Imaging chiral symmetry breaking from Kekulé bond order in graphene

Gutié,rrez, Christopher,Kim, Cheol-Joo,Brown, Lola,Schiros, Theanne,Nordlund, Dennis,Lochocki, Edward ,B.,Shen, Kyle M.,Park, Jiwoong,Pasupathy, Abhay N. Nature Publishing Group, a division of Macmillan P 2016 NATURE PHYSICS Vol.12 No.10

Chirality—or ‘handedness’—is a symmetry property crucial to fields as diverse as biology, chemistry and high-energy physics. In graphene, chiral symmetry emerges naturally as a consequence of the carbon honeycomb lattice. This symmetry can be broken by interactions that couple electrons with opposite momenta in graphene. Here we directly visualize the formation of Kekulé bond order, one such phase of broken chiral symmetry, in an ultraflat graphene sheet grown epitaxially on a copper substrate. We show that its origin lies in the interactions between individual vacancies in the copper substrate that are mediated electronically by the graphene. We show that this interaction causes the bonds in graphene to distort, creating a phase with broken chiral symmetry. The Kekulé ordering is robust at ambient temperature and atmospheric conditions, indicating that intercalated atoms may be harnessed to drive graphene and other two-dimensional materials towards electronically desirable and exotic collective phases.

Klein tunnelling and electron trapping in nanometre-scale graphene quantum dots

Gutié,rrez, Christopher,Brown, Lola,Kim, Cheol-Joo,Park, Jiwoong,Pasupathy, Abhay N. Nature Publishing Group 2016 NATURE PHYSICS Vol.12 No.11

Relativistic fermions that are incident on a high potential barrier can pass through unimpeded, a striking phenomenon termed the ‘Klein paradox’ in quantum electrodynamics. Electrostatic potential barriers in graphene provide a solid-state analogue to realize this phenomenon. Here, we use scanning tunnelling microscopy to directly probe the transmission of electrons through sharp circular potential wells in graphene created by substrate engineering. We find that electrons in this geometry display quasi-bound states where the electron is trapped for a finite time before escaping via Klein tunnelling. We show that the continuum Dirac equation can be successfully used to model the energies and wavefunctions of these quasi-bound states down to atomic dimensions. We demonstrate that by tuning the geometry of the barrier it is possible to trap particular energies and angular momentum states with increased efficiency, showing that atomic-scale electrostatic potentials can be used to engineer quantum transport through graphene.

On the Strichartz Estimates for the Kinetic Transport Equation

Bennett, Jonathan,Bez, Neal,Gutié,rrez, Susana,Lee, Sanghyuk Marcel Dekker, Inc 2014 Communications in partial differential equations Vol.39 No.10

Light harvesting zinc naphthalocyanine–perylenediimide supramolecular dyads: long-lived charge-separated states in nonpolar media

El-Khouly, Mohamed E.,Gutié,rrez, Ana M.,Sastre-Santos, Á,ngela,Ferná,ndez-Lá,zaro, Fernando,Fukuzumi, Shunichi The Royal Society of Chemistry 2012 Physical chemistry chemical physics Vol.14 No.10

<P>Photoinduced electron-transfer dynamics of self-assembled donor–acceptor dyads formed by axial coordination of zinc naphthalocyanine, ZnNc, and perylenediimide (PDI) bearing either pyridine (py) or imidazole (im) coordinating ligands were investigated. The PDIim unit was functionalized with <I>tert</I>-octylphenoxy groups at the bay positions, which avoid aggregation providing solubility, to examine the effect of the bulky substituents at the bay positions on the rates of electron-transfer reactions. The combination between zinc naphthalocyanine and perylenediimide entities absorbs light over a wide region of the visible and near infrared (NIR) spectrum. The binding constants of the self-assembled ZnNc:PDIpy (<B>1</B>) and ZnNc:PDIim (<B>2</B>) in toluene were found to be 2.40 × 10<SUP>4</SUP> and 1.10 × 10<SUP>5</SUP> M<SUP>−1</SUP>, respectively, from the steady-state absorption and emission measurements, indicating formation of moderately stable complexes. The geometric and electronic calculations by using an <I>ab initio</I> B3LYP/6-311G method showed the majority of the highest occupied frontier molecular orbital (HOMO) on the zinc naphthalocyanine entity, while the lowest unoccupied molecular orbital (LUMO) was on the perylenediimide entities, suggesting that the charge-separated states of the supramolecular dyads are ZnNc&z.rad;<SUP>+</SUP>:PDI&z.rad;<SUP>−</SUP>. The electrochemical results suggest the exothermic charge-separation process <I>via</I> the singlet states of both ZnNc and PDI entities in nonpolar toluene. Upon coordination of perylenediimide to ZnNc, the main quenching pathway involved charge separation <I>via</I> the singlet-excited states of ZnNc and PDIs. Clear evidence of the intramolecular electron transfer from the singlet-excited state of ZnNc to PDI within the supramolecular dyads in toluene was monitored by the femtosecond laser photolysis by observing the characteristic absorption band of the PDI radical anion (PDI&z.rad;<SUP>−</SUP>) and the ZnNc radical cation (ZnNc&z.rad;<SUP>+</SUP>) in the visible and NIR regions. The rate constants of charge-separation (<I>k</I><SUB>CS</SUB>) processes of the self-assembled dyads <B>1</B> and <B>2</B> were determined to be 4.05 × 10<SUP>10</SUP> and 1.20 × 10<SUP>9</SUP> s<SUP>−1</SUP>, respectively. The rate constant of charge recombination (<I>k</I><SUB>CR</SUB>) and the lifetime of charge-separated states (<I>τ</I><SUB>CS</SUB>) of dyad <B>1</B> were determined to be 2.34 × 10<SUP>8</SUP> s<SUP>−1</SUP> and 4.30 ns, respectively. Interestingly, a slower charge recombination (2.20 × 10<SUP>7</SUP> s<SUP>−1</SUP>) and a longer lifetime of the charge separated state (45 ns) were observed in dyad <B>2</B> in nonpolar toluene by utilizing the nanosecond transient measurements. The absorption in a wide section of the solar spectrum and the high charge-separation/charge-recombination ratio suggest the usefulness of the self-assembled zinc naphthalocyanine–perylenediimide dyads as good photosynthetic models.</P> <P>Graphic Abstract</P><P>Good combination! Efficient electron transfer and relatively long-lived charge-separated states are achieved of light harvesting zinc naphthalocyanine:perylenediimide supramolecular dyads using the femtosecond transient absorption technique in nonpolar toluene. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c2cp23285e'> </P>

