Step Patterns on Vicinal Reconstructed Surfaces

Step patterns on vicinal $(2\times1)$ reconstructed surfaces of noble metals Au(110) and Pt(110), miscut towards the (100) orientation, are investigated. The free energy of the reconstructed surface with a network of crossing opposite steps is calculated in the strong chirality regime when the steps cannot make overhangs. It is explained why the steps are not perpendicular to the direction of the miscut but form in equilibrium a network of crossing steps which make the surface to look like a fish skin. The network formation is the consequence of competition between the -- predominantly elastic -- energy loss and entropy gain. It is in agreement with recent scanning-tunnelling-microscopy observations on vicinal Au(110) and Pt(110) surfaces.Comment: 11 pages with 5 eps figures in text. Uses psfig and elsart.sty (ELSEVIER Science). To be published in Surf. Sc

DNA Condensate Morphology - Examples from the Test Tube and Nature

DNA condensates have attracted the attention of biophysicists, biochemists and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g. gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. The thesis includes an analysis of the kinetic and thermodynamic factors governing DNA condensate morphology in solution, and discusses implications for future applications of DNA condensation in vitro as a model system for testing theories of polyelectrolyte collapse. In addition, DNA condensation by folded bovine protamine, a naturally occurring multivalent oligopeptide responsible for packing genomic DNA in bovine sperm cells, has been studied as well. The analysis of morphology, size, DNA strand packing density, and the stability of structural integrity of DNA condensates obtained with folded bovine protamines suggests that we have reconstituted native sperm cell chromatin. The results of this study were used to model the local structure of bovine sperm cell chromatin.Ph.D.Committee Chair: Nicholas V. Hud; Committee Member: Donald F. Doyle; Committee Member: Loren D. Willliams; Committee Member: Rigoberto Hernandez; Committee Member: Roger M. Wartel

Structure determination of the (3sqrt{3}x3sqrt{3}) reconstructed alpha-Al_2O_3(0001)

Grazing-incidence X-ray diffraction data are combined with energy-minimization calculations to analyse the atomic structure of the Al-rich (3sqrt{3} x 3sqrt{3})R 30 deg reconstructed surface of sapphire alpha-Al_2O_3(0001). The experiments on the BM32 beamline of the ESRF provide the non-integer-order diffraction intensities and, after Fourier transform, an incomplete Patterson map. The computer simulations are implemented to obtain structural information from this map. In the simulations, the interactions between the Al overlayer atoms were described with the Sutton-Chen potential and the interactions between the overlayer and the sapphire substrate with a laterally modulated Lennard-Jones potential. We have shown that the hexagonal reconstructed unit cell is composed of triangles where the two layers of Al adatoms are FCC(111) ordered whereas between the triangles the stacking is FCC(001).Comment: 9 pages, incl. 4 figures; submitted to Surface Science Letter

Rotational Reconstruction of Sapphire (0001)

The structure of the $(\sqrt{31}\times \sqrt{31})R\pm9^\circ$ reconstructed phase on sapphire (0001) surface is investigated by means of a simulation based on the energy minimization. The interaction between Al adatoms is described with the semi-empirical many-body Sutton-Chen potential, corrected for the charge transfer between the metallic overlayer and the substrate. The interactions between the Al adatoms and sapphire substrate are described with a simple three-dimensional potential field which has the hexagonal periodicity of sapphire surface. Our energy analysis gave evidence that the structure which is observed at room temperature is in fact a frozen high-temperature structure. In accordance with the X-ray scattering, a hexagonal domain pattern separated by domain walls has been found. The Al adatoms, distributed in two monolayers, are ordered and isomorphic to metallic Al(111) in the domains and disordered in the domain walls. The main reason for the rotational reconstruction is the lattice misfit between the metallic Al and sapphire.Comment: 15 pages with 4 eps figures in text. Uses psfig and elsart.cls (ELSEVIER Science). Submitted to Surf. Sc

Characterization of ciprofloxacin binding to the linear single- and doublestranded DNA

