An evolutionary algorithm for the surface structure problem

Many macroscopic properties: hardness, corrosion, catalytic activity, etc. are directly related to the surface structure, that is, to the position and chemical identity of the outermost atoms of the material. Current experimental techniques for its determination produce a “signature” from which the structure must be inferred by solving an inverse problem: a solution is proposed, its corresponding signature computed and then compared to the experiment. This is a challenging optimization problem where the search space and the number of local minima grows exponentially with the number of atoms, hence its solution cannot be achieved for arbitrarily large structures. Nowadays, it is solved by using a mixture of human knowledge and local search techniques: an expert proposes a solution that is refined using a local minimizer. If the outcome does not fit the experiment, a new solution must be proposed again. Solving a small surface can take from days to weeks of this trial and error method. Here we describe our ongoing work in its solution. We use an hybrid algorithm that mixes evolutionary techniques with trusted region methods and reuses knowledge gained during the execution to avoid repeated search of structures. Its parallelization produces good results even when not requiring the gathering of the full population, hence it can be used in loosely coupled environments such as grids. With this algorithm, the solution of test cases that previously took weeks of expert time can be automatically solved in a day or two of uniprocessor time

SVis: A computational steering visualization environment for surface structure determination

The arrangement of atoms at the surface of a solid accounts for many of its properties: Hardness, chemical activity, corrosion, etc. are dictated by the precise surface structure. Hence, finding it, has a broad range of technical and industrial applications. The ability to solve this problem opens the possibility of designing by computer materials with properties tailored to specific applications. Since the search space grows exponentially with the number of atoms, its solution cannot be achieved for arbitrarily large structures. Presently, a trial and error procedure is used: an expert proposes an structure as a candidate solution and tries a local optimization procedure on it. The solution relaxes to the local minimum in the attractor basin corresponding to the initial point, that might be the one corresponding to the global minimum or not. This procedure is very time consuming and, for reasonably sized surfaces, can take many iterations and much effort from the expert. Here we report on a visualization environment designed to steer this process in an attempt to solve bigger structures and reduce the time needed. The idea is to use an immersive environment to interact with the computation. It has immediate feedback to assess the quality of the proposed structure in order to let the expert explore the space of candidate solutions. The visualization environment is also able to communicate with the de facto local solver used for this problem. The user is then able to send trial structures to the local minimizer and track its progress as they approach the minimum. This allows for simultaneous testing of candidate structures. The system has also proved very useful as an educational tool for the field

On-Surface Hydrogen-Induced Covalent Coupling of Polycyclic Aromatic Hydrocarbons via a Superhydrogenated Intermediate

The activation and subsequent covalent coupling of polycyclic aromatic hydrocarbons (PAHs) are of great interest in fields like chemistry, energy, biology, or health, among others. However, this is not a trivial process. So far, it is based on the use of catalysts that drive and increase the efficiency of the reaction. Here, we report on an unprecedented method in which the dehydrogenation and covalent coupling is thermally activated in the presence of atomic hydrogen and a surface. This mechanism, which requires of the superhydrogenation of the PAHs, has been characterized by high-resolution scanning tunnelling microscopy (STM) and rationalized by density functional theory (DFT) calculations. This work opens a door toward the formation of covalent, PAH-based, macromolecular nanostructures on low-reactive surfaces, thus facilitating its applicability.Comment: This manuscript version is made available under the CC-BY-NC-ND 4.0 licens

Caracterización estructural y electrónica de films subnanométricos de carbono tipo diamante depositados sobre silicio mediante evaporación láser

Tesis doctoral inédita leida en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Física de la Materia Condensada. Fecha de lectura: 8-6-199

Nuevos materiales para retos sociales globales: el instituto de ciencia de materiales de Madrid (ICMM-CSIC)