Evolution of asexual and sexual reproduction in the aspergilli

Ojeda-Ló,pez, M.,Chen, W.,Eagle, C.E.,Gutié,rrez, G.,Jia, W.L.,Swilaiman, S.S.,Huang, Z.,Park, H.-S.,Yu, J.-H.,Cá,novas, D.,Dyer, P.S. CBS Fungal Biodiversity Centre 2018 Studies in mycology Vol.91 No.-

<P><I>Aspergillus nidulans</I> has long-been used as a model organism to gain insights into the genetic basis of asexual and sexual developmental processes both in other members of the genus <I>Aspergillus</I>, and filamentous fungi in general. Paradigms have been established concerning the regulatory mechanisms of conidial development. However, recent studies have shown considerable genome divergence in the fungal kingdom, questioning the general applicability of findings from <I>Aspergillus</I>, and certain longstanding evolutionary theories have been questioned. The phylogenetic distribution of key regulatory elements of asexual reproduction in <I>A. nidulans</I> was investigated in a broad taxonomic range of fungi. This revealed that some proteins were well conserved in the <I>Pezizomycotina</I> (<I>e.g.</I> AbaA, FlbA, FluG, NsdD, MedA, and some velvet proteins), suggesting similar developmental roles. However, other elements (<I>e.g.</I> BrlA) had a more restricted distribution solely in the <I>Eurotiomycetes</I>, and it appears that the genetic control of sporulation seems to be more complex in the aspergilli than in some other taxonomic groups of the <I>Pezizomycotina</I>. The evolution of the velvet protein family is discussed based on the history of expansion and contraction events in the early divergent fungi. Heterologous expression of the <I>A. nidulans abaA</I> gene in <I>Monascus ruber</I> failed to induce development of complete conidiophores as seen in the aspergilli, but did result in increased conidial production. The absence of many components of the asexual developmental pathway from members of the <I>Saccharomycotina</I> supports the hypothesis that differences in the complexity of their spore formation is due in part to the increased diversity of the sporulation machinery evident in the <I>Pezizomycotina</I>. Investigations were also made into the evolution of sex and sexuality in the aspergilli. <I>MAT</I> loci were identified from the heterothallic <I>Aspergillus</I> (<I>Emericella</I>) <I>heterothallicus</I> and <I>Aspergillus</I> (<I>Neosartorya</I>) <I>fennelliae</I> and the homothallic <I>Aspergillus pseudoglaucus</I> (=<I>Eurotium repens</I>). A consistent architecture of the <I>MAT</I> locus was seen in these and other heterothallic aspergilli whereas much variation was seen in the arrangement of <I>MAT</I> loci in homothallic aspergilli. This suggested that it is most likely that the common ancestor of the aspergilli exhibited a heterothallic breeding system. Finally, the supposed prevalence of asexuality in the aspergilli was examined. Investigations were made using <I>A. clavatus</I> as a representative ‘asexual’ species. It was possible to induce a sexual cycle in <I>A. clavatus</I> given the correct <I>MAT1-1</I> and <I>MAT1-2</I> partners and environmental conditions, with recombination confirmed utilising molecular markers. This indicated that sexual reproduction might be possible in many supposedly asexual aspergilli and beyond, providing general insights into the nature of asexuality in fungi.</P>