Atomic-level structure and deformation in metallic glasses

Metallic glasses (MGs) are a relatively new class of materials discovered in 1960 and lauded for its high strengths and superior elastic properties. Three major obstacles prevent their widespread use as engineering materials for nanotechnology and industry: 1) their lack of plasticity mechanisms for deformation beyond the elastic limit, 2) their disordered atomic structure, which prevents effective study of their structure-to-property relationships, and 3) their poor glass forming ability, which limits bulk metallic glasses to sizes on the order of centimeters. We focused on understanding the first two major challenges by observing the mechanical properties of nanoscale metallic glasses in order to gain insight into its atomic-level structure and deformation mechanisms. We found that anomalous stable plastic flow emerges in room-temperature MGs at the nanoscale in wires as little as ~100 nanometers wide regardless of fabrication route (ion-irradiated or not). To circumvent experimental challenges in characterizing the atomic-level structure, extensive molecular dynamics simulations were conducted using approximated (embedded atom method) potentials to probe the underlying processes that give rise to plasticity in nanowires. Simulated results showed that mechanisms of relaxation via the sample free surfaces contribute to tensile ductility in these nanowires. Continuing with characterizing nanoscale properties, we studied the fracture properties of nano-notched MGnanowires and the compressive response of MG nanolattices at cryogenic (~130 K) temperatures. We learned from these experiments that nanowires are sensitive to flaws when the (amorphous) microstructure does not contribute stress concentrations, and that nano-architected structures with MG nanoribbons are brittle at low temperatures except when elastic shell buckling mechanisms dominate at low ribbon thicknesses (~20 nm), which instead gives rise to fully recoverable nanostructures regardless of temperature. Finally, motivated by understanding structure-to-property relationships in MGs, we studied the disordered atomic structure using a combination of in-situ X-ray tomography and X-ray diffraction in a diamond anvil cell and molecular dynamics simulations. Synchrotron X-ray experiments showed the progression of the atomic-level structure (in momentum space) and macroscale volume under increasing hydrostatic pressures. Corresponding simulations provided information on the real space structure, and we found that the samples displayed fractal scaling (r^d ∝ V, d < 3) at short length scales (< ~8 Å), and exhibited a crossover to a homogeneous scaling (d = 3) at long length scales. We examined this underlying fractal structure of MGs with parallels to percolation clusters and discuss the implications of this structural analogy to MG properties and the glass transition phenomenon.

Crystal structure of human T cell leukemia virus type 1 gp21 ectodomain crystallized as a maltose-binding protein chimera reveals structural evolution of retroviral transmembrane proteins

Retroviral entry into cells depends on envelope glycoproteins, whereby receptor binding to the surface-exposed subunit triggers membrane fusion by the transmembrane protein (TM) subunit. We determined the crystal structure at 2.5-Angstrom resolution of the ectodomain of gp21, the TM from human T cell leukemia virus type 1. The gp21 fragment was crystallized as a maltose-binding protein chimera, and the maltose-binding protein domain was used to solve the initial phases by the method of molecular replacement. The structure of gp21 comprises an N-terminal trimeric coiled coil, an adjacent disulfide-bonded loop that stabilizes a chain reversal, and a C-terminal sequence structurally distinct from HIV type 1/simian immunodeficiency virus gp41 that packs against the coil in an extended antiparallel fashion. Comparison of the gp21 structure with the structures of other retroviral TMs contrasts the conserved nature of the coiled coil-forming region and adjacent disulfide-bonded loop with the variable nature of the C-terminal ectodomain segment. The structure points to these features having evolved to enable the dual roles of retroviral TMs: conserved fusion function and an ability to anchor diverse surface-exposed subunit structures to the virion envelope and infected cell surface. The structure of gp21 implies that the N-terminal fusion peptide is in close proximity to the C-terminal transmembrane domain and likely represents a postfusion conformation.

Functional implications of the human T-lymphotropic virus type 1 transmembrane glycoprotein helical hairpin structure

Retrovirus entry into cells follows receptor binding by the surface exposed envelope glycoprotein (Env) subunit (SU), which triggers the membrane fusion activity of the transmembrane (TM) protein. TM protein fragments expressed in the absence of SU adopt helical hairpin structures comprising a central coiled coil, a region of chain reversal containing a disulfide-bonded loop, and a C-terminal segment that packs onto the exterior of the coiled coil in an antiparallel manner. Here we used in vitro mutagenesis to test the functional role of structural elements observed in a model helical hairpin, gp21 of human T-lymphotropic virus type 1. Membrane fusion activity requires the stabilization of the N and C termini of the central coiled coil by a hydrophobic N cap and a small hydrophobic core, respectively. A conserved Gly-Gly hinge motif preceding the disulfide-bonded loop, a salt bridge that stabilizes the chain reversal region, and interactions between the C-terminal segment and the coiled coil are also critical for fusion activity. Our data support a model whereby the chain reversal region transmits a conformational signal from receptor-bound SU to induce the fusion-activated helical hairpin conformation of the TM protein.

