Shower approach in the simulation of ion scattering from solids

An efficient approach for the simulation of ion scattering from solids is proposed. For every encountered atom, we take multiple samples of its thermal displacements among those which result in scattering with high probability to finally reach the detector. As a result, the detector is illuminated by intensive “showers,” where each event of detection must be weighted according to the actual probability of the atom displacement. The computational cost of such simulation is orders of magnitude lower than in the direct approach, and a comprehensive analysis of multiple and plural scattering effects becomes possible. We use this method for two purposes. First, the accuracy of the approximate approaches, developed mainly for ion-beam structural analysis, is verified. Second, the possibility to reproduce a wide class of experimental conditions is used to analyze some basic features of ion-solid collisions: the role of double violent collisions in low-energy ion scattering; the origin of the “surface peak” in scattering from amorphous samples; the low-energy tail in the energy spectra of scattered medium-energy ions due to plural scattering; and the degradation of blocking patterns in two-dimensional angular distributions with increasing depth of scattering. As an example of simulation for ions of MeV energies, we verify the time reversibility for channeling and blocking of 1-MeV protons in a W crystal. The possibilities of analysis that our approach offers may be very useful for various applications, in particular, for structural analysis with atomic resolution.

Time-multiscale methods for the simulation of slow transport problems in atomistic systems

En esta tesis presentamos una teoría adaptada a la simulación de fenómenos lentos de transporte en sistemas atomísticos. En primer lugar, desarrollamos el marco teórico para modelizar colectividades estadísticas de equilibrio. A continuación, lo adaptamos para construir modelos de colectividades estadísticas fuera de equilibrio. Esta teoría reposa sobre los principios de la mecánica estadística, en particular el principio de máxima entropía de Jaynes, utilizado tanto para sistemas en equilibrio como fuera de equilibrio, y la teoría de las aproximaciones del campo medio. Expresamos matemáticamente el problema como un principio variacional en el que maximizamos una entropía libre, en lugar de una energía libre. La formulación propuesta permite definir equivalentes atomísticos de variables macroscópicas como la temperatura y la fracción molar. De esta forma podemos considerar campos macroscópicos no uniformes. Completamos el marco teórico con reglas de cuadratura de Monte Carlo, gracias a las cuales obtenemos modelos computables. A continuación, desarrollamos el conjunto completo de ecuaciones que gobiernan procesos de transporte. Deducimos la desigualdad de disipación entrópica a partir de fuerzas y flujos termodinámicos discretos. Esta desigualdad nos permite identificar la estructura que deben cumplir los potenciales cinéticos discretos. Dichos potenciales acoplan las tasas de variación en el tiempo de las variables microscópicas con las fuerzas correspondientes. Estos potenciales cinéticos deben ser completados con una relación fenomenológica, del tipo definido por la teoría de Onsanger. Por último, aportamos validaciones numéricas. Con ellas ilustramos la capacidad de la teoría presentada para simular propiedades de equilibrio y segregación superficial en aleaciones metálicas. Primero, simulamos propiedades termodinámicas de equilibrio en el sistema atomístico. A continuación evaluamos la habilidad del modelo para reproducir procesos de transporte en sistemas complejos que duran tiempos largos con respecto a los tiempos característicos a escala atómica. ABSTRACT In this work, we formulate a theory to address simulations of slow time transport effects in atomic systems. We first develop this theoretical framework in the context of equilibrium of atomic ensembles, based on statistical mechanics. We then adapt it to model ensembles away from equilibrium. The theory stands on Jaynes' maximum entropy principle, valid for the treatment of both, systems in equilibrium and away from equilibrium and on meanfield approximation theory. It is expressed in the entropy formulation as a variational principle. We interpret atomistic equivalents of macroscopic variables such as the temperature and the molar fractions, wich are not required to be uniform, but can vary from particle to particle. We complement this theory with Monte Carlo summation rules for further approximation. In addition, we provide a framework for studying transport processes with the full set of equations driving the evolution of the system. We first derive a dissipation inequality for the entropic production involving discrete thermodynamic forces and fluxes. This discrete dissipation inequality identifies the adequate structure for discrete kinetic potentials which couple the microscopic field rates to the corresponding driving forces. Those kinetic potentials must finally be expressed as a phenomenological rule of the Onsanger Type. We present several validation cases, illustrating equilibrium properties and surface segregation of metallic alloys. We first assess the ability of a simple meanfield model to reproduce thermodynamic equilibrium properties in systems with atomic resolution. Then, we evaluate the ability of the model to reproduce a long-term transport process in complex systems.

