Controlled Electronic and Magnetic Landscape in Self-Assembled Complex Oxide Heterostructures.

Complex oxide heterointerfaces contain a rich playground of novel physical properties and functionalities, which give rise to emerging technologies. Among designing and controlling the functional properties of complex oxide film heterostructures, vertically aligned nanostructure (VAN) films using a self-assembling bottom-up deposition method presents great promise in terms of structural flexibility and property tunability. Here, the bottom-up self-assembly is extended to a new approach using a mixture containing a 2Dlayer-by-layer film growth, followed by a 3D VAN film growth. In this work, the two-phase nanocomposite thin films are based on LaAlO3 :LaBO3 , grown on a lattice-mismatched SrTiO3001 (001) single crystal. The 2D-to-3D transient structural assembly is primarily controlled by the composition ratio, leading to the coexistence of multiple interfacial properties, 2D electron gas, and magnetic anisotropy. This approach provides multidimensional film heterostructures which enrich the emergent phenomena for multifunctional applications.

Spin waves in disordered materials.

We present an efficient methodology to study spin waves in disordered materials. The approach is based on a Heisenberg model and enables calculations of magnon properties in spin systems with disorder of an arbitrary kind and concentration of impurities. Disorder effects are taken into account within two complementary approaches. Magnons in systems with substitutional (uncorrelated) disorder can be efficiently calculated within a single-site coherent potential approximation for the Heisenberg model. From the computation point of view the method is inexpensive and directly applicable to systems like alloys and doped materials. It is shown that it performs exceedingly well across all concentrations and wave vectors. Another way is the direct numerical simulation of large supercells using a configurational average over possible samples. This approach is applicable to systems with an arbitrary kind of disorder. The effective interaction between magnetic moments entering the Heisenberg model can be obtained from first-principles using a self-consistent Green function method within the density functional theory. Thus, our method can be viewed as an ab initio approach and can be used for calculations of magnons in real materials.

Solar Absorption by Aerosol-Bound Nitrophenols Compared to Aqueous and Gaseous Nitrophenols.

Nitrophenols are well-known absorbers of near-UV/blue radiation and are considered to be a component of solar-absorbing organic aerosol material commonly labeled brown carbon. Nitrophenols have been identified in a variety of phases in earth's atmosphere, including the gaseous, aqueous, and aerosol bound, and these different environments alter their UV-vis absorption spectra, most dramatically when deprotonated forming nitrophenolates. We quantify the impact of these different absorption profiles by calculating the solar power absorbed per molecule for several nitrophenols. For instance, aqueous 2,4-dinitrophenol absorption varies dramatically over the pH range of cloud droplets with pH = 5.5 solutions absorbing three times the solar power compared to pH = 3.5 solutions. We also measured the UV-vis spectra of 2-nitrophenol adsorbed on several aerosol substrates representative of mineral dust, inorganic salts, and organic aerosol and compare these spectra to gaseous and aqueous 2-nitrophenol. 2-Nitrophenol adsorbed on mineral and chloride aerosol substrates exhibits a red-shifted absorption band (∼450-650 nm) consistent with 2-nitrophenolate and absorbs twice the solar power per molecule compared to gaseous, aqueous, and organic aerosol-bound 2-nitrophenol. We also discuss how different nitrophenol absorption profiles alter important atmospheric photolysis rate constants [e.g., J(NO2) and J(O3)] by attenuating solar flux.

Interface electronic complexes and Landau damping of magnons in ultrathin magnets.

The damping of magnons in ultrathin metallic magnets is studied from first-principles. We contrast Fe/Cu(100) and Fe/W(110) systems for which the influence of the substrate on the magnon life time differs strongly. We introduce the concept of Landau map in momentum space to assess the role of different electronic states in the attenuation. The formation of electronic complexes localized at the film-substrate interface leads to hot spots in the Landau maps and enhances the damping. This finding allows tuning the attenuation of high-frequency magnetization dynamics in nanostructures.

Standing spin waves as a basis for the control of terahertz spin dynamics: time dependent density functional theory study.

We report on the linear response density functional study of the magnetization dynamics in Co(100) film driven by a nonuniform magnetic field. At resonant frequencies in the terahertz range, the magnetic field excites standing spin waves of the system and the induced magnetization penetrates the whole volume of the film. The pattern of magnetization precession is strongly influenced by the spin-flip excitations of single electrons which lead to the Landau damping of the spin-wave modes. Our results pave the way for the precise control of terahertz magnetization dynamics in itinerant magnets.

Energies and lifetimes of magnons in complex ferromagnets: a first-principle study of Heusler alloys.

