ITN FELLOWSHIP'S PROJECTS
List of the ITN projects that are being developed by our fellows. The duration of the projects are 36 months.
This PhD project will be carried in cotutelle by the University of Pisa (PI: Prof. Benedetta Mennucci) and by the University of Vienna (PI: Prof. Leticia González)
Secondment: Barcelona Supercomputing Center (BSC)
Energy transfer by light absorption represents the fundamental processes in both natural and artificial light-harvesting (LH) systems.
The most striking example is the initial step of photosynthesis, in which plants, algae and bacteria are able to transfer the absorbed light to the reaction centers with almost 100% quantum efficiency.
The electronic energy transfer (EET) process is indeed ubiquitous, being used also for the amplification of fluorescence-based sensors, the optimization of organic light-emitting diodes, and the measurement of structure in biological systems.
The focus of the present project will be on the accurate modeling of the light-harvesting process in both natural and artificial systems. Addressing this problem calls for new theoretical and computational approaches able to reproduce the microscopic process based on an accurate description of the playing actors, i.e. the interacting pigments and the environment. Such an approach is formidably challenging due to the large network of interactions that couple all the parts of the system, making the dynamics of the process a complex competition of random fluctuations and coherences.
Only a strategy based upon an integration of models with different length and time scales can achieve the required completeness of the description.
The results of these three tasks will be synergically exchanged with the non-academic partner (PLC system) in a 3 months secondment, so to achieve an optimal computational protocol which can be used, not only to get a knowledge of the fundamental molecular-level mechanisms beyond the light-harvesting process, but also to suggest rules on how to design effective artificial LH devices.
- Month 1-16: University of Pisa (Italy)
- Month 17-19: Secondment at Barcelona (Spain)
- Month 20-36: University of Vienna (Austria)
This PhD project will be carried in cotutelle by the University of Groningen (PI: Prof. Remco Havenith) and by the University of Valencia (PI: Dr. Daniel Roca Sanjuan)
The improvement of materials with application in organic photovoltaics (OPV) requires the detailed understanding of the processes that occur during and after the photo-excitation.
These processes include charge-transfer and the formation of free charge-carriers, but also the recombination processes that leads to losses. Important parameters that determine the efficiency of photo-current generation are the energetics of the states involved and the rates with which energy is transferred from one particular state to another.
This will be investigated using a combined QM/MM approach: a central part of the system (a PCBM molecule and part of the polymer) is treated quantum mechanically, while the remainder of the system is described classically (MM) by either the Frozen Density Embedding (FDE) scheme or the Discrete Reaction Field (DRF) method. Charge-transfer rates will be calculated using Markus theory, in which the rate is proportional to the electronic coupling between the diabatic states. In this way, key features of the materials for efficient charge separation can be determined.
This work will be done in Amsterdam, under the daily co-supervision of SCM (10 months) the developer of the ADF code.
- Month 1-10: Secondment at SCM (Netherlands)
- Month 11-24: University of Groningen (Netherlands)
- Month 25-36: University of Valencia (Spain)
This PhD project will be carried in cotutelle by the University of Groningen (PI: Prof. Remco Havenith) and by the University of Pisa (PI: Prof. Maurizio Persico)
Multiple exciton generation (MEG) is the phenomenon wherein the absorption of a single photon leads to the excitation of multiple electrons. MEG has high potential use in photovoltaic materials: if this process can be controlled, higher efficiencies can be reached since multiple excitons may lead to multiple charge carriers after absorption of one photon.
This project is aimed at the design of materials for organic solar cells with efficient MEG. Important aspects that have to be studied are the potential energy surfaces (PES) of the relevant excited states in the diabatic and in the adiabatic representation, the couplings between them, and the nonadiabatic dynamics. Accurate PESs and couplings will be obtained by a method we have developed, based on nonorthogonal configuration interaction.