Imaging of spin waves in atomically designed nanomagnets

The spin dynamics of all ferromagnetic materials are governed by two types of collective phenomenon: spin waves and domain walls. The fundamental processes underlying these collective modes, such as exchange interactions and magnetic anisotropy, all originate at the atomic scale. However, conventional probing techniques based on neutron1 and photon scattering2 provide high resolution in reciprocal space, and thereby poor spatial resolution. Here we present direct imaging of standing spin waves in individual chains of ferromagnetically coupled S = 2 Fe atoms, assembled one by one on a Cu2N surface using a scanning tunnelling microscope. We are able to map the spin dynamics of these designer nanomagnets with atomic resolution in two complementary ways. First, atom-to-atom variations of the amplitude of the quantized spin-wave excitations are probed using inelastic electron tunnelling spectroscopy. Second, we observe slow stochastic switching between two opposite magnetization states3, 4, whose rate varies strongly depending on the location of the tip along the chain. Our observations, combined with model calculations, reveal that switches of the chain are initiated by a spin-wave excited state that has its antinodes at the edges of the chain, followed by a domain wall shifting through the chain from one end to the other. This approach opens the way towards atomic-scale imaging of other types of spin excitation, such as spinon pairs and fractional end-states5, 6, in engineered spin chains.

Different routes to pure food allergens: extraction, recombinant techniques and total chemical synthesis for obtaining the plant-food pan-allergen LTP

La richiesta di allergeni puri è in continuo aumento per scopi diagnostici, come standard per metodi di rilevamento e di quantificazione, per l'immunoterapia e per lo studio a livello molecolare dei meccanismi delle reazioni allergiche, al fine di facilitare lo sviluppo di possibili cure. In questa tesi di dottorato sono descritte diverse strategie per l’ottenimento di forme pure di non-specific Lipid Transfer Proteins (nsLTPs), le quali sono state riconosciute essere rilevanti allergeni alimentari in molti frutti e verdure comunemente consumati e sono state definite come modello di veri allergeni alimentari. Una LTP potenzialmente allergenica, non nota in precedenza, è stata isolata dalle mandorle, mentre una LTP dall’allergenicità nota contenuta nelle noci è stata prodotta mediante tecniche di DNA ricombinante. Oltre a questi approcci classici, metodi per la sintesi chimica totale di proteine sono stati applicati per la prima volta alla produzione di un allergene, utilizzando Pru p 3, la LTP prototipica e principale allergene della pesca nell'area mediterranea, come modello. La sintesi chimica totale di proteinepermette di controllarne completamente la sequenza e di studiare la loro funzione a livello atomico. La sua applicazione alla produzione di allergeni costituisce perciò un importante passo avanti nel campo della ricerca sulle allergie alimentari. La proteina Pru p 3 è stata prodotta nella sua intera lunghezza e sono necessari solo due passaggi finali di deprotezione per ottenere il target nella sua forma nativa. Le condizioni sperimentali per tali deprotezioni sono state messe a punto durante la produzione dei peptidi sPru p 3 (1-37) e sPru p 3 (38-91), componenti insieme l'intera proteina. Tecniche avanzate di spettrometria di massa sono state usate per caratterizzare tutti i composti ottenuti, mentre la loro allergenicità è stata studiata attraverso test immunologici o approcci in silico.

