Ab-initio spin dynamics applied to nanoparticles: canted magnetism of a finite Co chain along a Pt(111) surface step edge

In order to search for the magnetic ground state of surface nanostructures we extended first principles adiabatic spin dynamics to the case of fully relativistic electron scattering. Our method relies on a constrained density functional theory whereby the evolution of the orientations of the spin-moments results from a semi-classical Landau-Lifshitz equation. This approach is applied to a study of the ground state of a finite Co chain placed along a step edge of a Pt(111) surface. As far as the ground state spin orientation is concerned we obtain excellent agreement with the experiment. Furthermore we observe noncollinearity of the atom-resolved spin and orbital moments. In terms of magnetic force theorem calculations we also demonstrate how a reduction of symmetry leads to the existence of canted magnetic states.Comment: 4 pages, ReVTeX + 3 figures (Encapsulated Postscript), submitted to PR

Interacting with the biomolecular solvent accessible surface via a haptic feedback device

Background: From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results: A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion: By using the software, named HaptiMol ISAS (available from http://​www.​haptimol.​co.​uk), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software

Structural Characterization of Protein Folding Intermediates by Oxidative Labeling and Mass Spectrometry

A key challenge associated with protein folding studies is the characterization of short-lived intermediates that become populated en route to the native state. In this work, a covalent labeling method was developed that provides insights into the structures of these transient species. Hydroxyl radical (·OH) reacts with solvent-exposed side chains, whereas buried residues are protected. Mass spectrometry is used for monitoring the locations and the extent of labeling. Pulsed ·OH labeling of proteins at selected time points during folding results in high temporal and spatial resolution when compared to existing other labeling methods. This novel technique was validated by studying the kinetic unfolding and refolding of holomyoglobin (hMb) and cytochrome c (cyt c), respectively. The noncovalent prosthetic heme group in hMb was shown to drastically affect the unfolding pathway. Cyt c refolding was found to fold in a stepwise manner. The population of a misfolded cyt c intermediate was also detected. Results in both cases were in accord with published data. Many cellular proteins exist as oligomers. Pulsed ·OH labeling method was therefore extended to monitor the folding and assembly of a 22 kDa homodimeric protein, S100A11. Prior to this study very little information regarding the folding mechanism of this protein was available. ·OH labeling reveals that disruption of the native dimer is followed by the formation of non-native hydrophobic contacts within the denatured monomers. The folding/binding pathway was shown to progress through monomeric and dimeric intermediates. In the final section of this study we applied ·OH labeling to a large monomeric protein that folds to a metastable state. The folding pathway of the 44 kDa protease inhibitor, α1-antitrypsin, was characterized and compared with complementary data from hydrogen/deuterium exchange studies. Our results show that the formation of early tertiary contacts and specific hydrogen bonds guide the protein towards its active, metastable structure. Structural correlation is also seen between a late kinetic species and a previously characterized equilibrium intermediate of a pathogenic mutant. Overall, the results presented highlight the ability of the technique developed in this work to provide in-depth information about the mechanisms of protein folding

Spin-correlations and magnetic structure in an Fe monolayer on 5d transition metal surfaces

We present a detailed first principles study on the magnetic structure of an Fe monolayer on different surfaces of 5d transition metals. We use the spin-cluster expansion technique to obtain parameters of a spin model, and predict the possible magnetic ground state of the studied systems by employing the mean field approach and in certain cases by spin dynamics calculations. We point out that the number of shells considered for the isotropic exchange interactions plays a crucial role in the determination of the magnetic ground state. In the case of Ta substrate we demonstrate that the out-of-plane relaxation of the Fe monolayer causes a transition from ferromagnetic to antiferromagnetic ground state. We examine the relative magnitude of nearest neighbour Dzyaloshinskii-Moriya (D) and isotropic (J) exchange interactions in order to get insight into the nature of magnetic pattern formations. For the Fe/Os(0001) system we calculate a very large D/J ratio, correspondingly, a spin spiral ground state. We find that, mainly through the leading isotropic exchange and Dzyaloshinskii-Moriya interactions, the inward layer relaxation substantially influences the magnetic ordering of the Fe monolayer. For the Fe/Re(0001) system characterized by large antiferromagnetic interactions we also determine the chirality of the $120^{\circ}$ N\'eel-type ground state.Comment: 15 pages, 8 figures, 2 table

Can’t get you out of my mind: Empathy, Distress, and Recurring Thoughts about a Person in Need

Research suggests that empathic concern and distress give rise to different patterns of helping behavior. It has been proposed that this difference is caused by the effects of these emotions on recurrent thoughts about the person in need. However, no research has directly investigated this potential explanation. To remedy this, we tested the hypotheses that distress, but not empathic concern, is associated with both anticipated recurring thoughts (Study 1) and experienced recurring thoughts (Study 2) about a victim. We also tested the hypothesis that distress is associated with thoughts about the victim, whereas empathic concern is associated with thoughts about the victim’s situation (Study 3), which is potentially a consequence of the motives associated with each emotion. Lastly, we assessed the causal relations between distress, empathic concern, and recurrent thoughts (Study 4). Overall, results demonstrate a distinctive, and important, pattern of associations among empathic concern, distress, and different forms of recurrent thoughts about an emotion-eliciting stimulus

Exchange interaction between magnetic adatoms on surfaces of noble metals

We present first-principles calculations of the exchange interactions between magnetic impurities deposited on (001), (110), and (111) surfaces of Cu and Au and analyze them, in particular, in the asymptotic regime. For the (110) and the (111) surfaces, we demonstrate that the interaction shows an oscillatory behavior as a function of the distance, R, of the impurities and that the amplitude of the oscillations decays as 1/R(2). Furthermore, the frequency of the oscillations is closely related to the length of the Fermi vector of the surface states existing on these surfaces. Due to the asymmetry of the surface-states dispersion, the frequency of the oscillations becomes also asymmetric on the (110) surfaces, while on the Au(111) surface two distinct frequencies are found in the oscillations as a consequence of the Bychkov-Rashba splitting of the surface states. Remarkably, no long-range oscillations of the exchange interaction are observed for the (001) surfaces where the surface states are unoccupied. When burying the impurities beneath the surface layer, oscillations mediated by the bulk states become visible