Atomistic mechanisms for the ordered growth of Co nano-dots on Au(788): comparison of VT-STM experiments and multi-scaled calculations

Hetero-epitaxial growth on a strain-relief vicinal patterned substrate has revealed unprecedented 2D long range ordered growth of uniform cobalt nanostructures. The morphology of a Co sub-monolayer deposit on a Au(111) reconstructed vicinal surface is analyzed by Variable Temperature Scanning Tunneling Microscopy (VT-STM) experiments. A rectangular array of nano-dots (3.8 nm x 7.2 nm) is found for a particularly large deposit temperature range lying from 60 K to 300 K. Although the nanodot lattice is stable at room temperature, this paper focus on the early stage of ordered nucleation and growth at temperatures between 35 K and 480 K. The atomistic mechanisms leading to the nanodots array are elucidated by comparing statistical analysis of VT-STM images with multi-scaled numerical calculations combining both Molecular Dynamics for the quantitative determination of the activation energies for the atomic motion and the Kinetic Monte Carlo method for the simulations of the mesoscopic time and scale evolution of the Co submonolayer

Dynamical Properties and Plasmon Dispersion of a Weakly Degenerate Correlated One-Component Plasma

Classical Molecular Dynamics (MD) simulations for a one-component plasma (OCP) are presented. Quantum effects are included in the form of the Kelbg potential. Results for the dynamical structure factor are compared with the Vlasov and RPA (random phase approximation) theories. The influence of the coupling parameter $\Gamma$, degeneracy parameter $\rho \Lambda^3$ and the form of the pair interaction on the optical plasmon dispersion is investigated. An improved analytical approximation for the dispersion of Langmuir waves is presented.Comment: 23 pages, includes 7 ps/eps-figures and 2 table

Exploring the Leo II dSph I.: The Variable Star Content

We present the first comprehensive catalogue of variable stars in the Leo II dwarf spheroidal galaxy. We have identified 148 RR Lyrae type variables, of which 140 were amenable to derivation of variability parameters with our data. We have also confirmed the existence of four anomalous Cepheids as identified in previous studies. The average period of the RR Lyrae ab variables (0.62 days), the fraction of c variables (0.24) and the minimum period of the RR Lyrae ab variables (0.51 days) all define Leo II as an "Oosterhoff intermediate" galaxy. We have used the properties of these variables to derive a metallicity for Leo II of approximately [Fe/H]=-1.9. The presence of longer period, higher amplitude RR Lyrae variable implies a metallicity distribution that extends to as poor as [Fe/H]=-2.3. Leo II's location on the period-metallicity relation of clusters, like that of other ``Ootershoff intermediate'' objects, falls between the Oosterhoff Class I and Oosterhoff Class II clusters. The properties of the variable populations of these objects are consistent with the idea that the Oosterhoff "dichotomy" is a continuum. The gap between the classes seems to be explained by the horizontal branch of Galactic globular clusters shifting away from the instability strip at at intermediate metallicities. However, Leo II, as well as other Oosterhoff intermediate objects, has a second parameter effect strong enough to leave horizontal branch stars in the instability strip.Comment: 44 pages, 8 figures, 3 tables, accepted in Astronomical Journa

An orbital-free molecular dynamics study of melting in K_20, K_55, K_92, K_142, Rb_55 and Cs_55 clusters

The melting-like transition in potasium clusters K_N, with N=20, 55, 92 and 142, is studied by using an orbital-free density-functional constant-energy molecular dynamics simulation method, and compared to previous theoretical results on the melting-like transition in sodium clusters of the same sizes. Melting in potasium and sodium clusters proceeds in a similar way: a surface melting stage develops upon heating before the homogeneous melting temperature is reached. Premelting effects are nevertheless more important and more easily established in potasium clusters, and the transition regions spread over temperature intervals which are wider than in the case of sodium. For all the sizes considered, the percentage melting temperature reduction when passing from Na to K clusters is substantially larger than in the bulk. Once those two materials have been compared for a number of different cluster sizes, we study the melting-like transition in Rb_55 and Cs_55 clusters and make a comparison with the melting behavior of Na_55 and K_55. As the atomic number increases, the height of the specific heat peaks decreases, their width increases, and the melting temperature decreases as in bulk melting, but in a more pronounced way.Comment: LaTeX file. 6 pages with 17 pictures. Final version with minor change

