School of Biotechnology
Department of
Theoretical Chemistry
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Royal Institute of Technology
School of Biotechnology Department of Theoretical Chemistry |
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Major projects
PhotonicsPhotonics will play a critical role in the emergence of the information society. In this technology photons play the same role as electrons in electronics, and form the basis for new products like UV-lasers, 3D ultra-compact storage devices, opto-electronic conductors, wave-guides, switches and displays. In order to predict new materials with certain photonic properties it is essential to master and simulate the basic photon-matter interaction. This is a central goal in our research in which we use own developed methodology, in particular analytic response theory. A large effort is thus devoted to simulations of various non-linear optical properties and to obtain their structure-to-property relationships. Multi-photon excitation processes are special non-linear optical properties that we combine with solutions of wave equations into a powerful dynamic laser methodology. We use this methodology to simulate how laser pulses propagate through macroscopic media, which in general are non-linear. We furthermore explore so-called photonic crystals, which are well-ordered nanostructured materials that can be viewed as optical analogies of semiconductors that modify the properties of light propagation, and especially how such crystals operate in the non-linear regime. A new research direction is biophotonics, which in general deals with interactions between light and biological matter, and where we perform modeling design of new types of molecular and nano-particle biomarkers with particular non-linear optical response properties. ElectronicsIn the last 35 years, Moore's law, which now states that the number of transistors on a chip doubles every 18 months, has enjoyed a great success. However, this "law" seems to reach a point of breakdown because the current density of silicon-based transistors on a chip is approaching the limits imposed by the laws of physics. Molecular electronics should be the solution to this problem, providing a new and better "Moore's law" that will operate in a foreseeable future. It can be estimated that by using a transistor based on molecules, one can place 10,000 times more transistors on the present chip. However, while one has witnessed many exciting breakthroughs in the field of molecular electronics in the recent years, the underlying physical principles are still largely unknown. The goal of our studies in the field of molecular electronics is to gain more of the necessary understanding of the physical and chemical processes involved, to develop efficient computational approaches to simulate the electron transportation of molecular devices and finally to use these to optimize the performance of the devices. Read more about our theoretical models and simulations. CatalysisTheoretical studies are playing an increasingly important role in understanding enzymatic catalysis. In the last few years, accurate models to treat the active sites of enzymes have emerged. Theoretical studies provide some advantages in that short-lived intermediates can be located and characterized, and different possible reaction pathways can be studied and compared. With the computer power of today, one is able to accurately treat systems of up to ca 100 atoms. This is a considerable improvement compared to just a couple of years ago. Many enzyme active sites can be modeled with this size, and indeed many biochemical questions have so become addressed. We put much effort in this research using first principles quantum calculations. In this context we also emphasize our concept of spin catalysis which comprises a wide range of phenomena in which chemical reactions are promoted by substances assisting to overcome spin-prohibition. It has recently found rewarding applications in explaining some biochemical problems, for instance it led to the proposal of a new mechanism for oxygen activation in enzymes like in glucose oxidase and in copper amino oxidase. Laser and X-ray ScienceThe world-wide development of synchrotron radiation sources has created a revolution in X-ray science nearly analogous to the breakthrough with lasers in the optical region in the 60'ies. The further development of 4th generation sources, X-ray lasers and -in some years to come- free electron lasers with outstanding performances, is believed to produce a paradigm shift in areas like materials science and structural biology, with possibilities to study single membrane proteins and to follow structural dynamics at atomic dimensions. Our studies in this area include basic theory development, coding and applications. The theory work has mostly concerned the description of resonant X-ray scattering as a coherent ultra-fast excitation process, with direct reference to the most modern and coming (free-electron) light sources and with reference to the new area of X-ray femtochemistry. On the applicative side we take advantage of the fact that X-ray spectroscopies, like X-ray emission and absorption spectroscopy, are element specific and locally probing of electronic and conformation structures, which together with simulations make them sharp tools for studies of bio-molecules, solid materials and solutions. Magnetic ResonanceMagnetic resonance parameters are useful for diagnostics of bioradicals that play vital roles in the catalytic activity of enzymes, for instance, for the various intermediate amino acid radicals that are important for the enzymatic function of RNR. Such diagnostics lead to better understanding of the reaction mechanisms and may so enhance the possibilities to produce synthetic enzymes and well-designed pharmaceuticals. With the development of simulation methods for paramagnetic nuclear magnetic resonance pNMR, electron paramagnetic resonance EPR and optically detected magnetic resonance ODMR spectroscopies, we aim to contribute to important pieces of knowledge for bio-radicals like metalloproteins and artificially spin-labeled protein complexes. With the so-called electronic g-tensor and the electronic spin-spin coupling parameters, D-tensor, we have now completed the full spin Hamiltonian with response theory, including the previously coded hyperfine A-tensor, giving us unique possibilities to obtain property-structure relations through first principles computations of these parameters and through analyzing the corresponding measurements in pNMR, EPR, and ODMR spectroscopies. Nanoparticle TechnologyThe overall objective is focussed on designing nanostructured metamaterials by incorporating nanoparticles to address fundamental issues limiting current photonics technologies. We study, design, and apply excitonic and surface-plasmonic polaritons in nanostructures including inorganic semiconducting and metallic nanoparticles as well as organic molecules in terms of active photonic metamaterials. With fundamental revisions with respect to electromagnetic properties, we shall be able to drastically reduce the optical loss as well as the spatial dimension of the metamaterial-based optical components.
The project will deliver blueprint meta-photonic components with the following
extraordinary optical properties:
Visions:
The project involves an in-house experimental lab for chemical synthesizing and conjugating colloidal II-VI QDs in organic nanostructure. Protein Dynamics
The overall research objective is to use computational simulations to study biomolecular recognition and complex forming mechanisms. Multiscale ModelingAb-initio methods have been used over the years to successfully predict properties and model behavior of small molecular systems - see above for a long list of noteworthy accomplishments. However, these methods frequently were derived and implemented in a way that makes the computation time grow much faster than the system size. As the researchers' ambitions grew a need to re-derive and re-implement the theory in a more computation-friendly manner became more and more clear. We focus in our group on various aspects of application of Density Functional Theory (DFT) to systems ranging from one to few thousand of atoms. Our aim is to compute not only total energies and stationary geometries of large molecules on ab-initio levels but also evaluate their interaction with light and magnetic field. The list of applications include also non-linear effects appearing in strong fields and direct simulations of solution, and to generally apply this multiscale methodology throughout entire DALTON quantum chemistry package. Read more about multiscale methods. We are also trying to increase the understanding of functional nucleic acid systems using first-principles and hybrid QM/MM molecular dynamics simulations. Read more about these projects! Yet another area of interest is the development of computational models for predicting drug solubility. Read more about this project! Computer ProgramsWe develop following programs at our department:
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