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Catalysis of chemical reactions by nanosized clusters of transition metals holds the key to the provision of sustainable energy and materials. However, the atomistic behaviour of nanocatalysts still remains largely unknown due to uncertainties associated with the highly labile metal nanoclusters changing their structure during the reaction. In this study, we reveal and explore reactions of nm-sized clusters of 14 technologically important metals in carbon nano test tubes using time-series imaging by atomically-resolved transmission electron microscopy (TEM), employing the electron beam simultaneously as an imaging tool and stimulus of the reactions. Defect formation in nanotubes and growth of new structures promoted by metal nanoclusters enable the ranking of the different metals both in order of their bonding with carbon and their catalytic activity, showing significant variation across the Periodic Table of Elements. Metal nanoclusters exhibit complex dynamics shedding light on atomistic workings of nanocatalysts, with key features mirroring heterogeneous catalysis.

We report an approach – named chemTEM – to follow chemical transformations at the single-molecule level with the electron beam of a transmission electron microscope (TEM) applied as both a tuneable source of energy and a sub-Angstrom imaging probe. Deposited on graphene, disk-shaped perchlorocoronene molecules are precluded from intermolecular interactions. This allows monomolecular transformations to be studied at the single-molecule level in real time and reveals chlorine elimination and reactive aryne formation as a key initial stage of multi-step reactions initiated by the 80 keV e-beam. Under the same conditions, perchlorocoronene confined within a nanotube cavity, where the molecules are situated in very close proximity to each other, enables imaging of intermolecular reactions, starting with the Diels-Alder cycloaddition of a generated aryne, followed by rearrangement of the angular adduct to a planar polyaromatic structure and the formation of a perchlorinated zigzag nanoribbon of graphene as the final product. ChemTEM enables the entire process of polycondensation, including the formation of metastable intermediates, to be captured in a one-shot ‘movie’. A molecule with a similar size and shape but with a different chemical composition, octathio[8]circulene, under the same conditions undergoes another type of polycondensation via thiyl biradical generation and subsequent reaction leading to polythiophene nanoribbons with irregular edges incorporating bridging sulphur atoms. Graphene or carbon nanotubes supporting the individual molecules during chemTEM studies ensure that the elastic interactions of the molecules with the e-beam are the dominant forces that initiate and drive the reactions we image. Our ab initio DFT calculations explicitly incorporating the e-beam in the theoretical model correlate with the chemTEM observations and give a mechanism for direct control not only of the type of the reaction but also of the reaction rate. Selection of the appropriate e-beam energy and control of the dose rate in chemTEM enabled imaging of reactions on a timeframe commensurate with TEM image capture rates, revealing atomistic mechanisms of previously unknown processes.

Ernogrammus zhirmunskii, sp. nov. Proposed English name — seven-lined prickleback. (Figs. 1–4 ) Holotype: ZIN 54444, female SL 75 mm, the Sea of Japan, Peter the Great Bay, Bol’shoy Pelis Island, bay on the northern coast of the island. 13 July 2008. Depth 5.9 m, boulders, SCUBA poison station, hand net, collector A.I. Markevich. Paratypes: ZIN 54757 males SL 59.5, 58.5, 56.5 mm and females 55.5, 54 mm, data as for holotype; ZMFESU IV 27577 / 1233 male SL 64 mm, data as for holotype; TINRO Centre Р 242 female SL 70.5 mm, data as for holotype; MIMB 20795 male SL 53.8 mm, data as for holotype; FEMBSNR 747 male SL 60 mm and female 61 mm, data as for holotype. Non-type material. FEMBSNR 748 female SL 61 mm, juvenile SL 34 mm, the Sea of Japan, Peter the Great Bay, Bol’shoy Pelis Island, Molchanskiy bay, 42 º 38.71´N, 131 º 26.72´E. 27 August 2008. Depth 7.9 m, boulders, SCUBA poison station, hand net, collector A.I. Markevich. Diagnosis. Anal fin with one spine anteriorly, a long series of soft rays, and one short rigid spine posteriorly. Seven longitudinal lateral line canals present; one canal runs along middle of belly. No branches ascend or descend from lateral line canals. In coloration one narrow white stripe between two wide black stripes on the base of pelvic fin, and one dark blotch on the dorsal fin anteriorly. Description. Proportional measurements are given in Table 1. Body moderately extended, laterally compressed. Maximum body height 6.2 times in SL, head large, measuring 