Anisotropic intrinsic spin relaxation in graphene due to flexural distortions

We propose an intrinsic spin scattering mechanism in graphene originated by the interplay of atomic spin-orbit interaction and the local curvature induced by flexural distortions of the atomic lattice. Starting from a multiorbital tight-binding Hamiltonian with spin-orbit coupling considered nonperturbatively, we derive an effective Hamiltonian for the spin scattering of the Dirac electrons due to flexural distortions. We compute the spin lifetime due to both flexural phonons and ripples and we find values in the microsecond range at room temperature. Interestingly, this mechanism is anisotropic on two counts. First, the relaxation rate is different for off-plane and in-plane spin quantization axis. Second, the spin relaxation rate depends on the angle formed by the crystal momentum with the carbon-carbon bond. In addition, the spin lifetime is also valley dependent. The proposed mechanism sets an upper limit for spin lifetimes in graphene and will be relevant when samples of high quality can be fabricated free of extrinsic sources of spin relaxation.

Quantum spin Hall phase in multilayer graphene

The so-called quantum spin Hall phase is a topologically nontrivial insulating phase that is predicted to appear in graphene and graphenelike systems. In this paper we address the question of whether this topological property persists in multilayered systems. We consider two situations: purely multilayer graphene and heterostructures where graphene is encapsulated by trivial insulators with a strong spin-orbit coupling. We use a four-orbital tight-binding model that includes full atomic spin-orbit coupling and we calculate the Z2 topological invariant of the bulk states as well as the edge states of semi-infinite crystals with armchair termination. For homogeneous multilayers we find that even when the spin-orbit interaction opens a gap for all possible stackings, only those with an odd number of layers host gapless edge states while those with an even number of layers are trivial insulators. For heterostructures where graphene is encapsulated by trivial insulators, it turns out that interlayer coupling is able to induce a topological gap whose size is controlled by the spin-orbit coupling of the encapsulating materials, indicating that the quantum spin Hall phase can be induced by proximity to trivial insulators.

Large spin splitting in the conduction band of transition metal dichalcogenide monolayers

We study the conduction band spin splitting that arises in transition metal dichalcogenide (TMD) semiconductor monolayers such as MoS2, MoSe2, WS2, and WSe2 due to the combination of spin-orbit coupling and lack of inversion symmetry. Two types of calculation are done. First, density functional theory (DFT) calculations based on plane waves that yield large splittings, between 3 and 30 meV. Second, we derive a tight-binding model that permits to address the atomic origin of the splitting. The basis set of the model is provided by the maximally localized Wannier orbitals, obtained from the DFT calculation, and formed by 11 atomiclike orbitals corresponding to d and p orbitals of the transition metal (W, Mo) and chalcogenide (S, Se) atoms respectively. In the resulting Hamiltonian, we can independently change the atomic spin-orbit coupling constant of the two atomic species at the unit cell, which permits to analyze their contribution to the spin splitting at the high symmetry points. We find that—in contrast to the valence band—both atoms give comparable contributions to the conduction band splittings. Given that these materials are most often n-doped, our findings are important for developments in TMD spintronics.

Edge states in graphene-like systems

The edges of graphene and graphene like systems can host localized states with evanescent wave function with properties radically different from those of the Dirac electrons in bulk. This happens in a variety of situations, that are reviewed here. First, zigzag edges host a set of localized non-dispersive state at the Dirac energy. At half filling, it is expected that these states are prone to ferromagnetic instability, causing a very interesting type of edge ferromagnetism. Second, graphene under the influence of external perturbations can host a variety of topological insulating phases, including the conventional quantum Hall effect, the quantum anomalous Hall (QAH) and the quantum spin Hall phase, in all of which phases conduction can only take place through topologically protected edge states. Here we provide an unified vision of the properties of all these edge states, examined under the light of the same one orbital tight-binding model. We consider the combined action of interactions, spin–orbit coupling and magnetic field, which produces a wealth of different physical phenomena. We briefly address what has been actually observed experimentally.

Julii Bernhards von Rohr Einleitung zu der allgemeinen Land- und Feld-Wirthschaffts-Kunst derer Teutschen : darinnen die allgemeinen Regeln und Anmerckungen die so wohl bey der Land und Feld-Oeconomie überhaupt als insonderheit [b]ey dem Ackerbau, der Viehzucht, Gärtne[re]y ... und Fischereyen fast in allen Provinzien Teutschlandes in acht zu nehmen [i]n einer guten Ordnung ohne Einmischung unnöthiger Sachen vorgetragen werden.