The energies and lifetimes of magnons in several Mn-based Heusler alloys are studied using linear response density functional theory. The number of the spin wave branches in Co(2)MnSi corresponds to the number of its magnetic sublattices in contrast with the NiMnSb case in which the induced Ni sublattice cannot support optical magnons. The half-metallicity of these systems results in long-living acoustic spin waves. The example of non-half-metallic Cu(2)MnAl shows that the hybridization with Stoner continuum leads not only to the damping of magnons but also to a renormalization of their energies.

Structural reorganization and the cooperative binding of single-stranded telomere DNA in Sterkiella nova.

In Sterkiella nova, alpha and beta telomere proteins bind cooperatively with single-stranded DNA to form a ternary alpha.beta.DNA complex. Association of telomere protein subunits is DNA-dependent, and alpha-beta association enhances DNA affinity. To further understand the molecular basis for binding cooperativity, we characterized several possible stepwise assembly pathways using isothermal titration calorimetry. In one path, alpha and DNA first form a stable alpha.DNA complex followed by the addition of beta in a second step. Binding energy accumulates with nearly equal free energy of association for each of these steps. Heat capacity is nonetheless dramatically different, with DeltaCp = -305 +/- 3 cal mol(-1) K(-1) for alpha binding with DNA and DeltaCp = -2010 +/- 20 cal mol(-1) K(-1) for the addition of beta to complete the alpha.beta.DNA complex. By examining alternate routes including titration of single-stranded DNA with a preformed alpha.beta complex, a significant portion of binding energy and heat capacity could be assigned to structural reorganization involving protein-protein interactions and repositioning of the DNA. Structural reorganization probably affords a mechanism to regulate high affinity binding of telomere single-stranded DNA with important implications for telomere biology. Regulation of telomere complex dissociation is thought to involve post-translational modifications in the lysine-rich C-terminal portion of beta. We observed no difference in binding energetics or crystal structure when comparing complexes prepared with full-length beta or a C-terminally truncated form, supporting interesting parallels between the intrinsically disordered regions of histones and this portion of beta.

Structure of conkunitzin-S1, a neurotoxin and Kunitz-fold disulfide variant from cone snail.

Cone snails (Conus) are predatory marine mollusks that immobilize prey with venom containing 50-200 neurotoxic polypeptides. Most of these polypeptides are small disulfide-rich conotoxins that can be classified into families according to their respective ion-channel targets and patterns of cysteine-cysteine disulfides. Conkunitzin-S1, a potassium-channel pore-blocking toxin isolated from C. striatus venom, is a member of a newly defined conotoxin family with sequence homology to Kunitz-fold proteins such as alpha-dendrotoxin and bovine pancreatic trypsin inhibitor (BPTI). While conkunitzin-S1 and alpha-dendrotoxin are 42% identical in amino-acid sequence, conkunitzin-S1 has only four of the six cysteines normally found in Kunitz proteins. Here, the crystal structure of conkunitzin-S1 is reported. Conkunitzin-S1 adopts the canonical 3(10)-beta-beta-alpha Kunitz fold complete with additional distinguishing structural features including two completely buried water molecules. The crystal structure, although completely consistent with previously reported NMR distance restraints, provides a greater degree of precision for atomic coordinates, especially for S atoms and buried solvent molecules. The region normally cross-linked by cysteines II and IV in other Kunitz proteins retains a network of hydrogen bonds and van der Waals interactions comparable to those found in alpha-dendrotoxin and BPTI. In conkunitzin-S1, glycine occupies the sequence position normally reserved for cysteine II and the special steric properties of glycine allow additional van der Waals contacts with the glutamine residue substituting for cysteine IV. Evolution has thus defrayed the cost of losing a disulfide bond by augmenting and optimizing weaker yet nonetheless effective non-covalent interactions.

Thermodynamic characterization of binding Oxytricha nova single strand telomere DNA with the alpha protein N-terminal domain.

The Oxytricha nova telemere binding protein alpha subunit binds single strand DNA and participates in a nucleoprotein complex that protects the very ends of chromosomes. To understand how the N-terminal, DNA binding domain of alpha interacts with DNA we measured the stoichiometry, enthalpy (DeltaH), entropy (DeltaS), and dissociation constant (K(D-DNA)) for binding telomere DNA fragments at different temperatures and salt concentrations using native gel electrophoresis and isothermal titration calorimetry (ITC). About 85% of the total free energy of binding corresponded with non-electrostatic interactions for all DNAs. Telomere DNA fragments d(T(2)G(4)), d(T(4)G(4)), d(G(3)T(4)G(4)), and d(G(4)T(4)G(4)) each formed monovalent protein complexes. In the case of d(T(4)G(4)T(4)G(4)), which has two tandemly repeated d(TTTTTGGGG) telomere motifs, two binding sites were observed. The high-affinity "A site" has a dissociation constant, K(D-DNA(A)) = 13(+/-4) nM, while the low-affinity "B site" is characterized by K(D-DNA(B)) = 5600(+/-600) nM at 25 degrees C. Nucleotide substitution variants verified that the A site corresponds principally with the 3'-terminal portion of d(T(4)G(4)T(4)G(4)). The relative contributions of entropy (DeltaS) and enthalpy (DeltaH) for binding reactions were DNA length-dependent as was heat capacity (DeltaCp). These trends with respect to DNA length likely reflect structural transitions in the DNA molecule that are coupled with DNA-protein association. Results presented here are important for understanding early intermediates and subsequent stages in the assembly of the full telomere nucleoprotein complex and how binding events can prepare the telomere DNA for extension by telomerase, a critical event in telomere biology.

