A Fluid Dynamics Calculation of Sputtering from a Cylindrical Thermal Spike

The sputtering yield, Y, from a cylindrical thermal spike is calculated using a two dimensional fluid dynamics model which includes the transport of energy, momentum and mass. The results show that the high pressure built-up within the spike causes the hot core to perform a rapid expansion both laterally and upwards. This expansion appears to play a significant role in the sputtering process. It is responsible for the ejection of mass from the surface and causes fast cooling of the cascade. The competition between these effects accounts for the nearly linear dependence of $Y$ with the deposited energy per unit depth that was observed in recent Molecular Dynamics simulations. Based on this we describe the conditions for attaining a linear yield at high excitation densities and give a simple model for this yield.Comment: 10 pages, 9 pages (including 9 figures), submitted to PR

Modeling of Martensitic Transformations in Pure Iron by a Phase Field Approach Using Information from Atomistic Simulation

A phase field approach for martensitic transformations is introduced. The parameters are determined due to results from molecular dynamic simulations for pure iron. The continuum model is provided with the atomistic input data to examine the evolution of microstructure in 2D, both under the influence of external load and for interface motion through the transformation induced eigenstrain. Therefore, different configurations of the two phases are used. In addition, the energy evolution of the system is studied in detail during the transformation process. The numerical implementation of the model is performed with finite elements while an implicit time integration scheme is applied for the transient terms

Melting of Al Induced by Laser Excitation of 2p Holes

Novel photon sources—such as XUV- or X-ray lasers—allow to selectively excite core excitations in materials. We study the response of a simple metal, Al, to the excitation of 2p holes using molecular dynamics simulations. During the lifetime of the holes, the interatomic interactions in the slab are changed; we calculate these using WIEN2k. We find that the melting dynamics after core-hole excitation is dominated by classical electron–phonon dynamics. The effects of the changed potential surface for excited Al atoms occur on the time scale of 100 fs, corresponding to the Debye time of the lattice

Origin of atomic clusters during ion sputtering

Previous studies have shown that the size distributions of small clusters ( n<=40 n = number of atoms/cluster) generated by sputtering obey an inverse power law with an exponent between -8 and -4. Here we report electron microscopy studies of the size distributions of larger clusters ( n>=500) sputtered by high-energy ion impacts. These new measurements also yield an inverse power law, but one with an exponent of -2 and one independent of sputtering yield, indicating that the large clusters are produced when shock waves, generated by subsurface displacement cascades, ablate the surface

Molecular dynamics simulations of non-equilibrium systems

Peer reviewe

A Structural Feature of the Non-Peptide Ligand Interactions with Mice Mu-Opioid Receptors

By binding to and activating the G-protein coupled μ−, κ− and δ−opioid receptors in the central nervous system, opiates are known to induce analgesic and sedative effects. In particular, non-peptide opioid ligands are often used in clinical applications to induce these therapeutically beneficial effects, due to their superior pharmacokinetics and bioavailability in comparison to endogenous neuropeptides. However, since opioid alkaloids are highly addictive substances, it is necessary to understand the exact mechanisms of their actions, specifically the ligand-binding properties of the target receptors, in order to safely apply opiates for therapeutic purposes. Using an in silico molecular docking approach (AutoDock Vina) combined with two-step cluster analysis, we have computationally obtained the docking scores and the ligand-binding pockets of twelve representative non-peptide nonendogenous agonists and antagonists at the crystallographically identified μ-opioid receptor. Our study predicts the existence of two main binding sites that are congruently present in all opioid receptor types. Interestingly, in terms of the agonist or antagonist properties of the substances on the receptors, the clustering analysis suggests a relationship with the position of the ligand-binding pockets, particularly its depth within the receptor structure. Furthermore, the binding affinity of the substances is directly correlated to the proximity of the binding pockets to the extracellular space. In conclusion, the results provide further insights into the structural features of the functional pharmacology of opioid receptors, suggesting the importance of the binding position of non-peptide agonists and antagonists- specifically the distance and the level of exposure to the extracellular space- to their dissociation kinetics and subsequent potency

Ethanol-induced conformational fluctuations of NMDA receptors

Alcohol addiction ranks among the leading global causes of preventable death and disabilities in human population. Understanding the sites of ethanol action that mediate its acute and chronic neural and behavioural effects is critical to develop appropriate treatment options for this disorder. The N-methyl-d-asparate (NMDA) receptors are ligand-gated heterotetrameric ion channels, which are known to directly interact with alcohol in a concentration-dependent manner. Yet, the exact molecular mechanisms and conformational dynamics of this interaction are not well understood. Here, we conducted a series of molecular dynamics simulations of the interaction of moderate ethanol concentrations with rat's wild-type GluN1–GluN2B NMDA Receptor under physiological conditions. The simulations suggest that glutamate or glycine alone induce an intermediate conformational state and point towards the transmembrane domain (TMD) as the site of action of ethanol molecules. Ethanol interacts by double hydrogen bonds with Trp635 and Phe638 at the transmembrane M3 helix of GluN2B. Alcohol not only reduces the pore radius of the ion channel within the TMD but also decreases accessibility of glutamate and glycine to the ligand-binding sites by altering the structure of the ligand-binding domain and significantly widening the receptor in that area