Thermostat Influence on the Structural Development and Material Removal during Abrasion of Nanocrystalline Ferrite

We consider a nanomachining process of hard, abrasive particles grinding on the rough surface of a polycrystalline ferritic work piece. Using extensive large-scale molecular dynamics (MD) simulations, we show that the mode of thermostatting, i.e., the way that the heat generated through deformation and friction is removed from the system, has crucial impact on tribological and materials related phenomena. By adopting an electron-phonon coupling approach to parametrize the thermostat of the system, thus including the electronic contribution to the thermal conductivity of iron, we can reproduce the experimentally measured values that yield realistic temperature gradients in the work piece. We compare these results to those obtained by assuming the two extreme cases of only phononic heat conduction and instantaneous removal of the heat generated in the machining interface. Our discussion of the differences between these three cases reveals that although the average shear stress is virtually temperature independent up to a normal pressure of approximately 1 GPa, the grain and chip morphology as well as most relevant quantities depend heavily on the mode of thermostatting beyond a normal pressure of 0.4 GPa. These pronounced differences can be explained by the thermally activated processes that guide the reaction of the Fe lattice to the external mechanical and thermal loads caused by nanomachining

Structural Studies of GABAA Receptor Binding Sites: Which Experimental Structure Tells us What?

Atomic resolution structures of cys-loop receptors, including one of a γ-aminobutyric acid type A receptor (GABA(A) receptor) subtype, allow amazing insights into the structural features and conformational changes that these pentameric ligand-gated ion channels (pLGICs) display. Here we present a comprehensive analysis of more than 30 cys-loop receptor structures of homologous proteins that revealed several allosteric binding sites not previously described in GABA(A) receptors. These novel binding sites were examined in GABA(A) receptor homology models and assessed as putative candidate sites for allosteric ligands. Four so far undescribed putative ligand binding sites were proposed for follow up studies based on their presence in the GABA(A) receptor homology models. A comprehensive analysis of conserved structural features in GABA(A) and glycine receptors (GlyRs), the glutamate gated ion channel, the bacterial homologs Erwinia chrysanthemi (ELIC) and Gloeobacter violaceus GLIC, and the serotonin type 3 (5-HT(3)) receptor was performed. The conserved features were integrated into a master alignment that led to improved homology models. The large fragment of the intracellular domain that is present in the structure of the 5-HT(3) receptor was utilized to generate GABA(A) receptor models with a corresponding intracellular domain fragment. Results of mutational and photoaffinity ligand studies in GABA(A) receptors were analyzed in the light of the model structures. This led to an assignment of candidate ligands to two proposed novel pockets, candidate binding sites for furosemide and neurosteroids in the trans-membrane domain were identified. The homology models can serve as hypotheses generators, and some previously controversial structural interpretations of biochemical data can be resolved in the light of the presented multi-template approach to comparative modeling. Crystal and cryo-EM microscopic structures of the closest homologs that were solved in different conformational states provided important insights into structural rearrangements of binding sites during conformational transitions. The impact of structural variation and conformational motion on the shape of the investigated binding sites was analyzed. Rules for best template and alignment choice were obtained and can generally be applied to modeling of cys-loop receptors. Overall, we provide an updated structure based view of ligand binding sites present in GABA(A) receptors

Thermostat Influence on the Structural Development and Material Removal during Abrasion of Nanocrystalline Ferrite

We consider a nanomachining process of hard, abrasive particles grinding on the rough surface of a polycrystalline ferritic work piece. Using extensive large-scale molecular dynamics (MD) simulations, we show that the mode of thermostatting, i.e., the way that the heat generated through deformation and friction is removed from the system, has crucial impact on tribological and materials related phenomena. By adopting an electron-phonon coupling approach to parametrize the thermostat of the system, thus including the electronic contribution to the thermal conductivity of iron, we can reproduce the experimentally measured values that yield realistic temperature gradients in the work piece. We compare these results to those obtained by assuming the two extreme cases of only phononic heat conduction and instantaneous removal of the heat generated in the machining interface. Our discussion of the differences between these three cases reveals that although the average shear stress is virtually temperature independent up to a normal pressure of approximately 1 GPa, the grain and chip morphology as well as most relevant quantities depend heavily on the mode of thermostatting beyond a normal pressure of 0.4 GPa. These pronounced differences can be explained by the thermally activated processes that guide the reaction of the Fe lattice to the external mechanical and thermal loads caused by nanomachining

Thermostat Influence on the Structural Development and Material Removal during Abrasion of Nanocrystalline Ferrite

We consider a nanomachining process of hard, abrasive particles grinding on the rough surface of a polycrystalline ferritic work piece. Using extensive large-scale molecular dynamics (MD) simulations, we show that the mode of thermostating, i.e., the way that the heat generated through deformation and friction is removed from the system, has crucial impact on tribological and materials related phenomena. By adopting an electron-phonon coupling approach to parametrize the thermostat of the system, thus including the electronic contribution to the thermal conductivity of iron, we can reproduce the experimentally measured values that yield realistic temperature gradients in the work piece. We compare these results to those obtained by assuming the two extreme cases of only phononic heat conduction and instantaneous removal of the heat generated in the machining interface. Our discussion of the differences between these three cases reveals that although the average shear stress is virtually temperature independent up to a normal pressure of approximately 1 GPa, the grain and chip morphology as well as most relevant quantities depend heavily on the mode of thermostating beyond a normal pressure of 0.4 GPa. These pronounced differences can be explained by the thermally activated processes that guide the reaction of the Fe lattice to the external mechanical and thermal loads caused by nanomachining

Applicability of Macroscopic Wear and Friction Laws on the Atomic Length Scale

Using molecular dynamics, we simulate the abrasion process of an atomically rough Fe surface with multiple hard abrasive particles. By quantifying the nanoscopic wear depth in a time-resolved fashion, we show that Barwell's macroscopic wear law can be applied at the atomic scale. We find that in this multiasperity contact system, the Bowden-Tabor term, which describes the friction force as a function of the real nanoscopic contact area, can predict the kinetic friction even when wear is involved. From this the Derjaguin-Amontons-Coulomb friction law can be recovered, since we observe a linear dependence of the contact area on the applied load in accordance with Greenwood-Williamson contact mechanics