Ab initio Simulations of Fe-based Ferric Wheels

Based on first-principles density-functional theory calculations we investigate the electronic structure of hexanuclear "ferric wheels" M Fe_6[N(CH_2 CH_2 O)_3]_6 Cl (M = Li, Na) in their antiferromagnetic ground state. The electronic structure is presented in form of spin- and site-resolved local densities of states. The latter clearly indicate that the magnetic moment is distributed over several sites. The local moment at the iron site is still the largest one with about 4 mu_B, thus indicating the valence state of iron to be closer to Fe(II) than to commonly accepted Fe(III). The local spin of S=5/2 per iron site, following from magnetization measurements, is perfectly reproduced if one takes the moments on the neighbor atoms into account. The largest magnetic polarization is found on the apical oxygen atom, followed by nitrogen bridging oxygens. These findings are confirmed by a map of spatial spin density. A further goal of the present study has been a comparative test of two different DFT implementations, Siesta and NRLMOL. They yield a very good agreement down to small details in the electronic structure.Comment: 10 pages, 3 embedded postscript figures, to be published in Molecular Physics Reports (proceedings of the Summer School on New Magnetics - Bedlewo, Poland, September 2003). Two references update

Role of basic and hydrophobic residues in the poliovirus polymerase elongation complex and the structure of a coxsackievirus polymerase elongation complex

2011 Fall.Includes bibliographical references.Picornaviruses encode for and require a viral RNA-dependent RNA polymerase (RdRP) for genome replication. This enzyme synthesizes negative-sense RNA from the infecting positive sense genome producing a replicative intermediate. The negative sense RNA then serves as a template for synthesis of additional positive-sense RNA. To efficiently replicate the genome, RdRPs must form a stable and processive elongation complex (EC) by binding RNA, incorporating the first templating nucleotide, and undergoing a necessary conformational. Upon completion of these steps that comprise initiation, the newly formed EC is capable of rapidly replicating the viral genome. The work presented in this thesis 1) investigates the role that several basic and hydrophobic residues serve in forming and maintaining the poliovirus (PV) EC and 2) presents the crystal structure of a coxsackievirus (CV) EC. To determine the role of that several arginines, lysines, and tyrosines play in the PV polymerase, we assessed whether mutations to these residues affect initiation, elongation, or stability of the EC. The data indicates the basic residues within the fingers domain of the PV polymerase have a major role in binding RNA. In addition, data shows two tyrosine residues in particular are critical for formation and maintenance of the EC. Overall, the data provides evidence the fingers domain interacts with the template RNA in a manner not captured by crystal structures. Finally, we have solved the structure of a CVEC stalled after incorporation of four nucleotides. The CVEC structure closely matches the previously solved PVEC structure. In addition, one crystal form produced an elongation complex trapped in a translocation intermediate state

Electronic structure, magnetic ordering and phonons in molecules and solids

The present work gives an overview of the authors work in the field of electronic structure calculations. The main objective is to show how electronic structure methods in particular density functional theory (DFT) can be used for the description and interpretation of experimental results in order to enhance our understanding of physical and chemical properties of materials. The recently found superconductor MgB2 is an example where the electronic structure was the key to our understanding of the surprising properties of this material. The experimental confirmation of the predicted electronic structure from first principles calculations was very important for the acceptance of earlier theoretical suggestions. Molecular crystals build from magnetic clusters containing a few transition metal ions and organic ligands show fascinating magnetic properties at the nanoscale. DFT allows for the investigation of magnetic ordering and magnetic anisotropy energies. The magnetic anisotropy which results mainly from the spin-orbit coupling determines many of the properties which make the single molecule magnets interesting

Masoński kod w twórczości Władimira Nabokowa. Próba interpretacji powieści „Zaproszenie na egzekucję” w kluczu symboliki masońskiej

This article is an attempt to interpet a work by Vladimir Nabokov, Invitation to a Beheading, with the most important determinants of Masonic culture. There are few studies that discuss this outstanding prose writer in terms of freemasonry and the author of this article discusses this issue with particular attention to the symbolism  of the Masonic initiation ritual.This article is an attempt to interpet a work by Vladimir Nabokov, Invitation to a Beheading, with the most important determinants of Masonic culture. There are few studies that discuss this outstanding prose writer in terms of freemasonry and the author of this article discusses this issue with particular attention to the symbolism  of the Masonic initiation ritual

Wavevector-dependent optical properties from wavevector-independent proper conductivity tensor

We discuss the calculation of the refractive index by means of the ab initio scalar dielectric function and point out its inherent limitations. To overcome these, we start from the recently proposed fundamental, microscopic wave equation in materials in terms of the frequency- and wavevector-dependent dielectric tensor, and investigate under which conditions the standard treatment can be justified. Thereby, we address the question of neglecting the wavelength dependence of microscopic response functions. Furthermore, we analyze in how far the fundamental, microscopic wave equation is equivalent to the standard wave equation used in theoretical optics. In particular, we clarify the relation of the "effective" dielectric tensor used there to the microscopic dielectric tensor defined in ab initio physics.Comment: consistent with published version in Eur. Phys. J. B (2020