Abstract: The time-dependent density functional based tight-binding (TD-DFTB) approach is generalized to account for fractional occupations. In addition, an on-site correction leads to marked qualitative and quantitative improvements over the original method. Especially, the known failure of TD-DFTB for the description of σ → π* and n → π* excitations is overcome. Benchmark calculations on a large set of organic molecules also indicate a better description of triplet states. The accuracy of the revised TD-DFTB method is found to be similar to first principles TD-DFT calculations at a highly reduced computational cost. As a side issue DFTB for water outperforms the recently introduced 3rd order DFTB with empirically adjusted 3rd order parameters. As application we report on combined excited-state theoretical simulations and experimental studies to investigate the degradation of NO and acetaldehyde on TiO2 under visible and UV irradiation revealing charge transfer complexes on TiO2 as new source for visible light activity.In this presentation, I will present the ability of conventional molecular dynamics (MD) simulation to evaluate protein stability upon mutation by conducting simulations in explicit 2 M urea solution for four apomyoglobin (ApoMb) variants namely wildtype (WT), E109A, E109G and G65A/G73A. Based on the simulations conducted, analyses such as variation in root-mean-square deviation (rmsd), native contacts and solvent accessible surface area with time were conducted to compare the stability of the ApoMb variants. Subsequently, the mechanism leading to the destabilization of the ApoMb variants were also studied through the calculation of correlation matrix, principal component analyses, hydrogen bond analyses and root-mean-square fluctuation (rmsf). The effect of mutation on the stability of ApoMb variants to urea unfolding had been conducted experimentally by Baldwin and Luo. The results obtained in this study correlates well with that acquired by Baldwin and Luo whereby E109A mutation was shown to stabilize ApoMb while E109G and G65A/G73A mutation showed otherwise. This positive observation showcases the feasibility of exploiting MD simulation in the determination of protein stability prior to protein synthesis.
About the Speaker: Prof. Thomas Frauenheim obtained his Ph.D. from Theoretical Physics Department, Technical University Dresden in 1976, supervised by Prof. Gerd Röpke. He is the Funding Director of the Bremen Center for Computational Material Sciences, University of Bremen. He is now the Chair Professor for Computational Material Science and Director of the German CECAM-node Multi-scale Modeling from First Principles. His research topics include: Development of highly efficient and chemically accurate quantum-mechanically based simulation meth-ods/tools having advanced functionality for dynamic atomistic treatment of many-atom (1000´s) nano-structures in electronic ground and excited states. Application of these methods to fundamental and techno-logical relevant problems in material science. The primary focus is to understand structure-property-function correlations of complex materials systems in physics, chemistry, biology and engineering.
Date&Time: March 12, 2014 (Wednesday)，10:30 -11:30 a.m.
Location: 606 Conference Room 
