Phonons in Ultrathin Oxide Films: 2D to 3D Transition in FeO on Pt(111).

The structural and magnetic properties of ultrathin FeO(111) films on Pt(111) with thicknesses from 1 to 16 monolayers (MLs) were studied using the nuclear inelastic scattering of synchrotron radiation. A distinct evolution of vibrational characteristics with thickness, revealed in the phonon density of states (PDOS), shows a textbook transition from 2D to 3D lattice dynamics. For the thinnest films of 1 and 2 ML, the low-energy part of the PDOS followed a linear ∝E dependence in energy that is characteristic for two-dimensional systems. This dependence gradually transforms with thickness to the bulk ∝E^{2} relationship. Density-functional theory phonon calculations perfectly reproduced the measured 1-ML PDOS within a simple model of a pseudomorphic FeO/Pt(111) interface. The calculations show that the 2D PDOS character is due to a weak coupling of the FeO film to the Pt(111) substrate. The evolution of the vibrational properties with an increasing thickness is closely related to a transient long-range magnetic order and stabilization of an unusual structural phase.

Transfer of magnetic anisotropy in epitaxial Co/NiO/Fe trilayers.

The magnetic properties of Co(10 Å)/NiO(40 Å)/Fe trilayer epitaxially grown on W(110) substrate were investigated with use of x-ray magnetic linear dichroism (XMLD) and x-ray magnetic circular dichroism (XMCD). We showed that magnetic anisotropy of Fe film that can be controlled by a thickness-driven spin reorientation transition is transferred via interfacial exchange coupling not only to NiO layer but further to ferromagnetic Co overlayer as well. Similarly, a temperature driven spin reorientation of Fe sublayer induces a reorientation of NiO spin orientation and simultaneous switching of the Co magnetization direction. Finally, by element specific XMCD and XMLD magnetic hysteresis loop measurements we proved that external magnetic field driven reorientation of Fe and Co magnetizations as well as NiO Néel vector are strictly correlated and magnetic anisotropy fields of Fe and Co sublayers are identical despite the different crystal structures.

The dynamics of the non-heme iron in bacterial reaction centers from Rhodobacter sphaeroides.

We investigate the dynamical properties of the non-heme iron (NHFe) in His-tagged photosynthetic bacterial reaction centers (RCs) isolated from Rhodobacter (Rb.) sphaeroides. Mössbauer spectroscopy and nuclear inelastic scattering of synchrotron radiation (NIS) were applied to monitor the arrangement and flexibility of the NHFe binding site. In His-tagged RCs, NHFe was stabilized only in a high spin ferrous state. Its hyperfine parameters (IS=1.06±0.01mm/s and QS=2.12±0.01mm/s), and Debye temperature (θ(D0)~167K) are comparable to those detected for the high spin state of NHFe in non-His-tagged RCs. For the first time, pure vibrational modes characteristic of NHFe in a high spin ferrous state are revealed. The vibrational density of states (DOS) shows some maxima between 22 and 33meV, 33 and 42meV, and 53 and 60meV and a very sharp one at 44.5meV. In addition, we observe a large contribution of vibrational modes at low energies. This iron atom is directly connected to the protein matrix via all its ligands, and it is therefore extremely sensitive to the collective motions of the RC protein core. A comparison of the DOS spectra of His-tagged and non-His-tagged RCs from Rb. sphaeroides shows that in the latter case the spectrum was overlapped by the vibrations of the heme iron of residual cytochrome c(2), and a low spin state of NHFe in addition to its high spin one. This enabled us to pin-point vibrations characteristic for the low spin state of NHFe.

Oxygen on an Fe monolayer on W(110): From chemisorption to oxidation.

The adsorption of oxygen on a pseudomorphic iron monolayer deposited on a W(110) surface was studied experimentally and theoretically. Standard surface characterization methods, such as Auger electron spectroscopy and low energy electron diffraction, and specific nuclear methods, such as conversion electron Mössbauer spectroscopy (CEMS) and nuclear resonant scattering of synchrotron radiation, combined with theoretical calculations based on the density functional theory allowed us to determine the structure of the oxygen adsorbate and the electronic properties of iron atoms with different oxygen coordinations. The oxygen-(3 × 2) structure on the iron monolayer was recognized and was interpreted to be a state with oxygen chemisorbed on the non-reconstructed surface with modest electron transfer from iron to oxygen. A transition from chemisorbed oxygen to the onset of Fe-oxidation is revealed by distinct changes in the CEMS spectra.

