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This is made possible by the EU reverse charge method. Edited by Lichang Wang. Edited by Dongbin Lee. Edited by Jan Awrejcewicz. Edited by Bishnu Pal. Edited by Alexander Kokorin. Edited by Theophanides Theophile. Edited by Kresimir Delac. Edited by Sergey Mikhailov.

Published: April 5th DOI: Hudson Open access peer-reviewed 3. Sofianos Open access peer-reviewed 8.

Introduction to Computational Electrostatics for Biological Applications (CEBA'13)

Gonzalez-Wasaff Open access peer-reviewed Dunlap Open access peer-reviewed Therefore many open questions in the fundamental understanding of photovoltaic and photo-catalytic processes remain, whose resolution would expedite progress in device design. This is the domain of theoretical spectroscopy - the domain of quantum-mechanical calculations of elementary excitations on the atomic scale and clearly the domain of application of the present DynaPlex project. The goal of the project has been divided in three main subjects according to the nature of the activities being performed.

First, Fundamental issues and methodological developments to handle charge-transfer processes, highly correlated oxides and Mott-insulators, and develop new algorithms to address molecular dynamics including non-adiabatic effects, electron delocalization, and bond-breaking phenomena. Second, a set of Practical objectives ranging from photocatalysis to thermoelectricity and energy harvesting in hybrid solar cells. Finally, Biophysics and biotechnology looks at the control of nanocapilarity by light, the photophysics of fluorescent proteins, and the microscopic mechanisms behind the first step of photosynthesis towards "artificial photosynthetic" units.

Achieving a "first-principles spatially and time resolved multi-scale spectroscopic modelling tool-box" not only means meeting the challenges of clean energy solutions, but also many other old and new challenges appearing in material science, chemistry, biomedicine, and nanotechnology as well. Our goal with this project is to consolidate an interdisciplinary world-reference Spanish collaborative team in Theoretical Condensed Matter and Computational Physics in what is now starting to be known as Theoretical Spectroscopy.

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With this goal in mind, we will provide a general ab-initio toolbox theoretical framework , that can be used to describe, explain, and predict the structural, chemical, and spectroscopic properties of atoms, molecules, clusters, surfaces, and solids, without the inclusion of any external, semi-empirical or empirical, parameters in order not to bias its predictions or its interpretations of experiments. Besides theoretical and consequent computing implementations we will address highly relevant topics in nano- and bio-physics and material science.

Spectroscopy essentially deals with the excitation of a system as a response to an external perturbation. To interpret or design this kind of experiments, one needs to make use of theoretical approaches beyond the present standard model of solid-state physics, namely density-functional theory DFT. In fact, DFT is a ground-state theory and, in principle, by solving the Kohn-Sham KS equations one can have access to properties like the electronic density or the total energy of the system. These calculations can be done in a very efficient way adopting the local-density approximation LDA or even more sophisticated approximations.

However, the eigenvalues of the Kohn-Sham equations cannot be interpreted as excitation energies.

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An accurate description of such excited states can be obtained in the framework of many-body perturbation theory MBPT or, in certain cases, using time-dependent density functional theory TDDFT. They are complementary approaches.

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MBPT has a relative conceptual clarity and therefore allows one to find good approximations, but calculations are in general very demanding. For these reasons, a great effort in the last years has been made in combining the advantages of both methods. In MBPT the key variables are the Green's functions, which describe the propagation of effective particles "quasiparticles" and give access to one-particle excitations, as measured in photoemission, or to neutral excitations, as measured e.

In the GW approximation one takes for the self-energy, which is a non-local, non-Hermitian, and frequency-dependent potential, the product of the Green's function G and the dynamically screened Coulomb interaction W. In this way, one neglects the so-called vertex corrections, which are responsible, for instance, for excitonic effects in the screening. Then, in the BSE one further takes into account the interaction between the electron and the hole, which constitute the neutral excitations that are directly probed by absorption experiments.


One can use TDDFT to address neutral excitations, but then one has to find reliable approximations to describe the electron exchange and correlation XC terms. This has the added difficulty of it being necessary to have the correct description of the dynamic effects within the XC potential, which is also indispensable to analyze nonlinear phenomena e.

Concerning the linear-response regime there have been very interesting progresses in the representation of the dynamic part of the XC kernel, which have provided a way of describing adequately excitonic effects in a broad class of materials, ranging from nanosystems to bulk solids. In correlated materials, thanks to their extreme sensitivity, even local excitations with light can trigger a macroscopic phase transition by virtue of a cooperative interaction of the different degrees of freedom of the system e.

Hence, photoinduced phase transitions provide an important approach to investigate the physical pathway connecting different correlated electron states as well as their mutual competition. On the other side, time-resolved spectroscopy measurements of photoinduced phase transitions are very demanding, because they require a simultaneous access to the femtosecond dynamics of more than one degree of freedom of the system.

There have been impressive improvements in this field during the last few years, including new theoretical paradigms and the development of more efficient computational tools from our presently running national project fancy-nano. This allows us to tackle the ab-initio description of a wide range of systems, which combine structural complexity and a rich phenomenology.

