Hybrid density functional study of small Rh-n (n=2-15) clusters

The physical properties of small rhodium clusters, Rh-n, have been in debate due to the shortcomings of density functional theory (DFT). To help in the solution of those problems, we obtained a set of putative lowest energy structures for small Rh-n (n = 2-15) clusters employing hybrid-DFT and the generalized gradient approximation (GGA). For n = 2-6, both hybrid and GGA functionals yield similar ground-state structures (compact), however, hybrid favors compact structures for n = 7-15, while GGA favors open structures based on simple cubic motifs. Thus, experimental results are crucial to indicate the correct ground-state structures, however, we found that a unique set of structures (compact or open) is unable to explain all available experimental data. For example, the GGA structures (open) yield total magnetic moments in excellent agreement with experimental data, while hybrid structures (compact) have larger magnetic moments compared with experiments due to the increased localization of the 4d states. Thus, we would conclude that GGA provides a better description of the Rh-n clusters, however, a recent experimental-theoretical study [ Harding et al., J. Chem. Phys. 133, 214304 (2010)] found that only compact structures are able to explain experimental vibrational data, while open structures cannot. Therefore, it indicates that the study of Rh-n clusters is a challenging problem and further experimental studies are required to help in the solution of this conundrum, as well as a better description of the exchange and correlation effects on the Rh n clusters using theoretical methods such as the quantum Monte Carlo method.

Spin Orbit Effects in the Electronic Transport Properties of Adsorbed Graphene Nanoribbons

Graphene has received great attention due to its exceptional properties, which include corners with zero effective mass, extremely large mobilities, this could render it the new template for the next generation of electronic devices. Furthermore it has weak spin orbit interaction because of the low atomic number of carbon atom in turn results in long spin coherence lengths. Therefore, graphene is also a promising material for future applications in spintronic devices - the use of electronic spin degrees of freedom instead of the electron charge. Graphene can be engineered to form a number of different structures. In particular, by appropriately cutting it one can obtain 1-D system -with only a few nanometers in width - known as graphene nanoribbon, which strongly owe their properties to the width of the ribbons and to the atomic structure along the edges. Those GNR-based systems have been shown to have great potential applications specially as connectors for integrated circuits. Impurities and defects might play an important role to the coherence of these systems. In particular, the presence of transition metal atoms can lead to significant spin-flip processes of conduction electrons. Understanding this effect is of utmost importance for spintronics applied design. In this work, we focus on electronic transport properties of armchair graphene nanoribbons with adsorbed transition metal atoms as impurities and taking into account the spin-orbit effect. Our calculations were performed using a combination of density functional theory and non-equilibrium Greens functions. Also, employing a recursive method we consider a large number of impurities randomly distributed along the nanoribbon in order to infer, for different concentrations of defects, the spin-coherence length.

Rafael Moneo: la complessità del vuoto. Dalle matrici formali dell'opera di Oteiza e Chillida

