Search

We present a linear-scaling method based on the use of density-functional theory (DFT) for the system-wide optimization of x-ray structural coordinates and apply it to optimize the 150 000 atoms of the photosystem-I (PS-I) trimer. The method is based on repetitive applications of a multilevel ONIOM procedure using the PW91/6-31G(d) DFT calculations for the high level and PM3 for the lower level; this method treats all atoms in the structure equivalently, a structure in which the majority of the atoms can be considered as part of some internal "active site." To obtain a realistic single structure, some changes to the original protein model were necessary but these are kept to a minimum in order that the optimized structure most closely resembles the original x-ray one. Optimization has profound effects on the perceived electronic properties of the cofactors, with, e.g., optimization lowering the internal energy of the chlorophylls by on average 53 kcal mol-1 and eliminates the enormous 115 kcal -1 energy spread depicted by the original x-ray heavy-atom coordinates. A highly precise structure for PS-I results that is suitable for analysis of device function. Significant qualitative features of the structure are also improved such as correction of an error in the stereochemistry of one of the chlorophylls in the "special pair" of the reaction center, as well as the replacement of a water molecule with a metal cation in a critical region on the C3 axis. The method also reveals other unusual features of the structure, leading both to suggestions concerning device functionality and possible mutations between gene sequencing and x-ray structure determination. The optimization scheme is thus shown to augment the molecular modeling schemes that are currently used to add medium-resolution structural information to the raw scattering data in order to obtain atomically resolved structures. System-wide optimization is now a feasible process and its use within protein x-ray data refinement should be considered. [ABSTRACT FROM AUTHOR]

The [Q.sub.y] absorption of photosystem-I from Thermosynecochoccus elongatus is measured by using the CAM-B3LYP density functional and INDO methods. The results are shown to be a realistic first-principles prediction of the absorption band that has identified the nature of the red-shifted chlorophylls as well as the energies of the reaction-center chlorophylls and the exciton couplings acting between them.

The main objective of the AtmoFlow experiment is the investigation of convective flows in thespherical gap geometry. Gaining fundamental knowledge on the origin and behavior of flowphenomena such as global cells and planetary waves is interesting not only from ameteorological perspective. Understanding the interaction between atmosphericcirculation and a planet’s climate, be it Earth, Mars, Jupiter, or a distant exoplanet,contributes to various fields of research such as astrophysics, geophysics, fluidphysics, and climatology. The main feature of AtmoFlow is its spherical geometry andaims to observe flows in a thin gap that are subjected to a central force field. Sucha condition, obviously impossible to reach on ground, is achieved by simulatingbuoyancy driven convection through a central dielectrophoretic field in micro-gravityconditions e.g. on the ISS. Without losing its overall view on the complex physics,circulation in planetary atmospheres can be reduced to a simple model of the in- andoutgoing energy (e.g. radiation) and rotational effects. Both input parameters aredetermined by the boundaries of the system. This strongly simplified assumptionmakes it possible to break some generic cases down to test models which can beinvestigated by laboratory experiments and numerical simulations. Varying differentialrotation rates and temperature boundary conditions represent different types ofplanets. This is a very basic approach, but various open questions regarding localpattern formation or global planetary cells can be investigated with that setup. Aconcept has been defined for developing a payload that could be installed and utilizedon-board the International Space Station. This concept is based on the micro-gravityexperiment GeoFlow, which has been conducted successfully between 2008 and 2016 onthe ISS. We present the scientific goals, the experimental setup, the concept forimplementation of the AtmoFlow experiment on the ISS and first numerical results. [ABSTRACT FROM AUTHOR]