TY - JOUR A1 - Chipman, Ariel D. A1 - Ferrier, David E. K. A1 - Brena, Carlo A1 - Qu, Jiaxin A1 - Hughes, Daniel S. T. A1 - Schroeder, Reinhard A1 - Torres-Oliva, Montserrat A1 - Znassi, Nadia A1 - Jiang, Huaiyang A1 - Almeida, Francisca C. A1 - Alonso, Claudio R. A1 - Apostolou, Zivkos A1 - Aqrawi, Peshtewani A1 - Arthur, Wallace A1 - Barna, Jennifer C. J. A1 - Blankenburg, Kerstin P. A1 - Brites, Daniela A1 - Capella-Gutierrez, Salvador A1 - Coyle, Marcus A1 - Dearden, Peter K. A1 - Du Pasquier, Louis A1 - Duncan, Elizabeth J. A1 - Ebert, Dieter A1 - Eibner, Cornelius A1 - Erikson, Galina A1 - Evans, Peter D. A1 - Extavour, Cassandra G. A1 - Francisco, Liezl A1 - Gabaldon, Toni A1 - Gillis, William J. A1 - Goodwin-Horn, Elizabeth A. A1 - Green, Jack E. A1 - Griffiths-Jones, Sam A1 - Grimmelikhuijzen, Cornelis J. P. A1 - Gubbala, Sai A1 - Guigo, Roderic A1 - Han, Yi A1 - Hauser, Frank A1 - Havlak, Paul A1 - Hayden, Luke A1 - Helbing, Sophie A1 - Holder, Michael A1 - Hui, Jerome H. L. A1 - Hunn, Julia P. A1 - Hunnekuhl, Vera S. A1 - Jackson, LaRonda A1 - Javaid, Mehwish A1 - Jhangiani, Shalini N. A1 - Jiggins, Francis M. A1 - Jones, Tamsin E. A1 - Kaiser, Tobias S. A1 - Kalra, Divya A1 - Kenny, Nathan J. A1 - Korchina, Viktoriya A1 - Kovar, Christie L. A1 - Kraus, F. Bernhard A1 - Lapraz, Francois A1 - Lee, Sandra L. A1 - Lv, Jie A1 - Mandapat, Christigale A1 - Manning, Gerard A1 - Mariotti, Marco A1 - Mata, Robert A1 - Mathew, Tittu A1 - Neumann, Tobias A1 - Newsham, Irene A1 - Ngo, Dinh N. A1 - Ninova, Maria A1 - Okwuonu, Geoffrey A1 - Ongeri, Fiona A1 - Palmer, William J. A1 - Patil, Shobha A1 - Patraquim, Pedro A1 - Pham, Christopher A1 - Pu, Ling-Ling A1 - Putman, Nicholas H. A1 - Rabouille, Catherine A1 - Ramos, Olivia Mendivil A1 - Rhodes, Adelaide C. A1 - Robertson, Helen E. A1 - Robertson, Hugh M. A1 - Ronshaugen, Matthew A1 - Rozas, Julio A1 - Saada, Nehad A1 - Sanchez-Gracia, Alejandro A1 - Scherer, Steven E. A1 - Schurko, Andrew M. A1 - Siggens, Kenneth W. A1 - Simmons, DeNard A1 - Stief, Anna A1 - Stolle, Eckart A1 - Telford, Maximilian J. A1 - Tessmar-Raible, Kristin A1 - Thornton, Rebecca A1 - van der Zee, Maurijn A1 - von Haeseler, Arndt A1 - Williams, James M. A1 - Willis, Judith H. A1 - Wu, Yuanqing A1 - Zou, Xiaoyan A1 - Lawson, Daniel A1 - Muzny, Donna M. A1 - Worley, Kim C. A1 - Gibbs, Richard A. A1 - Akam, Michael A1 - Richards, Stephen T1 - The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima JF - PLoS biology N2 - Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. Y1 - 2014 U6 - https://doi.org/10.1371/journal.pbio.1002005 SN - 1545-7885 VL - 12 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Utecht, Manuel Martin A1 - Palmer, Richard E. A1 - Klamroth, Tillmann T1 - Quantum chemical approach to atomic manipulation of chlorobenzene on the Si(111)-7 x 7 surface BT - Resonance localization, vibrational activation, and surface dynamics JF - Physical review materials N2 - We present a cluster model to describe the localization of hot charge carriers on the Si(111)-7 x 7 surface, which leads to (nonlocal) desorption of chlorobenzene molecules in scanning tunneling microscope (STM) manipulation experiments. The localized charge carriers are modeled by a small cluster. By means of quantum chemical calculations, this cluster model explains many experimental findings from STM manipulation. We show that the negative charge is mainly localized in the surface, while the positive one also resides on the molecule. Both resonances boost desorption: In the negative