The experience of void, essential to the production of forms and to make use them, can be considered as the base of the activities that attend to the formative processes. If void and matter constitutes the basic substances of architecture. Their role in the definition of form, the symbolic value and the constructive methods of it defines the quality of the space. This job inquires the character of space in the architecture of Moneo interpreting the meaning of the void in the Basque culture through the reading of the form matrices in the work of Jorge Oteiza and Eduardo Chillida. In the tie with the Basque culture a reading key is characterized by concurring to put in relation some of the theoretical principles expressed by Moneo on the relationship between place and time, in an unique and specific vision of the space. In the analysis of the process that determines the genesis of the architecture of Moneo emerges a trajectory whose direction is constructed on two pivos: on the one hand architecture like instrument of appropriation of the place, gushed from an acquaintance process who leans itself to the reading of the relations that define the place and of the resonances through which measuring it, on the other hand the architecture whose character is able to represent and to extend the time in which he is conceived, through the autonomy that is conferred to them from values. Following the trace characterized from this hypothesis, that is supported on the theories elaborated from Moneo, surveying deepens the reading of the principles that construct the sculptural work of Oteiza and Chillida, features from a search around the topic of the void and to its expression through the form. It is instrumental to the definition of a specific area that concurs to interpret the character of the space subtended to a vision of the place and the time, affine to the sensibility of Moneo and in some way not stranger to its cultural formation. The years of the academic formation, during which Moneo enters in contact with the Basque artistic culture, seem to be an important period in the birth of that knowledge that will leads him to the formulation of theories tied to the relationship between time, place and architecture. The values expressed through the experimental work of Oteiza and Chillida during years '50 are valid bases to the understanding of such relationships. In tracing a profile of the figures of Oteiza and Chillida, without the pretension that it is exhaustive for the reading of the complex historical period in which they are placed, but with the needs to put the work in a context, I want to be evidenced the important role carried out from the two artists from the Basque cultural area within which Moneo moves its first steps. The tie that approaches Moneo to the Basque culture following the personal trajectory of the formative experience interlaces to that one of important figures of the art and the Spanish architecture. One of the more meaningful relationships is born just during the years of his academic formation, from 1958 to the 1961, when he works like student in the professional office of the architect Francisco Sáenz de Oiza, who was teaching architectural design at the ETSAM. In these years many figures of Basque artists alternated at the professional office of Oiza that enjoys the important support of the manufacturer and maecenas Juan Huarte Beaumont, introduced to he from Oteiza. The tie between Huarte and Oteiza is solid and continuous in the years and it realizes in a contribution to many of the initiatives that makes of Oteiza a forwarder of the Basque culture. In the four years of collaboration with Oiza, Moneo has the opportunity to keep in contact with an atmosphere permeated by a constant search in the field of the plastic art and with figures directly connected to such atmosphere. It’s of a period of great intensity as in the production like in the promotion of the Basque art. The collective “Blanco y Negro”, than is held in 1959 at the Galería Darro to Madrid, is only one of the many times of an exhibition of the work of Oteiza and Chillida. The end of the Fifties is a period of international acknowledgment for Chillida that for Oteiza. The decade of the Fifties consecrates the hypotheses of a mythical past of the Basque people through the spread of the studies carried out in the antecedent years. The archaeological discoveries that join to a context already rich of signs of the prehistoric era, consolidate the knowledge of a strong cultural identity. Oteiza, like Chillida and other contemporary artists, believe in a cosmogonist conception belonging to the Basques, connected to their matriarchal mythological past. The void in its meaning of absence, in the Basque culture, thus as in various archaic and oriental religions, is equivalent to the spiritual fullness as essential condition to the revealing of essence. Retracing the archaic origins of the Basque culture emerges the deep meaning that the void assumes as key element in the religious interpretation of the passage from the life to the death. The symbology becomes rich of meaningful characters who derive from the fact that it is a chthonic cult. A representation of earth like place in which divine manifest itself but also like connection between divine and human, and this manipulation of the matter of which the earth it is composed is the tangible projection of the continuous search of the man towards God. The search of equilibrium between empty and full, that characterizes also the development of the form in architecture, in the Basque culture assumes therefore a peculiar value that returns like constant in great part of the plastic expressions, than in this context seem to be privileged regarding the other expressive forms. Oteiza and Chillida develop two original points of view in the representation of the void through the form. Both use of rigorous systems of rules sensitive to the physics principles and the characters of the matter. The last aim of the Oteiza’s construction is the void like limit of the knowledge, like border between known and unknown. It doesn’t means to reduce the sculptural object to an only allusive dimension because the void as physical and spiritual power is an active void, that possesses that value able to reveal the being through the trace of un-being. The void in its transcendental manifestation acts at the same time from universal and from particular, like in the atomic structure of the matter, in which on one side it constitutes the inner structure of every atom and on the other one it is necessary condition to the interaction between all the atoms. The void can be seen therefore as the action field that concurs the relations between the forms but is also the necessary condition to the same existence of the form. In the construction of Chillida the void represents that counterpart structuring the matter, inborn in it, the element in absence of which