In this project, this method will be explored further and extended such that electron correlation effects can be incorporated. The dynamics will be based on the surface hopping method, with a semi-empirical QM/MM representation of the electronic energies and wavefunctions. For various representative systems, the mechanism of multiple exciton generation will be studied. Crystal packing effects will also be considered.
The student works on the following tasks: 1) Derivation, implementation and application of a correlated nonorthogonal CI method for diabatic electronic couplings (performed at UGRO (18 months) and in collaboration with Simune (3 months)), and 2) Investigation of PESs of relevant states for different classes of molecules and reparameterization of a semiempirical Hamiltonian for the excited state dynamics, and performing the excited state dynamics simulations (15 months, performed at UNIPI).
- Month 1-18: University of Groningen (Netherlands)
- Month 19-21: Secondment at SIMUNE (Spain)
- Month 22-36: University of Pisa (Italy
This PhD project will be carried in cotutelle by the University of Perugia (PI: Prof. Antonio Laganà) and by the University of Toulouse (PI: Prof. Stefano Evangelisti)
Secondment: PL System
Distributed computing will be exploited to the end of carrying out ab initio simulations of chemical processes (electronic structure, nuclei dynamics, rate coefficients) by means of workflow managed applications (Grid empowered molecular simulation) combining the selected usage of High Performance and High Throughput computers.
Simulations will be focused on processes related to the storage of alternative energies as chemical energy thanks to the reduction of carbon dioxide.
During the Thesis work the students will be trained to develop concurrent software on innovative platforms, to assemble his/her own applications out of packages developed by the members of the COMPCHEM community.
Three months in PL System to have access to a prototype apparatus on which testing experimental and theoretical features of the project.
- Month 1-8: University of Perugia (Italy)
- Month 9-11:Secondment at PLC System (Italy)
- Month 12-20: University of Perugia (Italy)
- Month 21-36: University Paul Sabatier Tolouse III (France)
This PhD project will be carried in cotutelle by the University of Toulouse (PI: Prof. Thierry Leininger) and by the University of Perugia (PI: Dr. Noelia Faginas-Lago)
Carbon nanotubes (CNT) have been suggested as very promising materials for hydrogen fuel cell applications, because of their great adsorption capability.
Such structures exhibit a variety of shapes and size, and the further possibility of modifying their geometrical properties has made them widely studied materials, in order to achieve the most efficient storage.
Despite these interesting features, sufficiently high capacities have not yet been obtained, either experimentally or theoretically, and there are still many discrepancies between the available experimental data and the corresponding computational simulations.
The CINECA non-academic partner will host the PhD student(s) for a three-month training period on HPC Scientific Computing and Scientific Visualization. The CINECA computing facilities will also be used during the whole PhD thesis period for those applications having an intensive computional character.
- Month 01-05: University Paul Sabatier Toulouse III (France)
- Month 06-08:Secondment at CINECA (Italy)
- Month 09-17: University Paul Sabatier Toulouse III (France)
- Month 18-36: University of Perugia (Italy)
This PhD project will be carried in cotutelle by the University of Toulouse (PI: Prof. Martial Boggio-Pasqua) and by the University of Vienna (PI: Leticia González)
Ruthenium nitrosyl complexes have found utility in a variety of applications, such as optical switches and data storage, or medicine. Depending on the ancillary ligands, environment, and irradiation wavelength, these complexes can undergo either intramolecular N-O linkage photoisomerization or NO photorelease.
However, the mechanism behind these two competing processes is lacking. Preliminary results obtained by the leading partner on the [RuClNO(py)4]2+ complex using density functional theory (DFT) revealed two excited-state pathways on the lowest triplet potential energy surface (PES), which correspond to N-O linkage photoisomerization and NO photorelease, respectively.
However, these two pathways display unexpectedly high activation energies (ca. 100 kJ/mol), raising serious concerns about how they can be accessed. To unravel these photoisomerization and photorelease mechanisms, we propose to study the photodynamics of different ruthenium nitrosyl complexes using ab initio or TD-DFT molecular dynamics (MD), including the description of the intersystem crossings (ISC) between initially populated singlet states to the lower triplet states.