El Instituto de Ciencia de Materiales de Madrid (ICM), perteneciente al Consejo Superior de Investigaciones Científicas (CSIC), es un centro de investigación de renombre internacional comprometido con la realización de investigación sinérgica a la vanguardia del conocimiento para abordar desafíos sociales para los que es esencial contar con nuevos materiales. Las temáticas que se desarrollan abarcan desde la investigación fundamental hasta las aplicaciones tecnológicas, e involucran a investigadores de diferentes campos, como la química, la física y la ingeniería; además combinan estudios tanto teóricos como experimentales. El gran número de investigadores vinculados al ICMM permite enfrentar problemas sinérgicos, compartiendo instrumentación y conocimiento. Este entorno ha convertido al ICMM en un atractor de jóvenes talentos que, de manera creciente, se están desplazando al ICMM para desarrollar sus carreras profesionale

Abasic analogues of TSAO-T as the first sugar derivatives that specifically inhibit HIV-1 reverse transcriptase

With the aim of assessing the role that the thymine base of TSAO-T may play in the interaction of TSAO compounds with HIV-1 reverse transcriptase (RT), we have designed, synthesized, and evaluated for their anti-HIV-1 activity a series of 3-spiro sugar derivatives substituted at the anomeric position with nonaromatic rings or with amine, amide, urea, or thiourea moieties that mimic parts or the whole thymine base of TSAO-T. Also, a dihydrouracil TSAO analogue and O-glycosyl 3-spiro sugar derivatives substituted at the anomeric position with methyloxy or benzyloxy groups have been prepared. Compounds substituted at the anomeric position with an azido, amino, or methoxy group, respectively, were devoid of marked antiviral activity (EC50:10-200 íM). However, the substituted urea sugar derivatives led to an increase in antiviral potency (EC50: 0.35-4 íM), among them those urea derivatives that mimic most closely the intact TSAO-T molecule retained the highest antiviral activity. Also, the dihy- drouracil TSAO derivative retained pronounced anti-HIV-1 activity. None of the compounds showed any anti-HIV-2 activity. The results described herein represent the first examples of sugar derivatives that interact in a specific manner with HIV-1 RT. Molecular modeling studies carried out with a prototype urea derivative indicate that a heteroaromatic ring is not an absolute requirement for a favorable interaction between TSAO-T and HIV-1 RT. Urea derivatives, which can mimic to a large extent both the shape and the electrostatic potential of a thymine ring, can effectively replace this nucleic acid base when incorporated into a TSAO molecular framework with only moderate loss of activity.We thank Francisco Caballero for editorial assistance and Lizette van Berckelaer and Ann Absillis for excellent technical assistance. This research was supported in part by grants from the Spanish CICYT (Project SAF97-0048-C02-01), the NATO Collaborative Research (Grant No. CRG 920777), and the Biomedical Research Programme of the European Commission (Project BMH4-CT97-2161).Peer reviewe

Physicochemical characterization of Acidiphilium sp. biofilms

The biofilm formation of a strain of the extremophile bacterium Acidiphilium sp., capable of donating electrons directly to electrodes, was studied by different surface characterization techniques. We develop a method that allows the simultaneous study of bacterial biofilms by means of fluorescence microscopy and atomic force microscopy (AFM), in which transparent graphitic flakes deposited on a glass substrate are used as a support for the biofilm. The majority of the cells present on the surface were viable, and the growth of the biofilms over time showed a critical increase of the extracellular polymeric substances (EPS) as well as the formation of nanosized particles inside the biofilm. Also, the presence of Fe in Acidiphilium biofilms was determined by X-ray photoelectron spectroscopy (XPS), whereas surface-enhanced infrared absorption spectroscopy indicated the presence of redox-active proteins. Acidiphilium biofilms are grown on graphitic flakes and are characterized by different physicochemical techniques. Combined fluorescence-AFM microscopy is applied to study the biofilm formation over time and to detect nanosized particles that are, in turn, analyzed by X-ray photoelectron spectroscopy and attenuated total reflection surface-enhanced infrared absorption spectroscopy. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.Spanish Ministerio de Ciencia e Innovación (projects CTQ2009-12649, MAT2011-26534, MAT2010-18432); Fundación Ramón Areces (project 20100272)Peer Reviewe