An integrated metric physical map of human chromosome 19.

A metric physical map of human chromosome 19 has been generated. The foundation of the map is sets of overlapping cosmids (contigs) generated by automated fingerprinting spanning over 95% of the euchromatin, about 50 megabases (Mb). Distances between selected cosmid clones were estimated using fluorescence in situ hybridization in sperm pronuclei, providing both order and distance between contigs. An average inter-marker separation of 230 kb has been obtained across the non-centromeric portion of the chromosome. Various types of larger insert clones were used to span gaps between contigs. Currently, the map consists of 51 'islands' containing multiple clone types, whose size, order and relative distance are known. Over 450 genes, genetic markers, sequence tagged sites (STSs), anonymous cDNAs, and other markers have been localized. In addition, EcoRI restriction maps have been generated for > 41 Mb (approximately 83%) of the chromosome.

Tunable interplay between exchange coupling and uniaxial magnetic anisotropy in epitaxial CoO/Au/Fe trilayers.

We show that the interaction between ferromagnetic Fe(110) and antiferromagnetic CoO(111) sublayers can be mediated and precisely tuned by a nonmagnetic Au spacer. Our results prove that the thickness of the Fe and Au layers can be chosen to modify the effective anisotropy of the Fe layer and the strength of the exchange bias interaction between Fe and CoO sublayers. Well-defined and tailorable magnetic anisotropy of the ferromagnet above Néel temperature of the antiferromagnet is a determining factor that governs exchange bias and interfacial CoO spins orientation at low temperatures. In particular, depending on the room temperature magnetic state of Fe, the low-temperature exchange bias in a zero-field cooled system can be turned "off" or "on". The other way around, we show that exchange bias can be the dominating magnetic anisotropy source for the ferromagnet and it is feasible to induce a 90-degree rotation of the easy axis as compared to the initial, exchange bias-free easy axis orientation.

Tunable magnetic anisotropy of antiferromagnetic NiO in (Fe)/NiO/MgO/Cr/MgO(001) epitaxial multilayers.

We report on the magnetic properties of antiferromagnetic NiO(001) thin films in epitaxially grown NiO/MgO(dMgO)/Cr/MgO(001) system for different thicknesses of MgO, dMgO. Results of X-ray Magnetic Linear Dichroism show that together with an increase of dMgO, rotation of NiO spins from in-plane towards out-of-plane direction occurs. Furthermore, we investigated how the proximity of Fe modifies the magnetic state of NiO in Fe/NiO/MgO(dMgO)/Cr/MgO(001). We proved the existence of a multidomain state in NiO as a result of competition between the ferromagnet/antiferromagnet exchange coupling and strain exerted on the NiO by the MgO buffer layer.

From Termination Dependent Chemical Sensitivity of Spin Orientation in All-bcc Fe/Co Magnetic Superlattices toward the Concept of an Artificial Surface of a Ferromagnet.

Adsorption of gases on the surface of all-bcc (Fe/Co)N superlattices drives the in-plane, 90° magnetization rotation of the bulk-like Fe(110) supporting ferromagnet. Both experimental and theoretical results prove that terminating the surface of (Fe/Co)N superlattices either by Co or by Fe switches "ON" or "OFF" the spin orientation sensitivity to adsorption. Results indicate that purely surface limited adsorption processes strongly modify the magnetic anisotropy of the entire (Fe/Co)N superlattice, which acts as a kind of "artificial" surface of the bulky Fe(110) ferromagnet. Such an artificial magnetic surface anisotropy concept not only enhances the surface contribution in classical surface-bulk competition but also provides its additional chemical sensitivity.

Coupling of collective motions of the protein matrix to vibrations of the non-heme iron in bacterial photosynthetic reaction centers.

