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11th RES Users' Conference: Poster presentations

Chemistry and Materials Sciences and Technology

1. Selective conversion of biomass by Mo-based compounds

M. Rellán-Piñeiroa and N. Lópeza
aInstitute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans 16, 43007 Tarragona, Spain

By means of DFT studies we illustrate the important catalytic properties of Mo-based oxides for biomass conversion. Through the investigation of the oxidation of methanol, reduction of glycerol and epimerization of glucose we show the versatility of Mo-based oxides as catalyst for biomass conversion.
Formaldehyde is industrially obtained by the selective methanol oxidation in the FormoxTM process.1 The used catalyst is composed by two phases, MoO3 and Fe2(MoO4)3.2 The active phase and the reasons for the observed selectivity are still unknown. We calculate the route that drives the selective conversion and determine the role of Mo and Fe phases to explain the activity and selectivity of the catalyst.3 On the other hand, reduced MoO3 has been experimentally shown as a selective catalyst to glycerol reduction to propylene.4,5 Through a hydrodeoxygenation (HDO) process the selective C-O bond cleavage over C-C bonds leads to the formation of the desired product. A study of the reaction network has been performed to illustrate this selective bond cleavage and pave the way to a better understanding of these HDO processes. In addition, experimental studies have shown the Keggin cluster Mo-based polyoxometalate (POM), H3PMo12O40, as selective catalyst for glucose epimerization to mannose, through a 1,2 C-shif,t with a good performance in terms of activity and selectivity.6 We determine the mechanism and show as the activity depends of the redox properties of Mo centers.

1. www.formox.com, April 2015.
2. C. Brookes et al., ACS Catal., 2014, 4, 243-250.
3. M. Rellán-Piñeiro and N. López, ChemSusChem, 2015,8, 2231–2239.
4. T. Prasomsri et al., Energy Environ. Sci., 2014, 7, 2660-2669.
5. V. Zacharopoulou et al., Green Chem., 2015, 17, 903-912.
6. F. Ju et al. ACS Catal., 2014, 4 (5), 1358–1364


Life and Health Sciences

2. Study of cluster phases in attractive micro-swimmer suspensions

Francisco Alarcón Oseguera (Universidad Complutense de Madrid), Eloy Navarro Argemí (Universitat de Barcelona), Ignacio Pagonabarraga (Universitat de Barcelona) and Chantal Valeriani (Universidad Complutense de Madrid).

Swimming microorganisms play a fundamental role in a lot of biological, medical and engineering processes; bacteria, algae and spermatozoa are just some examples. Micro-swimmers and their individual and collective behavior has inspired researchers to deepen the understanding of the physics of motility to engineer complex emergent behaviors in model systems that promise advances in technological applications. We are particularly interested to asses the effect of hydrodynamics in the assembly of active attractive spheres, thus we simulate a semi-dilute suspension of attractive self-propelled spherical particles comparing the case with and without hydrodynamics interactions. Such a fundamental understanding will help us to identify new routes to design micro-robots that can imitate micro-organisms. The results show that our simulations can reproduce several regimes of emerging collective behavior , from isotropic to aligned suspensions; with qualitatively different distributions of cluster-sizes depending on the symmetry of the induced active stresses that characterize the active suspension. Specifically, we have reproduced the living clusters observed by experimentalists for both artificial active colloids and for some types of bacteria. The intrinsic non-equilibrium nature of the systems, and their tendency to develop long range correlations require the use of large scale suspensions, where we were able to explore the evolution of the suspensions over long time windows. To do such studies it is important to have high performance computing; in our case we had access to the MareNostrum Supercomputer at Barcelona Supercomputing Center (BSC) and also through the Partnership for Advanced Computing in Europe (PRACE).


3. Study of cyclic peptide nanotubes in a membrane environment via Molecular Dynamics simulations

M. Calvelo,1 J. R. Granja,1 R. Garcia-Fandino1,2
1Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), University of Santiago de Compostela 15782 Santiago de Compostela, Spain
2CIQUP, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, R. Campo Alegre s/n, P-4169-007 Porto, Portugal.