Editorial overview:new protein production tools for structural biology

Full text: The idea of producing proteins from recombinant DNA hatched almost half a century ago. In his PhD thesis, Peter Lobban foresaw the prospect of inserting foreign DNA (from any source, including mammalian cells) into the genome of a λ phage in order to detect and recover protein products from Escherichia coli [ 1 and 2]. Only a few years later, in 1977, Herbert Boyer and his colleagues succeeded in the first ever expression of a peptide-coding gene in E. coli — they produced recombinant somatostatin [ 3] followed shortly after by human insulin. The field has advanced enormously since those early days and today recombinant proteins have become indispensable in advancing research and development in all fields of the life sciences. Structural biology, in particular, has benefitted tremendously from recombinant protein biotechnology, and an overwhelming proportion of the entries in the Protein Data Bank (PDB) are based on heterologously expressed proteins. Nonetheless, synthesizing, purifying and stabilizing recombinant proteins can still be thoroughly challenging. For example, the soluble proteome is organized to a large part into multicomponent complexes (in humans often comprising ten or more subunits), posing critical challenges for recombinant production. A third of all proteins in cells are located in the membrane, and pose special challenges that require a more bespoke approach. Recent advances may now mean that even these most recalcitrant of proteins could become tenable structural biology targets on a more routine basis. In this special issue, we examine progress in key areas that suggests this is indeed the case. Our first contribution examines the importance of understanding quality control in the host cell during recombinant protein production, and pays particular attention to the synthesis of recombinant membrane proteins. A major challenge faced by any host cell factory is the balance it must strike between its own requirements for growth and the fact that its cellular machinery has essentially been hijacked by an expression construct. In this context, Bill and von der Haar examine emerging insights into the role of the dependent pathways of translation and protein folding in defining high-yielding recombinant membrane protein production experiments for the common prokaryotic and eukaryotic expression hosts. Rather than acting as isolated entities, many membrane proteins form complexes to carry out their functions. To understand their biological mechanisms, it is essential to study the molecular structure of the intact membrane protein assemblies. Recombinant production of membrane protein complexes is still a formidable, at times insurmountable, challenge. In these cases, extraction from natural sources is the only option to prepare samples for structural and functional studies. Zorman and co-workers, in our second contribution, provide an overview of recent advances in the production of multi-subunit membrane protein complexes and highlight recent achievements in membrane protein structural research brought about by state-of-the-art near-atomic resolution cryo-electron microscopy techniques. E. coli has been the dominant host cell for recombinant protein production. Nonetheless, eukaryotic expression systems, including yeasts, insect cells and mammalian cells, are increasingly gaining prominence in the field. The yeast species Pichia pastoris, is a well-established recombinant expression system for a number of applications, including the production of a range of different membrane proteins. Byrne reviews high-resolution structures that have been determined using this methylotroph as an expression host. Although it is not yet clear why P. pastoris is suited to producing such a wide range of membrane proteins, its ease of use and the availability of diverse tools that can be readily implemented in standard bioscience laboratories mean that it is likely to become an increasingly popular option in structural biology pipelines. The contribution by Columbus concludes the membrane protein section of this volume. In her overview of post-expression strategies, Columbus surveys the four most common biochemical approaches for the structural investigation of membrane proteins. Limited proteolysis has successfully aided structure determination of membrane proteins in many cases. Deglycosylation of membrane proteins following production and purification analysis has also facilitated membrane protein structure analysis. Moreover, chemical modifications, such as lysine methylation and cysteine alkylation, have proven their worth to facilitate crystallization of membrane proteins, as well as NMR investigations of membrane protein conformational sampling. Together these approaches have greatly facilitated the structure determination of more than 40 membrane proteins to