Atomic parity nonconservation, neutron radii, and effective field theories of nuclei

Accurately calibrated effective field theories are used to compute atomic parity nonconserving (APNC) observables. Although accurately calibrated, these effective field theories predict a large spread in the neutron skin of heavy nuclei. Whereas the neutron skin is strongly correlated to numerous physical observables, in this contribution we focus on its impact on new physics through APNC observables. The addition of an isoscalar-isovector coupling constant to the effective Lagrangian generates a wide range of values for the neutron skin of heavy nuclei without compromising the success of the model in reproducing well-constrained nuclear observables. Earlier studies have suggested that the use of isotopic ratios of APNC observables may eliminate their sensitivity to atomic structure. This leaves nuclear structure uncertainties as the main impediment for identifying physics beyond the standard model. We establish that uncertainties in the neutron skin of heavy nuclei are at present too large to measure isotopic ratios to better than the 0.1% accuracy required to test the standard model. However, we argue that such uncertainties will be significantly reduced by the upcoming measurement of the neutron radius in 208^Pb at the Jefferson Laboratory.

Atomic parity nonconservation, neutron radii, and effective field theories of nuclei

Accurately calibrated effective field theories are used to compute atomic parity nonconserving (APNC) observables. Although accurately calibrated, these effective field theories predict a large spread in the neutron skin of heavy nuclei. Whereas the neutron skin is strongly correlated to numerous physical observables, in this contribution we focus on its impact on new physics through APNC observables. The addition of an isoscalar-isovector coupling constant to the effective Lagrangian generates a wide range of values for the neutron skin of heavy nuclei without compromising the success of the model in reproducing well-constrained nuclear observables. Earlier studies have suggested that the use of isotopic ratios of APNC observables may eliminate their sensitivity to atomic structure. This leaves nuclear structure uncertainties as the main impediment for identifying physics beyond the standard model. We establish that uncertainties in the neutron skin of heavy nuclei are at present too large to measure isotopic ratios to better than the 0.1% accuracy required to test the standard model. However, we argue that such uncertainties will be significantly reduced by the upcoming measurement of the neutron radius in 208^Pb at the Jefferson Laboratory.

Imaging the structure of activated carbon using aberration corrected TEM

The precise atomic structure of activated carbon is unknown, despite its commercial importance. Here we show that the structure of a commercial activated carbon can be imaged directly using aberration corrected transmission electron microscopy. Images are presented both of the as-produced carbon and of the carbon following heat- treatment at 2000°C. In the 2000°C carbon clear evidence is found for the presence of pentagonal rings, suggesting that the carbons have a fullerene-related structure.

Local order and electronic structure of Pb1-xLaxZr0.40Ti0.60O3 materials and its relation with ferroelectric properties

The knowledge of electronic and local structures is a fundamental step towards understanding the properties of ferroelectric ceramics. X-ray absorption near-edge structure (XANES) of Pb1-xLaxZr0.40Ti0.60O3 ferroelectric samples was measured in order to know how the local order and electronic structure are related to their ferroelectric property, which was tailored by the substitution of lead by lanthanum atoms. The analysis of XANES spectra collected at Ti K- and L-edges XANES showed that the substitution of Pb by La leads to a decrement of local distortion around Ti atoms on the TiO6 octahedron. The analysis of O K-edge XANES spectra showed that the hybridization between O 2p and Pb 6sp states is related to the displacement of Ti atoms in the TiO6 octahedra. Based on these results, it is possible to determine that the degree of ferroelectricity in these samples and the manifestation of relaxor behavior are directly related to the weakening of O 2p and Pb 6sp hybridization. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4720472]

