been verified theoretically are highlighted, and theoretical predictions of universal behaviour that require experimental validation are pointed out.
### [Can all-atom protein dynamics be reconstructed from the knowledge of C-alpha time evolution?](http://arxiv.org/abs/1901.06864v1) (1901.06864v1)
<b>Jiaojiao Liu, Jin Dai, Jianfeng He, Xubiao Peng, Antti J. Niemi</b>
<i>2019-01-21</i>
> We inquire to what extent protein peptide plane and side chain dynamics can be reconstructed from knowledge of C-alpha dynamics. Due to lack of experimental data we analyze all atom molecular dynamics trajectories from Anton supercomputer, and for clarity we limit our attention to the peptide plane O atoms and side chain C-beta atoms. We try and reconstruct their dynamics using four different approaches. Three of these are the publicly available reconstruction programs Pulchra, Remo Scwrl4. The fourth, Statistical Method, builds entirely on statistical analysis of Protein Data Bank (PDB) structures. All four methods place the O and C-beta atoms accurately along the Anton trajectories. However, the Statistical Method performs best. The results suggest that under physiological conditions, the all atom dynamics is slaved to that of C-alpha atoms. The results can help improve all atom force fields, and advance reconstruction and refinement methods for reduced protein structures. The results provide impetus for development of effective coarse grained force fields in terms of reduced coordinates.
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