Self-assembling cyclic peptide nanotubes (SCPNs) have attracted a great amount of attention from the scientific community in recent years due to their important applications in biology, chemistry and material science.[1] They are based on cyclic structures that adopt a planar form with the amide groups arranged perpendicular to the plane of the cycle so that they are stacked by the formation of β-sheets. The radial disposition of the side chains outwards the channel modifies the external properties of the nanotube, allowing to control their formation and properties. The modulation of the external properties of SCPNs allows the design of cyclic peptides (CPs) that self-assemble into lipid membranes, changing their permeability and
resistance properties.[2] Depending on the sequences the formed SCPNs can be oriented perpendicularly to the lipid membrane (hydrophobic CPs) or in a parallel fashion (amphiphilic CPs). The consequences of this orientation determine the response caused in the lipid membrane and confer them important properties, such as a high antimicrobial activity.
Using Molecular Dynamics simulations (both using atomistic-AA and coarse-grained-CG resolution) we have studied the effect of the inner-functionalization of the SCPNs cavities, as well as the modulation of their external properties when they are inserted into a lipid bilayer. Different examples carried out recently in our research group will be presented, showing the power of combining experimental and computational methods in the field of supramolecular chemistry and demonstrating the power of theoretical calculations when acting as an atomic microscope to analyze the fine details of a complex supramolecular structure.

[1] (a) A. Stavrakoudis, Peptide, 92, 143 (2009). (b) A. Khalfa, J. Phys. Chem. B. 114, 2676 (2010)
[2] D. Seebach, Helv. Chim. Acta, 80, 173 (1997).
[3] (a) M. R. Ghadiri, Nature, 412, 452 (2001). (b) L. Motiei, Chem. Commun., 3693 (2009).


4. Microbial community analysis in wastewater N-removal technologies by 16S rRNA gene metagenomics

N. Fernandez-Gonzaleza, A. Pedrousoa, A. Val del Ríoa, N. Moralesb, J.R. Vázquez-Padínb, J.L. Camposa,c, R. Méndezaand A. Mosquera-Corrala,

a Department of Chemical Engineering, School of Engineering, University of Santiago de Compostela, Spain.

b FCC Aqualia, Guillarei WWTP, Tui, Spain.

c Faculty of Engineering and Science, Universidad Adolfo Ibáñez, Viña del Mar, Chile.

The use of next generation sequencing (NGS) technologies in the field of microbial ecology has impacted the way we study and comprehend microbial ecosystems. The combination of molecular biology approaches and NGS during the last decade has allowed the study microorganisms that are otherwise very difficult or impossible to characterize. As a result, ecologists have discovered an outstanding diversity of microorganisms. At the same time, the large amount of data that is produced by the NGS platforms has required the development of new analytical techniques and the use of large computational resources. In this study, the bacterial community of a bioreactor where the autotrophic removal of nitrogen from wastewater took place has been studied by means of the 16S rRNA gene, a housekeeping marker gene that is the gold standard for bacterial phylogeny and taxonomy in microbial ecology. Autotrophic nitrogen removal biotechnological processes, based on simultaneous partial nitritation (oxidation of ammonia to nitrite by ammonia oxidizing bacteria, AOB) and anammox processes, will contribute to achieve self-energy-sufficient wastewater treatment plants. To achieve an appropriated performance of both processes, the suppression of nitrite oxidizing bacteria (NOB) is crucial. In this sense, the use of sodium azide to stimulate the accumulation free nitrous acid inside the reactor was successfully used to suppress NOBs. The microbiological analysis showed that this procedure changed the bacterial community profile without affecting the reactor performance and that the predominant NOB, Nitrospira sp., was effectively washed out from the system.