Computational analyses on the structure-function relation in ion channels

Ion channels are protein molecules, embedded in the lipid bilayer of the cell membranes. They act as powerful sensing elements switching chemicalphysical stimuli into ion-fluxes. At a glance, ion channels are water-filled pores, which can open and close in response to different stimuli (gating), and one once open select the permeating ion species (selectivity). They play a crucial role in several physiological functions, like nerve transmission, muscular contraction, and secretion. Besides, ion channels can be used in technological applications for different purpose (sensing of organic molecules, DNA sequencing). As a result, there is remarkable interest in understanding the molecular determinants of the channel functioning. Nowadays, both the functional and the structural characteristics of ion channels can be experimentally solved. The purpose of this thesis was to investigate the structure-function relation in ion channels, by computational techniques. Most of the analyses focused on the mechanisms of ion conduction, and the numerical methodologies to compute the channel conductance. The standard techniques for atomistic simulation of complex molecular systems (Molecular Dynamics) cannot be routinely used to calculate ion fluxes in membrane channels, because of the high computational resources needed. The main step forward of the PhD research activity was the development of a computational algorithm for the calculation of ion fluxes in protein channels. The algorithm - based on the electrodiffusion theory - is computational inexpensive, and was used for an extensive analysis on the molecular determinants of the channel conductance. The first record of ion-fluxes through a single protein channel dates back to 1976, and since then measuring the single channel conductance has become a standard experimental procedure. Chapter 1 introduces ion channels, and the experimental techniques used to measure the channel currents. The abundance of functional data (channel currents) does not match with an equal abundance of structural data. The bacterial potassium channel KcsA was the first selective ion channels to be experimentally solved (1998), and after KcsA the structures of four different potassium channels were revealed. These experimental data inspired a new era in ion channel modeling. Once the atomic structures of channels are known, it is possible to define mathematical models based on physical descriptions of the molecular systems. These physically based models can provide an atomic description of ion channel functioning, and predict the effect of structural changes. Chapter 2 introduces the computation methods used throughout the thesis to model ion channels functioning at the atomic level. In Chapter 3 and Chapter 4 the ion conduction through potassium channels is analyzed, by an approach based on the Poisson-Nernst-Planck electrodiffusion theory. In the electrodiffusion theory ion conduction is modeled by the drift-diffusion equations, thus describing the ion distributions by continuum functions. The numerical solver of the Poisson- Nernst-Planck equations was tested in the KcsA potassium channel (Chapter 3), and then used to analyze how the atomic structure of the intracellular vestibule of potassium channels affects the conductance (Chapter 4). As a major result, a correlation between the channel conductance and the potassium concentration in the intracellular vestibule emerged. The atomic structure of the channel modulates the potassium concentration in the vestibule, thus its conductance. This mechanism explains the phenotype of the BK potassium channels, a sub-family of potassium channels with high single channel conductance. The functional role of the intracellular vestibule is also the subject of Chapter 5, where the affinity of the potassium channels hEag1 (involved in tumour-cell proliferation) and hErg (important in the cardiac cycle) for several pharmaceutical drugs was compared. Both experimental measurements and molecular modeling were used in order to identify differences in the blocking mechanism of the two channels, which could be exploited in the synthesis of selective blockers. The experimental data pointed out the different role of residue mutations in the blockage of hEag1 and hErg, and the molecular modeling provided a possible explanation based on different binding sites in the intracellular vestibule. Modeling ion channels at the molecular levels relates the functioning of a channel to its atomic structure (Chapters 3-5), and can also be useful to predict the structure of ion channels (Chapter 6-7). In Chapter 6 the structure of the KcsA potassium channel depleted from potassium ions is analyzed by molecular dynamics simulations. Recently, a surprisingly high osmotic permeability of the KcsA channel was experimentally measured. All the available crystallographic structure of KcsA refers to a channel occupied by potassium ions. To conduct water molecules potassium ions must be expelled from KcsA. The structure of the potassium-depleted KcsA channel and the mechanism of water permeation are still unknown, and have been investigated by numerical simulations. Molecular dynamics of KcsA identified a possible atomic structure of the potassium-depleted KcsA channel, and a mechanism for water permeation. The depletion from potassium ions is an extreme situation for potassium channels, unlikely in physiological conditions. However, the simulation of such an extreme condition could help to identify the structural conformations, so the functional states, accessible to potassium ion channels. The last chapter of the thesis deals with the atomic structure of the !- Hemolysin channel. !-Hemolysin is the major determinant of the Staphylococcus Aureus toxicity, and is also the prototype channel for a possible usage in technological applications. The atomic structure of !- Hemolysin was revealed by X-Ray crystallography, but several experimental evidences suggest the presence of an alternative atomic structure. This alternative structure was predicted, combining experimental measurements of single channel currents and numerical simulations. This thesis is organized in two parts, in the first part an overview on ion channels and on the numerical methods adopted throughout the thesis is provided, while the second part describes the research projects tackled in the course of the PhD programme. The aim of the research activity was to relate the functional characteristics of ion channels to their atomic structure. In presenting the different research projects, the role of numerical simulations to analyze the structure-function relation in ion channels is highlighted.