Two months in SCM to work on the interfacing SHARC/ADF
- Month 1-: University Paul Sabatier Tolouse III (France)
- Month 21-22: Secondment at SCM (Netherlands)
- Month 23-36: University of Vienna (Austria)
This PhD project will be carried in cotutelle by the University of Vienna (PI: Prof. Leticia González) and by the Autonomous University of Madrid (PI: Dr. Inés Corral)
Light-induced singlet oxygen generation is the key step in photodynamic therapy (PDT) against cancer. After administration of a photosensitizer (PS) and irradiation with light, the commonly accepted mechanism for singlet oxygen generation consists in an energy transfer process between the first triplet excited state of the PS, accessed after intersystem crossing from a singlet excited state, and the triplet oxygen from the environment.
Despite its importance, a comprehensive mechanism at molecular level for PDT is still missing. Only a detailed understanding of the radiationless photodynamical processes, as well as the interaction between the PS and the environment can help the design of novel functional drugs.
This project aims at modelling the deactivation mechanisms and modes of action of promising PSs envisioned by Biolitec research GmbH, one of the leading specialists in the sector of PDT.
Six moths in Biolitec will provide feedback on potential PS and discuss the feasibility and suitability of the studied PSs, allowing for a better rational design of drugs for PDT.
- Month 01-14: Autonomous University of Madrid (Spain)
- Month 15-21: University of Vienna (Austria)
- Month 22-27: Secondment at Biolitec Research GmbH (Germany)
- Month 28-36: University of Vienna (Austria)
This PhD project will be carried in cotutelle by the Autonomous University of Madrid (PI: Dr. Inés Corral) and by the University of Pisa (PI: Prof. Giovanni Granucci)
Light interaction with drugs and pharmaceutical excipients can result in the loss of potency, inactivation or in the formation of cytotoxic metabolites with side effects for the patients.
In the course of manufacture, storage or after administration, pharmaceuticals may be exposed to different light sources driving these formulations to their excited states. In the absence of efficient decay mechanisms, the temporary energy trapping of these systems in stable singlet or triplet excited intermediates would enhance the probability of undergoing photoreactions.
In particular, if long-lived triplet excited states happen to be populated, they could initiate photosensitization and/or charge or energy transfer reactions with other surrounding molecules, leading to cytotoxic side products, such as singlet oxygen or free radicals, able to oxidize a large number of substances, including cell components.
The aim of the present project is to explore the photostability/phototoxicity of several organic systems used as excipients or drugs in pharmaceutical formulations.
The two beneficiary groups UAM and UNIPI, have already collaborated in a study of the phototoxicity of 6-thioguanine, a drug prescribed to treat cancer and autoimmune diseases.
One secondment at GSK (10 months) to learn the know-how in photostability studies in the context of a pharmaceutical laboratory. GSK will also contribute to the research by providing experimental data to validate the theoretical models developed in (A) and (B) such as spectra, and preclinical or clinical toxicological results.
- Month 1-14: Autonomous University of Madrid (Spain)
- Month 15-24:Secondment at GSK (United Kingdom)
- Month 25-36: University of Pisa (Italy)
This PhD project will be carried in cotutelle by the Autonomous University of Madrid (PI: Prof. Manuel Alcamí) and by the University of Porto (PI: Prof. Maria Joao Ramos)
Secondment: Stockholm and Smartligs
To simulate the complex dynamics induced when a molecule is exposed to ionization radiations. In these processes highly charged species can be formed.
The main mechanism to relax the energy excess transfer to the biomolecule is fragmentation, but when the molecule is surrounded by solvent or by other biomolecules other process as bond formation may also occur.
Intramolecular bond formation could be also possible when considering large biomolecules.
The project proposed will identify the relative importance of these different mechanisms and their role in different applied areas as radiation damage or astrobiology.
