Friedel oscillations responsible for stacking fault of adatoms: The case of Mg(0001) and Be(0001)

We perform a first-principles study of Mg adatom and adislands on the Mg(0001) surface, and Be adatom on Be(0001), to obtain further insights into the previously reported energetic preference of the fcc faulty stacking of Mg monomers on Mg(0001). We first provide a viewpoint on how Friedel oscillations influence ionic relaxation on these surfaces. Our three-dimensional charge-density analysis demonstrates that Friedel oscillations have maxima which are more spatially localized than what one-dimensional average density or two-dimensional cross sectional plots could possibly inform: The well-known charge-density enhancement around the topmost surface layer of Mg(0001) is strongly localized at its fcc hollow sites. The charge accumulation at this site explains the energetically preferred stacking fault of the Mg monomer, dimer and trimer. Yet, larger islands prefer the normal hcp stacking. Surprisingly, the mechanism by which the fcc site becomes energetically more favorable is not that of enhancing the surface-adatom bonds but rather those between surface atoms. To confirm our conclusions, we analyze the stacking of Be adatom on Be(0001) - a surface also largely influenced by Friedel oscillations. We find, in fact, a much stronger effect: The charge enhancement at the fcc site is even larger and, consequently, the stacking-fault energy favoring the fcc site is quite large, 44 meV.Comment: Submitted to Physical Review

Theoretical Studies Of Nanostructure Formation And Transport On Surfaces

This dissertation undertakes theoretical and computational research to characterize and understand in detail atomic configurations and electronic structural properties of surfaces and interfaces at the nano-scale, with particular emphasis on identifying the factors that control atomic-scale diffusion and transport properties. The overarching goal is to outline, with examples, a predictive modeling procedure of stable structures of novel materials that, on the one hand, facilitates a better understanding of experimental results, and on the other hand, provide guidelines for future experimental work. The results of this dissertation are useful in future miniaturization of electronic devices, predicting and engineering functional novel nanostructures. A variety of theoretical and computational tools with different degrees of accuracy is used to study problems in different time and length scales. Interactions between the atoms are derived using both ab-initio methods based on Density Functional Theory (DFT), as well as semiempirical approaches such as those embodied in the Embedded Atom Method (EAM), depending on the scale of the problem at hand. The energetics for a variety of surface phenomena (adsorption, desorption, diffusion, and reactions) are calculated using either DFT or EAM, as feasible. For simulating dynamic processes such as diffusion of adatoms on surfaces with dislocations the Molecular Dynamics (MD) method is applied. To calculate vibrational mode frequencies, the infinitesimal displacement method is employed. The combination of non-equilibrium Green’s function (NEGF) and DFT is used to calculate electronic transport properties of molecular devices as well as interfaces and junctions

Effect of misfit dislocation on surface diffusion

We apply molecular dynamics and molecular static methods to study the effect of misfit dislocations on adatom diffusion in close proximity to the dislocation core in heteroepitaxial systems, using many-body interaction potentials. Our system consists of several layers (three-seven) of Cu on top of a Ni(111) substrate. The misfit dislocations are created with the core located at the interface between the Cu film and the Ni substrate, using the repulsive biased potential method described earlier. We find that presence of the defect under the surface strongly affects the adatom trajectory, creating anisotropy in atomic diffusion, independent of the thickness of the Cu film. We also calculate the potential energy surface available to the adatom and compare the energy barriers for adatom diffusion in the proximity of the core region and on the defect-free surface

In Silico Analysis of the Multi-Targeted Mode of Action of Ivermectin and Related Compounds

Some clinical studies have indicated activity of ivermectin, a macrocyclic lactone, against COVID-19, but a biological mechanism initially proposed for this anti-viral effect is not applicable at physiological concentrations. This in silico investigation explores potential modes of action of ivermectin and 14 related compounds, by which the infectivity and morbidity of the SARS-CoV-2 virus may be limited. Binding affinity computations were performed for these agents on several docking sites each for models of (1) the spike glycoprotein of the virus, (2) the CD147 receptor, which has been identified as a secondary attachment point for the virus, and (3) the alpha-7 nicotinic acetylcholine receptor (α7nAChr), an indicated point of viral penetration of neuronal tissue as well as an activation site for the cholinergic anti-inflammatory pathway controlled by the vagus nerve. Binding affinities were calculated for these multiple docking sites and binding modes of each compound. Our results indicate the high affinity of ivermectin, and even higher affinities for some of the other compounds evaluated, for all three of these molecular targets. These results suggest biological mechanisms by which ivermectin may limit the infectivity and morbidity of the SARS-CoV-2 virus and stimulate an α7nAChr-mediated anti-inflammatory pathway that could limit cytokine production by immune cells