wouldn’t be variations neither distinctive characters to define the phenomenal variety of the world. The physics laws become the subject of the sculptural representation, the void are the instrument that concurs to catch up the equilibrium. Chillida dedicate himself to experience the space through the senses, to perceive of the qualities, to tell the physics laws which forge the matter in the form and the form arranges the places. From the artistic experience of the two sculptors they can be transposed, to the architectonic work of Moneo, those matrices on which they have constructed their original lyric expressions, where the void is absolute protagonist. An ambit is defined thus within which the matrices form them drafts from the work of Oteiza and Chillida can be traced in the definition of the process of birth and construction of the architecture of Moneo, but also in the relation that the architecture establishes with the place and in the time. The void becomes instrument to read the space constructed in its relationships that determine the proportions, rhythms, and relations. In this way the void concurs to interpret the architectonic space and to read the value of it, the quality of the spaces constructing it. This because it’s like an instrument of the composition, whose role is to maintain to the separation between the elements putting in evidence the field of relations. The void is that instrument that serves to characterize the elements that are with in the composition, related between each other, but distinguished. The meaning of the void therefore pushes the interpretation of the architectonic composition on the game of the relations between the elements that, independent and distinguished, strengthen themselves in their identity. On the one hand if void, as measurable reality, concurs all the dimensional changes quantifying the relationships between the parts, on the other hand its dialectic connotation concurs to search the equilibrium that regulated such variations. Equilibrium that therefore does not represent an obtained state applying criteria setting up from arbitrary rules but that depends from the intimate nature of the matter and its embodiment in the form. The production of a form, or a formal system that can be finalized to the construction of a building, is indissolubly tied to the technique that is based on the acquaintance of the formal vocation of the matter, and what it also can representing, meaning, expresses itself in characterizing the site. For Moneo, in fact, the space defined from the architecture is above all a site, because the essence of the site is based on the construction. When Moneo speaks about “birth of the idea of plan” like essential moment in the construction process of the architecture, it refers to a process whose complexity cannot be born other than from a deepened acquaintance of the site that leads to the comprehension of its specificity. Specificity arise from the infinite sum of relations, than for Moneo is the story of the oneness of a site, of its history, of the cultural identity and of the dimensional characters that that they are tied to it beyond that to the physical characteristics of the site. This vision is leaned to a solid made physical structure of perceptions, of distances, guideline and references that then make that the process is first of all acquaintance, appropriation. Appropriation that however does not happen for directed consequence because does not exist a relationship of cause and effect between place and architecture, thus as an univocal and exclusive way does not exist to arrive to a representation of an idea. An approach that, through the construction of the place where the architecture acquires its being, searches an expression of its sense of the truth. The proposal of a distinction for areas like space, matter, spirit and time, answering to the issues that scan the topics of the planning search of Moneo, concurs a more immediate reading of the systems subtended to the composition principles, through which is related the recurrent architectonic elements in its planning dictionary. From the dialectic between the opposites that is expressed in the duality of the form, through the definition of a complex element that can mediate between inside and outside as a real system of exchange, Moneo experiences the form development of the building deepening the relations that the volume establishes in the site. From time to time the invention of a system used to answer to the needs of the program and to resolve the dual character of the construction in an only gesture, involves a deep acquaintance of the professional practice. The technical aspect is the essential support to which the construction of the system is indissolubly tied. What therefore arouses interest is the search of the criteria and the way to construct that can reveal essential aspects of the being of the things. The constructive process demands, in fact, the acquaintance of the formative properties of the matter. Property from which the reflections gush on the relations that can be born around the architecture through the resonance produced from the forms. The void, in fact, through the form is in a position to constructing the site establishing a reciprocity relation. A reciprocity that is determined in the game between empty and full and of the forms between each other, regarding around, but also with regard to the subjective experience. The construction of a background used to amplify what is arranged on it and to clearly show the relations between the parts and at the same time able to tie itself with around opening the space of the vision, is a system that in the architecture of Moneo has one of its more effective applications in the use of the platform used like architectonic element. The spiritual force of this architectonic gesture is in the ability to define a place whose projecting intention is perceived and shared with who experience and has lived like some instrument to contact the cosmic forces, in a delicate process that lead to the equilibrium with them, but in completely physical way. The principles subtended to the construction of the form taken from the study of the void and the relations that it concurs, lead to express human values in the construction of the site. The validity of these principles however is tested from the time. The time is what Moneo considers as filter that every architecture is subordinate to and the survival of architecture, or any of its formal characters, reveals them the validity of the principles that have determined it. It manifests thus, in the tie between the spatial and spiritual dimension, between the material and the worldly dimension, the state of necessity that leads, in the construction of the architecture, to establish a contact with the forces of the universe and the intimate world, through a process that translate that necessity in elaboration of a formal system.