5. Binding of Amantadine to the M2 proton channel: Molecular basis of the inhibition mechanism

Carolina Estarellas,1 Jordi Juarez-Jimenez,2 Elnaz Adelavood,1 Adrian Roitberg,3 F. Javier Luque1

1Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Prat de la Riba, 171, Santa Coloma de Gramenet, E-08921 (Spain)

2 School of Chemistry, University of Edinburgh, David Brewster Road, EdinburghEH9 3FJ, United Kingdom

3Department of Chemistry, University of Florida, 440 Leigh Hall, Gainesville, FL. 32611-7200

The M2 protein of the influenza A virus is a homotetramer that functions as a pH-gated proton channel essential for virus replication [1]. The influenza virus enters its target cells by receptormediated endocytosis, which is followed by acid-induced fusion of the viral and endosomal membranes. The endosomal pH activates the membrane-spanning M2 protein, which acts as a proton channel to conduct protons into the virion interior. The channel function of wild type (wt) M2 is efficiently inhibited by amantadine (Amt) and rimantadine (Rmt). The single amino acid substitutions associated with Amt resistance, such as V27A or S31N, suggests that these residues contribute to delineate the binding pocket for the inhibitors [2].
We have recently examined the mechanism of binding of Amt to the wt M2 channel and its V27A variant [3]. On the one hand, the binding of Amt involves two distinct binding modes, up and down, which orient the Amt protonated amine toward the His37 tetrad, respectively. The stabilization of the down state is carried out by the presence of chloride anions, which thus compensates the repulsive electrostatic repulsion between Amt and the diprotonated His37 tetrad.
It may be speculated, however, that binding of Amt may alter the protonation state of the His37 tetrad, leading to a distinct inhibition mechanism. To explore the feasibility of this possibility, we have performed a series of calculations to examine the effect of ligand binding on the protonated state of the His37 tetrad. In particular, pH-constant replica exchange simulations [4] have been planned for the apo form of the M2 channel and the results have been compared with the available experimental data. These computations have been extended to the ligandbound state, and they will be compared with the inhibition mechanism proposed recently for the binding of Amt [3].

[1] Lamb, R. A.; et al. Cell 1985, 40, 627.
[2] a) Cady, S. D.; et al. Nature 2010, 463, 689. b) Jing, X.; et al. Proc. Natl. Acad. Sci. U S A 2008, 105, 10967. c) Khurana, E.; et al. Proc. Natl. Acad. Sci. U S A 2009, 106, 1069. d) Stouffer, A. L.; et al. Nature 2008,  451, 596.
[3] Llabrés, S., et al. J. Am. Chem. Soc. 2016, 138, 15345.
[4] Project BCV-2017-1-0018 (Constant pH Replica Exchange Molecular Dynamics of the M2 Channel of Influenza A Virus)


6. Exploring the action mechanism of aniline-based inhibitors of influenza A Hemagglutinin

Tiziana Ginex and F. Javier Luque

Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Campus de l'Alimentació de Torribera, Universitat de Barcelona, Av. Prat de la Riba, 171, 08921 Santa Coloma de Gramenet, Spain.

Cell infection by Influenza A virus is a multi-stage process culminating in formation of fusion pores that allow the transfer of the viral material into the host cell, where replication takes place. Fusion of virus envelope to the endosome is promoted by exposure of the fusion peptide as a consequence of low pH-induced conformational changes occurring on hemagglutinin (HA), a glycoprotein embedded in the viral membrane. Fusion inhibitors may block conformational changes required for the exposure of the fusion peptide, thus stabilizing HA in its prefusogenic architecture. However, very little is known about the mechanism by which these molecules exert their inhibitory activity.

An in silico protocol1 was set up to investigate the action mechanism of a new class of amantadine- and aniline-derivatives on the influenza A/PuertoRico/8 (H1N1), A/Virginia/ATCC3/2009 (H1N1) and A/HongKong/7/87 (H3N2) subtypes: homology modeling, docking and molecular dynamic (MD) simulations were carried out to elucidate the structural and physicochemical features responsible of their experimentally observed H1 selectivity. In this regard, a common binding site close to the HA1-HA2 interface, and to the HA fusion peptide was modeled on these three strains and then targeted by docking and MD simulations. The results provide a preliminary basis to explain the H1-selectivity of these compounds. 


1 Redesigning anti-influenza compounds: Novel anilines with multi-target activity (RES project BCV-2017-1-0016)


Mathematics, Physics and Engineering

7. GPU-based Stochastic Problem Solving and Scalability in Superconductivity

Juan Rodríguez García 1, Manuel Rodríguez-Pascual 2, Jose Antonio Moríñigo 2, Rafael Mayo-García 2.

