Lorentz Center - Modeling natural and artificial photosynthesis from 7 Mar 2011 through 11 Mar 2011
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    Modeling natural and artificial photosynthesis
    from 7 Mar 2011 through 11 Mar 2011




Victor Salvador Batista

“Studies of Oxomanganese Complexes for Natural and Artificial Photosynthesis”


Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies of oxomanganese complexes. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy, and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based, but comprises important modifications due to structural refinement, hydration, and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting as described by the intermediate oxidation states of oxomanganese complexes. This talk summarizes recent advances on studies of the OEC of PSII and biomimetic oxomanganese complexes for artificial photosynthesis.




David Coker

“Quantum Simulation of Environmental Effects on Excitation Energy Transfer in Photosynthetic Light Harvesting and Reaction Center Systems"


A general quantum dynamical simulation approach, the Iterative Linearized Density Matrix (ILDM) propagation scheme, is employed to explore the behavior of detailed microscopic models of energy transfer in photosynthetic light harvesting, and reaction center systems. This general approach can treat non-markovian dynamics beyond the limits of perturbation theory. The Influence of high and low frequency structures in bath - multi-chromophore spectral density, and the effects of correlations between the bath modes of different chromophores on the excitation energy transfer dynamics are be explored. We observe the ubiquitous effects of stochastic resonance phenomena on the rates of energy transfer between chromophores and explore how these rates are maximized as a function of the solvent reorganization energy parameter and features of the local spectral density.  Authors: D.F. Coker* and P. Huo





Leslie Dutton

“Prospects for natural photochemistry in man-made proteins”


Biological photosynthesis is a rich source of inspiration for any intensions to produce solar fuels in man-made devices. Our own research intensions combine two approaches. The first endeavors to reveal engineering and structural principles on which stand the impressive light-driven oxidations and reductions catalyzed by natural proteins. The second endeavors to apply these principles to reproduce the same functions in artificial proteins designed and constructed from scratch.

Johnson Research Foundation and Department of Biochemistry and Biophysics

University of Pennsylvania, Philadelphia PA 19104





Pietro Liò (poster)

“Automating the Biological Design of C3 Carbon Metabolism for Enhanced Photosynthetic Productivity Minimizing the Nitrogen Employed”


Giovanni Stracquadanio1, Renato Umeton2, Alessio Papini3, Pietro Liò4 and Giuseppe Nicosia1

1 Dept. of Mathematics & Computer Science - University of Catania, Italy, {stracquadanio, nicosia}@dmi.unict.it 2 Dept. of Biological Engineering - MIT, Cambridge, MA, USA, umeton@mit.edu 3 Dept. of Plant Biology - University of Florence, Italy, alessio.papini@unifi.it 4 Computer Laboratory - University of Cambridge, UK, pl219@cam.ac.uk


We present a general-purpose methodology for the robust design of synthetic biochemical pathways and has application in synthetic and systems biology. The procedure relies on a flexible combination of sensitivity analysis and Pareto optimality, which generate a remarkably refined specification of biological robustness. The proposed methodology, directly inspired from Electronic Design Automation research field, is used to design manufacturable molecular biological parts, for instance pathways and networks. Bringing together skills from different areas of engineering and of systems biology, we combine robustness and system properties persistence to operate a careful choice of the system variables with respect to local and global perturbations. The Pareto optimality would then operate on these properties as a trade-off of multiple objective functions. We demonstrate its effectiveness in the analysis and robust design of C3 photosynthetic carbon metabolism. Exhaustive tests show that our procedure outperforms all the currently widely used algorithms. Over performing "newly designed leaf" has its strength in a small set of enzymes that boost an increase of the rate of photosynthetic CO2 leaf uptake per unit area. We justify a high investment in Rubisco, SBPase, ADPGPP and FBP aldolase to generate a CO2 uptake increase of 135% with respect to optimal natural conditions (from 15.486 μmol m-2 s-1, the natural leaf, to 36.489 μmol m-2 s-1). The investigation of past and predicted near/distant future intercellular CO2 concentrations and an enzyme-wise rearrangement of resource allocation unveil a trade-off between the maximization of CO2 uptake and the minimization of the total protein-nitrogen employed in the leaf. For a given model (e.g., biomolecular pathways), the procedure we propose for designing flow would identify sensitive and less sensitive variables (e.g., genes, enzymes), optimize the set of objective functions (e.g., photosynthetic-rate, nitrogen-use efficiency, water-use efficiency, visible light, light energy) and assess the robustness and fragility of the system (e.g., the designed leaf).




José Luis Vallés Pardo (poster)

“Synthesis, characterization and modeling of ruthenium catalysts for water oxidation”


José Luis Vallés Pardo, Marieke C. Guijt, Khurram S. Joya, Francesco Buda and Huub J.M. de Groot - Leiden Institute of Chemistry, Leiden University


Recently, various ruthenium complexes have shown catalytic activity for water oxidation in order to generate molecular oxygen [1]. We have synthesized novel mono site ruthenium catalysts and their activity for water splitting has been studied both homogeneously as well as electrochemically [2,3]. In addition, various complexes have been modeled theoretically to study the possible reaction pathway. Here, the focus is on the formation of the O-O bond, which is a key step in the water splitting reaction. For this purpose, the metadynamics approach was used. In this approach, a time-dependent bias potential is added to overcome the reaction barrier. The aim of the modeling is to gain a better understanding for the reaction mechanism and attempt to design new catalysts in-silico.


[1] Sala, X., Romero, I., Rodríguez, M., Escriche, L. and Llobet A., Angew. Chem. Int. Ed. 48 (2009) 2842

[2] Joya, K.S and de Groot, H.J.M. (2010) Submitted.

[3] Joya, K.S and de Groot, H.J.M. (2010) Submitted.




Alexander V. Soudackov

“Theoretical modeling of the ultrafast photoinduced proton-coupled electron transfer reactions”


Photoinduced proton-coupled electron transfer (PCET) reactions are important in a broad range of energy conversion devices, such as solar cells, as well as in both natural and artificial photosynthesis. We present a theoretical formulation for modeling photoinduced nonequilibrium PCET reactions in solution. In this formulation, the PCET system is described by electron-proton vibronic free energy surfaces that depend on collective solvent coordinates. The ultrafast nonadiabatic dynamics following photoexcitation is simulated using a surface hopping method in conjunction with the Langevin equation of motion for solvent coordinates. This methodology is used to examine a series of representative model systems inspired by recent time-resolved experiments on PCET systems related to artificial photosynthesis.

Analysis of the dynamical trajectories provides insight into the mechanism and interplay between the solvent dynamics and the electron-proton transfer for these types of processes. Authors: Alexander V. Soudackov (speaker), Anirban Hazra, and Sharon Hammes-Schiffer. Department of Chemistry, Pennsylvania State University, University Park, PA 16802, United States.