Enhanced Operational Semantics in Systems Biology

We are faced with a great challenge: the cross-fertilization between the fields of formal methods for concurrency, in the computer science domain, and systems biology in the biological realm

Far infrared study of the two dimensional dimer spin system SrCu_2(BO_3)_2

Using far-infrared spectroscopy in magnetic fields up to 12T we have studied a two-dimensional dimer spin gap system SrCu_2(BO_3)_2. We found several infrared active modes in the dimerized state (below 10K) in the frequency range from 3 to 100cm^-1. The measured splitting from the ground state to the excited triplet M_S=0 sublevel is Delta_1=24.2cm^-1 and the other two triplet state sublevels in zero magnetic field are 1.4cm^-1 below and above the M_S=0 sublevel. Another multiplet is at Delta_2=37.6cm^-1 from the ground state. A strong electric dipole active transition polarized in the (ab)-plane is activated in the dimer spin system below 15K at 52cm^-1.Comment: 4 pages including 5 figures, submitted to PRB, instrumental arte facts remove

Conservation agriculture with optimum fertilizer nitrogen rate reduces GWP for rice cultivation in floodplain soils

Wetland rice cultivation contributes significantly to global warming potential (GWP), an effect which is largely attributed to emissions of methane (CH4). Emerging technologies for wetland rice production such as conservation agriculture (CA) may mitigate greenhouse gas (GHG) emissions, but the effects are not well defined. Investigations were carried out in an irrigated rice (Boro rice) field in the fifth crop after conversion of conventional tillage (CT) to strip tillage (ST). Two crop residue levels (low versus high, LR versus HR) and three nitrogen (N) application rates (N1 = 108, N2 = 144, and N3 = 180 kg N ha−1) were laid out in a split-plot experiment with three replicates. Yield-scaled GHG emissions and GWP were estimated to evaluate the impacts of CA on mitigating CH4 and N2O emissions in the rice paddy field. There was a 55% higher N2O emission in ST with HR coupled with N3 than that in CT with LR coupled with N1. The N2O emission factors ranged from 0.43 to 0.75% in ST and 0.45 to 0.59% in CT, irrespective of the residue level and N rate. By contrast, CH4 emissions were significantly lower in CA than in the conventional practices (CT plus LR). The ST with LR in N2 reduced the GWP by 39% over the GWP in CT with HR in N1 and 16% over the conventional practices. Based on our investigation of the combination of tillage, residue, and N rate treatments, the adoption of CA with high and low residue levels reduced the GWP by 10 and 16%, respectively, because of lower CH4 and N2O emissions than the current management practices. The relatively high N2O emission factors suggest that mitigation of this GHG in wetland rice systems needs greater attention

Influence of micro-patterning of the growth template on defect reduction and optical properties of non-polar (11-20) GaN

We investigate the influence of different types of template micro-patterning on defect reduction and optical properties of non-polar GaN using detailed luminescence studies. Non-polar (11-20) (or a-plane) GaN exhibits a range of different extended defects compared with its more commonly used c-plane counterpart. In order to reduce the number of defects and investigate their impact on luminescence uniformity, non-polar GaN was overgrown on four different GaN microstructures. The micro-patterned structures consist of a regular microrod array; a microrod array where the -c-side of the microrods has been etched to suppress defect generation; etched periodic stripes and finally a subsequent combination of etched stripes and etched microrods (double overgrowth). Overall the presence of extended defects, namely threading dislocations and stacking faults (SFs) is greatly reduced for the two samples containing stripes compared with the two microrod samples. This is evidenced by more uniform emission and reduction in dark regions of non-radiative recombination in room temperature cathodoluminescence imaging as well as a reduction of the SF emission line in low temperature photoluminescence. The observed energy shifts of the GaN near band edge emission are related to anisotropic strain relaxation occurring during the overgrowth on these microstructures. A combination of stripes and microrods is a promising approach for defect reduction and emission uniformity in non-polar GaN for applications in light-emitting devices as well as power electronics

Femto-Photography of Protons to Nuclei with Deeply Virtual Compton Scattering

Developments in deeply virtual Compton scattering allow the direct measurements of scattering amplitudes for exchange of a highly virtual photon with fine spatial resolution. Real-space images of the target can be obtained from this information. Spatial resolution is determined by the momentum transfer rather than the wavelength of the detected photon. Quantum photographs of the proton, nuclei, and other elementary particles with resolution on the scale of a fraction of a femtometer is feasible with existing experimental technology.Comment: To be published in Physical Review D. Replaces previous version with minor changes in presentatio

Tunneling spectra of submicron Bi2_2Sr2_2CaCu2_2O8+δ_{8+\delta} intrinsic Josephson junctions: evolution from superconducting gap to pseudogap