Thus, theoretical spectroscopy has become a powerful tool with predictive accuracy. Nevertheless, still there are many open theoretical questions, the need of new methodological implementations of the latest theoretical developments and, what is more important, application fields basically within the nano- and bio-technology, functionalized materials design and, in general, in complex systems that ask for an extensive use of ab-initio tools. Based on these motivations the proposed project, Dynamical processes in complex quantum systems: from theoretical developments to energy harvesting and storage DynaPlex , will directly address fundamental problems related to the characterization of the electronic properties and its application to complex systems.

These properties, regardless of the object being studied and their static structural or dynamic character response or transport , will be determined by applying and developing common theoretical DFT, TDDFT, MBPT and computational tools where the participating researchers have a well-recognized expertise. To organize the description of the planed activities we have divided the project in three different, although interconnected, branches. First, we will consider basic research challenges concerning the development of new theoretical tools and its implementation on suitable computer codes.

This includes the critical discussion of the approximations that build the state-of-the-art ab-initio calculations of electronic structure and the theoretical spectroscopy. Second, we will tackle the study of specific problems having special relevance in applied nanoscience such as molecular electronics, new photovoltaic materials, thermoelectricity, and photocatalysis.

Finally, a third research line will be devoted to applications in biological processes, a field where one of the partners Donostia has gained a worldwide recognition in the last years.

Research Interests

The collaboration with other groups will be essential for the successful enforcement of the whole research. The ETSF is a distributed knowledge network that provides theoretical expertise to further the understanding of the properties of materials, chemicals, and biological processes for applications across both public and private sectors.

Donostia hosts the Vice-presidency for Scientific Development of the ETSF, and its activities will greatly help the proper attainment of the different research lines within the DynaPlex project. Reciprocally, some of the research objectives of the proposed project will contribute to the consolidation of the leading scientific role of Spain in the ESTF venture. This international projection constitutes a significant benefit for the project, whose main scientific aspects are described in the following.

Then, theoretical developments will constitute an essential part of the proposed activities that, on the other hand, are required ingredients to fulfil the more applied objectives. The simulation of molecular systems as energy-conserving, closed quantum mechanical objects is an idealization since every system interacts with its environment to a certain degree. However, due to obvious reasons, most of the molecular electronic structure approaches to date have concentrated on the simulation of time-independent or time-dependent systems that do not interact with quantum environments.

To fill this gap, we will pursue a consistent formulation of time-dependent DFT for open quantum systems F1 , an activity that will be complemented with a more fundamental study of quantum phase transitions F2. The study of molecular aggregates has opened a number of questions about the intrinsic nature of the chemical bond F3 , which explains their stability and chemical properties.

Many of these aggregates lie in the nanoscale and, therefore, their chemical properties show remarkable differences with respect to the basic molecular constituents. Although quantum-chemistry calculations are feasible for these systems, we want to address a more fundamental understanding of the chemical bond in such systems. We will study the electron localization in molecular bonds and the electronic delocalization that appears in molecular aggregates.

The study of degenerate confined systems F5 is closely related to this research line, as it provides a stringent assessment of existing functional approaches and provides clues for further improvement, with relevance in the characterization of biomolecular systems and molecular dissociation. Another objective is a better understanding of strong electronic correlation in transition-metal oxides F6. Shlomo Ruschin : Micro-electrooptics Prof. Arie Ruzin : Solid state detectocs and devices laboratory Prof.

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

Jacob Scheuer : Integrated nano-photonics, slow light and polymer optics Prof. Yosi Shacham-Diamand : Nano-chemical processes for microelectronics and integration of biological material on chip for acute toxicity detection Prof. Natan Shaked : Interferometry, microscopy and nanoscopy in biological cells and tisues Dr. Tamir Tuller : Predictive computational modeling, simulation, and systems biology analysis of intracellular biophysical processes.

Meital Zilberman : Polymeric biomaterials and implants, controlled drug release, tissue engineering Dr. Ari Barzilai : The molecular mechanism of optic nerve degeneration and regeneration Prof. Itai Benhar : Targeted drug-carrying phage nanoparicles Prof. Tal Dvir : Nanotechnologies for engineering 3D complex tissues Prof.

Chanoch Carmeli : Application of the photosynthetic reaction center proteins, PS I in the fabrication of a novel nano-bio-photovoltaic devices Dr. Avigdor Eldar : Sub-micron light-guided protein localization and super-resolution microscopy for studying division and signaling in bacteria Prof. Amihay Freeman : Biotemplating of stabilized protein crystals; directed metallization of biologically active proteins and cells Prof. Ehud Gazit : Self-assembly of short aromatic peptides: from amyloid disease to nanotechnology Prof.

Jonathan M. Gershoni : Nano-optical sensing of protein: Protein interactions Dr. Rimona Margalit : Drug delivery by nano-particles based on biomaterials: biophysical properties, cell-particle interactions and therapeutic responses Dr. Iftach Nachman : Microfluidic approaches to study cell developmental decisions Prof.

Dan Peer : Selective targeting and reprogramming of leukocytes using fully degradable nanomedicines Prof. Judith Rishpon : Application of nano technologies in electrochemical biosensors Prof. Vered Padler-Karavani : Glycans in immune recognition and response Prof. Daniel Segal : Determinants of protein misfolding and self-assembly in amyloid diseases, and development of novel inhibitors as candidate therapeutics. Dafna Benayahu : Nano manipulation of stem cells differentiation to become biomedical devices Dr.

Eran Perlson : Nanomotors and microfluidic platforms reveal neurodegeneration mechanisms Prof.