The structure of the two amino-terminal domains of human ICAM-1 suggests how it functions as a rhinovirus receptor and as an LFA-1 integrin ligand

The normal function of human intercellular adhesion molecule-1 (ICAM-1) is to provide adhesion between endothelial cells and leukocytes after injury or stress. ICAM-1 binds to leukocyte function-associated antigen (LFA-1) or macrophage-1 antigen (Mac-1). However, ICAM-1 is also used as a receptor by the major group of human rhinoviruses and is a catalyst for the subsequent viral uncoating during cell entry. The three-dimensional atomic structure of the two amino-terminal domains (D1 and D2) of ICAM-1 has been determined to 2.2-Å resolution and fitted into a cryoelectron microscopy reconstruction of a rhinovirus–ICAM-1 complex. Rhinovirus attachment is confined to the BC, CD, DE, and FG loops of the amino-terminal Ig-like domain (D1) at the end distal to the cellular membrane. The loops are considerably different in structure to those of human ICAM-2 or murine ICAM-1, which do not bind rhinoviruses. There are extensive charge interactions between ICAM-1 and human rhinoviruses, which are mostly conserved in both major and minor receptor groups of rhinoviruses. The interaction of ICAMs with LFA-1 is known to be mediated by a divalent cation bound to the insertion (I)-domain on the α chain of LFA-1 and the carboxyl group of a conserved glutamic acid residue on ICAMs. Domain D1 has been docked with the known structure of the I-domain. The resultant model is consistent with mutational data and provides a structural framework for the adhesion between these molecules.

An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated β-sheet structure for amyloid

X-ray diffraction and other biophysical tools reveal features of the atomic structure of an amyloid-like crystal. Sup35, a prion-like protein in yeast, forms fibrillar amyloid assemblies intrinsic to its prion function. We have identified a polar peptide from the N-terminal prion-determining domain of Sup35 that exhibits the amyloid properties of full-length Sup35, including cooperative kinetics of aggregation, fibril formation, binding of the dye Congo red, and the characteristic cross-β x-ray diffraction pattern. Microcrystals of this peptide also share the principal properties of the fibrillar amyloid, including a highly stable, β-sheet-rich structure and the binding of Congo red. The x-ray powder pattern of the microcrystals, extending to 0.9-Å resolution, yields the unit cell dimensions of the well-ordered structure. These dimensions restrict possible atomic models of this amyloid-like structure and demonstrate that it forms packed, parallel-stranded β-sheets. The unusually high density of the crystals shows that the packed β-sheets are dehydrated, despite the polar character of the side chains. These results suggest that amyloid is a highly intermolecularly bonded, dehydrated array of densely packed β-sheets. This dry β-sheet could form as Sup35 partially unfolds to expose the peptide, permitting it to hydrogen-bond to the same peptide of other Sup35 molecules. The implication is that amyloid-forming units may be short segments of proteins, exposed for interactions by partial unfolding.

Quantum interference in atomic-sized point contacts

The conductance of atomic-sized metallic point contacts is shown to be strongly voltage dependent due to quantum interference with impurities even in samples with low impurity concentrations. Transmission through these small contacts depends not only on the local atomic structure at the contact but also on the distribution of impurities or defects within a coherence length of the contact. In contrast with other mesoscopic systems we show that transport through atomic contacts is coherent even at room temperature. The use of a scanning tunneling microscope (STM) makes it possible to fabricate one atom contacts of gold whose transmission can be controlled by manipulation of the contact allowing inelastic spectroscopy in such small contacts.

Analysis of the Kondo effect in ferromagnetic atomic-sized contacts

Atomic contacts made of ferromagnetic metals present zero-bias anomalies in the differential conductance due to the Kondo effect. These systems provide a unique opportunity to perform a statistical analysis of the Kondo parameters in nanostructures since a large number of contacts can be easily fabricated using break-junction techniques. The details of the atomic structure differ from one contact to another so a large number of different configurations can be statistically analyzed. Here we present such a statistical analysis of the Kondo effect in atomic contacts made from the ferromagnetic transition metals Ni, Co, and Fe. Our analysis shows clear differences between materials that can be understood by fundamental theoretical considerations. This combination of experiments and theory allows us to extract information about the origin and nature of the Kondo effect in these systems and to explore the influence of geometry and valence in the Kondo screening of atomic-sized nanostructures.