Goldsmiths'-Kress no. 05628.10, suppl.

Structural studies on antifolate drugs

Single crystal X-ray structure determinations are reported for eleven compounds all of which are either biologically active or potentially biologically important. The compounds fall into two distinct classes:- 1. Substituted diaminopyrimidines 2. Substituted aminopyrimidinones The first class of compounds were all selected on the basis of their common diaminopyrimidine nucleus which has been demonstrated to be a vital requirement for antifolate activity. They may all be described as non-classical or small molecule lipophilic dihydrofolate reductase (DHFR) inhibitors, as opposed to the classical folate analogues, having the ability to cross the blood-brain barrier, enter cells via a rapid passive diffusion process, and achieve high intracellular concentrations. Thus they are an excellent choice in the search for crystallography in the solid state, providing geometrical and distance data not available from any other analytical techniques to date; supporting and enhancing data obtained in the lower resolution studies of protein crystallography. The biological importance of these compounds is discussed and an attempt is made to relate/predict their pharmacological activity to observed structural features in the crystalline environment. Special attention is focussed on hydrogen bonding, confirmational flexibility and hydrophobicity of substituents; each of which appear to make contributions to tight binding in the enzyme active site. Chapter 9 describes the use of data from the literature and the solid state modelling of an observed enzyme-substrate interaction in an attempt to define it more accurately in terms of its geometric flexibility. Of the second class, one compound (ABPP) is reported; studies in two different crystal forms. In demonstrating both antiviral and high interferon inducing activity it is possible that this compound could be useful against cancer and also viral infections.

Thermalized polarization dynamics of a discrete optical-waveguide system with four-wave mixing

Statistical mechanics of two coupled vector fields is studied in the tight-binding model that describes propagation of polarized light in discrete waveguides in the presence of the four-wave mixing. The energy and power conservation laws enable the formulation of the equilibrium properties of the polarization state in terms of the Gibbs measure with positive temperature. The transition line T=∞ is established beyond which the discrete vector solitons are created. Also in the limit of the large nonlinearity an analytical expression for the distribution of Stokes parameters is obtained, which is found to be dependent only on the statistical properties of the initial polarization state and not on the strength of nonlinearity. The evolution of the system to the final equilibrium state is shown to pass through the intermediate stage when the energy exchange between the waveguides is still negligible. The distribution of the Stokes parameters in this regime has a complex multimodal structure strongly dependent on the nonlinear coupling coefficients and the initial conditions.

Proprietà di conduzione elettrica in campioni di grafene poroso

Il grafene, allotropo del carbonio costituito da un reticolo bidimensionale, è uno dei nanomateriali più promettenti allo stato attuale della ricerca nei campi della Fisica e della Chimica, ma anche dell'Ingegneria e della Biologia. Isolato e caratterizzato per la prima volta nel 2004 dai ricercatori russi Andre Geim e Konstantin Novoselov presso l'Università di Manchester, ha aperto la via sia a studi teorici per comprendere con gli strumenti della Meccanica Quantistica gli effetti di confinamento in due dimensioni (2D), sia ad un vastissimo panorama di ricerca applicativa che ha l'obiettivo di sfruttare al meglio le straordinarie proprietà meccaniche, elettriche, termiche ed ottiche mostrate da questo materiale. Nella preparazione di questa tesi ho personalmente seguito presso l'Istituto per la Microelettronica e i Microsistemi (IMM) del CNR di Bologna la sintesi mediante Deposizione Chimica da Fase Vapore (CVD) di grafene "tridimensionale" (3D) o "poroso" (denominato anche "schiuma di grafene", in inglese "graphene foam"), ossia depositato su una schiuma metallica dalla struttura non planare. In particolare l'obiettivo del lavoro è stato quello di misurare le proprietà di conduttività elettrica dei campioni sintetizzati e di confrontarle con i risultati dei modelli che le descrivono teoricamente per il grafene planare. Dopo un primo capitolo in cui descriverò la struttura cristallina, i livelli energetici e la conduzione dei portatori di carica nel reticolo ideale di grafene 2D (utilizzando la teoria delle bande e l'approssimazione "tight-binding"), illustrerò le differenti tecniche di sintesi, in particolare la CVD per la produzione di grafene poroso che ho seguito in laboratorio (cap.2). Infine, nel capitolo 3, presenterò la teoria di van der Pauw su cui è basato il procedimento per eseguire misure elettriche su film sottili, riporterò i risultati di conduttività delle schiume e farò alcuni confronti con le previsioni della teoria.