Abstract The binding of ciprofloxacin to natural and synthetic polymeric DNAs was investigated at different solvent conditions using a combination of spectroscopic and hydrodynamic techniques. In 10 mM cacodylate buffer (pH 7.0) containing 108.6 mM Na + , no sequence preferences in the interaction of ciprofloxacin with DNA was detected, while in 2 mM cacodylate buffer (pH 7.0) containing only 1.7 mM Na + , a significant binding of ciprofloxacin to natural and synthetic linear double-stranded DNA was observed. At low ionic strength of solution, ciprofloxacin binding to DNA duplex containing alternating AT base pairs is accompanied by the largest enhancement in thermal stability (e.g

Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site

Peer reviewe

Reinitiated viral RNA-dependent RNA polymerase resumes replication at a reduced rate

RNA-dependent RNA polymerases (RdRP) form an important class of enzymes that is responsible for genome replication and transcription in RNA viruses and involved in the regulation of RNA interference in plants and fungi. The RdRP kinetics have been extensively studied, but pausing, an important regulatory mechanism for RNA polymerases that has also been implicated in RNA recombination, has not been considered. Here, we report that RdRP experience a dramatic, long-lived decrease in its elongation rate when it is reinitiated following stalling. The rate decrease has an intriguingly weak temperature dependence, is independent of both the nucleotide concentration during stalling and the length of the RNA transcribed prior to stalling; however it is sensitive to RNA structure. This allows us to delineate the potential factors underlying this irreversible conversion of the elongation complex to a less active mode

Elongation-competent pauses govern the fidelity of a viral RNA-dependent RNA polymerase

Peer reviewe

An RNA toolbox for single-molecule force spectroscopy studies

Precise, controllable single-molecule force spectroscopy studies of RNA and RNA-dependent processes have recently shed new light on the dynamics and pathways of RNA folding and RNA-enzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Such a construct is typically subject to several criteria. First, single-molecule force spectroscopy techniques often require an RNA construct that is longer than the RNA molecules used for bulk biochemical studies. Next, the incorporation of modified nucleotides into the RNA construct is required for its surface immobilization. In addition, RNA constructs for single-molecule studies are commonly assembled from different single-stranded RNA molecules, demanding good control of hybridization or ligation. Finally, precautions to prevent RNase- and divalent cation-dependent RNA digestion must be taken. The rather limited selection of molecular biology tools adapted to the manipulation of RNA molecules, as well as the sensitivity of RNA to degradation, make RNA construct preparation a challenging task. We briefly illustrate the types of single-molecule force spectroscopy experiments that can be performed on RNA, and then present an overview of the toolkit of molecular biology techniques at one's disposal for the assembly of such RNA constructs. Within this context, we evaluate the molecular biology protocols in terms of their effectiveness in producing long and stable RNA constructs

Analysis of fluid flow around a beating artificial cilium

Biological cilia are found on surfaces of some microorganisms and on surfaces of many eukaryotic cells where they interact with the surrounding fluid. The periodic beating of the cilia is asymmetric, resulting in directed swimming of unicellular organisms or in generation of a fluid flow above a ciliated surface in multicellular ones. Following the biological example, externally driven artificial cilia have recently been successfully implemented as micropumps and mixers. However, biomimetic systems are useful not only in microfluidic applications, but can also serve as model systems for the study of fundamental hydrodynamic phenomena in biological samples. To gain insight into the basic principles governing propulsion and fluid pumping on a micron level, we investigated hydrodynamics around one beating artificial cilium. The cilium was composed of superparamagnetic particles and driven along a tilted cone by a varying external magnetic field. Nonmagnetic tracer particles were used for monitoring the fluid flow generated by the cilium. The average flow velocity in the pumping direction was obtained as a function of different parameters, such as the rotation frequency, the asymmetry of the beat pattern, and the cilium length. We also calculated the velocity field around the beating cilium by using the analytical far-field expansion. The measured average flow velocity and the theoretical prediction show an excellent agreement