One secondment at Stockholm (8 months) to learn the techniques to treat the collisional process and to have a direct access to the experimental results. A 2 month secondment in SmartLigs, a SME specialized in modelling, where the researcher will get familiar with the modellization procedures and protocols used when applied to the industry needs.
- Month 1-8: Secondment at University of Stockholm (Sweden)
- Month 9-20:University of Porto (Portugal)
- Month 21-28: Autonomous University of Madrid (Spain)
- Month 29-30: Secondment at SmartLigs (Spain)
- Month 31-36:Autonomous University of Madrid (Spain)
This PhD project will be carried in cotutelle by the University of Porto (PI: Prof. Maria Joao Ramos) and by the Autonomous University of Madrid (PI: Prof. Manuel Yáñez)
Drug metabolites are typically identified using a combination of mass spectrometry (MS) and nuclear magnetic metabolites resonance spectroscopy (NMR) techniques.
Collaborations between GlaxoSmithKline (GSK) and Waters MS Technologies Group have demonstrated the ability to differentiate between isomers of a drug based on their “collisional cross-sections” (CCS) using IMS-MS and in silico modelling. Compared to NMR, this methodology has the advantages of requiring less sample volumes, ultimately leading to reduced animal numbers in pre-clinical studies and the analysis of samples from lower dosed clinical studies. However, it relies on the quality of in silico methods to predict high quality CCS.
The project will focus on the refinement of current protocols and development of alternative methods for the calculation of CCS with the aim of reducing the error associated with its in silico prediction.
One secondment at GSK (10 months) with the objectives indicated in the "Exepected results" section.
- Month 1-10: Secondment at GSK (United kingdom)
- Month 11-24:University of Porto (Portugal)
- Month 25-36: Autonomous University of Madrid (Spain)
This PhD project will be carried in cotutelle by the University Pierre et Marie Curie (Paris) (PI: Prof. Monica Calatayud) and by the University of Barcelona (PI: Dr. Stefan Bromley)
Understanding the structure-reactivity relationship at the nanoscale is crucial to be able to design materials with selected properties.
We are particularly interested in the non-bulk-like properties of nanoclusters and how they thus may provide the inspiration for novel low density (nanostructured) materials.
The final goal is to bring fundamental understanding in complex nanostructures for uniquely tailored applications in nanoelectronics, gas-sensing or (photo)catalysis.
To do so, mixed metal oxides will be modellend and investigated by means of theoretical methods.
Two months in Simune which will provide contact with industrial partners interested in developing mixed materials with technological applications.
- Month 01-16: University of Barcelona (Spain)
- Month 17-18: Secondment at SIMUNE (Spain)
- Month 19-36: University Pierre et Marie Curie Paris VI (France)
This PhD project will be carried in cotutelle by the University of Leuven (PI: Prof. Jeremy Harvey) and by the University of the Basque Country (PI: Prof. Jesús Ugalde)
Computational chemistry is frequently used to assess reaction mechanisms qualitatively. Catalytic reactions in organometallic chemistry are one frequent area of application – as experimental data can be hard to acquire. Quantitative predictions of reactivity, i.e. computational kinetics studies of catalysis, are harder to perform, as they require very accurate electronic structure methods.
In recent work, we have shown that such calculations are now starting to be possible, provided that accurate explicitly-correlated coupled-cluster methods are used to compute energies. Hydroformylation of alkenes has been extensively studied previously, the new work enables us to make much firmer conclusions about turnover-limiting steps.
This project will extend this work in two ways: by going beyond reactivity in the catalysis to consider also selectivity – a most important factor experimentally – and by studying further catalytic processes, e.g. hydrocyanation.
The ESR will do a secondment of 3 months in Matgas to be in contact with the catalysis industrial needs and their simulations.