date. It may be an advantage to produce a target protein in mammalian cells, especially if authentic post-translational modifications such as glycosylation are required for proper activity. Chinese Hamster Ovary (CHO) cells and Human Embryonic Kidney (HEK) 293 cell lines have emerged as excellent hosts for heterologous production. The generation of stable cell-lines is often an aspiration for synthesizing proteins expressed in mammalian cells, in particular if high volumetric yields are to be achieved. In his report, Buessow surveys recent structures of proteins produced using stable mammalian cells and summarizes both well-established and novel approaches to facilitate stable cell-line generation for structural biology applications. The ambition of many biologists is to observe a protein's structure in the native environment of the cell itself. Until recently, this seemed to be more of a dream than a reality. Advances in nuclear magnetic resonance (NMR) spectroscopy techniques, however, have now made possible the observation of mechanistic events at the molecular level of protein structure. Smith and colleagues, in an exciting contribution, review emerging ‘in-cell NMR’ techniques that demonstrate the potential to monitor biological activities by NMR in real time in native physiological environments. A current drawback of NMR as a structure determination tool derives from size limitations of the molecule under investigation and the structures of large proteins and their complexes are therefore typically intractable by NMR. A solution to this challenge is the use of selective isotope labeling of the target protein, which results in a marked reduction of the complexity of NMR spectra and allows dynamic processes even in very large proteins and even ribosomes to be investigated. Kerfah and co-workers introduce methyl-specific isotopic labeling as a molecular tool-box, and review its applications to the solution NMR analysis of large proteins. Tyagi and Lemke next examine single-molecule FRET and crosslinking following the co-translational incorporation of non-canonical amino acids (ncAAs); the goal here is to move beyond static snap-shots of proteins and their complexes and to observe them as dynamic entities. The encoding of ncAAs through codon-suppression technology allows biomolecules to be investigated with diverse structural biology methods. In their article, Tyagi and Lemke discuss these approaches and speculate on the design of improved host organisms for ‘integrative structural biology research’. Our volume concludes with two contributions that resolve particular bottlenecks in the protein structure determination pipeline. The contribution by Crepin and co-workers introduces the concept of polyproteins in contemporary structural biology. Polyproteins are widespread in nature. They represent long polypeptide chains in which individual smaller proteins with different biological function are covalently linked together. Highly specific proteases then tailor the polyprotein into its constituent proteins. Many viruses use polyproteins as a means of organizing their proteome. The concept of polyproteins has now been exploited successfully to produce hitherto inaccessible recombinant protein complexes. For instance, by means of a self-processing synthetic polyprotein, the influenza polymerase, a high-value drug target that had remained elusive for decades, has been produced, and its high-resolution structure determined. In the contribution by Desmyter and co-workers, a further, often imposing, bottleneck in high-resolution protein structure determination is addressed: The requirement to form stable three-dimensional crystal lattices that diffract incident X-ray radiation to high resolution. Nanobodies have proven to be uniquely useful as crystallization chaperones, to coax challenging targets into suitable crystal lattices. Desmyter and co-workers review the generation of nanobodies by immunization, and highlight the application of this powerful technology to the crystallography of important protein specimens including G protein-coupled receptors (GPCRs). Recombinant protein production has come a long way since Peter Lobban's hypothesis in the late 1960s, with recombinant proteins now a dominant force in structural biology. The contributions in this volume showcase an impressive array of inventive approaches that are being developed and implemented, ever increasing the scope of recombinant technology to facilitate the determination of elusive protein structures. Powerful new methods from synthetic biology are further accelerating progress. Structure determination is now reaching into the living cell with the ultimate goal of observing functional molecular architectures in action in their native physiological environment. We anticipate that even the most challenging protein assemblies will be tackled by recombinant technology in the near future.