Optische Spektroskopie an Fermium (Z=100)

Im Rahmen der vorliegenden Arbeit wurde erstmals Laser-Atomspektroskopie an einem Element durchgeführt, für das bisher keine atomaren Niveaus bekannt waren. Die Experimente wurden am Element Fermium mit der Ordnungszahl Z=100 mit der Resonanzionisationsspektroskopie (RIS) in einer Puffergaszelle durchgeführt. Verwendet wurde das Isotop 255Fm mit einer Halbwertszeit von 20.1 h, das im Hochflusskernreaktor des ORNL, Oak Ridge, USA, hergestellt wurde. Die von einem elektrochemischen Filament in das Argon-Puffergas bei einer Temperatur von 960(20)°C abgedampften Fm-Atome wurden mit Lasern in einem Zweistufenprozess resonant ionisiert. Dazu wurde das Licht eines Excimerlaser gepumpten Farbstofflasers für den ersten Anregungsschritt um die Wellenlänge 400 nm durchgestimmt. Ein Teil des Excimer (XeF) Laser Pumplichtes mit den Wellenlänge 351/353 nm wurde für die nicht-resonante Ionisation verwendet. Die Ionen wurden mit Hilfe elektrischer Felder aus der optischen Zelle extrahiert und nach einem Quadrupol Massenfilter mit einem Channeltron-Detektor massenselektiv nachgewiesen. Trotz der geringen Probenmenge von 2.7 x 10^10 eingesetzten Atomen wurden zwei atomare Resonanzen bei Energien von 25099.8(2) cm-1 und 25111.8(2) cm-1 gefunden und das Sättigungsverhalten dieser Linien gemessen. Es wurde ein theoretisches Modell entwickelt, dass sowohl das spektrale Profil der sättigungsverbreiterten Linien als auch die Sättigungskurven beschreibt. Durch Anpassung an die Messdaten konnten die partiellen Übergangsraten in den 3H6 Grundzustand Aki=3.6(7) x 10^6/s und Aki=3.6(6) x 10^6/s bestimmt werden. Der Vergleich der Niveauenergien und Übergangsraten mit Multikonfigurations Dirac-Fock Rechnungen legt die spektroskopische Klassifizierung der beobachteten Niveaus als 5f12 7s7p 5I6 und 5G6 Terme nahe. Weiterhin wurde ein Übergang bei 25740 cm-1 gefunden, der aufgrund der beobachteten Linienbreite von 1000 GHz als Rydbergzustand Zustand mit der Niveauenergie 51480 cm-1 interpretiert wurde und über einen Zweiphotonen Prozess angeregt werden kann. Basierend auf dieser Annahme wurde die Obergrenze für die Ionisationsenergie IP = 52140 cm-1 = 6.5 eV abgeschätzt. In den Messungen wurden Verschiebungen in den Zeitverteilungsspektren zwischen den mono-atomaren Ionen Fm+ und Cf+ und dem Molekül-Ion UO+ festgestellt und auf Driftzeitunterschiede im elektrischen Feld der gasgefüllten optischen Zelle zurückgeführt. Unter einfachen Modellannahmen wurde daraus auf die relativen Unterschiede Delta_r(Fm+,Cf+)/r(Cf+) ˜ -0.2 % und Delta_r(UO+,Cf+)/r(Cf+) ˜ 20 % in den Ionenradien geschlossen. Über die Bestimmung der Abnahme der Fm-a Aktivität des Filamentes auf der einen Seite und die Messung der Resonanzzählrate auf der anderen Seite, wurde die Nachweiseffizienz der Apparatur zu 4.5(3) x 10^-4 bestimmt. Die Nachweisapparatur wurde mit dem Ziel weiterentwickelt, Laserspektroskopie am Isotop 251Fm durchzuführen, das über die Reaktion 249Cf(a,2n)251Fm direkt in der optischen Zelle erzeugt werden soll. Das Verfahren wurde am chemischen Homolog Erbium getestet. Dabei wurde das Isotop 163Er über die Reaktion 161Dy(a,2n)163Er erzeugt und nach Resonanzionisation nachgewiesen. Die Nachweiseffizienz der Methode wurde zu 1 x 10^-4 bestimmt.