Non-heme iron is a conservative component of type II photosynthetic reaction centers of unknown function. We found that in the reaction center from Rba. sphaeroides it exists in two forms, high and low spin ferrous states, whereas in Rsp. rubrum mostly in a low spin state, in line with our earlier finding of its low spin state in the algal photosystem II reaction center (Burda et al., 2003). The temperature dependence of the non-heme iron displacement studied by Mössbauer spectroscopy shows that the surrounding of the high spin iron is more flexible (Debye temperature ~165K) than that of the low spin atom (~207K). Nuclear inelastic scattering measurements of the collective motions in the Rba. sphaeroides reaction center show that the density of vibrational states, originating from non-heme iron, has well-separated modes between lower (4-17meV) and higher (17-25meV) energies while in the one from Rsp. rubrum its distribution is more uniform with only little contribution of low energy (~6meV) vibrations. It is the first experimental evidence that the fluctuations of the protein matrix in type II reaction center are correlated to the spin state of non-heme iron. We propose a simple mechanism in which the spin state of non-heme iron directly determines the strength of coupling between the two quinone acceptors (Q(A) and Q(B)) and fast collective motions of protein matrix that play a crucial role in activation and regulation of the electron and proton transfer between these two quinones. We suggest that hydrogen bond network on the acceptor side of reaction center is responsible for stabilization of non-heme iron in different spin states.

Noncollinear magnetization structure at the thickness-driven spin-reorientation transition in epitaxial Fe films on W(110).

An in-plane spin-reorientation transition occurring during the growth of epitaxial Fe films on W(110) was studied in situ by using the nuclear resonant scattering of synchrotron radiation. The spin-reorientation transition originates at the Fe/W(110) interface and proceeds via a noncollinear spin structure resembling a planar domain wall that propagates towards the surface with increasing film thickness.

Fine tuning of ferromagnet/antiferromagnet interface magnetic anisotropy for field-free switching of antiferromagnetic spins.

We show that in a uniform thickness NiO(111)/Fe(110) epitaxial bilayer system, at given temperature near 300 K, two magnetic states with orthogonal spin orientations can be stabilized in antiferromagnetic NiO. Field-free, reversible switching between these two antiferromagnetic states is demonstrated. The observed phenomena arise from the unique combination of precisely tuned interface magnetic anisotropy, thermal hysteresis of spin reorientation transition and interfacial ferromagnet/antiferromagnet exchange coupling. The possibility of field-free switching between two magnetic states in an antiferromagnet is fundamentally interesting and can lead to new ideas in heat assisted magnetic recording technology.

Driving the polar spin reorientation transition of ultrathin ferromagnets with antiferromagnetic-ferromagnetic phase transition of nearby FeRh alloy film.

We show that in-plane to out-of-plane magnetization switching of a ferromagnetic layer can be driven by antiferromagnetic-ferromagnetic phase transition in a nearby FeRh system. For FeRh/Au/FeAu trilayers, the impact of the magnetic phase transition of FeRh onto the perpendicular magnetization of monoatomic FeAu superlattices is transferred across the Au spacer layer via interlayer magnetic coupling. The polar spin reorientation process of the FeAu spins driven by the magnetic phase transition in the FeRh reveals its major features; namely it is reversible and displays hysteresis.

Correction: Fine tuning of ferromagnet/antiferromagnet interface magnetic anisotropy for field-free switching of antiferromagnetic spins.

Correction for 'Fine tuning of ferromagnet/antiferromagnet interface magnetic anisotropy for field-free switching of antiferromagnetic spins' by M. Slezak et al., Nanoscale, 2020, DOI: 10.1039/d0nr04193a.

MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications.

Knowledge of toxins, virulence factors and antibiotic resistance genes is essential for bio-defense applications aimed at identifying 'functional' signatures for characterizing emerging or engineered pathogens. Whereas genetic signatures identify a pathogen, functional signatures identify what a pathogen is capable of. To facilitate rapid identification of sequences and characterization of genes for signature discovery, we have collected all publicly available (as of this writing), organized sequences representing known toxins, virulence factors, and antibiotic resistance genes in one convenient database, which we believe will be of use to the bio-defense research community. MvirDB integrates DNA and protein sequence information from Tox-Prot, SCORPION, the PRINTS virulence factors, VFDB, TVFac, Islander, ARGO and a subset of VIDA. Entries in MvirDB are hyperlinked back to their original sources. A blast tool allows the user to blast against all DNA or protein sequences in MvirDB, and a browser tool allows the user to search the database to retrieve virulence factor descriptions, sequences, and classifications, and to download sequences of interest. MvirDB has an automated weekly update mechanism. Each protein sequence in MvirDB is annotated using our fully automated protein annotation system and is linked to that system's browser tool. MvirDB can be accessed at http://mvirdb.llnl.gov/.