resonance the adatom is elevated; in the positive one the chemisorption bond between the silicon surface adatom and chlorobenzene is broken. We find normal modes promoting desorption matching experimental low-temperature activation energies for electron-and hole-induced desorption. Y1 - 2017 U6 - https://doi.org/10.1103/PhysRevMaterials.1.026001 SN - 2475-9953 VL - 1 IS - 2 PB - American Physical Society CY - College Park ER - TY - JOUR A1 - Gaebel, Tina A1 - Bein, Daniel A1 - Mathauer, Daniel A1 - Utecht, Manuel A1 - Palmer, Richard E. A1 - Klamroth, Tillmann T1 - Nonlocal STM manipulation of chlorobenzene on Si(111)-7 x 7 BT - Potentials, kinetics, and first-principles molecular dynamics calculations for open systems JF - The journal of physical chemistry : C, Nanomaterials and interfaces N2 - We use quantum chemical cluster models together with constrained density STM Ph CI functional theory (DFT) and ab initio molecular dynamics (AIMD) for open system to simulate tip and rationalize nonlocal scanning tunneling microscope (STM) manipulation experiments for Philh ci chlorobenzene (PhCl) on a Si(111)-7 X 7 surface. We consider three different processes, namely, the electron-induced dissociation of the carbon-chlorine bond for physisorbed PhCl molecules at low temperatures and the electron- or hole-induced desorption of chemisorbed PhCl at 300 K. All processes can be induced nonlocally, i.e., up to several nanometers (nm) away from the injection site, in STM experiments. We rationalize and explain the experimental findings regarding the STM-induced dissociation using constrained DFT. The coupling of STM-induced ion resonances to nuclear degrees of freedom is simulated with AIMD using the Gadzuk averaging approach for open systems. From this data, we predict a 4 fs lifetime for the cationic resonance. For the anion model, desorption could not be observed. In addition, the same cluster models are used for transition-state theory calculations, which are compared to and validated against time-lapse STM experiments. Y1 - 2021 U6 - https://doi.org/10.1021/acs.jpcc.1c02612 SN - 1932-7447 SN - 1932-7455 VL - 125 IS - 22 SP - 12175 EP - 12184 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Utecht, Manuel Martin A1 - Pan, Tianluo A1 - Klamroth, Tillmann A1 - Palmer, Richard E. T1 - Quantum chemical cluster models for chemi- and physisorption of chlorobenzene on Si(111)-7x7 JF - The journal of physical chemistry : A, Molecules, spectroscopy, kinetics, environment & general theory N2 - Motivated by recent atomic manipulation experiments, we report quantum chemical calculations for chemi- and physisorption minima of chlorobenzene on the Si(111)-7x7 surface. A density functional theory cluster approach is applied, using the B3LYP hybrid functional alongside Grimme's empirical dispersion corrections (D3). We were able to identify chemisorption sites of binding energies of 1.6 eV and physisorption energies of 0.6 eV, both in encouraging agreement with the trend of experimental data. The cluster approach opens up the possibility of a first-principles based dynamical description of STM manipulation experiments on this system, the interpretation of which involves both the chemi- and physisorbed states. However, we found that special care has to be taken regarding the choice of clusters, basis sets, and the evaluation of the dispersion corrections. Y1 - 2014 U6 - https://doi.org/10.1021/jp504208d SN - 1089-5639 VL - 118 IS - 33 SP - 6699 EP - 6704 PB - American Chemical Society CY - Washington ER -