3.7 times in SL. Dorsal and anal fins long; dorsal slightly connected to tail. Dorsal fin composed of 41–42 spines, thin in the anterior part of the fin and more rigid and thick originating from 15 th spine (behind vertical line to origin of anal fin). Anal fin with one long spine anteriorly, one short rigid spine posteriorly and 28–30 soft rays. Pelvic fins on thoracic, originating before pectoral fins and reaching past their bases consisting of one spine and 3 branched rays. All these fins low: hD 6.6 % in SL, hA 7.5 %, hV 10.3 % in SL. Pectoral fins more higher, hP 17.4 % in SL, with 14 branched rays. Caudal fin slightly extended, with rounded margin, and has 7 – 6 + 6–7 principal rays. Vertebrae 44–47 (14–16 + 30–31), with urostyl. Head rather large, 3.7 times (26.9 %) in SL, slightly conical. Eyes large, 4.2 times in head length; eye orbits slightly jutting out above the top head profile. Interorbital space rather wide, 4.6 % in SL (6.1 times in head length), and flat. Edge of snout with noticeable dermal nostril tubes. Mouth terminal, large, not reaching vertical below middle of eye; oral extends slightly oblique upwards. Branchiostegal membranes not connected; isthmus free up to vertical from posterior edge of eye. Gill rakers on first arch 6 + 6, short. Head naked, except strip ahead of dorsal fin to occipital sensory canal. Body and bases of fins covered with overlapping small oval cycloid scales. Number of scales 30–33 in oblique row in the line of highest body depth, 155–160 in the middle lateral line. Teeth on both jaws, vomer and palatines present. Large conical teeth form one row on maxilla, ahead of this row some small teeth settle down irregularly, these teeth 3–5 times smaller than teeth of the row. Mandible has two rows of large conical teeth, teeth of the 1 -st row a little smaller than those of the 2 -nd row. Sensory system consists of numerous canals on body and head. Body with 7 longitudinal lateral line canals: 3 lateral line canals (upper, middle, and lower) on each body side plus one unpaired ventral canal. Upper canal originating above dorsal margin of operculum and running along base of dorsal fin, almost reaching insertion of dorsal fin. Middle canal originating behind base of pectoral fin, running along middle of body and ending at base of caudal fin. Lower canal originating anterior to base of pelvic fin and running along base of anal fin to its posterior margin. Lower paired lateral canals not connected anteriorly. Pores of all longitudinal canals on short branches, pointed obliquely posteriorly. Vertical branches and those connecting lateral canals absent. Ventral canal short; originating behind posterior edge of pelvic fin, running along midline of belly, branching before anus and connecting with lower lateral line canals. Cephalic sensory canals well developed. Pores of supraorbital canal 6, infraorbital 4, postorbital 4, preoperculo-mandibular 4, preopercular 7, occipital 6. Each dorsal fin ray is supported one pterygiophore locating between neural spines of adjacent vertebrae, posteriormost pterygiophore bears two rays. A wide variety in the position of the anteriormost pterygiophores of the anal fin is observed. Pterygiophores implant in the interval between haemal spines of the posteriormost body vertebrae, or between the posterior body vertebra and the anterior caudal vertebra. Posteriormost anal fin pterygiophore bears posterior soft ray and rigid spine. The majority of the type specimens (9 of 11) have 4 free caudal vertebrae. Three epurals present, upper marginal rays not branched, 3–5 (mode 3). Hypurals 3–4 are separated, and bear 6–7 (mode 7) upper principal rays. Hypurals 1–2 are connected in hypural plate bearing 6–7 (mode 6) lower principal rays. Lower marginal rays 2–4, usually 3, not branched. Total number of the caudal fin rays 17–23 = 3–5 + 7 – 6 + 6–7 + 2–4. Color of live specimens. Background body color brown in life, with numerous small grayish-white spots and dots. Dorsum sometimes with 7–8 narrow (no more than diameter of eye) and short white vertical stripes extending to dorsal fin; row of rounded white spots under these stripes on ventral body part. Two wide black stripes with narrow white stripe between them near base of pectoral; these stripes followed by alternating indistinct black and white stripes. Four type specimens including holotype with clearly visible dark blotch on the dorsal fin anteriorly but others fish not. Caudal base with wide vertical yellow stripe and 3 brown stripes alternating narrow white stripes; caudal margin white. Head with irregularly placed small white dots, stripes absent. No significant differences among sexes in morphological characters and coloration were found. Distribution. The only known locality of the fish is the coast of Bol’shoy Pelis Island. In addition to the typical