Coupling of magnetic, strain and electric polarization fields in the structure of multiferroic material

The comprehensive study on the coupling of magnetism, electrical polarization and the crystalline lattice with the off-stoichiometric effects in self-doped multiferroic hexagonal h-LuMnxO3±δ (0.92≤x≤1.12) ceramic oxides was carried out for the PhD work. There is a complex coupling of the three ferroic degrees. The cancelation of the magnetic moments of ions in the antiferromagnetic order, electric polarization with specific vortex/antivortex topology and lattice properties have pushed researchers to find out ways to disclose the underlying physics and chemistry of magneto-electric and magneto-elastic couplings of h-RMnO3 multiferroic materials. In this research work, self-doping of Lu-sites or Mn-sites of h-LuMnxO3±δ ceramics prepared via solid state route was done to pave a way for deeper understanding of the antiferromagnetic transition, the weak ferromagnetism often reported in the same crystalline lattices and the ferroelectric properties coupled to the imposed lattice changes. Accordingly to the aim of the PhD thesis, the objectives set for the sintering study in the first chapter on experimental results were two. First, study of sintering off-stoichiometric samples within conditions reported in the bibliography and also extracted from the phase diagrams of the LuMnxO3±δ, with a multiple firings ending with a last high temperature step at 1300ºC for 24 hours. Second, explore longer annealing times of up to 240 hours at the fixed temperature of 1300 ºC in a search for improving the properties of the solid solution under study. All series of LuMnxO3±δ ceramics for each annealing time were characterized to tentatively build a framework enabling comparison of measured properties with results of others available in literature. XRD and Rietveld refinement of data give the evolution the lattice parameters as a function to x. Shrinkage of the lattice parameters with increasing x values was observed, the stability limit of the solid solution being determined by analysis of lattice parameters. The evolution of grain size and presence of secondary phases have been investigated by means of TEM, SEM, EDS and EBSD techniques. The dependencies of grain growth and regression of secondary phases on composition x and time were further characterized. Magnetic susceptibility of samples and magnetic irreversibility were extensively examined in the present work. The dependency of magnetic susceptibility, Neel ordering transition and important magnetic parameters are determined and compared to observation in other multiferroics in the following chapter of the thesis. As a tool of high sensitivity to detect minor traces of the secondary phase hausmannite, magnetic measurements are suggested for cross-checking of phase diagrams. Difficulty of previous studies on interpreting the magnetic anomaly below 43 K in h-RMnO3 oxides was discussed and assigned to the Mn3O4 phase, with supported of the electron microscopy. Magneto-electric coupling where AFM ordering is coupled to dielectric polarization is investigated as a function of x and of sintering condition via frequency and temperature dependent complex dielectric constant measurements in the final chapter of the thesis. Within the limits of solid solubility, the crystalline lattice of off-stoichiometric ceramics was shown to preserve the magneto-electric coupling at TN. It represents the first research work on magneto-electric coupling modified by vacancy doping to author’s knowledge. Studied lattices would reveal distortions at the atomic scale imposed by local changes of x dependent on sintering conditions which were widely inspected by using TEM/STEM methods, complemented with EDS and EELS spectroscopy all together to provide comprehensive information on cross coupling of distortions, inhomogeneity and electronic structure assembled and discussed in a specific chapter. Internal interfaces inside crystalline grains were examined. Qualitative explanations of the measured magnetic and ferroelectric properties were established in relation to observed nanoscale features of h-LuMnxO3±δ ceramics. Ferroelectric domains and topological defects are displayed both in TEM and AFM/PFM images, the later technique being used to look at size, distribution and switching of ferroelectric domains influenced by vacancy doping at the micron scale bridging to complementary TEM studies on the atomic structure of ferroelectric domains. In support to experimental study, DFT simulations using Wien2K code have been carried out in order to interpret the results of EELS spectra of O K-edge and to obtain information on the cation hybridization to oxygen ions. The L3,2 edges of Mn is used to access the oxidation state of the Mn ions inside crystalline grains. In addition, rehybridization driven ferroelectricity is also evaluated by comparing the partial density of states of the orbitals of all ions of the samples, also the polarization was calculated and correlated to the off-stoichiometric effect.