Tunneling spectra of near optimally doped, submicron Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ intrinsic Josephson junctions are presented, and examined in the region where the superconducting gap evolves into pseudogap. The spectra are analyzed using a self-energy model, proposed by Norman {\it et al.}, in which both quasiparticle scattering rate $\Gamma$ and pair decay rate $\Gamma_{\Delta}$ are considered. The density of states derived from the model has the familiar Dynes' form with a simple replacement of $\Gamma$ by $\gamma_+$ = ($\Gamma$ + $\Gamma_{\Delta}$)/2. The $\gamma_+$ parameter obtained from fitting the experimental spectra shows a roughly linear temperature dependence, which puts a strong constraint on the relation between $\Gamma$ and $\Gamma_{\Delta}$. We discuss and compare the Fermi arc behavior in the pseudogap phase from the tunneling and angle-resolved photoemission spectroscopy experiments. Our results indicate an excellent agreement between the two experiments, which is in favor of the precursor pairing view of the pseudogap.Comment: 7 pages, 6 figure

A molecular dynamics study on the equilibrium magnetization properties and structure of ferrofluids

We investigate in detail the initial susceptibility, magnetization curves, and microstructure of ferrofluids in various concentration and particle dipole moment ranges by means of molecular dynamics simulations. We use the Ewald summation for the long-range dipolar interactions, take explicitly into account the translational and rotational degrees of freedom, coupled to a Langevin thermostat. When the dipolar interaction energy is comparable with the thermal energy, the simulation results on the magnetization properties agree with the theoretical predictions very well. For stronger dipolar couplings, however, we find systematic deviations from the theoretical curves. We analyze in detail the observed microstructure of the fluids under different conditions. The formation of clusters is found to enhance the magnetization at weak fields and thus leads to a larger initial susceptibility. The influence of the particle aggregation is isolated by studying ferro-solids, which consist of magnetic dipoles frozen in at random locations but which are free to rotate. Due to the artificial suppression of clusters in ferro-solids the observed susceptibility is considerably lowered when compared to ferrofluids.Comment: 33 pages including 12 figures, requires RevTex

Magnetic Anisotropy in the Molecular Complex V15

We apply degenerate perturbation theory to investigate the effects of magnetic anisotropy in the magnetic molecule V15. Magnetic anisotropy is introduced via Dzyaloshinskii-Moriya (DM) interaction in the full Hilbert space of the system. Our model provides an explanation for the rounding of transitions in the magnetization as a function of applied field at low temperature, from which an estimate for the DM interaction is found. We find that the calculated energy differences of the lowest energy states are consistent with the available data. Our model also offers a novel explanation for the hysteretic nature of the time-dependent magnetization data.Comment: Final versio

Q-dependence of the inelastic neutron scattering cross section for molecular spin clusters with high molecular symmetry

For powder samples of polynuclear metal complexes the dependence of the inelastic neutron scattering intensity on the momentum transfer Q is known to be described by a combination of so called interference terms. They reflect the interplay between the geometrical structure of the compound and the spatial properties of the wave functions involved in the transition. In this work, it is shown that the Q-dependence is strongly interrelated with the molecular symmetry of molecular nanomagnets, and, if the molecular symmetry is high enough, is actually completely determined by it. A general formalism connecting spatial symmetry and interference terms is developed. The arguments are detailed for cyclic spin clusters, as experimentally realized by e.g. the octanuclear molecular wheel Cr8, and the star like tetranuclear cluster Fe4.Comment: 8 pages, 1 figures, REVTEX

Squalenyl Hydrogen Sulfate Nanoparticles for Simultaneous Delivery of Tobramycin and an Alkylquinolone Quorum Sensing Inhibitor Enable the Eradication of P. aeruginosa Biofilm Infections

Elimination of pulmonary Pseudomonas aeruginosa (PA) infections is challenging to accomplish with antibiotic therapies, mainly due to resistance mechanisms. Quorum sensing inhibitors (QSIs) interfering with biofilm formation can thus complement antibiotics. For simultaneous and improved delivery of both active agents to the infection sites, self-assembling nanoparticles of a newly synthesized squalenyl hydrogen sulfate (SqNPs) were prepared. These nanocarriers allowed for remarkably high loading capacities of hydrophilic antibiotic tobramycin (Tob) and a novel lipophilic QSI at 30 % and circa 10 %, respectively. The drug-loaded SqNPs showed improved biofilm penetration and enhanced efficacy in relevant biological barriers (mucin/human tracheal mucus, biofilm), leading to complete eradication of PA biofilms at circa 16-fold lower Tob concentration than Tob alone. This study offers a viable therapy optimization and invigorates the research and development of QSIs for clinical use