A simple model of epitaxial growth

A discrete solid-on-solid model of epitaxial growth is introduced which, in a simple manner, takes into account the effect of an Ehrlich-Schwoebel barrier at step edges as well as the local relaxation of incoming particles. Furthermore a fast step edge diffusion is included in 2+1 dimensions. The model exhibits the formation of pyramid-like structures with a well-defined constant inclination angle. Two regimes can be distinguished clearly: in an initial phase (I) a definite slope is selected while the number of pyramids remains unchanged. Then a coarsening process (II) is observed which decreases the number of islands according to a power law in time. Simulations support self-affine scaling of the growing surface in both regimes. The roughness exponent is alpha =1 in all cases. For growth in 1+1 dimensions we obtain dynamic exponents z = 2 (I) and z = 3 (II). Simulations for d=2+1 seem to be consistent with z= 2 (I) and z= 2.3 (II) respectively.Comment: 8 pages Latex2e, 4 Postscript figures included, uses packages a4wide,epsfig,psfig,amsfonts,latexsy

Dislocation Kinks in Copper: Widths, Barriers, Effective Masses, and Quantum Tunneling

We calculate the widths, migration barriers, effective masses, and quantum tunneling rates of kinks and jogs in extended screw dislocations in copper, using an effective medium theory interatomic potential. The energy barriers and effective masses for moving a unit jog one lattice constant are close to typical atomic energies and masses: tunneling will be rare. The energy barriers and effective masses for the motion of kinks are unexpectedly small due to the spreading of the kinks over a large number of atoms. The effective masses of the kinks are so small that quantum fluctuations will be important. We discuss implications for quantum creep, kink--based tunneling centers, and Kondo resonances

Self-diffusion of adatoms, dimers, and vacancies on Cu(100)

We use ab initio static relaxation methods and semi-empirical molecular-dynamics simulations to investigate the energetics and dynamics of the diffusion of adatoms, dimers, and vacancies on Cu(100). It is found that the dynamical energy barriers for diffusion are well approximated by the static, 0 K barriers and that prefactors do not depend sensitively on the species undergoing diffusion. The ab initio barriers are observed to be significantly lower when calculated within the generalized-gradient approximation (GGA) rather than in the local-density approximation (LDA). Our calculations predict that surface diffusion should proceed primarily via the diffusion of vacancies. Adatoms are found to migrate most easily via a jump mechanism. This is the case, also, of dimers, even though the corresponding barrier is slightly larger than it is for adatoms. We observe, further, that dimers diffuse more readily than they can dissociate. Our results are discussed in the context of recent submonolayer growth experiments of Cu(100).Comment: Submitted to the Physical Review B; 15 pages including postscript figures; see also http://www.centrcn.umontreal.ca/~lewi

Are Vicinal Metal Surfaces Stable?

Quantum Matter and Optic

Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction

<p>Abstract</p> <p>Background</p> <p>Reliable predictions of Cytotoxic T lymphocyte (CTL) epitopes are essential for rational vaccine design. Most importantly, they can minimize the experimental effort needed to identify epitopes. NetCTL is a web-based tool designed for predicting human CTL epitopes in any given protein. It does so by integrating predictions of proteasomal cleavage, TAP transport efficiency, and MHC class I affinity. At least four other methods have been developed recently that likewise attempt to predict CTL epitopes: EpiJen, MAPPP, MHC-pathway, and WAPP. In order to compare the performance of prediction methods, objective benchmarks and standardized performance measures are needed. Here, we develop such large-scale benchmark and corresponding performance measures and report the performance of an updated version 1.2 of NetCTL in comparison with the four other methods.</p> <p>Results</p> <p>We define a number of performance measures that can handle the different types of output data from the five methods. We use two evaluation datasets consisting of known HIV CTL epitopes and their source proteins. The source proteins are split into all possible 9 mers and except for annotated epitopes; all other 9 mers are considered non-epitopes. In the RANK measure, we compare two methods at a time and count how often each of the methods rank the epitope highest. In another measure, we find the specificity of the methods at three predefined sensitivity values. Lastly, for each method, we calculate the percentage of known epitopes that rank within the 5% peptides with the highest predicted score.</p> <p>Conclusion</p> <p>NetCTL-1.2 is demonstrated to have a higher predictive performance than EpiJen, MAPPP, MHC-pathway, and WAPP on all performance measures. The higher performance of NetCTL-1.2 as compared to EpiJen and MHC-pathway is, however, not statistically significant on all measures. In the large-scale benchmark calculation consisting of 216 known HIV epitopes covering all 12 recognized HLA supertypes, the NetCTL-1.2 method was shown to have a sensitivity among the 5% top-scoring peptides above 0.72. On this dataset, the best of the other methods achieved a sensitivity of 0.64. The NetCTL-1.2 method is available at <url>http://www.cbs.dtu.dk/services/NetCTL</url>.</p> <p>All used datasets are available at <url>http://www.cbs.dtu.dk/suppl/immunology/CTL-1.2.php</url>.</p