- Month 01-09: Catholic University of Leuven (Belgium)
- Month 10-12: Secondment at AlyaTech (Spain)
- Month 13-21: Catholic University of Leuven (Belgium)
- Month 22-36: University of Basque Country (Spain)
This PhD project will be carried in cotutelle by the University of Barcelona (PI: Prof. Juan Novoa) and by the University of Groningen (PI: Prof. Ria Broer)
Secondment: Simune and University of Groningen
Among the strategies that have been developed for designing magnetic systems involving intermolecular coupling of organic spins, the “metal-radical” approach has led to promising results.
This approach, proposed by Gatteschi and co-workers, consists in getting strong direct metal-ligand magnetic exchange interactions from the coordination of paramagnetic transition-metal ions with stable free radicals.
Recently magnetism has been discovered in graphene derivatives and one may expect new interesting properties from the coordination of these magnetic graphene units with paramagnetic transition metal ions.
The ESR will do a secondment of 3 months in Simune to work in the spin-polarized transport in collaboration with UGRO.
- Month 01-21: University of Barcelona (Spain)
- Month 22-24: Secondment at SIMUNE (Spain)
- Month 25-36: University of Groningen (Netherlands)
This PhD project will be carried in cotutelle by the University of the Basque Country (PI: Prof. Xabi López) and by the University of Porto (PI: Prof. Maria Joao Ramos)
Due to its industrial applications, Aluminiun's bioavailability has increased to the point that it can be easily incorporated into biological systems, producing human neurodegenerative diseases. How Al(III) can access the human organism is therefore, of primary importance.
Al is able to form a variety of hydrolysis products as a function of pH, and complexes with a variety of ligands. In serum, Al(III) interacts with high molecular mass species, serum-transferrin, and low molecular mass ligands, mainly citrate and phosphates. The presence of Al(III) can alter the cell's biochemistry, including promotion of substantial pro-oxidant activity.
We propose the study of interactions of Aluminum with phosphates of biological interest, such as AMP, ADP, ATP, DNA, RNA and NAD(P). In particular the following areas will be covered: Interaction of Al(III) with biophosphates, using DFT to outline a map of the intrinsic affinities of Al towards phosphate structural motifs, such as mono/di/tri-ester phosphates, di- and bis-phosphates and triphosphates.
Conformational changes induced by Al, by analyzing the influence that Al has in the conformation of key phosphates for several metabolic pathways, such as NADH and ATP, by means of a combination of activated classical MD simulations and QM/MM calculations.
Phosphoryl Transfer Reactivity and Al(III), by characterizing phosphoryl transfer pathways in the presence and abscence of Al, focussing primarily in the phosphorylation of Ser/Thr by ATP, for which experimental data are available.
The ESR will do a secondment of 3 months in Smarligs to work in the simulation of other biochemical systems.
- Month 1-11: University of Basque Country (Spain)
- Month 12-14: Secondment at SmartLigs (Spain)
- Month 14-20: University of Basque Country (Spain)
- Month 21-36: University of Porto (Portugal)
This PhD project will be carried in cotutelle by the University of Valencia (PI: Prof. Alfredo Sánchez de Meras) and by the University of Perugia (PI: Dr. Noelia Faginas-Lago)
In spite of the interest received by the possibility of using graphene as adsorbent for hydrogen and other gases, there still exist discrepancies between experimental and theoretical results.
A multi-scale computational study covering from highly accurate ab initio calculations to long Molecular Dynamics simulations is missing.
The goal of the proposed Thesis is, then, to fill that gap, not only by carrying out the appropriated applications but also by developing the required methodology if needed.
The non-academic partner, MATGAS, will take care of the Monte Carlo set of calculations. Computational studies will be performed in terms of modelling the adsorbate-adsorbent and adsorbate-adsorbate interactions. Simulation will calculate, at molecular level, the adsorption process and the kinetic properties under different conditions. MATGAS will suggest, as well, other gases and pollutants to be considered according to their industrial interest.
- Month 1-9: University of Valencia (Spain)
- Month 10-19: Secondment at AlyaTech (Spain)
- Month 20-24: University of Valencia (Spain)
- Month 25-36: University of Perugia (Italy)