locality in the bay on the northern coast of the island, 2 specimens FEMBSNR 748 were collected at the southwestern tip of the same island, in the Molchanskiy bay. Biology. Conducted visual underwater observations of senior author show that Ernogrammus zhirmunskii occurs in rocky substrate of a depth 2.5 to 11.3 m at water temperature from 14 ºC to 21 ºC during July to September. It is a secretive species, and under ordinary condition the fish seldom leave their shelters under boulders in the daytime, usually they expose only the anterior part of the body. During the collection, from 1 to 3 fish were usually found under one boulder 0.3 × 0.3 m in size, so the common density reached 8 fish/m 2. This species is inactive at night, unlike E. hexagrammus, which commonly occurs in the same rocky habitat (Markevich 2004). Specimens of the type series had average body weight 1.425 g (1.100–1.900 g), the smallest collected fish (FEMBSNR 748 juvenile SL 34 mm) had body weight 0.350 g. The stomachs of the collected fishes contained the remains of shells small mollusk Falsicingula mundana (Gastropoda: Discopoda: Falsicingulidae), the remains of unidentified fish and lumps of tiny fish eggs. Etymology. The species is named after an outstanding scientist who worked in marine biology, ecology, and comparative physiology, Member of the Russian Academy of Sciences Alexey V. Zhirmunsky (1921–2000). He was the founder and director of the Institute of Marine Biology (Far Eastern Branch of the Russian Academy of Sciences, Vladivostok), and the initiator of the Far Eastern Marine Reserve. He contributed significantly to the development of marine biology in the Russian Far East. His talent as of a scientist and organizer turned the Institute of Marine Biology and the Far Eastern Marine Biosphere Reserve to large scientific and nature preservation organizations.

Markevich, Alexander I., Kharin, Vladimir E. (2011): A new species of prickleback Ernogrammus zhirmunskii (Acanthopterygii: Perciformes: Stichaeidae) from the Sea of Japan, Russia. Zootaxa 2814: 59-66, DOI: 10.5281/zenodo.203484

Mestrado em Ciência e Engenharia de Materiais Esta tese apresenta os resultados de um programa de investigação sobre a difusão da lacuna, bi-lacuna e tri-lacuna em silício utilizando simulações numéricas pelo método da teoria do funcional da densidade. Este método está implementado na forma de um programa informático referido como AIMPRO (Ab Initio Modelling PROgram). Para o cálculo dos pontos cela dos mecanismos de difusão foi usado o método “Nudged Elastic Band”. As condições fronteira dos problemas foram impostas recorrendo à utilização de agregados esféricos de silício com 275 atomos, cuja superfície foi saturada por ligações Si-H. As lacunas foram então introduzidas no centro destes agregados. Os valores calculados das barreiras de difusão para a lacuna simples e para a bi-lacuna são respectivamente 0.68 e 1.75 eV. Estes valores apresentam um acordo razoável com os obtidos experimentalmente e obtidos em outros cálculos anteriores. A barreira de difusão da tri-lacuna foi, de acordo com a literatura disponível, calculada pela primeira vêz. O mecanismo de difusão mais favorável apresenta uma barreira de 2.2 eV. No seguimento dos resultados para a lacuna e bi-lacuna, pensamos que este resultado sobrestima a barreira em cerca de 0.25 eV, colocando a nossa melhor estimativa em 1.9- 2.0 eV. Varias fontes de erro nos resultados são comentadas, assim como são sugeridas várias formas de as evitar. ABSTRACT: This work presents the results of a computational investigation into the diffusion of the single vacancy (V) and small vacancy clusters, divacancy (V2) and trivacancy (V3), in silicon. The calculations were performed principally using local density functional theory as implemented by the AIMPRO (Ab Initio Modelling PROgram) code. The Nudged Elastic Band Method was used for elucidating diffusion paths and obtaining the energy barriers for diffusion of the defects considered. Based on ab-initio calculations with H-terminated Si clusters with 275 host atoms, diffusion paths for neutral Vn (n = 1 to 3) defects were found. Calculated values of the activation energy for the diffusion of the Si vacancy and divacancy are 0.68 and 1.75 eV, respectively. These values are in a reasonable agreement with those derived from experimental and previous ab-initio modelling studies. The diffusion of trivacancy in Si has been modelled for the first time. The diffusion barrier of V3 along the proposed diffusion path was found to be about 2.2 eV. This result comes overestimated as the experimental data indicates that the values of diffusion barriers for divacancy and trivacancy in Si should be similar. Probable sources of the calculation errors have been considered and possible ways to surmount these difficulties are proposed.