1 UAM, 2 CIEMAT. Spain

In Nb films fabricated on top of array of Ni nanodots, the array of periodic pinning potentials modifies the vortex lattice for specific values of the external applied magnetic field. With GPU computer simulations based on the vortex–vortex and the vortex–nanodot interactions, it is possible to determine the total interaction between vortices and pinning sites as well as the position of the vortices in the array unit cell, the latter of which is not possible to be figured out from the experiments. The code can simulate square, rectangular or triangular arrays of nanodefects of different size and make use of several stochastic processes to find out the final solution.


8. Introduction of obstacles in bidimensional Vicsek model

Raul Martinez, Francisco Alarcon, Chantal Valeriani
Universidad Complutense de Madrid

A situation where objects are introduced in Vicsek model was studied, using a collision rule between objects and walls consisting in the allignment of the colliding particle with the direction that is tangent to the wall. Two shapes of objects were considered: funnel-shaped and circular ones.

Funnel shaped objects have been previously used in theoretical and experimental studies aimed at trapping active particles. Particles with run-and-tumble behaviour had already been reported to concentrate in the concave side of the funnels, as simulations and a experimental work done with bacteria have proved. We have obtained an unexpected result for Vicsek particles: particles tend to be confined in the convex part of the funnels. Simple circular traps for vicsek particles were designed on the basis of this result, and a brief study on the conditions necessary to trap the particles was carried out.

Using circular objects, the counterintuitive result of the existence of a noise value which maximizes order was reproduced when the circle radius is of the same order than the Vicsek interaction distance. As an explanation, formation of clusters for low values of noise was observed: when noise is low, clusters are formed and, as each one of them takes a different direction, the order parameter is small, but if noise increases, these clusters don't appear, and all the particles tend to flock in the same direction. The influence of some parameters in the size of these clusters was studied.

Curently the influence of the Vicsek particles size is being studied: the study is being repeated using, instead of puntual particles, disk-shaped particles.

This studies, developed with Vicsek model, will later be repeated with another system of active particles where the hydridynamics are explicitly considered. In this more realistic case we plan to make use of supercomputers, being hydrodynamic interactions quite demanding to simulate.


9. Dynamic task migration in HPC for Exascale challenge

Manuel Rodríguez-Pascual, Jose Antonio Moríñigo, Rafael Mayo-García.


Counting with a robust and efficient checkpoint/restart mechanism in a Slurm cluster can enable a wide set of possibilities. In this work, a work on the support for DMTCP (a robust and efficient checkpoint library) on Slurm will be presented, which shows the new possibilities enabled by this integration: besides fault tolerance, being able to checkpoint any serial or parallel job and restart it somewhere else (thus "migrating" it) is of high interest on job preemption, scheduling and system administration.


Astronomy, Space and Earth Sciences

10. Off-line lagrangian particle tracking: Efficient implementation of a Vertical Dispersion algorithm

Ignacio Vidal-Franco1, Manuel Ruiz-Villarreal2 and Andrés Gómez-Tato3

1 Galician Network of Cloud and Big Data technologies for HPC (UDC-IEO)

2 Spanish Institute of Oceanography (IEO)

3 Galician Centre for Supercomputing (CESGA)

In the context of physical oceanographic modelling, the vertical dispersion process is key to simulate particle trajectories using a lagrangian individual based model. As our main goal is to study the recruitment of Sardine in the north west of the Iberian Peninsula, we extended the Ichthyop java tool for simulation of ichthyoplankton dynamics by implementing the Vertical Dispersion Algorithm proposed by Visser in 1997. The starting point was a previously multithreaded but not satisfactorily performant version of Ichthyop v3.1. HPC suitability was achieved by means of codebase revision and extensive tests on the Finisterrae II computer cluster at the Galician Centre for Supercomputing (CESGA). Algorithm reordering, pseudo-random number generation management and serial I/O play here a key role on performance. The present work allowed for a higher number of particles to be simulated within a significantly reduced wall time.