Encapsulated membrane proteins:a simplified system for molecular simulation

Over the past 50 years there has been considerable progress in our understanding of biomolecular interactions at an atomic level. This in turn has allowed molecular simulation methods employing full atomistic modeling at ever larger scales to develop. However, some challenging areas still remain where there is either a lack of atomic resolution structures or where the simulation system is inherently complex. An area where both challenges are present is that of membranes containing membrane proteins. In this review we analyse a new practical approach to membrane protein study that offers a potential new route to high resolution structures and the possibility to simplify simulations. These new approaches collectively recognise that preservation of the interaction between the membrane protein and the lipid bilayer is often essential to maintain structure and function. The new methods preserve these interactions by producing nano-scale disc shaped particles that include bilayer and the chosen protein. Currently two approaches lead in this area: the MSP system that relies on peptides to stabilise the discs, and SMALPs where an amphipathic styrene maleic acid copolymer is used. Both methods greatly enable protein production and hence have the potential to accelerate atomic resolution structure determination as well as providing a simplified format for simulations of membrane protein dynamics.

Atomic configurations of dislocation core and twin boundaries in 3C-SiC studied by high-resolution electron microscopy

The defects in 3C-SiC film grown on (001) plane of Si substrate were studied using a 200 kV high-resolution electron microscope with point resolution of 0.2 nm. A posterior image processing technique, the image deconvolution, was utilized in combination with the image contrast analysis to distinguish atoms of Si from C distant from each other by 0.109 nm in the [110] projected image. The principle of the image processing technique utilized and the related image contrast theory is briefly presented. The procedures of transforming an experimental image that does not reflect the crystal structure intuitively into the structure map and of identifying Si and C atoms from the map are described. The atomic configurations for a 30 degrees partial dislocation and a microtwin have been derived at atomic level. It has been determined that the 30 degrees partial dislocation terminates in C atom and the segment of microtwin is sandwiched between two 180 degrees rotation twins. The corresponding stacking sequences are derived and atomic models are constructed according to the restored structure maps for both the 30 degrees partial dislocation and microtwin. Images were simulated based on the two models to affirm the above-mentioned results.

RESOLUTION OF CLOSELY SPACED LINES WITH KALMAN FILTERING IN INDUCTIVELY COUPLED PLASMA ATOMIC EMISSION-SPECTROMETRY

Effects of some factors on the performance of our Kalman filter in discrimination of closely spaced overlapping signals were investigated. The resolution power of the filter for overlapping lines can be strengthened by reduction of the step size in scans. The minimum peak separation of two lines which the Kalman filter can effectively handle generally equals two to three times the step size in scans. Significant difference between the profiles of the analysis and interfering lines and multiple lines from matrix in the spectral window of the analysis line are very helpful for the Kalman filter to discern closely spaced analysis and interfering signals correctly, which allow the filter well to resolve the line pair with very small peak distance or even the entirely coincident lines.

KALMAN FILTERING FOR RESOLUTION OF OVERLAPPING LINES IN INDUCTIVELY COUPLED PLASMA ATOMIC EMISSION-SPECTROMETRY

A Kalman filter was developed for resolving overlapping lines in inductively coupled plasma atomic emission spectrometry (ICP-AES) and evaluated experimentally with the determination of La in the presence of Ho, and Cu in the presence of Pr. The whiteness of the innovation sequence for an optimal filter was explored to be the criterion for the correction of the wavelength positioning errors which may occur in spectral scans. Under the conditions of the medium-resolution spectrometer and 1.5 pm step size in scans, the filter effectively resolved the Cu/Pr line pair having a small peak separation of 4.8 pm. For the La/Ho line pair with a peak distance of 9.8 pm, an unbiased estimate for La concentration was still obtained even when the signal-to-background ratio was down to 0.048. Favourable detection limits for real samples were achieved. Unstructured backgrounds were modeled theoretically and all spectral scans therefore did not require the correction for solvent.