An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness

How COVID-19 Hijacks the Cytoskeleton: Therapeutic Implications

The SARS-CoV-2 virus invades and replicates within host cells by “hijacking” biomolecular machinery, gaining control of the microtubule cytoskeleton. After attaching to membrane receptors and entering cells, the SARS-CoV-2 virus co-opts the dynamic intra-cellular cytoskeletal network of microtubules, actin, and the microtubule-organizing center, enabling three factors that lead to clinical pathology: (1) viral load due to intra-cellular trafficking, (2) cell-to-cell spread by filopodia, and (3) immune dysfunction, ranging from hyper-inflammatory cytokine storm to ineffective or absent response. These factors all depend directly on microtubules and the microtubule-organizing center, as do cell functions such as mitosis and immune cell movement. Here we consider how the SARS-CoV-2 virus may “hijack” cytoskeletal functions by docking inside the microtubule-organizing center’s centriole “barrels”, enabling certain interactions between the virus’s positively charged spike (“S”) proteins and negatively charged C-termini of the microtubules that the centriole comprises, somewhat like fingers on a keyboard. This points to the potential benefit of therapies aimed not directly at the virus but at the microtubules and microtubule-organizing center of the host cell on which the virus depends. These therapies could range from anti-microtubule drugs to low-intensity ultrasound (megahertz mechanical vibrations) externally applied to the vagus nerve at the neck and/or to the spleen (since both are involved in mediating inflammatory response). Given that ultrasound imaging machines suitable for vagal/splenic ultrasound are available for clinical trials in every hospital, we recommend an alternative therapeutic approach for COVID-19 based on addressing and normalizing the host cell microtubules and microtubule-organizing centers co-opted by the SARS-CoV-2 virus

An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness

Revisiting The Surface Properties Of Mg(0001) Thin Films And Their Effect On The Adatom Binding Energy And Self-Diffusion

We perform first-principles calculations of the properties of the Mg(0001) surface of thin films to examine the giant oscillations of surface energy and interlayer relaxation of Mg(0001) films as a function of thickness reported previously. We find that, although overcoming the thin-film limit requires up to 25 layers, properties exclusive to the surface layer are well converged for 18-layer thick films (~ 4.1 nm). Furthermore, the fcc-stacking fault is found to be energetically favorable for the Mg adatom by 15 meV. We also find that the binding energy of the Mg adatom (~ 0.6 eV), well converged for 7-layer films, is significantly weaker than the value reported by previous calculations. In addition, our calculations show small diffusion barriers of 9 meV (hcp to fcc) and 25 meV (fcc to hcp) for the monomer

The Role Of Van Der Waals Interaction In The Tilted Binding Of Amine Molecules To The Au(111) Surface

We present the results of ab initio electronic structure calculations for the adsorption characteristics of three amine molecules on Au(111), which show that the inclusion of vanderWaals interactions between the isolated molecule and the surface leads in general to good agreement with experimental data on the binding energies. Each molecule, however, adsorbs with a small tilt angle (between 5 and 9°). For the specific case of 1,4-diaminobenzene (BDA) our calculations reproduce the larger tilt angle (close to 24°) measured by photoemission experiments, when intermolecular (vanderWaals) interactions (for about 8% coverage) are included. These results point not only to the important contribution of vanderWaals interactions to moleculesurface binding energy, but also that of intermolecular interactions, often considered secondary to that between the molecule and the surface, in determining the adsorption geometry and pattern formation. © 2012 IOP Publishing Ltd

Growth Of Aligned Mo6S6 Nanowires On Cu(111)

Based on density functional theory (DFT) predictions and scanning tunneling microscopy (STM) measurements we report the possibility of using the Cu(111) surface for growth of molybdenum sulfide nanowires (Mo6S 6). Strong substrate interactions coupled with small lattice mismatch lead to epitaxial growth of the nanowires parallel to a set of substrate high symmetry directions. We observe a propensity for creation of aligned and equally spaced arrays of nanowires and use DFT to elucidate interaction strength both in the absence and presence of the substrate. © 2013 Elsevier B.V