Finite-size versus Surface effects in nanoparticles

We study the finite-size and surface effects on the thermal and spatial behaviors of the magnetisation of a small magnetic particle. We consider two systems: 1) A box-shaped isotropic particle of simple cubic structure with either periodic or free boundary conditions. This case is treated analytically using the isotropic model of D-component spin vectors in the limit $D\to \infty$, including the magnetic field. 2) A more realistic particle ($\gamma$-Fe$_{2}$O$_{3}$) of ellipsoidal (or spherical) shape with open boundaries. The magnetic state in this particle is described by the anisotropic classical Dirac-Heisenberg model including exchange and dipolar interactions, and bulk and surface anisotropy. This case is dealt with by the classical Monte Carlo technique. It is shown that in both systems finite-size effects yield a positive contribution to the magnetisation while surface effects render a larger and negative contribution, leading to a net decrease of the magnetisation of the small particle with respect to the bulk system. In the system 2) the difference between the two contributions is enhanced by surface anisotropy. The latter also leads to non saturation of the magnetisation at low temperatures, showing that the magnetic order in the core of the particle is perturbed by the magnetic disorder on the surface. This is confirmed by the profile of the magnetisation.Comment: 6 pages of RevTex including 4 Figures, invited paper to 3rd EuroConference on Magnetic Properties of Fine Nanoparticles, Barcelona, October 9

Boundary and finite-size effects in small magnetic systems

We study the effect of free boundaries in finite magnetic systems of cubic shape on the field and temperature dependence of the magnetization within the isotropic model of D-component spin vectors in the limit D \to \infty. This model is described by a closed system of equations and captures the Goldstone-mode effects such as global rotation of the magnetic moment and spin-wave fluctuations. We have obtained an exact relation between the intrinsic (short-range) magnetization M = M(H,T) of the system and the supermagnetization m = m(H,T) which is induced by the field. We have shown, analytically at low temperatures and fields and numerically in a wide range of these parameters, that boundary effects leading to the decrease of M with respect to the bulk value are stronger than the finite-size effects making a positive contribution to M. The inhomogeneities of the magnetization caused by the boundaries are long ranged and extend far into the depth of the system.Comment: 15 pages, 5 figures, To appear in Physica

Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases

BACKGROUND: Manually finding subtle yet statistically significant links to distantly related homologues becomes practically impossible for very populated protein families due to the sheer number of similarity searches to be invoked and analyzed. The unclear evolutionary relationship between classical mammalian lipases and the recently discovered human adipose triglyceride lipase (ATGL; a patatin family member) is an exemplary case for such a problem. RESULTS: We describe an unsupervised, sensitive sequence segment collection heuristic suitable for assembling very large protein families. It is based on fan-like expanding, iterative database searches. To prevent inclusion of unrelated hits, additional criteria are introduced: minimal alignment length and overlap with starting sequence segments, finding starting sequences in reciprocal searches, automated filtering for compositional bias and repetitive patterns. This heuristic was implemented as FAMILYSEARCHER in the ANNIE sequence analysis environment and applied to search for protein links between the classical lipase family and the patatin-like group. CONCLUSION: The FAMILYSEARCHER is an efficient tool for tracing distant evolutionary relationships involving large protein families. Although classical lipases and ATGL have no obvious sequence similarity and differ with regard to fold and catalytic mechanism, homology links detected with FAMILYSEARCHER show that they are evolutionarily related. The conserved sequence parts can be narrowed down to an ancestral core module consisting of three β-strands, one α-helix and a turn containing the typical nucleophilic serine. Moreover, this ancestral module also appears in numerous enzymes with various substrate specificities, but that critically rely on nucleophilic attack mechanisms

MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins

We evaluated the evolutionary conservation of glycine myristoylation within eukaryotic sequences. Our large-scale cross-genome analyses, available as MYRbase, show that the functional spectrum of myristoylated proteins is currently largely underestimated. We give experimental evidence for in vitro myristoylation of selected predictions. Furthermore, we classify five membrane-attachment factors that occur most frequently in combination with, or even replacing, myristoyl anchors, as some protein family examples show

ANNIE: integrated de novo protein sequence annotation

Function prediction of proteins with computational sequence analysis requires the use of dozens of prediction tools with a bewildering range of input and output formats. Each of these tools focuses on a narrow aspect and researchers are having difficulty obtaining an integrated picture. ANNIE is the result of years of close interaction between computational biologists and computer scientists and automates an essential part of this sequence analytic process. It brings together over 20 function prediction algorithms that have proven sufficiently reliable and indispensable in daily sequence analytic work and are meant to give scientists a quick overview of possible functional assignments of sequence segments in the query proteins. The results are displayed in an integrated manner using an innovative AJAX-based sequence viewer. ANNIE is available online at: http://annie.bii.a-star.edu.sg. This website is free and open to all users and there is no login requirement