Spurenanalyse von Aktiniden in der Umwelt mittels Resonanzionisations-Massenspektrometrie

In dieser Arbeit wurde die Methode der resonanten Ionisation von neutralen Atomen mittels Laserstrahlung auf die leichten Aktinide Thorium, Uran, Neptunium und Plutonium angewendet und für die Ultraspurenanalyse optimiert. Der empfindliche Nachweis dieser Aktinide stellt eine Herausforderung für die Beobachtung und Bestimmung von radioaktiven Verunreinigungen aus kerntechnischen Anlagen in der Umwelt dar. In einem für diese Untersuchungen entwickelten Quadrupolmassenspektrometer konnte durch Resonanzionisationsspektroskopie jeweils eine Reihe unbekannter Energiezustände in der Elektronenhülle des neutralen Atoms der oben genannten Aktinide identifiziert, sowie effiziente Anregungsschemata für die resonante Ionisation entwickelt und charakterisiert werden. Durch die verwendete in-source-Ionisation, die aufgrund der guten Überlagerung von Laserstrahlung und Atomstrahl eine hohe Nachweiseffizienz gewährleistet, konnten diese Untersuchungen bereits mit einem, für Radionuklide notwendigen, geringen Probeneintrag erfolgen. Die resonante Ionisation erlaubt durch die selektiven resonanten Prozesse eine Unterdrückung unerwünschter Kontaminationen und wurde auf den analytischen Nachweis von Ultraspurengehalten in Umweltproben, sowie die Bestimmung der entsprechenden Isotopenzusammensetzung optimiert. Durch die effiziente in-source-Ionisation mit leistungsstarker gepulster Laserstrahlung, konnten Nachweiseffizienzen im Bereich von bis zu 1% erreicht werden. Dabei wurden für Plutonium in synthetischen Proben, aber auch in ersten Umweltproben, Nachweisgrenzen von 10^4-10^5 Atomen erzielt. Die Verwendung spektral schmalbandiger Dauerstrichlaser und eine Ionisation transversal zum frei propagierenden Atomstrahl ermöglicht durch Auflösung der Isotopieverschiebung eine hohe Selektivität gegenüber dominanten Nachbarisotopen, wohingegen die Ionisationseffizienz deutlich abnimmt. Hiermit konnte für das Ultraspurenisotop U-236 eine Nachweisgrenze bis hinab zu 10^-9 für das Isotopenverhältnis N(U-236)/N(U-238) bestimmt werden.