Generic helical edge states due to Rashba spin-orbit coupling in a topological insulator

We study the helical edge states of a two-dimensional topological insulator without axial spin symmetry due to the Rashba spin-orbit interaction. Lack of axial spin symmetry can lead to so-called generic helical edge states, which have energy-dependent spin orientation. This opens the possibility of inelastic backscattering and thereby nonquantized transport. Here we find analytically the new dispersion relations and the energy dependent spin orientation of the generic helical edge states in the presence of Rashba spin-orbit coupling within the Bernevig-Hughes-Zhang model, for both a single isolated edge and for a finite width ribbon. In the single-edge case, we analytically quantify the energy dependence of the spin orientation, which turns out to be weak for a realistic HgTe quantum well. Nevertheless, finite size effects combined with Rashba spin-orbit coupling result in two avoided crossings in the energy dispersions, where the spin orientation variation of the edge states is very significantly increased for realistic parameters. Finally, our analytical results are found to compare well to a numerical tight-binding regularization of the model.

Hepsine et matriptase activent l’hémagglutinine des virus influenza A et B et leur inhibition représente une nouvelle stratégie thérapeutique n’entraînant pas le développement de résistance

Résumé: Chaque année, les épidémies saisonnières d’influenza causent de 3 à 5 millions de cas sévères de maladie, entraînant entre 250 000 et 500 000 décès mondialement. Seulement deux classes d’antiviraux sont actuellement commercialisées pour traiter cette infection respiratoire : les inhibiteurs de la neuraminidase, tels que l’oseltamivir (Tamiflu) et les inhibiteurs du canal ionique M2 (adamantanes). Toutefois, leur utilisation est limitée par l’apparition rapide de résistance virale. Il est donc d’un grand intérêt de développer de nouvelles stratégies thérapeutiques pour le traitement de l’influenza. Le virus influenza dépend de l’activation de sa protéine de surface hémagglutinine (HA) pour être infectieux. L’activation a lieu par clivage protéolytique au sein d’une séquence d’acides aminés conservée. Ce clivage doit être effectué par une enzyme de l’hôte, étant donné que le génome du virus ne code pour aucune protéase. Pour les virus infectant l’humain, plusieurs études ont montré le potentiel de protéases à sérine transmembranaires de type II (TTSP) à promouvoir la réplication virale : TMPRSS2, TMPRSS4, HAT, MSPL, Desc1 et matriptase, identifiée récemment par notre équipe (Beaulieu, Gravel et al., 2013), activent l’HA des virus influenza A (principalement H1N1 et H3N2). Toutefois, il existe peu d’information sur le clivage de l’HA des virus influenza B, et seulement TMPRSS2 et HAT ont été identifiées comme étant capables d’activer ce type de virus. Les travaux de ce projet de maîtrise visaient à identifier d’autres TTSP pouvant activer l’HA de l’influenza B. L’efficacité de clivage par la matriptase, hepsine, HAT et Desc1 a été étudiée et comparée entre ces TTSP. Ces quatre protéases s’avèrent capables de cliver l’HA de l’influenza B in vitro. Cependant, seul le clivage par matriptase, hepsine et HAT promeut la réplication virale. De plus, ces TTSP peuvent aussi supporter la réplication de virus influenza A. Ainsi, l’utilisation d’un inhibiteur de TTSP, développé en collaboration avec notre laboratoire, permet de bloquer significativement la réplication virale dans les cellules épithéliales bronchiques humaines Calu-3. Cet inhibiteur se lie de façon covalente et lentement réversible au site actif de la TTSP par un mécanisme slow tight-binding. Puisque cet inhibiteur cible une composante de la cellule hôte, et non une protéine virale, il n’entraîne pas le développement de résistance après 15 passages des virus en présence de l’inhibiteur dans les cellules Calu-3. L’inhibition des TTSP activatrices d’HA dans le système respiratoire humain représente donc une nouvelle stratégie thérapeutique pouvant mener au développement d’antiviraux efficaces contre l’influenza.