Galvanic oxidation of bimetallic Zn-Fe nanoparticles for oxygen scavenging

Bimetallic nanoparticles (NP) have demonstrated outstanding multifunctional characteristics, which depend on their size, distribution and composition. In this study, we show the possibility of tailoring the oxidation behavior of Zn-Fe bimetallic nanoparticles produced by magnetron sputtering and gas agglomeration system. Zn and Fe metals were coupled to promote faster oxidation of Zn, stimulating a galvanic mechanism due to the dissimilar corrosion potential in the nanoparticles. The results revealed Zn dissolution occurring at high humidity environments for bimetallic Zn-Fe nanoparticles where no intermix exists between Zn and Fe; however, such dissolution is excluded for ZnFe alloys. The effect of the galvanic couple on the Zn dissolution was confirmed by molecular dynamic simulations. This bimetallic system can be exploited as moisture-activated oxygen scavenger materials due to the acceleration in the oxidation mechanism.This research is sponsored by FEDER funds through the program COMPETE – Programa Operacional Factores de Competitividade and by the Portuguese Foundation for Science and Technology (FCT) in the framework of the Strategic Funding UID/FIS/04650/2019, and UID/ EMS/00285/2013 and in the framework of ERA-SIINN/0004/2013, PTDC/CTM-NAN/4242/2014 and PTDC/NAN-MAT/30789/2017 projects, and through IDMEC, under LAETA, project UIDB/50022/2020. This research was supported by Norte Regional Operational Program 2014-2020 (Norte2020) through the European Regional Development Fund (ERDF) Nanotechnology based functional solutions (NORTE-01- 0145-FEDER-000019) and through European Social Fund (FSE), under the National Doctoral Program in “Surfaces Engineering and Protection”, NORTE-08-5369-FSE-000047. The authors would like to acknowledge that this project received funding from the EU Framework Programme for Research and Innovation H2020, scheme COFUND – Cofunding of Regional, National and International Programmes, under Grant Agreement 713640. The authors also thank the financial support by Portuguese Foundation for Science and Technology (FCT) in the framework of the HEALTHYDENT (co-financed via FEDER (PT2020) POCI-01-0145-FEDER-030708 and FCT (PIDDAC)), in the framework of the ATRITO-0 (co-financed via FEDER (PT2020) POCI-01-0145-FEDER030446 and FCT (PIDDAC)) and in the framework of the project NANOXYPACK co-financed via FEDER (PT2020) POCI-01-0145-FEDER030789

Atomic-scale modeling of the deformation of nanocrystalline metals

Nanocrystalline metals, i.e. metals with grain sizes from 5 to 50 nm, display technologically interesting properties, such as dramatically increased hardness, increasing with decreasing grain size. Due to the small grain size, direct atomic-scale simulations of plastic deformation of these materials are possible, as such a polycrystalline system can be modeled with the computational resources available today. We present molecular dynamics simulations of nanocrystalline copper with grain sizes up to 13 nm. Two different deformation mechanisms are active, one is deformation through the motion of dislocations, the other is sliding in the grain boundaries. At the grain sizes studied here the latter dominates, leading to a softening as the grain size is reduced. This implies that there is an ``optimal'' grain size, where the hardness is maximal. Since the grain boundaries participate actively in the deformation, it is interesting to study the effects of introducing impurity atoms in the grain boundaries. We study how silver atoms in the grain boundaries influence the mechanical properties of nanocrystalline copper.Comment: 10 pages, LaTeX2e, PS figures and sty files included. To appear in Mater. Res. Soc. Symp. Proc. vol 538 (invited paper). For related papers, see http://www.fysik.dtu.dk/~schiotz/publist.htm

Variational Approach to Molecular Kinetics

The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics

Germline MC1R status influences somatic mutation burden in melanoma

The major genetic determinants of cutaneous melanoma risk in the general population are disruptive variants (R alleles) in the melanocortin 1 receptor (MC1R) gene. These alleles are also linked to red hair, freckling, and sun sensitivity, all of which are known melanoma phenotypic risk factors. Here we report that in melanomas and for somatic C>T mutations, a signature linked to sun exposure, the expected single-nucleotide variant count associated with the presence of an R allele is estimated to be 42% (95% CI, 15-76%) higher than that among persons without an R allele. This figure is comparable to the expected mutational burden associated with an additional 21 years of age. We also find significant and similar enrichment of non-C>T mutation classes supporting a role for additional mutagenic processes in melanoma development in individuals carrying R alleles

The Free Energy Landscape of Small Molecule Unbinding

The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein) is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide) and eleven (5-diethylamino-2-pentanone) non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand) are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential) time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance) are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics) of ligand unbinding

In Vitro Dedifferentiation of Melanocytes from Adult Epidermis

In previous work we described a novel culture technique using a cholera toxin and PMA-free medium (Mel-mix) for obtaining pure melanocyte cultures from human adult epidermis. In Mel-mix medium the cultured melanocytes are bipolar, unpigmented and highly proliferative. Further characterization of the cultured melanocytes revealed the disappearance of c-Kit and TRP-1 and induction of nestin expression, indicating that melanocytes dedifferentiated in this in vitro culture. Cholera toxin and PMA were able to induce c-Kit and TRP-1 protein expressions in the cells, reversing dedifferentiation. TRP-1 mRNA expression was induced in dedifferentiated melanocytes by UV-B irradiated keratinocyte supernatants, however direct UV-B irradiation of the cells resulted in further decrease of TRP-1 mRNA expression. These dedifferentiated, easily accessible cultured melanocytes provide a good model for studying melanocyte differentiation and possibly transdifferentiation. Because melanocytes in Mel-mix medium can be cultured with human serum as the only supplement, this culture system is also suitable for autologous cell transplantation