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Radiative properties for warm and hot dense matter

We will present calculations of opacities for matter under LTE conditions. Opacities are needed in radiation transport codes to study processes like Inertial Confinement Fusion and plasma amplifiers in X-ray secondary sources. For the calculations we use the code BiGBART, with either a hydrogenic approximation with j-splitting or self-consistent data generated with the atomic physics code FAC. We calculate the atomic structure, oscillator strengths, radiative transition energies, including UTA computations, and photoionization cross-sections. A DCA model determines the configurations considered in the computation of the opacities. The opacities obtained with these two models are compared with experimental measurements.

Icosahedral Ni nanowires formed from nanocontacts breaking: Identification and characterization by Molecular Dynamics

We present and discuss an algorithm to identify and characterize the long icosahedral structures (staggered pentagonal nanowires with 1-5-1-5 atomic structure) that appear in Molecular Dynamics simulations of metallic nanowires of different species subjected to stretching. The use of this algorithm allows the identification of pentagonal rings forming the icosahedral structure as well as the determination of its number np , and the maximum length of the pentagonal nanowire Lpm. The algorithm is tested with some ideal structures to show its ability to discriminate between pentagonal rings and other ring structures. We applied the algorithm to Ni nanowires with temperatures ranging between 4K and 865K, stretched along the [111], [100] and [110] directions. We studied statistically the formation of pentagonal nanowires obtaining the distributions of length Lpm and number of rings np as function of the temperature. The Lpm distribution presents a peaked shape, with peaks located at fixed distances whose separation corresponds to the distance between two consecutive pentagonal rings.

Independent mobility of catalytic and regulatory domains of myosin heads

The recent determination of the myosin head atomic structure has led to a new model of muscle contraction, according to which mechanical torque is generated in the catalytic domain and amplified by the lever arm made of the regulatory domain [Fisher, A. J., Smith, C. A., Thoden, J., Smith, R., Sutoh, K., Holden, H. M. & Rayment, I. (1995) Biochemistry 34, 8960–8972]. A crucial aspect of this model is the ability of the regulatory domain to move independently of the catalytic domain. Saturation transfer–EPR measurements of mobility of these two domains in myosin filaments give strong support for this notion. The catalytic domain of the myosin head was labeled at Cys-707 with indane dione spin label; the regulatory domain was labeled at the single cysteine residue of the essential light chain and exchanged into myosin. The mobility of the regulatory domain in myosin filaments was characterized by an effective rotational correlation time (τR) between 24 and 48 μs. In contrast, the mobility of the catalytic domain was found to be τR = 5–9 μs. This difference in mobility between the two domains existed only in the filament form of myosin. In the monomeric form, or when bound to actin, the mobility of the two domains in myosin was indistinguishable, with τR = 1–4 μs and >1,000 μs, respectively. Therefore, the observed difference in filaments cannot be ascribed to differences in local conformations of the spin-labeled sites. The most straightforward interpretation suggests a flexible hinge between the two domains, which would have to stiffen before force could be generated.

Architecture and mechanism of the light-harvesting apparatus of purple bacteria

Photosynthetic organisms fuel their metabolism with light energy and have developed for this purpose an efficient apparatus for harvesting sunlight. The atomic structure of the apparatus, as it evolved in purple bacteria, has been constructed through a combination of x-ray crystallography, electron microscopy, and modeling. The detailed structure and overall architecture reveals a hierarchical aggregate of pigments that utilizes, as shown through femtosecond spectroscopy and quantum physics, elegant and efficient mechanisms for primary light absorption and transfer of electronic excitation toward the photosynthetic reaction center.