Mathematical equation correction to spectral and transport interferences in high-resolution continuum source flame atomic absorption spectrometry: determination of lead in phosphoric acid

Um método de correção de interferência espectral e de transporte é proposto, e foi aplicado para minimizar interferências por moléculas de PO produzidas em chama ar-acetileno e de transporte causada pela variação da concentração de ácido fosfórico. Átomos de Pb e moléculas de PO absorvem a 217,0005 nm, então Atotal217,0005 nm = A Pb217,0005 nm + A PO217,0005 nm. Monitorando o comprimento de onda alternativo de PO em 217,0458 nm, é possível calcular a contribuição relativa de PO na absorbância total a 217,0005 nm: A Pb217,0005 nm = Atotal217,0005 nm - A PO217,0005 nm = Atotal217,0005 nm - k (A PO217,0458 nm). O fator de correção k é a razão entre os coeficientes angulares de duas curvas analíticas para P obtidas a 217,0005 e 217,0458 nm (k = b217,0005 nm/b217,0458 nm). Fixando-se a taxa de aspiração da amostra em 5,0 ml min-1, e integrando-se a absorbância no comprimento de onda a 3 pixels, curvas analíticas para Pb (0,1 - 1,0 mg L-1) foram obtidas com coeficientes de correlação típicos > 0,9990. As correlações lineares entre absorbância e concentração de P nos comprimentos de onda 217,0005 e 217,0458 foram > 0,998. O limite de detecção de Pb foi 10 µg L-1. O método de correção proposto forneceu desvios padrão relativos (n=12) de 2,0 a 6,0%, ligeiramente menores que os obtidos sem correção (1,4-4,3%). As recuperações de Pb adicionado às amostras de ácido fosfórico variaram de 97,5 a 100% (com correção pelo método proposto) e de 105 a 230% (sem correção).

Fast sequential multi-element determination of Ca, Mg, K, Cu, Fe, Mn and Zn for foliar diagnosis using high-resolution continuum source flame atomic absorption spectrometry: Feasibility of secondary lines, side pixel registration and least-squares background correction

The fast sequential multi-element determination of Ca, Mg, K, Cu, Fe, Mn and Zn in plant tissues by high-resolution continuum source flame atomic absorption spectrometry is proposed. For this, the main lines for Cu (324.754 nm), Fe (248.327 nm), Mn (279.482 nm) and Zn (213.857 nm) were selected, and the secondary lines for Ca (239.856 nm), Mg (202.582 nm) and K (404.414 nm) were evaluated. The side pixel registration approach was studied to reduce sensitivity and extend the linear working range for Mg by measuring at wings (202.576 nm; 202.577 nm; 202.578 nm; 202.580 nm: 202.585 nm; 202.586 nm: 202.587 nm; 202.588 nm) of the secondary line. The interference caused by NO bands on Zn at 213.857 nm was removed using the least-squares background correction. Using the main lines for Cu, Fe, Mn and Zn, secondary lines for Ca and K, and line wing at 202.588 nm for Mg, and 5 mL min(-1) sample flow-rate, calibration curves in the 0.1-0.5 mg L-1 Cu, 0.5-4.0 mg L-1 Fe, 0.5-4.0 mg L-1 Mn, 0.2-1.0 mg L-1 Zn, 10.0-100.0 mg L-1 Ca, 5.0-40.0 mg L-1 Mg and 50.0-250.0 mg L-1 K ranges were consistently obtained. Accuracy and precision were evaluated after analysis of five plant standard reference materials. Results were in agreement at a 95% confidence level (paired t-test) with certified values. The proposed method was applied to digests of sugar-cane leaves and results were close to those obtained by line-source flame atomic absorption spectrometry. Recoveries of Ca, Mg, K, Cu, Fe, Mn and Zn in the 89-103%, 84-107%, 87-103%, 85-105%, 92-106%, 91-114%, 96-114% intervals, respectively, were obtained. The limits of detection were 0.6 mg L-1 Ca, 0.4 mg L-1 Mg, 0.4 mg L-1 K, 7.7 mu g L-1 Cu, 7.7 mu g L-1 Fe, 1.5 mu g L-1 Mn and 5.9 mu g L-1 Zn. (C) 2009 Elsevier B.V. All rights reserved.

Determination of macro- and micronutrients in plant leaves by high-resolution continuum source flame atomic absorption spectrometry combining instrumental and sample preparation strategies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evaluation of solid sampling high-resolution continuum source graphite furnace atomic absorption spectrometry for direct determination of chromium in medicinal plants

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)