Fermi level alignment in single molecule junctions and its dependence on interface structure

The alignment of the Fermi level of a metal electrode within the gap of the highest occupied and lowest unoccupied orbital of a molecule is a key quantity in molecular electronics. Depending on the type of molecule and the interface structure of the junction, it can vary the electron transparency of a gold/molecule/gold junction by at least one order of magnitude. In this article we will discuss how Fermi level alignment is related to surface structure and bonding configuration on the basis of density functional theory calculations for bipyridine and biphenyl dithiolate between gold leads. We will also relate our findings to quantum-chemical concepts such as electronegativity.Comment: 5 pages, 2 figures, presented at the ICN+T 2006 conferenc

Covariant spectator theory of np scattering: Effective range expansions and relativistic deuteron wave functions

We present the effective range expansions for the 1S_0 and 3S_1 scattering phase shifts, and the relativistic deuteron wave functions that accompany our recent high precision fits (with chi^2/N{data} approx 1) to the 2007 world np data below 350 MeV. The wave functions are expanded in a series of analytical functions (with the correct asymptotic behavior at both large and small arguments) that can be Fourier-transformed from momentum to coordinate space and are convenient to use in any application. A fortran subroutine to compute these wave functions can be obtained from the authors.Comment: 32 pages, 14 figure

Elucidating the Impact of Low Dissolved Oxygen Wastewater Treatment on Pharmaceutical Fate.

More than half of the energy in conventional wastewater treatment is consumed by aeration. To achieve substantial energy savings and comply with increasingly stringent effluent nutrient regulations, wastewater utilities are beginning to control and minimize aeration, thereby operating at a lower dissolved oxygen (DO) concentration. As utilities implement low DO processes, the impact of DO on non-regulated pollutants, such as pharmaceuticals, warrants attention to understand the impact of these technologies on pharmaceutical loads to the environment. This dissertation focuses on the impact of DO on pharmaceutical biotransformation during treatment. Low DO treatment could impact pharmaceutical biotransformation directly by acting as a limiting substrate and slowing the activity of microorganisms involved in biotransformation, and indirectly by selecting for a community that is more (or less) effective at biotransformation. The objective of this work was to evaluate and characterize both direct and indirect impacts of low DO conditions in wastewater treatment bioprocesses on pharmaceutical biotransformation. To characterize how DO concentration directly impacts pharmaceutical biotransformation rates, oxygen half-saturation constants (KO2) were determined for a suite of compounds that describe the impact of DO on a compound’s biotransformation rate. Indirect impacts of DO concentration on pharmaceutical biotransformation rates were demonstrated using bench-scale nitrifying bioreactors operated for over a year under low (~0.3 mg-DO/L) and high (>4 mg-DO/L) DO conditions. Results showed that long-term low DO conditions resulted in a greater biomass concentration in the low DO reactor compared to high DO reactor. The greater biomass concentration in the low DO reactor resulted in a community with lower specific pharmaceutical biotransformation rates but greater net biotransformation rates under non-limiting DO conditions. In addition, the low DO reactor supported the growth of a more diverse microbial community. To follow up on this finding, a direct test of how microbial diversity affects pharmaceutical biotransformation was performed using a dilution-to-extinction approach. The results showed a strong positive association between biodiversity and collective pharmaceutical biotransformation rates. Taken together, these studies demonstrate that that substantial energy savings can be achieved by operating at lower bulk liquid DO concentrations (0.5 - 1 mg/L) without compromising net pharmaceutical biotransformation rates.PhDEnvironmental EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/120642/1/lstadler_1.pd

Structural basis for sequence specific DNA binding and protein dimerization of HOXA13.

The homeobox gene (HOXA13) codes for a transcription factor protein that binds to AT-rich DNA sequences and controls expression of genes during embryonic morphogenesis. Here we present the NMR structure of HOXA13 homeodomain (A13DBD) bound to an 11-mer DNA duplex. A13DBD forms a dimer that binds to DNA with a dissociation constant of 7.5 nM. The A13DBD/DNA complex has a molar mass of 35 kDa consistent with two molecules of DNA bound at both ends of the A13DBD dimer. A13DBD contains an N-terminal arm (residues 324 - 329) that binds in the DNA minor groove, and a C-terminal helix (residues 362 - 382) that contacts the ATAA nucleotide sequence in the major groove. The N370 side-chain forms hydrogen bonds with the purine base of A5* (base paired with T5). Side-chain methyl groups of V373 form hydrophobic contacts with the pyrimidine methyl groups of T5, T6* and T7*, responsible for recognition of TAA in the DNA core. I366 makes similar methyl contacts with T3* and T4*. Mutants (I366A, N370A and V373G) all have decreased DNA binding and transcriptional activity. Exposed protein residues (R337, K343, and F344) make intermolecular contacts at the protein dimer interface. The mutation F344A weakens protein dimerization and lowers transcriptional activity by 76%. We conclude that the non-conserved residue, V373 is critical for structurally recognizing TAA in the major groove, and that HOXA13 dimerization is required to activate transcription of target genes

Influence of a transverse static magnetic field on the magnetic hyperthermia properties and high-frequency hysteresis loops of ferromagnetic FeCo nanoparticles

The influence of a transverse static magnetic field on the magnetic hyperthermia properties is studied on a system of large-losses ferromagnetic FeCo nanoparticles. The simultaneous measurement of the high-frequency hysteresis loops and of the temperature rise provides an interesting insight into the losses and heating mechanisms. A static magnetic field of only 40 mT is enough to cancel the heating properties of the nanoparticles, a result reproduced using numerical simulations of hysteresis loops. These results cast doubt on the possibility to perform someday magnetic hyperthermia inside a magnetic resonance imaging setup.Comment: 6 pages, 3 figure

Metastable States in High Order Short-Range Spin Glasses

The mean number of metastable states in higher order short-range spin glasses is estimated analytically using a variational method introduced by Tanaka and Edwards for very large coordination numbers. For lattices with small connectivities, numerical simulations do not show any significant dependence on the relative positions of the interacting spins on the lattice, indicating thus that these systems can be described by a few macroscopic parameters. As an extremely anisotropic model we consider the low autocorrelated binary spin model and we show through numerical simulations that its landscape has an exceptionally large number of local optima

Escalation of error catastrophe for enzymatic self-replicators

It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication, we analyze highly specific enzymatic self-replication mediated through an otherwise neutral recognition region, which leads to frequency-dependent replication rates. We find a significant reduction of the maximally tolerable error rate, because the replication rate of the fittest molecules decreases with the fraction of functional enzymes. Our analysis is extended to hypercyclic couplings as an example for catalytic networks.Comment: 6 pages, 4 figures; accepted at Europhys. Let