Vacancy-induced magnetism in graphene and graphene ribbons

We address the electronic structure and magnetic properties of vacancies and voids both in graphene and graphene ribbons. By using a mean-field Hubbard model, we study the appearance of magnetic textures associated with removing a single atom (vacancy) and multiple adjacent atoms (voids) as well as the magnetic interactions between them. A simple set of rules, based on the Lieb theorem, link the atomic structure and the spatial arrangement of the defects to the emerging magnetic order. The total spin S of a given defect depends on its sublattice imbalance, but some defects with S=0 can still have local magnetic moments. The sublattice imbalance also determines whether the defects interact ferromagnetically or antiferromagnetically with one another and the range of these magnetic interactions is studied in some simple cases. We find that in semiconducting armchair ribbons and two-dimensional graphene without global sublattice imbalance, there is a maximum defect density above which local magnetization disappears. Interestingly, the electronic properties of semiconducting graphene ribbons with uncoupled local moments are very similar to those of diluted magnetic semiconductors, presenting giant Zeeman splitting.

Proceedings of the Cambridge Philosophical Society.

Mode of access: Internet.

Expression and biochemical analysis of the entire HIV-2 gp41 ectodomain: determinants of stability map to N- and C-terminal sequences outside the 6-helix bundle core

The folding of HIV gp41 into a 6-helix bundle drives virus-cell membrane fusion. To examine the structural relationship between the 6-helix bundle core domain and other regions of gp41, we expressed in Escherichia coli, the entire ectodomain of HIV-2(ST) gp41 as a soluble, trimeric maltose-binding protein (MBP)/gp41 chimera. Limiting proteolysis indicated that the Cys-591-Cys-597 disulfide-bonded region is outside a core domain comprising two peptides, Thr-529-Trp-589 and Val-604-Ser-666. A biochemical examination of MBP/gp41 chimeras encompassing these core peptides; indicated that the N-terminal polar segment, 521-528, and C-terminal membrane-proximal segment, 658-666, cooperate in stabilizing the ectodomain. A functional interaction between sequences outside the gp41 core may contribute energy to membrane fusion. (C) 2004 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

Scattering and tangential momentum accommodation at a 2D adsorbate-solid interface

We calculate tangential momentum coefficients for the exchange of momentum between molecules in transport and the internal surface of a membrane pore, modelled as a simple atomic structure. We introduce a local specular reflection (LSR) hypothesis, which states that impinging molecules undergo mirror-like reflection in a plane tangent to a surface atom at the point of impact. As a consequence, the components of the velocity, parallel to the direction of flow will (in general) change on impact. The overall effect is a loss of tangential momentum, since more is lost in the upstream direction than is gained in the downstream direction. The loss of tangential momentum is greater when the size ratio of fluid to solid atom is small, allowing more steeply inclined impact planes to become accessible to the fluid phase molecules. (c) 2005 Elsevier B.V. All rights reserved.

theta-defensins prevent HIV-1 Env-mediated fusion by binding gp41 and blocking 6-helix bundle formation

Retrocyclin-1, a 0-defensin, protects target cells from human immunodeficiency virus, type 1 (HIV-1) by preventing viral entry. To delineate its mechanism, we conducted fusion assays between susceptible target cells and effector cells that expressed HIV-1 Env. Retrocyclin-1 (4 mu M) completely blocked fusion mediated by HIV-1 Envs that used CXCR4 or CCR5 but had little effect on cell fusion mediated by HIV-2 and simian immunodeficiency virus Envs. Retrocyclin-1 inhibited HIV-1 Env-mediated fusion without impairing the lateral mobility of CD4, and it inhibited the fusion of CD4-deficient cells with cells bearing CD4-independent HIV-1 Env. Thus, it could act without cross-linking membrane proteins or inhibiting gp120-CD4 interactions. Retrocyclin-1 acted late in the HIV-1 Env fusion cascade but prior to 6-helix bundle formation. Surface plasmon resonance experiments revealed that retrocyclin bound the ectodomain of gp41 with high affinity in a glycan-independent manner and that it bound selectively to the gp41 C-terminal heptad repeat. Native-PAGE, enzyme-linked immunosorbent assay, and CD spectroscopic analyses all revealed that retrocyclin-1 prevented 6-helix bundle formation. This mode of action, although novel for an innate effector molecule, resembles the mechanism of peptidic entry inhibitors based on portions of the gp41 sequence.