Disorder driven transitions in non-equilibrium quantum systems

This thesis presents studies of the role of disorder in non-equilibrium quantum systems. The quantum states relevant to dynamics in these systems are very different from the ground state of the Hamiltonian. Two distinct systems are studied, (i) periodically driven Hamiltonians in two dimensions, and (ii) electrons in a one-dimensional lattice with power-law decaying hopping amplitudes. In the first system, the novel phases that are induced from the interplay of periodic driving, topology and disorder are studied. In the second system, the Anderson transition in all the eigenstates of the Hamiltonian are studied, as a function of the power-law exponent of the hopping amplitude.

In periodically driven systems the study focuses on the effect of disorder in the nature of the topology of the steady states. First, we investigate the robustness to disorder of Floquet topological insulators (FTIs) occurring in semiconductor quantum wells. Such FTIs are generated by resonantly driving a transition between the valence and conduction band. We show that when disorder is added, the topological nature of such FTIs persists as long as there is a gap at the resonant quasienergy. For strong enough disorder, this gap closes and all the states become localized as the system undergoes a transition to a trivial insulator.

Interestingly, the effects of disorder are not necessarily adverse, disorder can also induce a transition from a trivial to a topological system, thereby establishing a Floquet Topological Anderson Insulator (FTAI). Such a state would be a dynamical realization of the topological Anderson insulator. We identify the conditions on the driving field necessary for observing such a transition. We realize such a disorder induced topological Floquet spectrum in the driven honeycomb lattice and quantum well models.

Finally, we show that two-dimensional periodically driven quantum systems with spatial disorder admit a unique topological phase, which we call the anomalous Floquet-Anderson insulator (AFAI). The AFAI is characterized by a quasienergy spectrum featuring chiral edge modes coexisting with a fully localized bulk. Such a spectrum is impossible for a time-independent, local Hamiltonian. These unique characteristics of the AFAI give rise to a new topologically protected nonequilibrium transport phenomenon: quantized, yet nonadiabatic, charge pumping. We identify the topological invariants that distinguish the AFAI from a trivial, fully localized phase, and show that the two phases are separated by a phase transition.

The thesis also present the study of disordered systems using Wegner's Flow equations. The Flow Equation Method was proposed as a technique for studying excited states in an interacting system in one dimension. We apply this method to a one-dimensional tight binding problem with power-law decaying hoppings. This model presents a transition as a function of the exponent of the decay. It is shown that the the entire phase diagram, i.e. the delocalized, critical and localized phases in these systems can be studied using this technique. Based on this technique, we develop a strong-bond renormalization group that procedure where we solve the Flow Equations iteratively. This renormalization group approach provides a new framework to study the transition in this system.

Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase

Archaeal transcription utilizes a complex multisubunit RNA polymerase and the basal transcription factors TBP and TF(II)B, closely resembling its eukaryal counterpart. We have uncovered a tight physical and functional interaction between RNA polymerase and the single-stranded DNA-binding protein SSB in Sulfolobus solfataricus. SSB stimulates transcription from promoters in vitro under TBP-limiting conditions and supports transcription in the absence of TBP. SSB also rescues transcription from repression by reconstituted chromatin. We demonstrate the potential for promoter melting by SSB, suggesting a plausible basis for the stimulation of transcription. This stimulation requires both the single-stranded DNA-binding domain and the acidic C-terminal tail of the SSB. The tail forms a stable interaction with RNA polymerase. These data reveal an unexpected role for single-stranded DNA-binding proteins in transcription in archaea.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ihfA and ihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

A provably tight delay-driven concurrently congestion mitigating global routing algorithm

Routing is a very important step in VLSI physical design. A set of nets are routed under delay and resource constraints in multi-net global routing. In this paper a delay-driven congestion-aware global routing algorithm is developed, which is a heuristic based method to solve a multi-objective NP-hard optimization problem. The proposed delay-driven Steiner tree construction method is of O(n(2) log n) complexity, where n is the number of terminal points and it provides n-approximation solution of the critical time minimization problem for a certain class of grid graphs. The existing timing-driven method (Hu and Sapatnekar, 2002) has a complexity O(n(4)) and is implemented on nets with small number of sinks. Next we propose a FPTAS Gradient algorithm for minimizing the total overflow. This is a concurrent approach considering all the nets simultaneously contrary to the existing approaches of sequential rip-up and reroute. The algorithms are implemented on ISPD98 derived benchmarks and the drastic reduction of overflow is observed. (C) 2014 Elsevier Inc. All rights reserved.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli Delta ihfA and Delta ihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF alpha beta. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.