Binding linkage in a telomere DNA-protein complex at the ends of Oxytricha nova chromosomes.

Alpha and beta protein subunits of the telomere end binding protein from Oxytricha nova (OnTEBP) combine with telomere single strand DNA to form a protective cap at the ends of chromosomes. We tested how protein-protein interactions seen in the co-crystal structure relate to DNA binding through use of fusion proteins engineered as different combinations of domains and subunits derived from OnTEBP. Joining alpha and beta resulted in a protein that bound single strand telomere DNA with high affinity (K(D-DNA)=1.4 nM). Another fusion protein, constructed without the C-terminal protein-protein interaction domain of alpha, bound DNA with 200-fold diminished affinity (K(D-DNA)=290 nM) even though the DNA-binding domains of alpha and beta were joined through a peptide linker. Adding back the alpha C-terminal domain as a separate protein restored high-affinity DNA binding. The binding behaviors of these fusion proteins and the native protein subunits are consistent with cooperative linkage between protein-association and DNA-binding equilibria. Linking DNA-protein stability to protein-protein contacts at a remote site may provide a trigger point for DNA-protein disassembly during telomere replication when the single strand telomere DNA must exchange between a very stable OnTEBP complex and telomerase.

Total chemical synthesis and oxidative folding of delta-conotoxin PVIA containing an N-terminal propeptide.

Small disulfide-rich peptides are translated as larger precursors typically containing an N-terminal prepro sequence. In this study, we investigated the role of a propeptide in the oxidative folding of an extremely hydrophobic delta-conotoxin, PVIA. delta-Conotoxin PVIA (delta-PVIA) is a 29-amino acid neurotoxin stabilized by three disulfide bridges. Previous folding studies on delta-conotoxins revealed that their poor folding properties resulted from their hydrophobicity. However, low folding yields of delta-PVIA could be improved by the presence of a nonionic detergent, which acted as a chemical chaperone. delta-PVIA provided an attractive model to investigate whether the hydrophilic propeptide region could function as an intramolecular chaperone. A 58-amino acid precursor for delta-PVIA (pro-PVIA), containing the N-terminal propeptide covalently attached to the mature conotoxin, was synthesized using native chemical ligation. Oxidative folding of pro-PVIA resulted in a very low accumulation of the correctly folded form, comparable to that for the mature conotoxin delta-PVIA. Our results are in accord with the relevant data previously observed for alpha- and omega-conotoxins, indicating that conotoxin prepro sequences are so-called class II propeptides, which are not directly involved in the oxidative folding. We hypothesize that these propeptide regions may be important for interactions with protein folding catalysts and sorting receptors during the secretory process.

Cosolvent-assisted oxidative folding of a bicyclic alpha-conotoxin ImI.

alpha-Conotoxin ImI is a 12-amino acid peptide, found in the venom of the marine snail Conus imperialis. This conotoxin is a selective antagonist of alpha7 nicotinic acetylcholine receptors. To produce biologically active alpha-ImI, disulfide bonds must be formed between Cys2-Cys8 and Cys3-Cys12. Oxidative folding of bicyclic conotoxins, such as alpha-ImI, has been traditionally achieved using two-step oxidation protocols with orthogonal protection on two native pairs of cysteines. In this work, two alternative oxidation protocols were explored: (1) the recently described one-pot oxidation of t-butyl/4-methylbenzyl protected Cys pairs and (2) direct oxidative folding. In contrast to the first method, the latter one resulted in high yields of correctly folded alpha-ImI. The addition of organic cosolvents, such as methanol, ethanol or isopropanol into the folding mixture significantly increased the accumulation of the native peptide. This effect was also observed for another conotoxin, alpha-PnIA. It is suggested that cosolvent-assisted direct oxidation might be of general use for other bicyclic alpha-conotoxins, but efficiency should be assessed on a case-by-case basis.