How a ferromagnet drives an antiferromagnet in exchange biased CoO/Fe(110) bilayers.

Antiferromagnet/ferromagnet (AFM/FM) bilayers that display the exchange bias (EB) effect have been subjected to intensive material research, being the key elements of novel spintronics systems. In a commonly accepted picture, the antiferromagnet, considered as a rigid material due to its high anisotropy and magnetic hardness, controls the magnetic properties of the ferromagnet, such as a shift of the hysteresis loop or coercivity. We show that this AFM-FM master-slave hierarchy is not generally valid and that the influence of the ferromagnet on the magnetic anisotropy (MA) of the neighbouring antiferromagnet must be considered. Our computer simulation and experimental studies of EB in an epitaxial CoO/Fe(110) bilayer show that the ferromagnetic layer with strong uniaxial magnetic anisotropy determines the interfacial spin orientations of the neighbouring AFM layer and rotates its easy axis. This effect has a strong feedback on the EB effect experienced by the FM layer. Our results show new physics behind the EB effect, providing a route for grafting a desired anisotropy onto the AFM and for precise tailoring of EB in AFM/FM systems.

AS2TS system for protein structure modeling and analysis.

We present a set of programs and a website designed to facilitate protein structure comparison and protein structure modeling efforts. Our protein structure analysis and comparison services use the LGA (local-global alignment) program to search for regions of local similarity and to evaluate the level of structural similarity between compared protein structures. To facilitate the homology-based protein structure modeling process, our AL2TS service translates given sequence-structure alignment data into the standard Protein Data Bank (PDB) atom records (coordinates). For a given sequence of amino acids, the AS2TS (amino acid sequence to tertiary structure) system calculates (e.g. using PSI-BLAST PDB analysis) a list of the closest proteins from the PDB, and then a set of draft 3D models is automatically created. Web services are available at http://as2ts.llnl.gov/.

A computer-based data analysis system for enzyme-linked immunosorbent assays.

A computerized system is presented for automating the data collection, processing, and displaying tasks involved in enzyme-linked immunosorbent assays. This system uses a through-the-well absorbance reader of microtiter plates interfaced to a minicomputer running the UNIX operating system. Optical density in each well of a 96-well microtiter plate is recorded as a function of time for up to 10 time points. These data are automatically transmitted to the remote computer. The rate of product formation is then calculated for each well, and a battery of analysis, display, and comparison programs can then be used by the researcher for data presentation. Using the initial rate of reaction as the basis for quantifying enzyme-linked immunosorbent assays focuses on the catalytic property of the enzyme and allows a large dynamic range of the assay on any plate. These programs can be adapted to virtually any mini- or microcomputer with a graphics display or a plotting device. Assuming moderately powerful computing hardware, throughputs of 50 plates per day are easily achieved. The programs work equally well with peroxidase, beta-galactosidase, or alkaline phosphatase conjugated second antibodies, and with whole cell or soluble antigens.

DataFoundry: information management for scientific data.

Data warehouses and data marts have been successfully applied to a multitude of commercial business applications. They have proven to be invaluable tools by integrating information from distributed, heterogeneous sources and summarizing this data for use throughout the enterprise. Although the need for information dissemination is as vital in science as in business, working warehouses in this community are scarce because traditional warehousing techniques do not transfer to scientific environments. There are two primary reasons for this difficulty. First, schema integration is more difficult for scientific databases than for business sources, because of the complexity of the concepts and the associated relationships. While this difference has not yet been fully explored, it is an important consideration when determining how to integrate autonomous sources. Second, scientific data sources have highly dynamic data representations (schemata). When a data source participating in a warehouse changes its schema, both the mediator transferring data to the warehouse and the warehouse itself need to be updated to reflect these modifications. The cost of repeatedly performing these updates in a traditional warehouse, as is required in a dynamic environment, is prohibitive. This paper discusses these issues within the context of the DataFoundry project, an ongoing research effort at Lawrence Livermore National Laboratory. DataFoundry utilizes a unique integration strategy to identify corresponding instances while maintaining differences between data from different sources, and a novel architecture and an extensive meta-data infrastructure, which reduce the cost of maintaining a warehouse.